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is really type IPLDKind, but the documentation generates something a bit strange since IPLDKind is a type union. """ - @abstractmethod - def save_raw(self, data: bytes) -> IPLDKind: - """Take any set of bytes, save it to the storage mechanism, and return an ID in the type of IPLDKind that can be used to retrieve those bytes later.""" + async def save(self, data: bytes, codec: Literal["raw", "dag-cbor"]) -> IPLDKind: + """Take any set of bytes, save it to the storage mechanism, and reutrn an ID in the type of IPLDKind which can be used to retrieve those bytes later. This also includes extra information in `codec` on whether to mark this data as special linked data.""" @abstractmethod - def save_dag_cbor(self, data: bytes) -> IPLDKind: - """Take a set of bytes and save it just like `save_raw`, except this method has additional context that the data is in a dag-cbor format.""" - - @abstractmethod - def load(self, id: IPLDKind) -> bytes: + async def load(self, id: IPLDKind) -> bytes: """Retrieve the bytes based on an ID returned earlier by the save function.""" @@ -36,25 +33,16 @@ class DictStore(Store): """@private""" def __init__(self): - self.store = {} + self.store = dict() self.hash_alg = multihash.get("blake3") - def save(self, data: bytes) -> bytes: + async def save(self, data: bytes, codec: Literal["raw", "dag-cbor"]) -> bytes: hash = self.hash_alg.digest(data, size=32) self.store[hash] = data return hash - def save_raw(self, data: bytes) -> bytes: - """""" - return self.save(data) - - def save_dag_cbor(self, data: bytes) -> bytes: - """""" - return self.save(data) - # Ignore the type error since bytes is in the IPLDKind type - def load(self, id: bytes) -> bytes: # type: ignore - """""" + async def load(self, id: bytes) -> bytes: # type: ignore since bytes is a subset of the IPLDKind type if id in self.store: return self.store[id] else: @@ -73,133 +61,69 @@ class IPFSStore(Store): - API Key: Provide an API key to the `api_key` parameter. You can customize the header name for the API key by setting the `api_key_header` parameter. """ + KUBO_DEFAULT_LOCAL_GATEWAY_BASE_URL = "http://127.0.0.1:8080" + KUBO_DEFAULT_LOCAL_RPC_BASE_URL = "http://127.0.0.1:5001" + + # Take in a aiohttp session that can be reused across POSTs and GETs to a specific ipfs daemon, also allow for not doing that and creating our own single request lifetime session instead def __init__( self, - timeout_seconds: int = 30, - gateway_uri_stem: str = "http://127.0.0.1:8080", - rpc_uri_stem: str = "http://127.0.0.1:5001", + gateway_session: aiohttp.ClientSession | None = None, + rpc_session: aiohttp.ClientSession | None = None, hasher: str = "blake3", - pin_on_add: bool = False, - debug: bool = False, - # Authentication parameters - basic_auth: tuple[str, str] | None = None, # (username, password) - bearer_token: str | None = None, - api_key: str | None = None, - api_key_header: str = "X-API-Key", # Customizable API key header ): - self.timeout_seconds = timeout_seconds - """ - You can modify this variable directly if you choose. - - This sets the timeout in seconds for all HTTP requests. - """ - self.gateway_uri_stem = gateway_uri_stem """ - URI stem of the IPFS HTTP gateway that IPFSStore will retrieve blocks from. + TODO write about user needing to close the aiohttp session at the end of IPFSStore's use if this thing is being used in a long running program """ - self.rpc_uri_stem = rpc_uri_stem - """URI Stem of the IPFS RPC API that IPFSStore will send data to.""" + # Don't initialize a self-managed ClientSession here, so that they are only created when needed, a lot of clients will only ever read from IPFS + self.gateway_session = gateway_session + self.rpc_session = rpc_session + self.hasher = hasher """The hash function to send to IPFS when storing bytes.""" - self.pin_on_add: bool = pin_on_add - """Whether IPFSStore should tell the daemon to pin the generated CIDs in API calls. This can be changed in between usage, but should be kept the same value for the lifetime of the program.""" - self.debug: bool = debug - """If true, this records the total number of bytes sent in and out of IPFSStore to the network. You can access this information in `total_sent` and `total_received`. Bytes are counted in terms of either how much was sent to IPFS to store a CID, or how much data was inside of a retrieved IPFS block. This does not include the overhead of the HTTP requests themselves.""" - self.total_sent: None | int = 0 if debug else None - """Total bytes sent to IPFS. Used for debugging purposes.""" - self.total_received: None | int = 0 if debug else None - """Total bytes in responses from IPFS for blocks. Used for debugging purposes.""" - - # Authentication settings - self.basic_auth = basic_auth - """Tuple of (username, password) for Basic Authentication""" - self.bearer_token = bearer_token - """Bearer token for token-based authentication""" - self.api_key = api_key - """API key for API key-based authentication""" - self.api_key_header = api_key_header - """Header name to use for API key authentication""" - - def save(self, data: bytes, cid_codec: str) -> CID: - """ - This saves the data to an ipfs daemon by calling the RPC API, and then returns the CID, with a multicodec set by the input cid_codec. We need to do this since the API always returns either a multicodec of raw or dag-pb if it had to shard the input data. - - By default, `save` pins content it adds. - ```python - from py_hamt import IPFSStore - - ipfs_store = IPFSStore() - cid = ipfs_store.save("foo".encode(), "raw") - print(cid.human_readable) - ``` - """ - pin_string: str = "true" if self.pin_on_add else "false" - - # Apply authentication based on provided credentials - headers = {} - if self.bearer_token: - headers["Authorization"] = f"Bearer {self.bearer_token}" - elif self.api_key: - headers[self.api_key_header] = self.api_key - - # Prepare request parameters - url = f"{self.rpc_uri_stem}/api/v0/add?hash={self.hasher}&pin={pin_string}" - - # Make the request with appropriate authentication - response = requests.post( - url, - files={"file": data}, - headers=headers, - auth=self.basic_auth, - timeout=self.timeout_seconds, - ) - response.raise_for_status() - - cid_str: str = json.decode(response.content)["Hash"] # type: ignore - cid = CID.decode(cid_str) - # If it's dag-pb it means we should not reset the cid codec, since this is a UnixFS entry for a large amount of data that thus had to be sharded - # We don't worry about HAMT nodes being larger than 1 MB - # with a conservative calculation of 256 map keys * 10 (bucket size of 9 and 1 link per map key)*100 bytes huge size for a cid=0.256 MB, so we can always safely recodec those as dag-cbor, which is what they are - # 0x70 means dag-pb - if cid.codec.code != 0x70: - cid = cid.set(codec=cid_codec) - - # if everything is succesful, record debug information - if self.debug: - self.total_sent += len(data) # type: ignore - - return cid - - def save_raw(self, data: bytes) -> CID: - """See `save`""" - return self.save(data, "raw") - - def save_dag_cbor(self, data: bytes) -> CID: - """See `save`""" - return self.save(data, "dag-cbor") + self.rpc_url = f"/api/v0/add?hash={self.hasher}&pin=false" + + # TODO make this a future feature for IPFSStore after all the HAMT stuff is already done + # self.debug: bool = debug + # """If true, this records the total number of bytes sent in and out of IPFSStore to the network. You can access this information in `total_sent` and `total_received`. Bytes are counted in terms of either how much was sent to IPFS to store a CID, or how much data was inside of a retrieved IPFS block. This does not include the overhead of the HTTP requests themselves.""" + # self.total_sent: None | int = 0 if debug else None + # """Total bytes sent to IPFS. Used for debugging purposes.""" + # self.total_received: None | int = 0 if debug else None + # """Total bytes in responses from IPFS for blocks. Used for debugging purposes.""" + + async def save(self, data: bytes, codec: Literal["raw", "dag-cbor"]) -> CID: + if self.rpc_session is None: + self.rpc_session = aiohttp.ClientSession( + base_url=IPFSStore.KUBO_DEFAULT_LOCAL_RPC_BASE_URL + ) + + async with self.rpc_session.request( + method="POST", url=self.rpc_url, data={"file": data} + ) as response: + response.raise_for_status() + json_bytes = await response.read() + cid_str: str = json.decode(json_bytes)["Hash"] + cid = CID.decode(cid_str) + # If it's dag-pb it means we should not reset the cid codec, since this is a UnixFS entry for a large amount of data that thus had to be sharded + # 0x70 means dag-pb + if cid.codec.code != 0x70: + cid = cid.set(codec=codec) + + return cid # Ignore the type error since CID is in the IPLDKind type - def load(self, id: CID) -> bytes: # type: ignore - """ - This retrieves the raw bytes by calling the provided HTTP gateway. - ```python - from py_hamt import IPFSStore - from multiformats import CID - - ipfs_store = IPFSStore() - # This is just an example CID - cid = CID.decode("bafybeiaysi4s6lnjev27ln5icwm6tueaw2vdykrtjkwiphwekaywqhcjze") - data = ipfs_store.load(cid) - print(data) - ``` - """ - response = requests.get( - f"{self.gateway_uri_stem}/ipfs/{str(id)}", timeout=self.timeout_seconds - ) - response.raise_for_status() - - if self.debug: - self.total_received += len(response.content) # type: ignore - - return response.content + async def load( # type: ignore + self, + id: CID, + session: aiohttp.ClientSession | None = None, + ) -> bytes: + if self.gateway_session is None: + self.gateway_session = aiohttp.ClientSession( + base_url=IPFSStore.KUBO_DEFAULT_LOCAL_GATEWAY_BASE_URL + ) + + async with self.gateway_session.request( + method="GET", url=f"/ipfs/{str(id)}" + ) as response: + response.raise_for_status() + return await response.read() From ce758661a2f9d87f6f26e7a891ec361855d5062a Mon Sep 17 00:00:00 2001 From: Abid Sikder <41392423+abidsikder@users.noreply.github.com> Date: Mon, 5 May 2025 20:14:08 -0400 Subject: [PATCH 003/118] address aiohttp deprecation warning --- py_hamt/store.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/py_hamt/store.py b/py_hamt/store.py index 8d0064c..7afe105 100644 --- a/py_hamt/store.py +++ b/py_hamt/store.py @@ -1,3 +1,4 @@ +import io from typing import Literal from abc import ABC, abstractmethod from dag_cbor.ipld import IPLDKind @@ -98,7 +99,7 @@ async def save(self, data: bytes, codec: Literal["raw", "dag-cbor"]) -> CID: ) async with self.rpc_session.request( - method="POST", url=self.rpc_url, data={"file": data} + method="POST", url=self.rpc_url, data={"file": io.BytesIO(data)} ) as response: response.raise_for_status() json_bytes = await response.read() From 6d734694d6a942ae053addbf213fc95c8f42c40c Mon Sep 17 00:00:00 2001 From: Abid Sikder <41392423+abidsikder@users.noreply.github.com> Date: Mon, 5 May 2025 20:14:28 -0400 Subject: [PATCH 004/118] move common testing utils into single file --- tests/test_hamt.py | 30 +----------- tests/test_zarr_ipfs.py | 64 ------------------------- tests/testing_utils.py | 102 ++++++++++++++++++++++++++++++++++++++++ 3 files changed, 103 insertions(+), 93 deletions(-) create mode 100644 tests/testing_utils.py diff --git a/tests/test_hamt.py b/tests/test_hamt.py index 0b95501..1a53e0b 100644 --- a/tests/test_hamt.py +++ b/tests/test_hamt.py @@ -7,41 +7,13 @@ from multiformats import CID from hypothesis import given from hypothesis import strategies as st -from hypothesis.strategies import SearchStrategy import pytest from py_hamt import HAMT, DictStore from py_hamt.hamt import Node from py_hamt.store import Store - -def cid_strategy() -> SearchStrategy: - """Generate random CIDs for testing.""" - - # Strategy for generating random hash digests - digests = st.binary(min_size=32, max_size=32).map( - lambda d: bytes.fromhex("1220") + d # 0x12 = sha2-256, 0x20 = 32 bytes - ) - - # Generate CIDv1 (more flexible) - cidv1 = st.tuples(st.just("base32"), st.just(1), st.just("dag-cbor"), digests) - - # Combine the strategies and create CIDs - return cidv1.map(lambda args: CID(*args)) - - -def ipld_strategy() -> SearchStrategy: - return st.one_of( - [ - st.none(), - st.booleans(), - st.integers(min_value=-9223372036854775808, max_value=9223372036854775807), - st.floats(allow_infinity=False, allow_nan=False), - st.text(), - st.binary(), - cid_strategy(), - ] - ) +from .testing_utils import ipld_strategy key_value_lists = st.lists( diff --git a/tests/test_zarr_ipfs.py b/tests/test_zarr_ipfs.py index f23b5aa..c8fd7f2 100644 --- a/tests/test_zarr_ipfs.py +++ b/tests/test_zarr_ipfs.py @@ -60,70 +60,6 @@ def random_zarr_dataset(): yield ds -def find_free_port() -> int: - with socket.socket() as s: - s.bind(("", 0)) # Bind to a free port provided by the host. - return int(s.getsockname()[1]) # Return the port number assigned. - - -@pytest.fixture -def create_ipfs(): - # Create temporary directory, set it as the IPFS Path - temp_dir = Path(tempfile.mkdtemp()) - custom_env = os.environ.copy() - custom_env["IPFS_PATH"] = str(temp_dir) - - # IPFS init - subprocess.run( - ["ipfs", "init", "--profile", "pebbleds"], check=True, env=custom_env - ) - - # Edit the config file so that it serves on randomly selected and available ports to not conflict with any currently running ipfs daemons - swarm_port = find_free_port() - rpc_port = find_free_port() - gateway_port = find_free_port() - - config_path = temp_dir / "config" - config: dict - with open(config_path, "r") as f: - config = json.load(f) - - swarm_addrs: list[str] = config["Addresses"]["Swarm"] - new_port_swarm_addrs = [s.replace("4001", str(swarm_port)) for s in swarm_addrs] - config["Addresses"]["Swarm"] = new_port_swarm_addrs - - rpc_multiaddr = config["Addresses"]["API"] - gateway_multiaddr = config["Addresses"]["Gateway"] - - config["Addresses"]["API"] = rpc_multiaddr.replace("5001", str(rpc_port)) - config["Addresses"]["Gateway"] = gateway_multiaddr.replace( - "8080", str(gateway_port) - ) - - with open(config_path, "w") as f: - json.dump(config, f, indent=2) - - # Start the daemon - rpc_uri_stem = f"http://127.0.0.1:{rpc_port}" - gateway_uri_stem = f"http://127.0.0.1:{gateway_port}" - - ipfs_process = subprocess.Popen(["ipfs", "daemon"], env=custom_env) - while True: - try: - requests.post(rpc_uri_stem + "/api/v0/id", timeout=1) - break - except requests.exceptions.ConnectionError: - time.sleep(1) - - yield rpc_uri_stem, gateway_uri_stem - - # Close the daemon - ipfs_process.kill() - - # Delete the temporary directory - shutil.rmtree(temp_dir) - - # This test also collects miscellaneous statistics about performance, run with pytest -s to see these statistics being printed out @pytest.mark.asyncio async def test_write_read(create_ipfs, random_zarr_dataset: xr.Dataset): diff --git a/tests/testing_utils.py b/tests/testing_utils.py new file mode 100644 index 0000000..18b5d1c --- /dev/null +++ b/tests/testing_utils.py @@ -0,0 +1,102 @@ +import json +import os +import shutil +import socket +import subprocess +import tempfile +import time +from pathlib import Path + +import pytest +from hypothesis import strategies as st +from hypothesis.strategies import SearchStrategy +from multiformats import CID + + +def cid_strategy() -> SearchStrategy: + """Generate random CIDs for testing.""" + + # Strategy for generating random hash digests + digests = st.binary(min_size=32, max_size=32).map( + lambda d: bytes.fromhex("1220") + d # 0x12 = sha2-256, 0x20 = 32 bytes + ) + + # Generate CIDv1 (more flexible) + cidv1 = st.tuples(st.just("base32"), st.just(1), st.just("dag-cbor"), digests) + + # Combine the strategies and create CIDs + return cidv1.map(lambda args: CID(*args)) + + +def ipld_strategy() -> SearchStrategy: + return st.one_of( + [ + st.none(), + st.booleans(), + st.integers(min_value=-9223372036854775808, max_value=9223372036854775807), + st.floats(allow_infinity=False, allow_nan=False), + st.text(), + st.binary(), + cid_strategy(), + ] + ) + + +def find_free_port() -> int: + with socket.socket() as s: + s.bind(("", 0)) # Bind to a free port provided by the host. + return int(s.getsockname()[1]) # Return the port number assigned. + + +@pytest.fixture(scope="module") +def create_ipfs(): + # Create temporary directory, set it as the IPFS Path + temp_dir = Path(tempfile.mkdtemp()) + custom_env = os.environ.copy() + custom_env["IPFS_PATH"] = str(temp_dir) + + # IPFS init + subprocess.run( + ["ipfs", "init", "--profile", "pebbleds"], check=True, env=custom_env + ) + + # Edit the config file so that it serves on randomly selected and available ports to not conflict with any currently running ipfs daemons + swarm_port = find_free_port() + rpc_port = find_free_port() + gateway_port = find_free_port() + + config_path = temp_dir / "config" + config: dict + with open(config_path, "r") as f: + config = json.load(f) + + swarm_addrs: list[str] = config["Addresses"]["Swarm"] + new_port_swarm_addrs = [s.replace("4001", str(swarm_port)) for s in swarm_addrs] + config["Addresses"]["Swarm"] = new_port_swarm_addrs + + rpc_multiaddr = config["Addresses"]["API"] + gateway_multiaddr = config["Addresses"]["Gateway"] + + config["Addresses"]["API"] = rpc_multiaddr.replace("5001", str(rpc_port)) + config["Addresses"]["Gateway"] = gateway_multiaddr.replace( + "8080", str(gateway_port) + ) + + with open(config_path, "w") as f: + json.dump(config, f, indent=2) + + # Start the daemon + rpc_uri_stem = f"http://127.0.0.1:{rpc_port}" + gateway_uri_stem = f"http://127.0.0.1:{gateway_port}" + + ipfs_process = subprocess.Popen(["ipfs", "daemon"], env=custom_env) + # Should be enough time for the ipfs daemon process to start up + time.sleep(5) + + yield rpc_uri_stem, gateway_uri_stem + + # Close the daemon + ipfs_process.kill() + + # Delete the temporary directory + shutil.rmtree(temp_dir) From 916df3c601e9a5775e7e88d98ec2eafd0ce8d1b0 Mon Sep 17 00:00:00 2001 From: Abid Sikder <41392423+abidsikder@users.noreply.github.com> Date: Mon, 5 May 2025 20:14:38 -0400 Subject: [PATCH 005/118] pass fuzz tested ipfsstore --- tests/test_ipfsstore.py | 28 ++++++++++++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 tests/test_ipfsstore.py diff --git a/tests/test_ipfsstore.py b/tests/test_ipfsstore.py new file mode 100644 index 0000000..177a17f --- /dev/null +++ b/tests/test_ipfsstore.py @@ -0,0 +1,28 @@ +import aiohttp +import dag_cbor +from dag_cbor import IPLDKind +from hypothesis import given +import pytest + +from py_hamt import IPFSStore + +from testing_utils import ipld_strategy, create_ipfs # noqa + + +@pytest.mark.asyncio +@given(data=ipld_strategy()) +async def test_ipfsstore(create_ipfs, data: IPLDKind): # noqa + rpc_uri_stem, gateway_uri_stem = create_ipfs + gateway_session = aiohttp.ClientSession(base_url=gateway_uri_stem) + rpc_session = aiohttp.ClientSession(base_url=rpc_uri_stem) + + try: + ipfsstore = IPFSStore(rpc_session=rpc_session, gateway_session=gateway_session) + + for codec in ["raw", "dag-cbor"]: + cid = await ipfsstore.save(dag_cbor.encode(data), codec=codec) # type: ignore + result = dag_cbor.decode(await ipfsstore.load(cid)) + assert data == result + finally: + await rpc_session.close() + await gateway_session.close() From 7dcc85269c9224a6104bc0ae2e30e31f9179b594 Mon Sep 17 00:00:00 2001 From: Abid Sikder <41392423+abidsikder@users.noreply.github.com> Date: Mon, 5 May 2025 20:54:19 -0400 Subject: [PATCH 006/118] move key_value_list into common testing utilities --- tests/test_hamt.py | 21 +++------------------ tests/testing_utils.py | 10 ++++++++++ 2 files changed, 13 insertions(+), 18 deletions(-) diff --git a/tests/test_hamt.py b/tests/test_hamt.py index 1a53e0b..25f9a73 100644 --- a/tests/test_hamt.py +++ b/tests/test_hamt.py @@ -13,18 +13,7 @@ from py_hamt.hamt import Node from py_hamt.store import Store -from .testing_utils import ipld_strategy - - -key_value_lists = st.lists( - st.tuples(st.text(), ipld_strategy()), - min_size=0, - max_size=10000, - unique_by=lambda x: x[ - 0 - ], # ensure unique keys, otherwise we can't do the length and size checks -) - +from .testing_utils import key_value_list # Just enough to make it that reading back a hamt without the proper transformer will scramble things _x = "x".encode() @@ -38,14 +27,10 @@ def transformer_decode_minimal(key: str, val: bytes) -> bytes: return val[1:] -@given(key_value_lists) +@given(key_value_list) def test_fuzz(kvs: list[tuple[str, IPLDKind]]): store = DictStore() - hamt = HAMT( - store=store, - transformer_encode=transformer_encode_minimal, - transformer_decode=transformer_decode_minimal, - ) + hamt = HAMT(store=store) assert isinstance(hamt, MutableMapping) # The HAMT should be able to withstand its bucket size changing in between operations diff --git a/tests/testing_utils.py b/tests/testing_utils.py index 18b5d1c..5975a7b 100644 --- a/tests/testing_utils.py +++ b/tests/testing_utils.py @@ -42,6 +42,16 @@ def ipld_strategy() -> SearchStrategy: ) +key_value_list = st.lists( + st.tuples(st.text(), ipld_strategy()), + min_size=0, + max_size=10000, + unique_by=lambda x: x[ + 0 + ], # ensure unique keys, otherwise we can't do the length and size checks when using these KVs for the HAMT +) + + def find_free_port() -> int: with socket.socket() as s: s.bind(("", 0)) # Bind to a free port provided by the host. From 7e0a162fccbf7544e4837ef74248d4387f8b985b Mon Sep 17 00:00:00 2001 From: Abid Sikder <41392423+abidsikder@users.noreply.github.com> Date: Mon, 5 May 2025 20:54:50 -0400 Subject: [PATCH 007/118] compact and simplify Node's dag-cbor representation --- py_hamt/hamt.py | 49 ++++++++++++++++------------------------------ tests/test_node.py | 20 +++++++++++++++++++ 2 files changed, 37 insertions(+), 32 deletions(-) create mode 100644 tests/test_node.py diff --git a/py_hamt/hamt.py b/py_hamt/hamt.py index 2b673f3..830c387 100644 --- a/py_hamt/hamt.py +++ b/py_hamt/hamt.py @@ -47,64 +47,49 @@ def extract_bits(hash_bytes: bytes, depth: int, nbits: int) -> int: class Node: # Use a dict for easy serializability with dag_cbor - data: dict[str, IPLDKind] + data: list[IPLDKind] def __init__(self): - data = {} - # Each "string" key for both buckets and CIDs is the bits as a string, e.g. str(0b1101) = '13' - buckets: dict[str, list[dict[str, IPLDKind]]] = {} - data["B"] = buckets + buckets: dict[str, dict[str, IPLDKind]] = dict() links: dict[str, Link] = {} - data["L"] = links - self.data = data + self.data = [buckets, links] # type: ignore # By having these two methods, the HAMT class has to know less about Node's internal structure and we get better type checking since we don't need to put #type:ignore everywhere - def get_buckets(self) -> dict[str, list[dict[str, IPLDKind]]]: - buckets: dict[str, list[dict[str, IPLDKind]]] = self.data["B"] # type: ignore + def get_buckets(self) -> dict[str, dict[str, IPLDKind]]: + # Buckets looks like + # {"0": {k1: v1, k2: v2, ...}, "1": ...} + buckets: dict[str, dict[str, IPLDKind]] = self.data[0] # type: ignore return buckets def get_links(self) -> dict[str, Link]: - links: dict[str, Link] = self.data["L"] # type: ignore + # Links looks like + # {"0": Link, "1": Link, ...} + links: dict[str, Link] = self.data[1] # type: ignore return links - def _replace_link(self, old_link: Link, new_link: Link): - links = self.get_links() - for str_key in list(links.keys()): - link = links[str_key] - if link == old_link: - links[str_key] = new_link - - def _remove_link(self, old_link: Link): - links = self.get_links() - for str_key in list(links.keys()): - link = links[str_key] - if link == old_link: - del links[str_key] - def serialize(self) -> bytes: return dag_cbor.encode(self.data) @classmethod def deserialize(cls, data: bytes) -> "Node": try: - decoded = dag_cbor.decode(data) + decoded_data = dag_cbor.decode(data) except: # noqa: E722 raise Exception( "Invalid dag-cbor encoded data from the store was attempted to be decoded" ) if ( - isinstance(decoded, dict) - and "B" in decoded - and isinstance(decoded["B"], dict) - and "L" in decoded - and isinstance(decoded["L"], dict) + isinstance(decoded_data, list) + and len(decoded_data) == 2 + and isinstance(decoded_data[0], dict) + and isinstance(decoded_data[1], dict) ): node = cls() - node.data = decoded + node.data = decoded_data return node else: - raise ValueError("Data not a valid Node serialization") + raise ValueError("Data does not contain a valid Node") b3 = multihash.get("blake3") diff --git a/tests/test_node.py b/tests/test_node.py new file mode 100644 index 0000000..8b30948 --- /dev/null +++ b/tests/test_node.py @@ -0,0 +1,20 @@ +from py_hamt.hamt import Node +from hypothesis import given + +from testing_utils import key_value_list + + +@given(buckets_data=key_value_list, links_data=key_value_list) +def test_node(buckets_data, links_data): + node = Node() + buckets = dict() + for k, v in buckets_data: + buckets[k] = v + links = dict() + for k, v in links_data: + links[k] = v + node.data = [buckets, links] + + new_node = Node.deserialize(node.serialize()) + assert buckets == new_node.get_buckets() + assert links == new_node.get_links() From ae0a3088143a1c2b76c63e448bf1f6988d4a6c99 Mon Sep 17 00:00:00 2001 From: Abid Sikder <41392423+abidsikder@users.noreply.github.com> Date: Mon, 5 May 2025 20:56:02 -0400 Subject: [PATCH 008/118] remove encryption transformers --- py_hamt/zarr_encryption_transformers.py | 154 --- pyproject.toml | 1 - uv.lock | 1302 +++++++++++------------ 3 files changed, 641 insertions(+), 816 deletions(-) delete mode 100644 py_hamt/zarr_encryption_transformers.py diff --git a/py_hamt/zarr_encryption_transformers.py b/py_hamt/zarr_encryption_transformers.py deleted file mode 100644 index 7b5033f..0000000 --- a/py_hamt/zarr_encryption_transformers.py +++ /dev/null @@ -1,154 +0,0 @@ -import json -from typing import Callable, Literal - -import dag_cbor -import xarray as xr -from Crypto.Cipher import ChaCha20_Poly1305 -from Crypto.Random import get_random_bytes - -type TransformerFN = Callable[[str, bytes], bytes] - - -def create_zarr_encryption_transformers( - encryption_key: bytes, - header: bytes, - exclude_vars: list[str] = [], - detect_exclude: xr.Dataset - | Literal["auto-from-read"] - | Literal[False] = "auto-from-read", -) -> tuple[TransformerFN, TransformerFN]: - """ - Uses XChaCha20_Poly1305 from the pycryptodome library to perform encryption, while ignoring zarr metadata files. - - https://pycryptodome.readthedocs.io/en/latest/src/cipher/chacha20_poly1305.html - - Note that the encryption key must be exactly 32 bytes long. A header is required by the underlying encryption algorithm. Every time a zarr chunk is encrypted, a random 24-byte nonce is generated. This is saved with the chunk for use when reading back. - - zarr.json metadata files in a zarr v3 are always ignored and passed through unencrypted. - - With `exclude_vars` you may also set some variables to be unencrypted. This allows for partially encrypted zarrs. This should generally include your coordinate variables, along with any data variables you want to keep open. - - `detect_exclude` allows you to put in a xarray Dataset. This will be used to automatically add coordinate variables to the exclusion list. When you reading back a dataset and you do not know the unencrypted variables ahead of time, you can set this to the default "auto-from-read", which will attempt to use any metadata or any decryption errors to detect unencrypted variables. - - To do no automatic detection, set `detect_exclude` to False. - - # Example code - ```python - from py_hamt import HAMT, IPFSStore, IPFSZarr3, create_zarr_encryption_transformers - - ds = ... # example xarray Dataset with precip and temp data variables - encryption_key = bytes(32) # change before using, only for demonstration purposes! - header = "sample-header".encode() - encrypt, decrypt = create_zarr_encryption_transformers( - encryption_key, header, exclude_vars=["temp"], detect_exclude=ds - ) - hamt = HAMT( - store=IPFSStore(), transformer_encode=encrypt, transformer_decode=decrypt - ) - ipfszarr3 = IPFSZarr3(hamt) - ds.to_zarr(store=ipfszarr3, mode="w") - - print("Attempting to read and print metadata of partially encrypted zarr") - wrong_key = bytes([0xAA]) * 32 - wrong_header = "".encode() - bad_encrypt, auto_detecting_decrypt = create_zarr_encryption_transformers( - wrong_key, - wrong_header, - ) - hamt = HAMT(store=IPFSStore(), transformer_encode=bad_encrypt, transformer_decode=auto_detecting_decrypt, root_node_id=ipfszarr3.hamt.root_node_id) - ipfszarr3 = IPFSZarr3(hamt, read_only=True) - enc_ds = xr.open_zarr(store=ipfszarr3) - print(enc_ds) - assert enc_ds.temp.sum() == ds.temp.sum() - try: - enc_ds.precip.sum() - except: - print("Couldn't read encrypted variable") - ``` - """ - if len(encryption_key) != 32: - raise ValueError("Encryption key is not 32 bytes") - - exclude_var_set = set(exclude_vars) - - if isinstance(detect_exclude, xr.Dataset): - ds = detect_exclude - for coord in list(ds.coords): - exclude_var_set.add(coord) # type: ignore - - def _should_transform(key: str) -> bool: - # Find the first directory name in the path since zarr v3 chunks are stored in a nested directory structure - # e.g. for "precip/c/0/0/1" this would find "precip" - first_slash = key.find("/") - if first_slash != -1: - var_name = key[0:first_slash] - if var_name in exclude_var_set: - return False - - # Don't transform metadata files, even for encrypted variables - if key[-9:] == "zarr.json": - return False - - return True - - def encrypt(key: str, val: bytes) -> bytes: - if not _should_transform(key): - return val - - nonce = get_random_bytes(24) - cipher = ChaCha20_Poly1305.new(key=encryption_key, nonce=nonce) - cipher.update(header) - ciphertext, tag = cipher.encrypt_and_digest(val) - # + concatenates two byte variables x,y so that it looks like xy - return nonce + tag + ciphertext - - seen_metadata: set[str] = set() - - def decrypt(key: str, val: bytes) -> bytes: - # Look through files, this relies on the fact that xarray itself will attempt to read the root zarr.json and other metadata files first before any data will ever be accessed - # Important that this goes before _should_transform since that will return before we get a chance to look at metadata, and it needs information that we can glean here - if ( - detect_exclude == "auto-from-read" - and key[-9:] == "zarr.json" - and key not in seen_metadata - ): - seen_metadata.add(key) - - # Assume the zarr.json is unencrypted, which it should be if made with zarr encryption transformers - metadata = json.loads(dag_cbor.decode(val)) # type: ignore - - # If the global zarr.json, check if it has the list of coordinates in the consolidated metadata - if ( - "consolidated_metadata" in metadata - and metadata["consolidated_metadata"] is not None - ): - variables = metadata["consolidated_metadata"]["metadata"] - for var in variables: - for dimension in variables[var]["dimension_names"]: - exclude_var_set.add(dimension) - # Otherwise just scan a variable's individual metadata, but first make sure it's not the root zarr.json - elif "dimension_names" in metadata: - for dimension in metadata["dimension_names"]: - exclude_var_set.add(dimension) - - if not _should_transform(key): - return val - - try: - nonce, tag, ciphertext = val[:24], val[24:40], val[40:] - cipher = ChaCha20_Poly1305.new(key=encryption_key, nonce=nonce) - cipher.update(header) - plaintext = cipher.decrypt_and_verify(ciphertext, tag) - return plaintext - except Exception as e: - # If if we are auto detecting coordinates, and there's an error with decrypting, then assume the issue is that this is a partially encrypted zarr, so we need to mark this variable as being one of the unencrypted ones and return like normal - if detect_exclude == "auto-from-read": - first_slash = key.find("/") - if first_slash != -1: - var_name = key[0:first_slash] - exclude_var_set.add(var_name) - return val - else: - raise e - - return (encrypt, decrypt) diff --git a/pyproject.toml b/pyproject.toml index 4b6fc92..0acbf65 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -9,7 +9,6 @@ dependencies = [ "dag-cbor>=0.3.3", "msgspec>=0.18.6", 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Tue, 6 May 2025 09:15:04 -0400 Subject: [PATCH 009/118] even more efficient node implementation --- py_hamt/hamt.py | 28 ++-------------------------- 1 file changed, 2 insertions(+), 26 deletions(-) diff --git a/py_hamt/hamt.py b/py_hamt/hamt.py index 830c387..95f5c85 100644 --- a/py_hamt/hamt.py +++ b/py_hamt/hamt.py @@ -46,27 +46,8 @@ def extract_bits(hash_bytes: bytes, depth: int, nbits: int) -> int: class Node: - # Use a dict for easy serializability with dag_cbor - data: list[IPLDKind] - def __init__(self): - # Each "string" key for both buckets and CIDs is the bits as a string, e.g. str(0b1101) = '13' - buckets: dict[str, dict[str, IPLDKind]] = dict() - links: dict[str, Link] = {} - self.data = [buckets, links] # type: ignore - - # By having these two methods, the HAMT class has to know less about Node's internal structure and we get better type checking since we don't need to put #type:ignore everywhere - def get_buckets(self) -> dict[str, dict[str, IPLDKind]]: - # Buckets looks like - # {"0": {k1: v1, k2: v2, ...}, "1": ...} - buckets: dict[str, dict[str, IPLDKind]] = self.data[0] # type: ignore - return buckets - - def get_links(self) -> dict[str, Link]: - # Links looks like - # {"0": Link, "1": Link, ...} - links: dict[str, Link] = self.data[1] # type: ignore - return links + self.data: list[IPLDKind] = [dict() for _ in range(0, 256)] def serialize(self) -> bytes: return dag_cbor.encode(self.data) @@ -79,12 +60,7 @@ def deserialize(cls, data: bytes) -> "Node": raise Exception( "Invalid dag-cbor encoded data from the store was attempted to be decoded" ) - if ( - isinstance(decoded_data, list) - and len(decoded_data) == 2 - and isinstance(decoded_data[0], dict) - and isinstance(decoded_data[1], dict) - ): + if (isinstance(decoded_data, list) and len(decoded_data) == 256): node = cls() node.data = decoded_data return node From 0ceede9bb492d091e4d31f25d04e0c83410cbf47 Mon Sep 17 00:00:00 2001 From: Abid Sikder <41392423+abidsikder@users.noreply.github.com> Date: Tue, 6 May 2025 09:15:30 -0400 Subject: [PATCH 010/118] remove node test, rely on hamt integration instead --- tests/test_node.py | 20 -------------------- 1 file changed, 20 deletions(-) delete mode 100644 tests/test_node.py diff --git a/tests/test_node.py b/tests/test_node.py deleted file mode 100644 index 8b30948..0000000 --- a/tests/test_node.py +++ /dev/null @@ -1,20 +0,0 @@ -from py_hamt.hamt import Node -from hypothesis import given - -from testing_utils import key_value_list - - -@given(buckets_data=key_value_list, links_data=key_value_list) -def test_node(buckets_data, links_data): - node = Node() - buckets = dict() - for k, v in buckets_data: - buckets[k] = v - links = dict() - for k, v in links_data: - links[k] = v - node.data = [buckets, links] - - new_node = Node.deserialize(node.serialize()) - assert buckets == new_node.get_buckets() - assert links == new_node.get_links() From 655f1afe4b0ae2fcc424f329dff0d20aa601bef3 Mon Sep 17 00:00:00 2001 From: Abid Sikder <41392423+abidsikder@users.noreply.github.com> Date: Tue, 6 May 2025 09:15:52 -0400 Subject: [PATCH 011/118] add abstract method decorator, remove unnecessary line --- py_hamt/store.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/py_hamt/store.py b/py_hamt/store.py index 7afe105..214c82b 100644 --- a/py_hamt/store.py +++ b/py_hamt/store.py @@ -16,8 +16,10 @@ class Store(ABC): The return type of save and input to load is really type IPLDKind, but the documentation generates something a bit strange since IPLDKind is a type union. """ + @abstractmethod async def save(self, data: bytes, codec: Literal["raw", "dag-cbor"]) -> IPLDKind: """Take any set of bytes, save it to the storage mechanism, and reutrn an ID in the type of IPLDKind which can be used to retrieve those bytes later. This also includes extra information in `codec` on whether to mark this data as special linked data.""" + # TODO add bit about its important that dag-cbor is only called for an internal data structure node, and ONLY that type @abstractmethod async def load(self, id: IPLDKind) -> bytes: @@ -116,7 +118,6 @@ async def save(self, data: bytes, codec: Literal["raw", "dag-cbor"]) -> CID: async def load( # type: ignore self, id: CID, - session: aiohttp.ClientSession | None = None, ) -> bytes: if self.gateway_session is None: self.gateway_session = aiohttp.ClientSession( From 149bae2f5b364a0c4dbfa46af72fb0fc290dc991 Mon Sep 17 00:00:00 2001 From: Abid Sikder <41392423+abidsikder@users.noreply.github.com> Date: Tue, 6 May 2025 18:01:10 -0400 Subject: [PATCH 012/118] add type definition to store codec input --- py_hamt/store.py | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/py_hamt/store.py b/py_hamt/store.py index 214c82b..eeeb31c 100644 --- a/py_hamt/store.py +++ b/py_hamt/store.py @@ -9,6 +9,8 @@ import aiohttp +type CodecInput = Literal["raw", "dag-cbor"] + class Store(ABC): """Abstract class that represents a storage mechanism the HAMT can use for keeping data. @@ -17,7 +19,7 @@ class Store(ABC): """ @abstractmethod - async def save(self, data: bytes, codec: Literal["raw", "dag-cbor"]) -> IPLDKind: + async def save(self, data: bytes, codec: CodecInput) -> IPLDKind: """Take any set of bytes, save it to the storage mechanism, and reutrn an ID in the type of IPLDKind which can be used to retrieve those bytes later. This also includes extra information in `codec` on whether to mark this data as special linked data.""" # TODO add bit about its important that dag-cbor is only called for an internal data structure node, and ONLY that type @@ -39,7 +41,7 @@ def __init__(self): self.store = dict() self.hash_alg = multihash.get("blake3") - async def save(self, data: bytes, codec: Literal["raw", "dag-cbor"]) -> bytes: + async def save(self, data: bytes, codec: CodecInput) -> bytes: hash = self.hash_alg.digest(data, size=32) self.store[hash] = data return hash @@ -94,7 +96,7 @@ def __init__( # self.total_received: None | int = 0 if debug else None # """Total bytes in responses from IPFS for blocks. Used for debugging purposes.""" - async def save(self, data: bytes, codec: Literal["raw", "dag-cbor"]) -> CID: + async def save(self, data: bytes, codec: CodecInput) -> CID: if self.rpc_session is None: self.rpc_session = aiohttp.ClientSession( base_url=IPFSStore.KUBO_DEFAULT_LOCAL_RPC_BASE_URL @@ -114,10 +116,8 @@ async def save(self, data: bytes, codec: Literal["raw", "dag-cbor"]) -> CID: return cid - # Ignore the type error since CID is in the IPLDKind type - async def load( # type: ignore - self, - id: CID, + async def load( # type: ignore CID is definitely in the IPLDKind type + self, id: CID ) -> bytes: if self.gateway_session is None: self.gateway_session = aiohttp.ClientSession( From 7dd2b9c38006d20ce8bcecaccaed69988cd640c9 Mon Sep 17 00:00:00 2001 From: Abid Sikder <41392423+abidsikder@users.noreply.github.com> Date: Tue, 6 May 2025 18:01:17 -0400 Subject: [PATCH 013/118] ignore .DS_Store --- .gitignore | 1 + 1 file changed, 1 insertion(+) diff --git a/.gitignore b/.gitignore index 87ee1b3..3b7b425 100644 --- a/.gitignore +++ b/.gitignore @@ -1,3 +1,4 @@ +.DS_Store pyrightconfig.json *.prof From 1a0324eef69cdf51e120698c6c1b92dee297cc6a Mon Sep 17 00:00:00 2001 From: Abid Sikder <41392423+abidsikder@users.noreply.github.com> Date: Tue, 6 May 2025 18:01:46 -0400 Subject: [PATCH 014/118] async alternatives to all methods, VirtualStore with cache and in memory tree, incomplete --- py_hamt/hamt.py | 652 ++++++++++++++++++++++++++++-------------------- 1 file changed, 384 insertions(+), 268 deletions(-) diff --git a/py_hamt/hamt.py b/py_hamt/hamt.py index 95f5c85..a1d98ba 100644 --- a/py_hamt/hamt.py +++ b/py_hamt/hamt.py @@ -1,7 +1,11 @@ +from abc import ABC, abstractmethod from collections.abc import MutableMapping from sys import getsizeof from threading import Lock -from typing import Callable +from typing import Callable, Iterator, AsyncIterator +import uuid +from random import shuffle +import asyncio import dag_cbor from dag_cbor.ipld import IPLDKind @@ -39,6 +43,23 @@ def extract_bits(hash_bytes: bytes, depth: int, nbits: int) -> int: return result +b3 = multihash.get("blake3") + + +def blake3_hashfn(input_bytes: bytes) -> bytes: + """ + This is provided as a default recommended hash function by py-hamt. It uses the blake3 hash function and uses 32 bytes as the hash size. + + To bring your own hash function, just create a function that takes in bytes and returns the hash bytes, and use that in the HAMT init method. + + It's important to note that the resulting hash must must always be a multiple of 8 bits since python bytes object can only represent in segments of bytes, and thus 8 bits. + """ + # 32 bytes is the recommended byte size for blake3 and the default, but multihash forces us to explicitly specify + digest = b3.digest(input_bytes, size=32) + raw_bytes = b3.unwrap(digest) + return raw_bytes + + # Used for readability, since a HAMT also stores IPLDKind objects # Store IDs are also IPLDKind, which makes the code harder to read if only using IPLDKind rather than this type alias type Link = IPLDKind @@ -48,6 +69,27 @@ def extract_bits(hash_bytes: bytes, depth: int, nbits: int) -> int: class Node: def __init__(self): self.data: list[IPLDKind] = [dict() for _ in range(0, 256)] + # empty dicts represent empty buckets, lists with one element are links, with the internal element being a link + + def iter_buckets(self) -> Iterator[int]: + """Return the list indices where there are buckets, empty or not.""" + for i in range(len(self.data)): + if isinstance(self.data[i], dict): + yield i + + def iter_links(self) -> Iterator[int]: + """Return the list indices where there are links.""" + for i in range(len(self.data)): + if isinstance(self.data[i], list): + yield i + + def get_link(self, index: int) -> IPLDKind: + link_wrapper: list[IPLDKind] = self.data[index] # type: ignore + return link_wrapper[0] + + def set_link(self, index: int, link: IPLDKind): + wrapped = [link] + self.data[index] = wrapped def serialize(self) -> bytes: return dag_cbor.encode(self.data) @@ -60,7 +102,7 @@ def deserialize(cls, data: bytes) -> "Node": raise Exception( "Invalid dag-cbor encoded data from the store was attempted to be decoded" ) - if (isinstance(decoded_data, list) and len(decoded_data) == 256): + if isinstance(decoded_data, list) and len(decoded_data) == 256: node = cls() node.data = decoded_data return node @@ -68,21 +110,161 @@ def deserialize(cls, data: bytes) -> "Node": raise ValueError("Data does not contain a valid Node") -b3 = multihash.get("blake3") +# For HAMT internal use for increaing performance with nodes +class VirtualStore(ABC): + @abstractmethod + async def save(self, original_id: IPLDKind, node: Node) -> IPLDKind: + pass + @abstractmethod + async def load(self, id: IPLDKind) -> Node: + pass -def blake3_hashfn(input_bytes: bytes) -> bytes: - """ - This is provided as a default recommended hash function by py-hamt. It uses the blake3 hash function and uses 32 bytes as the hash size. - To bring your own hash function, just create a function that takes in bytes and returns the hash bytes, and use that in the HAMT init method. +class ReadCacheStore(VirtualStore): + def __init__(self, hamt: "HAMT"): + self.cache: dict[IPLDKind, Node] = dict() + self.hamt = hamt - It's important to note that the resulting hash must must always be a multiple of 8 bits since python bytes object can only represent in segments of bytes, and thus 8 bits. - """ - # 32 bytes is the recommended byte size for blake3 and the default, but multihash forces us to explicitly specify - digest = b3.digest(input_bytes, size=32) - raw_bytes = b3.unwrap(digest) - return raw_bytes + def cache_eviction_lru(self): + while getsizeof(self.cache) > self.hamt.read_cache_limit: + if len(self.cache) == 0: + return + stalest_node_id = next(iter(self.cache.keys())) + del self.cache[stalest_node_id] + + async def save(self, original_id: IPLDKind, node: Node) -> IPLDKind: + raise Exception( + "Save called in virtual store ReadCacheStore, only supposed to be used for reading" + ) + + async def load(self, id: IPLDKind) -> Node: + # Cache Hit + if id in self.cache: + # Reinsert to put this key as the most recently used and last in the dict insertion order + node = self.cache[id] + del self.cache[id] + self.cache[id] = node + + return node + + # Cache Miss + node = Node.deserialize(await self.hamt.store.load(id)) + self.cache[id] = node + self.cache_eviction_lru() + return node + + +class InMemoryTreeStore(VirtualStore): + def __init__(self, hamt: "HAMT"): + self.hamt = hamt + + # The Store ID returned by the InMemoryTree to mark objects as being in memory looks like list[inmemory_marker, virtual store uuid int ID for that node, original Store ID] + self.inmemory_marker = uuid.uuid4().int + # This buffer goes from the node's virtual store uuid to a Node object, which we can return references to for mutating within the HAMT + self.buffer: dict[IPLDKind, Node] = dict() + + def is_buffer_id(self, id: IPLDKind) -> bool: + return isinstance(id, list) and len(id) == 3 and id[0] == self.inmemory_marker + + def children_in_memory(self, node: Node) -> Iterator[IPLDKind]: + for index in range(len(node.data)): + item = node.data[index] + if self.is_buffer_id(item): + yield item + + def has_children_in_memory(self, node: Node) -> bool: + for _ in self.children_in_memory(node): + return True + return False + + def needs_flushing(self) -> bool: + return getsizeof(self.buffer) > self.hamt.inmemory_tree_limit + + async def flush_buffer(self, flush_everything: bool = False): + if (not self.needs_flushing()) and (not flush_everything): + return + + # Start with the root node's children, which should always be in the in memory buffer if there's anything there + # there is an implicit assumption that the entire continuous line of branches up to an ancestor in the memory buffer, which will happen because of the DFS style traversal in all HAMT operations + # node stack is a list of tuples that look like (parent_id, self_id, node) + node_stack: list[tuple[IPLDKind, IPLDKind, Node]] = [] + root_node: Node = self.buffer[self.hamt.root_node_id] + for child_buffer_id in self.children_in_memory(root_node): + node = self.buffer[child_buffer_id] + node_stack.append((self.hamt.root_node_id, child_buffer_id, node)) + + shuffle(node_stack) # so that we don't always recurse down the rightmost branch + + while len(node_stack) > 0 and (self.needs_flushing() or flush_everything): + top_parent_buffer_id, top_buffer_id, top_node = node_stack[-1] + new_nodes_on_stack = [] + if self.has_children_in_memory(top_node): + for child_buffer_id in self.children_in_memory(top_node): + node = self.buffer[child_buffer_id] + new_nodes_on_stack.append((top_buffer_id, child_buffer_id, node)) + + shuffle( + new_nodes_on_stack + ) # avoid always recursing down the rightmost branch first + node_stack.extend(new_nodes_on_stack) + else: + # We can flush this one completely, we'll just have to reserialize its parents up to the root node + old_id = top_buffer_id + new_id = await self.hamt.store.save( + top_node.serialize(), codec="dag-cbor" + ) + parent_node = self.buffer[top_parent_buffer_id] + for i in range(len(parent_node.data)): + item = parent_node.data[i] + if self.is_buffer_id(item) and item == old_id: + parent_node.set_link(i, new_id) + break + + del self.buffer[top_buffer_id] # type: ignore + node_stack.pop() + + # Only flush the root node if our size limits are still too big, or we've been instructed to remove everything. Always keeping the root node is important for performance + if self.needs_flushing() or flush_everything: + del self.buffer[self.root_node_id] + self.root_node_id = await self.hamt.store.save( + root_node.serialize(), codec="dag-cbor" + ) + + if flush_everything: + assert len(self.buffer) == 0 + if self.needs_flushing(): + raise Exception( + "Could not flush in memory tree buffer enough to reach limit, consider raising limit to accomodate for python empty object overheads" + ) + + async def add_to_buffer(self, original_id: IPLDKind, node: Node) -> list: + # This is IPLDKind type, but not dag_cbor serializable due to int limits so this will throw errors early if the tree is written with the buffer_ids still in there + node_uuid = uuid.uuid4().int + buffer_id = [self.inmemory_marker, node_uuid, original_id] + # Returns the virtual store ID that was generated for this node + self.buffer[buffer_id] = node + + return buffer_id + + async def save(self, original_id: IPLDKind, node: Node) -> IPLDKind: + if self.is_buffer_id(original_id): + return original_id + + # This node was not in the buffer, don't save it to the backing store but rather add to it to the in memory buffer + buffer_id = await self.add_to_buffer(original_id, node) + return buffer_id + + async def load(self, id: IPLDKind) -> Node: + # Hit for something already in the in memory tree + if self.is_buffer_id(id): + node: Node = self.buffer[id] # type: ignore + return node + + # Miss, something that isn't in the in memory tree, add it + node = Node.deserialize(await self.hamt.store.load(id)) + await self.add_to_buffer(id, node) + return node class HAMT(MutableMapping): @@ -97,11 +279,6 @@ class HAMT(MutableMapping): In write enabled mode, all operations block and wait, so multiple threads can write to the HAMT but the operations will in reality happen one after the other. - # transformer_encode, transformer_decode - `transformer_encode` and `transformer_decode` are functions that are called right before sending raw data to the store, after being encoded with dag_cbor. They get access to the key that the value originally corresponded to. - - HAMT also sometimes sends its internal data structure objects to the store, those will not pass through these functions. - # dunder method documentation These are not generated by pdoc automatically so we are including their documentation here. @@ -122,9 +299,11 @@ class HAMT(MutableMapping): store: Store """@private""" + # Every call of this will look like self.hash_fn() and so the first argument will always take a self argument hash_fn: Callable[[bytes], bytes] """@private""" + # Only important for writing, when reading this will use buckets even if they are overly big max_bucket_size: int """@private""" @@ -133,6 +312,8 @@ class HAMT(MutableMapping): root_node_id: IPLDKind """DO NOT modify this directly. + TODO write about how you do need to read it at times, and it should only be read when the buffer has been flushed to the backing store + This is the ID that the store returns for the root node of the HAMT. This is exposed since it is sometimes useful to reconstruct other HAMTs later if using a persistent store. This is really type IPLDKind, but the documentation generates this strange type instead since IPLDKind is a type union. @@ -144,127 +325,104 @@ class HAMT(MutableMapping): For use in multithreading """ - read_only: bool - """ - DO NOT modify this directly. This is here for you to read and check. - - You can modify the read status of a HAMT through the `make_read_only` or `enable_write` functions, so that the HAMT will block on making a change until all mutating operations are done. - """ + async def write_raw(self, data: IPLDKind) -> IPLDKind: + return await self.store.save(dag_cbor.encode(data), codec="raw") - transformer_encode: None | Callable[[str, bytes], bytes] - """This function is called to transform the raw bytes of a value after it is encoded with dag_cbor but before it gets sent to the Store.""" - transformer_decode: None | Callable[[str, bytes], bytes] - """This function is called to transform the raw bytes of a value after it is retrieved from the store but before decoding with dag_cbor to python IPLDKind type objects.""" + async def read_raw(self, id: IPLDKind) -> IPLDKind: + return dag_cbor.decode(await self.store.load(id)) - cache: dict[StoreID, Node] - """@private""" - max_cache_size_bytes: int - """The maximum size of the internal cache of nodes. We expect that some Stores will be high latency, so it is useful to cache parts of the datastructure. + async def read_node(self, id: IPLDKind) -> Node: + # TODO handle having a cache as well, with cache limits + if self.inmemory_buffer is not None and id in self.inmemory_buffer: + return self.inmemory_buffer[id] - Set to 0 if you want no cache at all.""" + node = Node.deserialize(await self.store.load(id)) + await self.add_to_buffer(id, node) + return node - # We rely on python 3.7+'s dicts which keep insertion order of elements to do a basic LRU - def cache_eviction_lru(self): - while getsizeof(self.cache) > self.max_cache_size_bytes: - if len(self.cache) == 0: - return - stalest_node_id = next(iter(self.cache.keys())) - del self.cache[stalest_node_id] + async def write_node(self, old_id: IPLDKind, node: Node) -> IPLDKind: + if self.inmemory_buffer is not None and old_id in self.inmemory_buffer: + # Nodes hold a mutable pointer to their data, so we shouldn't even need to set the inmemory buffer to this new node + return old_id - def write_node(self, node: Node) -> IPLDKind: - """@private""" - node_id = self.store.save_dag_cbor(node.serialize()) - self.cache[node_id] = node - self.cache_eviction_lru() - return node_id - - def read_node(self, node_id: IPLDKind) -> Node: - """@private""" - node: Node - # cache hit - if node_id in self.cache: - node = self.cache[node_id] - # Reinsert to put this key as the most recently used and last in the dict insertion order - del self.cache[node_id] - self.cache[node_id] = node - # cache miss - else: - node = Node.deserialize(self.store.load(node_id)) - self.cache[node_id] = node - self.cache_eviction_lru() + new_id = await self.store.save(node.serialize(), codec="dag-cbor") + await self.add_to_buffer(new_id, node) + return new_id - return node + inmemory_buffer: dict[IPLDKind, Node] | None def __init__( self, store: Store, hash_fn: Callable[[bytes], bytes] = blake3_hashfn, - read_only: bool = False, root_node_id: IPLDKind = None, - max_cache_size_bytes=10_000_000, # default to 10 megabytes - transformer_encode: None | Callable[[str, bytes], bytes] = None, - transformer_decode: None | Callable[[str, bytes], bytes] = None, + read_only: bool = False, + max_bucket_size: int = 67, + inmemory_tree_limit: int = 10_000_000, # 10 MB default + read_cache_limit: int = 10_000_000, # 10 MB default ): self.store = store self.hash_fn = hash_fn - - self.cache = {} - self.max_cache_size_bytes = max_cache_size_bytes - - self.max_bucket_size = 4 - self.read_only = read_only self.lock = Lock() + self.read_only = read_only - self.transformer_encode = transformer_encode - self.transformer_decode = transformer_decode + if max_bucket_size < 1: + raise ValueError("Bucket size maximum must be a positive integer") + self.max_bucket_size = max_bucket_size - if root_node_id is None: - root_node = Node() - self.root_node_id = self.write_node(root_node) - else: - self.root_node_id = root_node_id - # Make sure the cache has our root node - self.read_node(self.root_node_id) + # TODO add documentation about buffer limit and cache limit minimums being 10 KB, to avoid strange boundary cases in the algorithms due to python object overhead meaning that an in memory buffer should just never be used + # Add documentation about how its values should not be positive, otherwise the HAMT will not work + # Specify a minimum size of a couple hundred bytes, since just an empty dict will consume some memory - # dunder for the python deepcopy module - def __deepcopy__(self, memo) -> "HAMT": - if not self.read_only: - self.lock.acquire(blocking=True) + if read_cache_limit < 10_000: + raise ValueError("Cache limit too small, less than 10 KB") + if inmemory_tree_limit < 10_000: + raise ValueError("In memory tree limit too small, less than 10 KB") - copy_hamt = HAMT( - store=self.store, - hash_fn=self.hash_fn, - read_only=self.read_only, - root_node_id=self.root_node_id, - transformer_encode=self.transformer_encode, - transformer_decode=self.transformer_decode, - ) + self.inmemory_tree_limit = inmemory_tree_limit + self.read_cache_limit = read_cache_limit - if not self.read_only: - self.lock.release() + # Create an empty in memory tree or read cache store + self.virtual_store: VirtualStore + if read_only: + self.virtual_store = ReadCacheStore(self) + else: + self.virtual_store = InMemoryTreeStore(self) - return copy_hamt + if root_node_id is None: + self.root_node_id = asyncio.run(self.write_node(None, Node())) + else: + self.root_node_id = root_node_id def make_read_only(self): - """Disables all mutation of this HAMT. When enabled, the HAMT will throw errors if set or delete are called. When a HAMT is only in read only mode, it allows for safe multithreaded reads, increasing performance.""" self.lock.acquire(blocking=True) self.read_only = True + asyncio.run(self.flush_buffer(flush_everything=True)) + self.inmemory_buffer = None + self.cache = dict() self.lock.release() def enable_write(self): self.lock.acquire(blocking=True) self.read_only = False + self.inmemory_buffer = dict() + self.cache = None self.lock.release() - def _reserialize_and_link(self, node_stack: list[tuple[Link, Node]]): + async def _reserialize_and_link(self, node_stack: list[tuple[Link, Node]]): + # TODO this, or the set_pointer and delitem functions must manage best when to flush the in memory tree, since that requires that traveling down the branch to an arbitrary node within the buffer is contiguous """ - For internal use This function starts from the node at the end of the list and reserializes so that each node holds valid new IDs after insertion into the store Takes a stack of nodes, we represent a stack with a list where the first element is the root element and the last element is the top of the stack Each element in the list is a tuple where the first element is the ID from the store and the second element is the Node in python If a node ends up being empty, then it is deleted entirely, unless it is the root node Modifies in place """ + # if we have just the root node, then don't operate at all and serialize it all the way + if len(node_stack) == 1: + self.cache[self.root_node_id] = node_stack[0][1] + return + # Iterate in the reverse direction, imitating going deeper into a stack for stack_index in range(len(node_stack) - 1, -1, -1): old_store_id, node = node_stack[stack_index] @@ -293,19 +451,21 @@ def _reserialize_and_link(self, node_stack: list[tuple[Link, Node]]): prev_node._replace_link(old_store_id, new_store_id) def __setitem__(self, key_to_insert: str, val_to_insert: IPLDKind): + asyncio.run(self.setitem(key_to_insert, val_to_insert)) + + async def setitem(self, key_to_insert: str, val_to_insert: IPLDKind): + val_ptr = await self.write_raw(val_to_insert) + await self.set_pointer(key_to_insert, val_ptr) + + async def set_pointer(self, key_to_insert: str, val_ptr: IPLDKind): if self.read_only: raise Exception("Cannot call set on a read only HAMT") if not self.read_only: self.lock.acquire(blocking=True) - val = dag_cbor.encode(val_to_insert) - if self.transformer_encode is not None: - val = self.transformer_encode(key_to_insert, val) - val_ptr = self.store.save_raw(val) - - node_stack: list[tuple[Link, Node]] = [] - root_node = self.read_node(self.root_node_id) + node_stack: list[tuple[IPLDKind, Node]] = [] + root_node = await self.read_node(self.root_node_id) node_stack.append((self.root_node_id, root_node)) # FIFO queue to keep track of all the KVs we need to insert @@ -313,83 +473,51 @@ def __setitem__(self, key_to_insert: str, val_to_insert: IPLDKind): kvs_queue: list[tuple[str, IPLDKind]] = [] kvs_queue.append((key_to_insert, val_ptr)) - created_change = False - # Keep iterating until we have no more KVs to insert - while len(kvs_queue) != 0: + while len(kvs_queue) > 0: _, top_node = node_stack[-1] - curr_key, curr_val = kvs_queue[0] + curr_key, curr_val_ptr = kvs_queue[0] raw_hash = self.hash_fn(curr_key.encode()) - map_key = str(extract_bits(raw_hash, len(node_stack) - 1, 8)) - - buckets = top_node.get_buckets() - links = top_node.get_links() + map_key = extract_bits(raw_hash, len(node_stack) - 1, 8) - if map_key in links and map_key in buckets: - self.lock.release() - raise Exception( - "Key in both buckets and links of the node, invariant violated" - ) - elif map_key in links: - next_node_id = links[map_key] - next_node = self.read_node(next_node_id) + item = top_node.data[map_key] + if isinstance(item, list): + next_node_id = item[0] + next_node = await self.read_node(next_node_id) node_stack.append((next_node_id, next_node)) - elif map_key in buckets: - bucket = buckets[map_key] - created_change = True - - # If this bucket already has this same key, just rewrite the value - # Since we can't use continues to go back to the top of the while loop, use this boolean flag instead - should_continue_at_while = False - for kv in bucket: - if curr_key in kv: - kv[curr_key] = curr_val - kvs_queue.pop(0) - should_continue_at_while = True - break - if should_continue_at_while: - continue + if isinstance(item, dict): + bucket: dict[str, IPLDKind] = item - bucket_has_space = len(bucket) < self.max_bucket_size - if bucket_has_space: - bucket.append({curr_key: curr_val}) + # If this bucket already has this same key, or has space, just rewrite the value and work on the others in the queue + if curr_key in bucket or len(bucket) < self.max_bucket_size: + bucket[curr_key] = curr_val_ptr kvs_queue.pop(0) - # If bucket is full and we need to add, then all these KVs need to be taken out of this bucket and reinserted throughout the tree - else: - # Empty the bucket of KVs into the queue - for kv in bucket: - for k, v in kv.items(): - kvs_queue.append((k, v)) - - # Delete empty bucket, there should only be a link now - del buckets[map_key] + continue - # Create a new link to a new node so that we can reflow these KVs into new buckets - new_node = Node() - new_node_id = self.write_node(new_node) + # The current key is not in the bucket and the bucket is too full, so empty KVs from the bucket and restart insertion + for k, v_ptr in bucket: + kvs_queue.append((k, v_ptr)) - links[map_key] = new_node_id + # Create a new link to a new node so that we can reflow these KVs into nodes + new_node = Node() + new_node_id = await self.write_node(None, new_node) - # We need to rerun from the top with the new queue, but this time this node will have a link to put KVs deeper down in the tree - node_stack.append((new_node_id, new_node)) - else: - # If there is no link and no bucket, then we can create a new bucket, insert, and be done with this key - bucket: list[dict[str, IPLDKind]] = [] - bucket.append({curr_key: curr_val}) - kvs_queue.pop(0) - buckets[map_key] = bucket - created_change = True + link = [new_node_id] + top_node.data[map_key] = link # Finally, reserialize and fix all links, deleting empty nodes as needed - if created_change: - self._reserialize_and_link(node_stack) - node_stack_top_id = node_stack[0][0] - self.root_node_id = node_stack_top_id + await self._reserialize_and_link(node_stack) + node_stack_top_id = node_stack[0][0] + self.root_node_id = node_stack_top_id if not self.read_only: self.lock.release() def __delitem__(self, key: str): + asyncio.run(self.delitem(key)) + + async def delitem(self, key: str): + """Also deletes the pointer at the same time.""" if self.read_only: raise Exception("Cannot call delete on a read only HAMT") @@ -398,54 +526,31 @@ def __delitem__(self, key: str): raw_hash = self.hash_fn(key.encode()) - node_stack: list[tuple[Link, Node]] = [] - root_node = self.read_node(self.root_node_id) + node_stack: list[tuple[IPLDKind, Node]] = [] + root_node = await self.read_node(self.root_node_id) node_stack.append((self.root_node_id, root_node)) created_change = False while True: - top_id, top_node = node_stack[-1] - map_key = str(extract_bits(raw_hash, len(node_stack) - 1, 8)) - - buckets = top_node.get_buckets() - links = top_node.get_links() - - if map_key in buckets and map_key in links: - self.lock.release() - raise Exception( - "Key in both buckets and links of the node, invariant violated" - ) - elif map_key in buckets: - bucket = buckets[map_key] - - # Delete from within this bucket - for bucket_index in range(len(bucket)): - kv = bucket[bucket_index] - if key in kv: - created_change = True - bucket.pop(bucket_index) - - # If this bucket becomes empty then delete this dict entry for the bucket - if len(bucket) == 0: - del buckets[map_key] + _, top_node = node_stack[-1] + map_key = extract_bits(raw_hash, len(node_stack) - 1, 8) - # This must be done to avoid IndexErrors after continuing to iterate since the length of the bucket has now changed - break + item = top_node.data[map_key] + if isinstance(item, dict): + bucket = item + if key in bucket: + del bucket[key] + created_change = True break - elif map_key in links: - link = links[map_key] - next_node = self.read_node(link) + if isinstance(item, list): + link = item[0] + next_node = await self.read_node(link) node_stack.append((link, next_node)) - continue - - else: - # This key is not even in the HAMT so just exit - break # Finally, reserialize and fix all links, deleting empty nodes as needed if created_change: - self._reserialize_and_link(node_stack) + await self._reserialize_and_link(node_stack) node_stack_top_id = node_stack[0][0] self.root_node_id = node_stack_top_id @@ -456,37 +561,41 @@ def __delitem__(self, key: str): raise KeyError def __getitem__(self, key: str) -> IPLDKind: + return asyncio.run(self.getitem(key)) + + async def getitem(self, key: str) -> IPLDKind: + pointer: IPLDKind = await self.get_pointer(key) + return await self.read_raw(pointer) + + async def get_pointer(self, key: str) -> IPLDKind: if not self.read_only: self.lock.acquire(blocking=True) raw_hash = self.hash_fn(key.encode()) - node_id_stack: list[Link] = [] - node_id_stack.append(self.root_node_id) + current_id = self.root_node_id + current_depth = 0 - # Don't check if result is none but use a boolean to indicate finding something, this is because None is a possible value the HAMT can store + # Don't check if result is none but use a boolean to indicate finding something, this is because None is a possible value of IPLDKind result_ptr: IPLDKind = None found_a_result: bool = False while True: - top_id = node_id_stack[-1] - top_node = self.read_node(top_id) - map_key = str(extract_bits(raw_hash, len(node_id_stack) - 1, 8)) - - # Check if this node is in one of the buckets - buckets = top_node.get_buckets() - if map_key in buckets: - bucket = buckets[map_key] - for kv in bucket: - if key in kv: - result_ptr = kv[key] - found_a_result = True - break - - # If it isn't in one of the buckets, check if there's a link to another serialized node id - links = top_node.get_links() - if map_key in links: - link_id = links[map_key] - node_id_stack.append(link_id) + top_id = current_id + top_node = await self.read_node(top_id) + map_key = extract_bits(raw_hash, current_depth, 8) + + # Check if this key is in one of the buckets + item = top_node.data[map_key] + if isinstance(item, dict): + bucket = item + if key in bucket: + result_ptr = bucket[key] + found_a_result = True + break + if isinstance(item, list): + link = item[0] + current_id = link + current_depth += 1 continue # Nowhere left to go, stop walking down the tree else: @@ -498,70 +607,77 @@ def __getitem__(self, key: str) -> IPLDKind: if not found_a_result: raise KeyError - result_bytes = self.store.load(result_ptr) - if self.transformer_decode is not None: - result_bytes = self.transformer_decode(key, result_bytes) - return dag_cbor.decode(result_bytes) + return result_ptr - def __len__(self) -> int: - key_count = 0 - for _ in self: - key_count += 1 - - return key_count - - def __iter__(self): + async def _iter_nodes(self) -> AsyncIterator[tuple[IPLDKind, Node]]: if not self.read_only: self.lock.acquire(blocking=True) node_id_stack = [] node_id_stack.append(self.root_node_id) - if not self.read_only: - self.lock.release() - while True: if len(node_id_stack) == 0: break top_id = node_id_stack.pop() - node = self.read_node(top_id) - - # Collect all keys from all buckets - buckets = node.get_buckets() - for bucket in buckets.values(): - for kv in bucket: - for k in kv: - yield k + node = await self.read_node(top_id) + yield (top_id, node) # Traverse down list of links - links = node.get_links() - for link in links.values(): + for link_index in node.iter_links(): + link = node.get_link(link_index) node_id_stack.append(link) - def ids(self): - """Generator of all IDs the backing store uses""" + if not self.read_only: + self.lock.release() + + def __iter__(self): if not self.read_only: self.lock.acquire(blocking=True) - node_id_stack: list[Link] = [] + node_id_stack = [] node_id_stack.append(self.root_node_id) + while True: + if len(node_id_stack) == 0: + break + + top_id = node_id_stack.pop() + node = asyncio.run(self.read_node(top_id)) + + for item_index in range(len(node.data)): + item = node.data[item_index] + if isinstance(item, dict): + bucket = item + for key in bucket: + yield key + elif isinstance(item, list): + link = item[0] + node_id_stack.append(link) + if not self.read_only: self.lock.release() - while len(node_id_stack) > 0: - top_id = node_id_stack.pop() - yield top_id - top_node = self.read_node(top_id) - - buckets = top_node.get_buckets() - for bucket in buckets.values(): - for kv in bucket: - for v in kv.values(): - yield v - - # Traverse down list of ids that are the store's links' - links = top_node.get_links() - for link in links.values(): - node_id_stack.append(link) + async def aiter_keys(self) -> AsyncIterator[str]: + async for _, node in self._iter_nodes(): + for item_index in range(len(node.data)): + item = node.data[item_index] + if isinstance(item, dict): + bucket = item + for key in bucket: + yield key + + def __len__(self) -> int: + count = 0 + for _ in self: + count += 1 + + return count + + async def async_len(self): + count = 0 + async for _ in self.aiter_keys(): + count += 1 + + return count From 9646367311fb04b3467ee84b8baf3defa06408f7 Mon Sep 17 00:00:00 2001 From: Abid Sikder <41392423+abidsikder@users.noreply.github.com> Date: Wed, 7 May 2025 08:36:13 -0400 Subject: [PATCH 015/118] finish reserialization and linking changes --- py_hamt/hamt.py | 106 +++++++++++++++++++++++++----------------------- 1 file changed, 55 insertions(+), 51 deletions(-) diff --git a/py_hamt/hamt.py b/py_hamt/hamt.py index a1d98ba..8264dda 100644 --- a/py_hamt/hamt.py +++ b/py_hamt/hamt.py @@ -91,6 +91,13 @@ def set_link(self, index: int, link: IPLDKind): wrapped = [link] self.data[index] = wrapped + def replace_link(self, old_link: IPLDKind, new_link: IPLDKind): + for link_index in self.iter_links(): + link = self.get_link(link_index) + if link == old_link: + self.data[link_index] = new_link + return + def serialize(self) -> bytes: return dag_cbor.encode(self.data) @@ -160,6 +167,7 @@ def __init__(self, hamt: "HAMT"): self.hamt = hamt # The Store ID returned by the InMemoryTree to mark objects as being in memory looks like list[inmemory_marker, virtual store uuid int ID for that node, original Store ID] + # TODO write about how a virtual store uuid int is used for every specific node since content addressed systems would normally return the same Store ID for every single empty Node self.inmemory_marker = uuid.uuid4().int # This buffer goes from the node's virtual store uuid to a Node object, which we can return references to for mutating within the HAMT self.buffer: dict[IPLDKind, Node] = dict() @@ -331,26 +339,6 @@ async def write_raw(self, data: IPLDKind) -> IPLDKind: async def read_raw(self, id: IPLDKind) -> IPLDKind: return dag_cbor.decode(await self.store.load(id)) - async def read_node(self, id: IPLDKind) -> Node: - # TODO handle having a cache as well, with cache limits - if self.inmemory_buffer is not None and id in self.inmemory_buffer: - return self.inmemory_buffer[id] - - node = Node.deserialize(await self.store.load(id)) - await self.add_to_buffer(id, node) - return node - - async def write_node(self, old_id: IPLDKind, node: Node) -> IPLDKind: - if self.inmemory_buffer is not None and old_id in self.inmemory_buffer: - # Nodes hold a mutable pointer to their data, so we shouldn't even need to set the inmemory buffer to this new node - return old_id - - new_id = await self.store.save(node.serialize(), codec="dag-cbor") - await self.add_to_buffer(new_id, node) - return new_id - - inmemory_buffer: dict[IPLDKind, Node] | None - def __init__( self, store: Store, @@ -382,6 +370,13 @@ def __init__( self.inmemory_tree_limit = inmemory_tree_limit self.read_cache_limit = read_cache_limit + self.root_node_id = root_node_id + # Create an empty node to use as the root node + if root_node_id is None: + self.root_node_id = asyncio.run( + self.store.save(Node().serialize(), "dag-cbor") + ) + # Create an empty in memory tree or read cache store self.virtual_store: VirtualStore if read_only: @@ -389,24 +384,24 @@ def __init__( else: self.virtual_store = InMemoryTreeStore(self) - if root_node_id is None: - self.root_node_id = asyncio.run(self.write_node(None, Node())) - else: - self.root_node_id = root_node_id - + # This is typically a massive blocking operation, you dont want to be running this concurrently with a bunch of other operations, so it's ok to have it not be async def make_read_only(self): self.lock.acquire(blocking=True) self.read_only = True - asyncio.run(self.flush_buffer(flush_everything=True)) - self.inmemory_buffer = None - self.cache = dict() + + # Swap in memory tree for a read cache + inmemory_tree: InMemoryTreeStore = self.virtual_store # type: ignore + asyncio.run(inmemory_tree.flush_buffer(flush_everything=True)) + + read_cache = ReadCacheStore(self) + self.virtual_store = read_cache + self.lock.release() def enable_write(self): self.lock.acquire(blocking=True) self.read_only = False - self.inmemory_buffer = dict() - self.cache = None + self.virtual_store = InMemoryTreeStore(self) self.lock.release() async def _reserialize_and_link(self, node_stack: list[tuple[Link, Node]]): @@ -418,37 +413,46 @@ async def _reserialize_and_link(self, node_stack: list[tuple[Link, Node]]): If a node ends up being empty, then it is deleted entirely, unless it is the root node Modifies in place """ - # if we have just the root node, then don't operate at all and serialize it all the way - if len(node_stack) == 1: - self.cache[self.root_node_id] = node_stack[0][1] - return - # Iterate in the reverse direction, imitating going deeper into a stack + # this range goes from n-1 to 0 for stack_index in range(len(node_stack) - 1, -1, -1): - old_store_id, node = node_stack[stack_index] - - # If this node is empty, and its not the root node, then we can delete it entirely from the list - buckets = node.get_buckets() - links = node.get_links() - is_empty = buckets == {} and links == {} + old_id, node = node_stack[stack_index] + + # If this node is empty, and it's not the root node, then we can delete it entirely from the list + is_empty = True + for i in range(len(node.data)): + item = node.data[i] + # If we have a nonempty bucket, or a link at all, then this is a nonempty node + if (isinstance(item, dict) and len(item) > 0) or isinstance(item, list): + is_empty = False + break is_not_root = stack_index > 0 if is_empty and is_not_root: # Unlink from the rest of the tree _, prev_node = node_stack[stack_index - 1] - prev_node._remove_link(old_store_id) + # When removing links, don't worry about two nodes having the same link since all nodes are guaranteed to be different by the design of the tree and the exclusion of empty nodes + for i in range(len(prev_node.data)): + item = prev_node.data + if isinstance(item, dict): + continue + link = item[0] + # Delete the link by making it an empty bucket + if link == old_id: + prev_node.data[i] = dict() # Remove from our stack node_stack.pop(stack_index) - else: - # Reserialize - new_store_id = self.write_node(node) - node_stack[stack_index] = (new_store_id, node) - - # If this is not the last i.e. root node, we need to change the linking of the node prior in the list - if stack_index > 0: - _, prev_node = node_stack[stack_index - 1] - prev_node._replace_link(old_store_id, new_store_id) + continue + + # If not an empty node, just reserialize like normal + new_store_id = await self.virtual_store.save(old_id, node) + node_stack[stack_index] = (new_store_id, node) + + # If this is not the last i.e. root node, we need to change the linking of the node prior in the list + if is_not_root: + _, prev_node = node_stack[stack_index - 1] + prev_node.replace_link(old_id, new_store_id) def __setitem__(self, key_to_insert: str, val_to_insert: IPLDKind): asyncio.run(self.setitem(key_to_insert, val_to_insert)) From bfb2a2d84edbee00e8cb13154caf1993b2a044b7 Mon Sep 17 00:00:00 2001 From: Abid Sikder <41392423+abidsikder@users.noreply.github.com> Date: Wed, 7 May 2025 08:38:09 -0400 Subject: [PATCH 016/118] convert all read node uses to use virtual store --- py_hamt/hamt.py | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/py_hamt/hamt.py b/py_hamt/hamt.py index 8264dda..883f4d8 100644 --- a/py_hamt/hamt.py +++ b/py_hamt/hamt.py @@ -469,7 +469,7 @@ async def set_pointer(self, key_to_insert: str, val_ptr: IPLDKind): self.lock.acquire(blocking=True) node_stack: list[tuple[IPLDKind, Node]] = [] - root_node = await self.read_node(self.root_node_id) + root_node = await self.virtual_store.load(self.root_node_id) node_stack.append((self.root_node_id, root_node)) # FIFO queue to keep track of all the KVs we need to insert @@ -487,7 +487,7 @@ async def set_pointer(self, key_to_insert: str, val_ptr: IPLDKind): item = top_node.data[map_key] if isinstance(item, list): next_node_id = item[0] - next_node = await self.read_node(next_node_id) + next_node = await self.virtual_store.load(next_node_id) node_stack.append((next_node_id, next_node)) if isinstance(item, dict): bucket: dict[str, IPLDKind] = item @@ -504,7 +504,7 @@ async def set_pointer(self, key_to_insert: str, val_ptr: IPLDKind): # Create a new link to a new node so that we can reflow these KVs into nodes new_node = Node() - new_node_id = await self.write_node(None, new_node) + new_node_id = await self.virtual_store.save(None, new_node) link = [new_node_id] top_node.data[map_key] = link @@ -531,7 +531,7 @@ async def delitem(self, key: str): raw_hash = self.hash_fn(key.encode()) node_stack: list[tuple[IPLDKind, Node]] = [] - root_node = await self.read_node(self.root_node_id) + root_node = await self.virtual_store.load(self.root_node_id) node_stack.append((self.root_node_id, root_node)) created_change = False @@ -549,7 +549,7 @@ async def delitem(self, key: str): break if isinstance(item, list): link = item[0] - next_node = await self.read_node(link) + next_node = await self.virtual_store.load(link) node_stack.append((link, next_node)) # Finally, reserialize and fix all links, deleting empty nodes as needed @@ -585,7 +585,7 @@ async def get_pointer(self, key: str) -> IPLDKind: found_a_result: bool = False while True: top_id = current_id - top_node = await self.read_node(top_id) + top_node = await self.virtual_store.load(top_id) map_key = extract_bits(raw_hash, current_depth, 8) # Check if this key is in one of the buckets @@ -625,7 +625,7 @@ async def _iter_nodes(self) -> AsyncIterator[tuple[IPLDKind, Node]]: break top_id = node_id_stack.pop() - node = await self.read_node(top_id) + node = await self.virtual_store.load(top_id) yield (top_id, node) # Traverse down list of links @@ -648,7 +648,7 @@ def __iter__(self): break top_id = node_id_stack.pop() - node = asyncio.run(self.read_node(top_id)) + node = asyncio.run(self.virtual_store.load(top_id)) for item_index in range(len(node.data)): item = node.data[item_index] From a42bdaf98e07883f9dbcdc2b88f8f9447dd28228 Mon Sep 17 00:00:00 2001 From: Abid Sikder <41392423+abidsikder@users.noreply.github.com> Date: Wed, 7 May 2025 18:34:44 -0400 Subject: [PATCH 017/118] remove transformers --- py_hamt/__init__.py | 2 -- 1 file changed, 2 deletions(-) diff --git a/py_hamt/__init__.py b/py_hamt/__init__.py index ac9b60f..a82d228 100644 --- a/py_hamt/__init__.py +++ b/py_hamt/__init__.py @@ -1,6 +1,5 @@ from .hamt import HAMT, blake3_hashfn from .store import Store, DictStore, IPFSStore -from .zarr_encryption_transformers import create_zarr_encryption_transformers from .ipfszarr3 import IPFSZarr3 __all__ = [ @@ -9,6 +8,5 @@ "Store", "DictStore", "IPFSStore", - "create_zarr_encryption_transformers", "IPFSZarr3", ] From f3cfd29914cf9e62f6fc51d980ae3dc0c92a6101 Mon Sep 17 00:00:00 2001 From: Abid Sikder <41392423+abidsikder@users.noreply.github.com> Date: Wed, 7 May 2025 18:35:12 -0400 Subject: [PATCH 018/118] detach from MutableMapping interface to allow for full async creation --- py_hamt/hamt.py | 521 ++++++++++++++++++++---------------------------- 1 file changed, 220 insertions(+), 301 deletions(-) diff --git a/py_hamt/hamt.py b/py_hamt/hamt.py index 883f4d8..1cd0699 100644 --- a/py_hamt/hamt.py +++ b/py_hamt/hamt.py @@ -1,8 +1,6 @@ from abc import ABC, abstractmethod -from collections.abc import MutableMapping from sys import getsizeof -from threading import Lock -from typing import Callable, Iterator, AsyncIterator +from typing import Callable, Iterator, AsyncIterator, Literal import uuid from random import shuffle import asyncio @@ -71,13 +69,13 @@ def __init__(self): self.data: list[IPLDKind] = [dict() for _ in range(0, 256)] # empty dicts represent empty buckets, lists with one element are links, with the internal element being a link - def iter_buckets(self) -> Iterator[int]: + def iter_bucket_indices(self) -> Iterator[int]: """Return the list indices where there are buckets, empty or not.""" for i in range(len(self.data)): if isinstance(self.data[i], dict): yield i - def iter_links(self) -> Iterator[int]: + def iter_link_indices(self) -> Iterator[int]: """Return the list indices where there are links.""" for i in range(len(self.data)): if isinstance(self.data[i], list): @@ -87,15 +85,19 @@ def get_link(self, index: int) -> IPLDKind: link_wrapper: list[IPLDKind] = self.data[index] # type: ignore return link_wrapper[0] + def iter_links(self) -> Iterator[IPLDKind]: + for i in self.iter_link_indices(): + yield self.get_link(i) + def set_link(self, index: int, link: IPLDKind): wrapped = [link] self.data[index] = wrapped def replace_link(self, old_link: IPLDKind, new_link: IPLDKind): - for link_index in self.iter_links(): + for link_index in self.iter_link_indices(): link = self.get_link(link_index) if link == old_link: - self.data[link_index] = new_link + self.set_link(link_index, new_link) return def serialize(self) -> bytes: @@ -118,7 +120,7 @@ def deserialize(cls, data: bytes) -> "Node": # For HAMT internal use for increaing performance with nodes -class VirtualStore(ABC): +class NodeStore(ABC): @abstractmethod async def save(self, original_id: IPLDKind, node: Node) -> IPLDKind: pass @@ -128,10 +130,10 @@ async def load(self, id: IPLDKind) -> Node: pass -class ReadCacheStore(VirtualStore): +class ReadCacheStore(NodeStore): def __init__(self, hamt: "HAMT"): - self.cache: dict[IPLDKind, Node] = dict() self.hamt = hamt + self.cache: dict[IPLDKind, Node] = dict() def cache_eviction_lru(self): while getsizeof(self.cache) > self.hamt.read_cache_limit: @@ -162,24 +164,21 @@ async def load(self, id: IPLDKind) -> Node: return node -class InMemoryTreeStore(VirtualStore): +class InMemoryTreeStore(NodeStore): + # Add note about how this initiates by adding the HAMT's root node to the in memory tree buffer + # TODO add notice about how flushing needs to be handled by the HAMT internally and called after every operation is finished def __init__(self, hamt: "HAMT"): self.hamt = hamt - - # The Store ID returned by the InMemoryTree to mark objects as being in memory looks like list[inmemory_marker, virtual store uuid int ID for that node, original Store ID] - # TODO write about how a virtual store uuid int is used for every specific node since content addressed systems would normally return the same Store ID for every single empty Node - self.inmemory_marker = uuid.uuid4().int - # This buffer goes from the node's virtual store uuid to a Node object, which we can return references to for mutating within the HAMT - self.buffer: dict[IPLDKind, Node] = dict() + # This buffer goes from the node's virtual store uuid to a tuple of (original store id, Node), we can return the original node + self.buffer: dict[int, Node] = dict() def is_buffer_id(self, id: IPLDKind) -> bool: - return isinstance(id, list) and len(id) == 3 and id[0] == self.inmemory_marker + return isinstance(id, int) and id in self.buffer - def children_in_memory(self, node: Node) -> Iterator[IPLDKind]: - for index in range(len(node.data)): - item = node.data[index] - if self.is_buffer_id(item): - yield item + def children_in_memory(self, node: Node) -> Iterator[int]: + for link in node.iter_links(): + if self.is_buffer_id(link): + yield link # type: ignore we know for sure this is an int if it's a buffer id def has_children_in_memory(self, node: Node) -> bool: for _ in self.children_in_memory(node): @@ -189,6 +188,7 @@ def has_children_in_memory(self, node: Node) -> bool: def needs_flushing(self) -> bool: return getsizeof(self.buffer) > self.hamt.inmemory_tree_limit + # TODO, reimplement without treating the root node specially, but do assume that the root node is always in the in memory buffer since it will always be called first in any operations doing tree traversal async def flush_buffer(self, flush_everything: bool = False): if (not self.needs_flushing()) and (not flush_everything): return @@ -196,45 +196,43 @@ async def flush_buffer(self, flush_everything: bool = False): # Start with the root node's children, which should always be in the in memory buffer if there's anything there # there is an implicit assumption that the entire continuous line of branches up to an ancestor in the memory buffer, which will happen because of the DFS style traversal in all HAMT operations # node stack is a list of tuples that look like (parent_id, self_id, node) - node_stack: list[tuple[IPLDKind, IPLDKind, Node]] = [] - root_node: Node = self.buffer[self.hamt.root_node_id] + node_stack: list[tuple[int, int, Node]] = [] + root_node: Node = self.buffer[self.hamt.root_node_id] # type: ignore for child_buffer_id in self.children_in_memory(root_node): - node = self.buffer[child_buffer_id] - node_stack.append((self.hamt.root_node_id, child_buffer_id, node)) + child_node = self.buffer[child_buffer_id] + node_stack.append((self.hamt.root_node_id, child_buffer_id, child_node)) # type: ignore - shuffle(node_stack) # so that we don't always recurse down the rightmost branch + shuffle(node_stack) # avoid always recursing down the rightmost branch while len(node_stack) > 0 and (self.needs_flushing() or flush_everything): - top_parent_buffer_id, top_buffer_id, top_node = node_stack[-1] + parent_buffer_id, top_buffer_id, top_node = node_stack[-1] new_nodes_on_stack = [] if self.has_children_in_memory(top_node): for child_buffer_id in self.children_in_memory(top_node): - node = self.buffer[child_buffer_id] - new_nodes_on_stack.append((top_buffer_id, child_buffer_id, node)) + child_node = self.buffer[child_buffer_id] + new_nodes_on_stack.append( + (top_buffer_id, child_buffer_id, child_node) + ) shuffle( new_nodes_on_stack - ) # avoid always recursing down the rightmost branch first + ) # avoid always recursing down the rightmost branch node_stack.extend(new_nodes_on_stack) else: - # We can flush this one completely, we'll just have to reserialize its parents up to the root node + # We can flush this one completely since it has no children in memory, we'll just have to edit its parent after serializing it old_id = top_buffer_id new_id = await self.hamt.store.save( top_node.serialize(), codec="dag-cbor" ) - parent_node = self.buffer[top_parent_buffer_id] - for i in range(len(parent_node.data)): - item = parent_node.data[i] - if self.is_buffer_id(item) and item == old_id: - parent_node.set_link(i, new_id) - break + parent_node = self.buffer[parent_buffer_id] + parent_node.replace_link(old_id, new_id) - del self.buffer[top_buffer_id] # type: ignore + del self.buffer[top_buffer_id] node_stack.pop() # Only flush the root node if our size limits are still too big, or we've been instructed to remove everything. Always keeping the root node is important for performance if self.needs_flushing() or flush_everything: - del self.buffer[self.root_node_id] + del self.buffer[self.root_node_id] # type: ignore self.root_node_id = await self.hamt.store.save( root_node.serialize(), codec="dag-cbor" ) @@ -246,10 +244,9 @@ async def flush_buffer(self, flush_everything: bool = False): "Could not flush in memory tree buffer enough to reach limit, consider raising limit to accomodate for python empty object overheads" ) - async def add_to_buffer(self, original_id: IPLDKind, node: Node) -> list: + async def add_to_buffer(self, node: Node) -> IPLDKind: # This is IPLDKind type, but not dag_cbor serializable due to int limits so this will throw errors early if the tree is written with the buffer_ids still in there - node_uuid = uuid.uuid4().int - buffer_id = [self.inmemory_marker, node_uuid, original_id] + buffer_id = uuid.uuid4().int # Returns the virtual store ID that was generated for this node self.buffer[buffer_id] = node @@ -260,7 +257,7 @@ async def save(self, original_id: IPLDKind, node: Node) -> IPLDKind: return original_id # This node was not in the buffer, don't save it to the backing store but rather add to it to the in memory buffer - buffer_id = await self.add_to_buffer(original_id, node) + buffer_id = await self.add_to_buffer(node) return buffer_id async def load(self, id: IPLDKind) -> Node: @@ -271,17 +268,18 @@ async def load(self, id: IPLDKind) -> Node: # Miss, something that isn't in the in memory tree, add it node = Node.deserialize(await self.hamt.store.load(id)) - await self.add_to_buffer(id, node) + await self.add_to_buffer(node) return node -class HAMT(MutableMapping): +class HAMT: """ This HAMT presents a key value interface, like a python dictionary. The only limits are that keys can only be strings, and values can only be types amenable with [IPLDKind](https://dag-cbor.readthedocs.io/en/stable/api/dag_cbor.ipld.html#dag_cbor.ipld.IPLDKind). IPLDKind is a fairly flexible data model, but do note that integers are must be within the bounds of a signed 64-bit integer. py-hamt uses blake3 with a 32 byte wide hash by default, but to bring your own, read more in the documentation of `blake3_hashfn`. # Some notes about thread safety + TODO write about it not being thread safe but async concurrency model safe, so dont use it in multiple threads but do use it within an async event loop Since modifying a HAMT changes all parts of the tree, due to reserializing and saving to the backing store, modificiations are not thread safe. Thus, we offer a read-only mode which allows for parallel accesses, or a thread safe write enabled mode. You can see what type it is from the `read_only` variable. HAMTs default to write enabled mode on creation. Calling mutating operations in read only mode will raise Exceptions. @@ -316,7 +314,6 @@ class HAMT(MutableMapping): max_bucket_size: int """@private""" - # Don't use the type alias here since this is exposed in the documentation root_node_id: IPLDKind """DO NOT modify this directly. @@ -327,18 +324,12 @@ class HAMT(MutableMapping): This is really type IPLDKind, but the documentation generates this strange type instead since IPLDKind is a type union. """ - lock: Lock + lock: asyncio.Lock """ @private For use in multithreading """ - async def write_raw(self, data: IPLDKind) -> IPLDKind: - return await self.store.save(dag_cbor.encode(data), codec="raw") - - async def read_raw(self, id: IPLDKind) -> IPLDKind: - return dag_cbor.decode(await self.store.load(id)) - def __init__( self, store: Store, @@ -351,7 +342,7 @@ def __init__( ): self.store = store self.hash_fn = hash_fn - self.lock = Lock() + self.lock = asyncio.Lock() self.read_only = read_only if max_bucket_size < 1: @@ -371,41 +362,35 @@ def __init__( self.read_cache_limit = read_cache_limit self.root_node_id = root_node_id - # Create an empty node to use as the root node - if root_node_id is None: - self.root_node_id = asyncio.run( - self.store.save(Node().serialize(), "dag-cbor") - ) - # Create an empty in memory tree or read cache store - self.virtual_store: VirtualStore + self.node_store: NodeStore if read_only: - self.virtual_store = ReadCacheStore(self) + self.node_store = ReadCacheStore(self) else: - self.virtual_store = InMemoryTreeStore(self) + self.node_store = InMemoryTreeStore(self) - # This is typically a massive blocking operation, you dont want to be running this concurrently with a bunch of other operations, so it's ok to have it not be async - def make_read_only(self): - self.lock.acquire(blocking=True) - self.read_only = True + @classmethod + async def build(cls, *args, **kwargs): + hamt = cls(*args, **kwargs) + if hamt.root_node_id is None: + hamt.root_node_id = await hamt.node_store.save(None, Node()) - # Swap in memory tree for a read cache - inmemory_tree: InMemoryTreeStore = self.virtual_store # type: ignore - asyncio.run(inmemory_tree.flush_buffer(flush_everything=True)) + # This is typically a massive blocking operation, you dont want to be running this concurrently with a bunch of other operations, so it's ok to have it not be async + async def make_read_only(self): + async with self.lock: + self.read_only = True - read_cache = ReadCacheStore(self) - self.virtual_store = read_cache + inmemory_tree: InMemoryTreeStore = self.node_store # type: ignore + await inmemory_tree.flush_buffer(flush_everything=True) - self.lock.release() + self.node_store = ReadCacheStore(self) - def enable_write(self): - self.lock.acquire(blocking=True) - self.read_only = False - self.virtual_store = InMemoryTreeStore(self) - self.lock.release() + async def enable_write(self): + async with self.lock: + self.read_only = False + self.node_store = InMemoryTreeStore(self) async def _reserialize_and_link(self, node_stack: list[tuple[Link, Node]]): - # TODO this, or the set_pointer and delitem functions must manage best when to flush the in memory tree, since that requires that traveling down the branch to an arbitrary node within the buffer is contiguous """ This function starts from the node at the end of the list and reserializes so that each node holds valid new IDs after insertion into the store Takes a stack of nodes, we represent a stack with a list where the first element is the root element and the last element is the top of the stack @@ -413,8 +398,7 @@ async def _reserialize_and_link(self, node_stack: list[tuple[Link, Node]]): If a node ends up being empty, then it is deleted entirely, unless it is the root node Modifies in place """ - # Iterate in the reverse direction, imitating going deeper into a stack - # this range goes from n-1 to 0 + # iterate in the reverse direction, this range goes from n-1 to 0, from the bottommost tree node to the root for stack_index in range(len(node_stack) - 1, -1, -1): old_id, node = node_stack[stack_index] @@ -426,262 +410,197 @@ async def _reserialize_and_link(self, node_stack: list[tuple[Link, Node]]): if (isinstance(item, dict) and len(item) > 0) or isinstance(item, list): is_empty = False break - is_not_root = stack_index > 0 - if is_empty and is_not_root: + is_root = stack_index == 0 + + if is_empty and not is_root: # Unlink from the rest of the tree _, prev_node = node_stack[stack_index - 1] - # When removing links, don't worry about two nodes having the same link since all nodes are guaranteed to be different by the design of the tree and the exclusion of empty nodes - for i in range(len(prev_node.data)): - item = prev_node.data - if isinstance(item, dict): - continue - link = item[0] - # Delete the link by making it an empty bucket + # When removing links, don't worry about two nodes having the same link since all nodes are guaranteed to be different by the removal of empty nodes after every single operation + for link_index in prev_node.iter_link_indices(): + link = prev_node.get_link(link_index) if link == old_id: - prev_node.data[i] = dict() + # Delete the link by making it an empty bucket + prev_node.data[link_index] = dict() + break - # Remove from our stack + # Remove from our stack, continue reserializing up the tree node_stack.pop(stack_index) continue - # If not an empty node, just reserialize like normal - new_store_id = await self.virtual_store.save(old_id, node) + # If not an empty node, just reserialize like normal and replace this one + new_store_id = await self.node_store.save(old_id, node) node_stack[stack_index] = (new_store_id, node) - # If this is not the last i.e. root node, we need to change the linking of the node prior in the list - if is_not_root: + # If this is not the last i.e. root node, we need to change the linking of the node prior in the list since we just reserialized + if not is_root: _, prev_node = node_stack[stack_index - 1] prev_node.replace_link(old_id, new_store_id) - def __setitem__(self, key_to_insert: str, val_to_insert: IPLDKind): - asyncio.run(self.setitem(key_to_insert, val_to_insert)) - - async def setitem(self, key_to_insert: str, val_to_insert: IPLDKind): - val_ptr = await self.write_raw(val_to_insert) - await self.set_pointer(key_to_insert, val_ptr) + async def set(self, key: str, val: IPLDKind): + val_ptr = await self.store.save(dag_cbor.encode(val), codec="raw") + await self._set_pointer(key, val_ptr) - async def set_pointer(self, key_to_insert: str, val_ptr: IPLDKind): + async def _set_pointer(self, key: str, val_ptr: IPLDKind): if self.read_only: raise Exception("Cannot call set on a read only HAMT") - if not self.read_only: - self.lock.acquire(blocking=True) - - node_stack: list[tuple[IPLDKind, Node]] = [] - root_node = await self.virtual_store.load(self.root_node_id) - node_stack.append((self.root_node_id, root_node)) - - # FIFO queue to keep track of all the KVs we need to insert - # This is important for if any buckets overflow and thus we need to reinsert all those KVs - kvs_queue: list[tuple[str, IPLDKind]] = [] - kvs_queue.append((key_to_insert, val_ptr)) - - while len(kvs_queue) > 0: - _, top_node = node_stack[-1] - curr_key, curr_val_ptr = kvs_queue[0] - - raw_hash = self.hash_fn(curr_key.encode()) - map_key = extract_bits(raw_hash, len(node_stack) - 1, 8) - - item = top_node.data[map_key] - if isinstance(item, list): - next_node_id = item[0] - next_node = await self.virtual_store.load(next_node_id) - node_stack.append((next_node_id, next_node)) - if isinstance(item, dict): - bucket: dict[str, IPLDKind] = item - - # If this bucket already has this same key, or has space, just rewrite the value and work on the others in the queue - if curr_key in bucket or len(bucket) < self.max_bucket_size: - bucket[curr_key] = curr_val_ptr - kvs_queue.pop(0) - continue - - # The current key is not in the bucket and the bucket is too full, so empty KVs from the bucket and restart insertion - for k, v_ptr in bucket: - kvs_queue.append((k, v_ptr)) - - # Create a new link to a new node so that we can reflow these KVs into nodes - new_node = Node() - new_node_id = await self.virtual_store.save(None, new_node) - - link = [new_node_id] - top_node.data[map_key] = link + async with self.lock: + node_stack: list[tuple[IPLDKind, Node]] = [] + root_node = await self.node_store.load(self.root_node_id) + node_stack.append((self.root_node_id, root_node)) + + # FIFO queue to keep track of all the KVs we need to insert + # This is needed if any buckets overflow and so we need to reinsert all those KVs + kvs_queue: list[tuple[str, IPLDKind]] = [] + kvs_queue.append((key, val_ptr)) + + while len(kvs_queue) > 0: + _, top_node = node_stack[-1] + curr_key, curr_val_ptr = kvs_queue[0] + + raw_hash = self.hash_fn(curr_key.encode()) + map_key = extract_bits(raw_hash, len(node_stack) - 1, 8) + + item = top_node.data[map_key] + if isinstance(item, list): + next_node_id = item[0] + next_node = await self.node_store.load(next_node_id) + node_stack.append((next_node_id, next_node)) + elif isinstance(item, dict): + bucket: dict[str, IPLDKind] = item + + # If this bucket already has this same key, or has space, just rewrite the value and then go work on the others in the queue + if curr_key in bucket or len(bucket) < self.max_bucket_size: + bucket[curr_key] = curr_val_ptr + kvs_queue.pop(0) + continue - # Finally, reserialize and fix all links, deleting empty nodes as needed - await self._reserialize_and_link(node_stack) - node_stack_top_id = node_stack[0][0] - self.root_node_id = node_stack_top_id + # The current key is not in the bucket and the bucket is too full, so empty KVs from the bucket and restart insertion + for k, v_ptr in bucket: + kvs_queue.append((k, v_ptr)) - if not self.read_only: - self.lock.release() + # Create a new link to a new node so that we can reflow these KVs into a new subtree + new_node = Node() + new_node_id = await self.node_store.save(None, new_node) + link = [new_node_id] + top_node.data[map_key] = link - def __delitem__(self, key: str): - asyncio.run(self.delitem(key)) + # Finally, reserialize and fix all links, deleting empty nodes as needed + await self._reserialize_and_link(node_stack) + self.root_node_id = node_stack[0][0] + # This needs to be called after the root node is set from the node stack, since this may change the root node if the memory buffer is too small to hold the root node + if isinstance(self.node_store, InMemoryTreeStore): + await self.node_store.flush_buffer() - async def delitem(self, key: str): - """Also deletes the pointer at the same time.""" + async def delete(self, key: str): + # Also deletes the pointer at the same time so this doesn't have a _delete_pointer duo if self.read_only: raise Exception("Cannot call delete on a read only HAMT") - if not self.read_only: - self.lock.acquire(blocking=True) - - raw_hash = self.hash_fn(key.encode()) - - node_stack: list[tuple[IPLDKind, Node]] = [] - root_node = await self.virtual_store.load(self.root_node_id) - node_stack.append((self.root_node_id, root_node)) + async with self.lock: + raw_hash = self.hash_fn(key.encode()) - created_change = False - while True: - _, top_node = node_stack[-1] - map_key = extract_bits(raw_hash, len(node_stack) - 1, 8) + node_stack: list[tuple[IPLDKind, Node]] = [] + root_node = await self.node_store.load(self.root_node_id) + node_stack.append((self.root_node_id, root_node)) - item = top_node.data[map_key] + created_change = False + while True: + _, top_node = node_stack[-1] + map_key = extract_bits(raw_hash, len(node_stack) - 1, 8) - if isinstance(item, dict): - bucket = item - if key in bucket: - del bucket[key] - created_change = True - break - if isinstance(item, list): - link = item[0] - next_node = await self.virtual_store.load(link) - node_stack.append((link, next_node)) - - # Finally, reserialize and fix all links, deleting empty nodes as needed - if created_change: - await self._reserialize_and_link(node_stack) - node_stack_top_id = node_stack[0][0] - self.root_node_id = node_stack_top_id - - if not self.read_only: - self.lock.release() - - if not created_change: - raise KeyError - - def __getitem__(self, key: str) -> IPLDKind: - return asyncio.run(self.getitem(key)) - - async def getitem(self, key: str) -> IPLDKind: - pointer: IPLDKind = await self.get_pointer(key) - return await self.read_raw(pointer) - - async def get_pointer(self, key: str) -> IPLDKind: - if not self.read_only: - self.lock.acquire(blocking=True) - - raw_hash = self.hash_fn(key.encode()) - - current_id = self.root_node_id - current_depth = 0 - - # Don't check if result is none but use a boolean to indicate finding something, this is because None is a possible value of IPLDKind - result_ptr: IPLDKind = None - found_a_result: bool = False - while True: - top_id = current_id - top_node = await self.virtual_store.load(top_id) - map_key = extract_bits(raw_hash, current_depth, 8) - - # Check if this key is in one of the buckets - item = top_node.data[map_key] - if isinstance(item, dict): - bucket = item - if key in bucket: - result_ptr = bucket[key] - found_a_result = True + item = top_node.data[map_key] + if isinstance(item, dict): + bucket = item + if key in bucket: + del bucket[key] + created_change = True + # Break out since whether or not the key is in the bucket, it should have been here so either now reserialize or raise a KeyError break - if isinstance(item, list): - link = item[0] - current_id = link - current_depth += 1 - continue - # Nowhere left to go, stop walking down the tree + elif isinstance(item, list): + link = item[0] + next_node = await self.node_store.load(link) + node_stack.append((link, next_node)) + + # Finally, reserialize and fix all links, deleting empty nodes as needed + if created_change: + await self._reserialize_and_link(node_stack) + self.root_node_id = node_stack[0][0] + # This needs to be called after the root node is set from the node stack, since this may change the root node if the memory buffer is too small to hold the root node + if isinstance(self.node_store, InMemoryTreeStore): + await self.node_store.flush_buffer() else: - break - - if not self.read_only: - self.lock.release() - - if not found_a_result: - raise KeyError - - return result_ptr - - async def _iter_nodes(self) -> AsyncIterator[tuple[IPLDKind, Node]]: - if not self.read_only: - self.lock.acquire(blocking=True) - - node_id_stack = [] - node_id_stack.append(self.root_node_id) - - while True: - if len(node_id_stack) == 0: - break - - top_id = node_id_stack.pop() - node = await self.virtual_store.load(top_id) - yield (top_id, node) - - # Traverse down list of links - for link_index in node.iter_links(): - link = node.get_link(link_index) - node_id_stack.append(link) - - if not self.read_only: - self.lock.release() - - def __iter__(self): - if not self.read_only: - self.lock.acquire(blocking=True) - - node_id_stack = [] - node_id_stack.append(self.root_node_id) - - while True: - if len(node_id_stack) == 0: - break - - top_id = node_id_stack.pop() - node = asyncio.run(self.virtual_store.load(top_id)) - - for item_index in range(len(node.data)): - item = node.data[item_index] + # If we didn't make a change, then this key must not exist within the HAMT + raise KeyError + + async def get(self, key: str) -> IPLDKind: + pointer: IPLDKind = await self._get_pointer(key) + return dag_cbor.decode(await self.store.load(pointer)) + + async def _get_pointer(self, key: str) -> IPLDKind: + async with self.lock: + raw_hash = self.hash_fn(key.encode()) + + current_id = self.root_node_id + current_depth = 0 + + # Don't check if result is none but use a boolean to indicate finding something, this is because None is a possible value of IPLDKind + result_ptr: IPLDKind = None + found_a_result: bool = False + while True: + top_id = current_id + top_node = await self.node_store.load(top_id) + map_key = extract_bits(raw_hash, current_depth, 8) + + # Check if this key is in one of the buckets + item = top_node.data[map_key] if isinstance(item, dict): bucket = item - for key in bucket: - yield key - elif isinstance(item, list): + if key in bucket: + result_ptr = bucket[key] + found_a_result = True + break + + if isinstance(item, list): link = item[0] - node_id_stack.append(link) + current_id = link + current_depth += 1 + continue - if not self.read_only: - self.lock.release() + # Nowhere left to go, stop walking down the tree + break - async def aiter_keys(self) -> AsyncIterator[str]: - async for _, node in self._iter_nodes(): - for item_index in range(len(node.data)): - item = node.data[item_index] - if isinstance(item, dict): - bucket = item - for key in bucket: - yield key + if isinstance(self.node_store, InMemoryTreeStore): + await self.node_store.flush_buffer() - def __len__(self) -> int: - count = 0 - for _ in self: - count += 1 + if not found_a_result: + raise KeyError - return count + return result_ptr - async def async_len(self): + async def _iter_nodes(self) -> AsyncIterator[tuple[IPLDKind, Node]]: + async with self.lock: + node_id_stack = [self.root_node_id] + while len(node_id_stack) > 0: + top_id = node_id_stack.pop() + node = await self.node_store.load(top_id) + yield (top_id, node) + node_id_stack.extend(list(node.iter_links())) + + # TODO documentation warning that iterating does not lock the HAMT so be careful, but this choice was made to allow for getting keys in the middle of iteration, otherwise you'd have to wait for the whole thing to finish + async def keys(self) -> AsyncIterator[str]: + async for _, node in self._iter_nodes(): + for bucket_index in node.iter_bucket_indices(): + bucket: dict[str, IPLDKind] = node.data[bucket_index] # type: ignore + for key in bucket: + yield key + + # TODO similar documentation warning that iterating does not lock the HAMT so don't modify the HAMT in the middle of this thing running or you will get incorrect results + async def len(self) -> int: + """Return the number of key value mappings in this HAMT.""" count = 0 - async for _ in self.aiter_keys(): + async for _ in self.keys(): count += 1 return count From 0fea571ff3d463448a58c1116cf0b598ea952956 Mon Sep 17 00:00:00 2001 From: Abid Sikder <41392423+abidsikder@users.noreply.github.com> Date: Wed, 7 May 2025 18:36:37 -0400 Subject: [PATCH 019/118] first round of passing tests with the new interface --- py_hamt/hamt.py | 3 +- tests/test_hamt.py | 168 ++++++++++++++++++--------------------------- 2 files changed, 67 insertions(+), 104 deletions(-) diff --git a/py_hamt/hamt.py b/py_hamt/hamt.py index 1cd0699..a3f66c2 100644 --- a/py_hamt/hamt.py +++ b/py_hamt/hamt.py @@ -370,10 +370,11 @@ def __init__( self.node_store = InMemoryTreeStore(self) @classmethod - async def build(cls, *args, **kwargs): + async def build(cls, *args, **kwargs) -> "HAMT": hamt = cls(*args, **kwargs) if hamt.root_node_id is None: hamt.root_node_id = await hamt.node_store.save(None, Node()) + return hamt # This is typically a massive blocking operation, you dont want to be running this concurrently with a bunch of other operations, so it's ok to have it not be async async def make_read_only(self): diff --git a/tests/test_hamt.py b/tests/test_hamt.py index 25f9a73..74c8f51 100644 --- a/tests/test_hamt.py +++ b/tests/test_hamt.py @@ -6,123 +6,85 @@ from dag_cbor import IPLDKind from multiformats import CID from hypothesis import given -from hypothesis import strategies as st import pytest from py_hamt import HAMT, DictStore from py_hamt.hamt import Node -from py_hamt.store import Store -from .testing_utils import key_value_list - -# Just enough to make it that reading back a hamt without the proper transformer will scramble things -_x = "x".encode() - - -def transformer_encode_minimal(key: str, val: bytes) -> bytes: - return _x + val - - -def transformer_decode_minimal(key: str, val: bytes) -> bytes: - return val[1:] +from testing_utils import key_value_list +@pytest.mark.asyncio @given(key_value_list) -def test_fuzz(kvs: list[tuple[str, IPLDKind]]): +async def test_fuzz(kvs: list[tuple[str, IPLDKind]]): store = DictStore() - hamt = HAMT(store=store) - assert isinstance(hamt, MutableMapping) + hamt = await HAMT.build(store=store) # The HAMT should be able to withstand its bucket size changing in between operations for key, value in kvs: hamt.max_bucket_size = random.randint(1, 10) - hamt[key] = value - assert hamt[key] == value - assert len(hamt) == len(kvs) - assert len(list(hamt)) == len(hamt) + await hamt.set(key, value) + assert (await hamt.get(key)) == value + assert (await hamt.len()) == len(kvs) + assert len([key async for key in hamt.keys()]) == (await hamt.len()) for key, _ in kvs: - del hamt[key] - assert len(hamt) == 0 - assert len(list(hamt)) == len(hamt) - # Re insert all items but now with a bucket size that forces linking, which actually runs the link following code branches, otherwise we would miss 100% code coverage - hamt.max_bucket_size = 1 - for key, value in kvs: - hamt[key] = value - assert hamt[key] == value - assert len(hamt) == len(kvs) - assert len(list(hamt)) == len(hamt) - - ks = [k for k, _ in kvs] - key_that_cannot_exist = "".join(ks).join( - "string to account for empty string key case" - ) - with pytest.raises(KeyError): - hamt[key_that_cannot_exist] - with pytest.raises(KeyError): - del hamt[key_that_cannot_exist] - - for key, value in kvs: - assert hamt[key] == value - - assert len(hamt) == len(kvs) - assert len(list(hamt)) == len(kvs) - - hamt_keys = list(hamt) - hamt_key_set = set(hamt_keys) - keys_set = set() - for key, _ in kvs: - keys_set.add(key) - - assert hamt_key_set == keys_set - - # Make sure all ids actually exist in the store, this should not raies any exceptions - store_ids: list[bytes] = list(hamt.ids()) # type: ignore - for id in store_ids: - store.load(id) - - hamt.make_read_only() - with pytest.raises(Exception, match="Cannot call set on a read only HAMT"): - hamt["foo"] = b"bar" - with pytest.raises(Exception, match="Cannot call delete on a read only HAMT"): - del hamt["foo"] - hamt.enable_write() - - copy_hamt = deepcopy(hamt) - - # Modify our current hamt and since the copy is a deep copy, they should be different - for key, _ in kvs: - del hamt[key] - assert len(hamt) == 0 - assert len(copy_hamt) == len(kvs) - - # Test that when a hamt has its root manually initialized by a user, that the key count is accurate - hamt_re_initialized = HAMT(store=store, root_node_id=copy_hamt.root_node_id) - assert len(hamt_re_initialized) == len(kvs) - - -class BadStore(Store): - """ " - Bad store implementation that should cause errors - """ - - def save_raw(self, data: bytes) -> IPLDKind: - return 0 - - def save_dag_cbor(self, data: bytes) -> IPLDKind: - return 0 - - def load(self, id: IPLDKind) -> bytes: - return bytes(0) - - -def test_bad_store(): - bad_store = BadStore() - hamt = HAMT(store=bad_store, max_cache_size_bytes=0) - with pytest.raises( - Exception, - match="Invalid dag-cbor encoded data from the store was attempted to be decoded", - ): - hamt["test"] = 3 + await hamt.delete(key) + assert (await hamt.len()) == 0 + # assert len(list(hamt)) == len(hamt) + # # Re insert all items but now with a bucket size that forces linking, which actually runs the link following code branches, otherwise we would miss 100% code coverage + # hamt.max_bucket_size = 1 + # for key, value in kvs: + # hamt[key] = value + # assert hamt[key] == value + # assert len(hamt) == len(kvs) + # assert len(list(hamt)) == len(hamt) + + # ks = [k for k, _ in kvs] + # key_that_cannot_exist = "".join(ks).join( + # "string to account for empty string key case" + # ) + # with pytest.raises(KeyError): + # hamt[key_that_cannot_exist] + # with pytest.raises(KeyError): + # del hamt[key_that_cannot_exist] + + # for key, value in kvs: + # assert hamt[key] == value + + # assert len(hamt) == len(kvs) + # assert len(list(hamt)) == len(kvs) + + # hamt_keys = list(hamt) + # hamt_key_set = set(hamt_keys) + # keys_set = set() + # for key, _ in kvs: + # keys_set.add(key) + + # assert hamt_key_set == keys_set + + # # Make sure all ids actually exist in the store, this should not raies any exceptions + # store_ids: list[bytes] = list(hamt.ids()) # type: ignore + # for id in store_ids: + # store.load(id) + + # hamt.make_read_only() + # with pytest.raises(Exception, match="Cannot call set on a read only HAMT"): + # hamt["foo"] = b"bar" + # with pytest.raises(Exception, match="Cannot call delete on a read only HAMT"): + # del hamt["foo"] + # hamt.enable_write() + + # copy_hamt = deepcopy(hamt) + + # # Modify our current hamt and since the copy is a deep copy, they should be different + # for key, _ in kvs: + # del hamt[key] + # assert len(hamt) == 0 + # assert len(copy_hamt) == len(kvs) + + # # Test that when a hamt has its root manually initialized by a user, that the key count is accurate + # hamt_re_initialized = HAMT(store=store, root_node_id=copy_hamt.root_node_id) + # assert len(hamt_re_initialized) == len(kvs) # Mostly for complete code coverage's sake From e1a69bd8ae040b451128ca54347cef833bf719f4 Mon Sep 17 00:00:00 2001 From: Abid Sikder <41392423+abidsikder@users.noreply.github.com> Date: Thu, 8 May 2025 17:15:40 -0400 Subject: [PATCH 020/118] node class convenience functions --- py_hamt/hamt.py | 24 ++++++++++++++++-------- 1 file changed, 16 insertions(+), 8 deletions(-) diff --git a/py_hamt/hamt.py b/py_hamt/hamt.py index a3f66c2..54e81e8 100644 --- a/py_hamt/hamt.py +++ b/py_hamt/hamt.py @@ -69,11 +69,11 @@ def __init__(self): self.data: list[IPLDKind] = [dict() for _ in range(0, 256)] # empty dicts represent empty buckets, lists with one element are links, with the internal element being a link - def iter_bucket_indices(self) -> Iterator[int]: - """Return the list indices where there are buckets, empty or not.""" + def iter_buckets(self) -> Iterator[dict]: for i in range(len(self.data)): - if isinstance(self.data[i], dict): - yield i + item = self.data[i] + if isinstance(item, dict): + yield item def iter_link_indices(self) -> Iterator[int]: """Return the list indices where there are links.""" @@ -81,18 +81,19 @@ def iter_link_indices(self) -> Iterator[int]: if isinstance(self.data[i], list): yield i - def get_link(self, index: int) -> IPLDKind: - link_wrapper: list[IPLDKind] = self.data[index] # type: ignore - return link_wrapper[0] - def iter_links(self) -> Iterator[IPLDKind]: for i in self.iter_link_indices(): yield self.get_link(i) + def get_link(self, index: int) -> IPLDKind: + link_wrapper: list[IPLDKind] = self.data[index] # type: ignore + return link_wrapper[0] + def set_link(self, index: int, link: IPLDKind): wrapped = [link] self.data[index] = wrapped + # This assumes that there is only one unique link matching the old link, which is valid since we prune empty Nodes when reserializing and relinking def replace_link(self, old_link: IPLDKind, new_link: IPLDKind): for link_index in self.iter_link_indices(): link = self.get_link(link_index) @@ -100,6 +101,13 @@ def replace_link(self, old_link: IPLDKind, new_link: IPLDKind): self.set_link(link_index, new_link) return + def is_empty(self) -> bool: + for i in range(len(self.data)): + item = self.data[i] + if (isinstance(item, dict) and len(item) > 0) or isinstance(item, list): + return False + return True + def serialize(self) -> bytes: return dag_cbor.encode(self.data) From 1aefd24fd3dc1eb79c7377628b48c7286774a418 Mon Sep 17 00:00:00 2001 From: Abid Sikder <41392423+abidsikder@users.noreply.github.com> Date: Thu, 8 May 2025 18:00:40 -0400 Subject: [PATCH 021/118] add encode/decode, bug fixes --- py_hamt/hamt.py | 229 ++++++++++++++++++++++++------------------------ 1 file changed, 115 insertions(+), 114 deletions(-) diff --git a/py_hamt/hamt.py b/py_hamt/hamt.py index 54e81e8..5299e07 100644 --- a/py_hamt/hamt.py +++ b/py_hamt/hamt.py @@ -181,7 +181,7 @@ def __init__(self, hamt: "HAMT"): self.buffer: dict[int, Node] = dict() def is_buffer_id(self, id: IPLDKind) -> bool: - return isinstance(id, int) and id in self.buffer + return id in self.buffer def children_in_memory(self, node: Node) -> Iterator[int]: for link in node.iter_links(): @@ -198,9 +198,27 @@ def needs_flushing(self) -> bool: # TODO, reimplement without treating the root node specially, but do assume that the root node is always in the in memory buffer since it will always be called first in any operations doing tree traversal async def flush_buffer(self, flush_everything: bool = False): - if (not self.needs_flushing()) and (not flush_everything): + if ( + (not self.needs_flushing()) + and (not flush_everything) + or len(self.buffer) == 0 + ): return + # Start by removing completely empty nodes, which will end up being unreferencing by anything else, but which will still be inside the buffer since this in memory tree assigns unique IDs to every node unlike a normal content-addressed system + empty_node_buffer_ids: list[ + int + ] = [] # we can't modify a dictionary while iterating so do the deletion in a separate step + for buffer_id in self.buffer: + # Just don't delete an empty root node + if buffer_id == self.hamt.root_node_id: + continue + node = self.buffer[buffer_id] + if node.is_empty(): + empty_node_buffer_ids.append(buffer_id) + for buffer_id in empty_node_buffer_ids: + del self.buffer[buffer_id] + # Start with the root node's children, which should always be in the in memory buffer if there's anything there # there is an implicit assumption that the entire continuous line of branches up to an ancestor in the memory buffer, which will happen because of the DFS style traversal in all HAMT operations # node stack is a list of tuples that look like (parent_id, self_id, node) @@ -240,8 +258,8 @@ async def flush_buffer(self, flush_everything: bool = False): # Only flush the root node if our size limits are still too big, or we've been instructed to remove everything. Always keeping the root node is important for performance if self.needs_flushing() or flush_everything: - del self.buffer[self.root_node_id] # type: ignore - self.root_node_id = await self.hamt.store.save( + del self.buffer[self.hamt.root_node_id] # type: ignore + self.hamt.root_node_id = await self.hamt.store.save( root_node.serialize(), codec="dag-cbor" ) @@ -281,62 +299,17 @@ async def load(self, id: IPLDKind) -> Node: class HAMT: - """ - This HAMT presents a key value interface, like a python dictionary. The only limits are that keys can only be strings, and values can only be types amenable with [IPLDKind](https://dag-cbor.readthedocs.io/en/stable/api/dag_cbor.ipld.html#dag_cbor.ipld.IPLDKind). IPLDKind is a fairly flexible data model, but do note that integers are must be within the bounds of a signed 64-bit integer. - - py-hamt uses blake3 with a 32 byte wide hash by default, but to bring your own, read more in the documentation of `blake3_hashfn`. - - # Some notes about thread safety - TODO write about it not being thread safe but async concurrency model safe, so dont use it in multiple threads but do use it within an async event loop - - Since modifying a HAMT changes all parts of the tree, due to reserializing and saving to the backing store, modificiations are not thread safe. Thus, we offer a read-only mode which allows for parallel accesses, or a thread safe write enabled mode. You can see what type it is from the `read_only` variable. HAMTs default to write enabled mode on creation. Calling mutating operations in read only mode will raise Exceptions. - - In write enabled mode, all operations block and wait, so multiple threads can write to the HAMT but the operations will in reality happen one after the other. - - # dunder method documentation - These are not generated by pdoc automatically so we are including their documentation here. - - ## `__len__` - Total number of keys. Note that this will have to scan the entire tree in order to count, which can take a while depending on the speed of the store retrieval. - - ## `__iter__` - Generator of all string keys. When initially called, this will freeze the root node and then start iteration, so subsequent sets and deletes that mutate will not be reflected in the keys returned in this iteration. - - ## `__deepcopy__` - For use with the python copy module. This creates deep copies of the current HAMT. The only thing it does not copy over is the cache. - ```python - from copy import deepcopy - hamt = # ... - copy_hamt = deepcopy(hamt) - ``` - """ - store: Store - """@private""" # Every call of this will look like self.hash_fn() and so the first argument will always take a self argument hash_fn: Callable[[bytes], bytes] - """@private""" # Only important for writing, when reading this will use buckets even if they are overly big max_bucket_size: int - """@private""" root_node_id: IPLDKind - """DO NOT modify this directly. - - TODO write about how you do need to read it at times, and it should only be read when the buffer has been flushed to the backing store - - This is the ID that the store returns for the root node of the HAMT. This is exposed since it is sometimes useful to reconstruct other HAMTs later if using a persistent store. - - This is really type IPLDKind, but the documentation generates this strange type instead since IPLDKind is a type union. - """ lock: asyncio.Lock - """ - @private - For use in multithreading - """ def __init__( self, @@ -344,7 +317,7 @@ def __init__( hash_fn: Callable[[bytes], bytes] = blake3_hashfn, root_node_id: IPLDKind = None, read_only: bool = False, - max_bucket_size: int = 67, + max_bucket_size: int = 4, inmemory_tree_limit: int = 10_000_000, # 10 MB default read_cache_limit: int = 10_000_000, # 10 MB default ): @@ -374,7 +347,6 @@ def __init__( self.node_store: NodeStore if read_only: self.node_store = ReadCacheStore(self) - else: self.node_store = InMemoryTreeStore(self) @classmethod @@ -412,17 +384,8 @@ async def _reserialize_and_link(self, node_stack: list[tuple[Link, Node]]): old_id, node = node_stack[stack_index] # If this node is empty, and it's not the root node, then we can delete it entirely from the list - is_empty = True - for i in range(len(node.data)): - item = node.data[i] - # If we have a nonempty bucket, or a link at all, then this is a nonempty node - if (isinstance(item, dict) and len(item) > 0) or isinstance(item, list): - is_empty = False - break - is_root = stack_index == 0 - - if is_empty and not is_root: + if node.is_empty() and not is_root: # Unlink from the rest of the tree _, prev_node = node_stack[stack_index - 1] # When removing links, don't worry about two nodes having the same link since all nodes are guaranteed to be different by the removal of empty nodes after every single operation @@ -446,14 +409,22 @@ async def _reserialize_and_link(self, node_stack: list[tuple[Link, Node]]): _, prev_node = node_stack[stack_index - 1] prev_node.replace_link(old_id, new_store_id) - async def set(self, key: str, val: IPLDKind): - val_ptr = await self.store.save(dag_cbor.encode(val), codec="raw") - await self._set_pointer(key, val_ptr) - - async def _set_pointer(self, key: str, val_ptr: IPLDKind): + # automatically skip encoding if the value provided is of the bytes variety + async def set(self, key: str, val: IPLDKind, skip_encode=False): + """TODO add something about how skip encoding can make large bytes setting much more efficient""" if self.read_only: raise Exception("Cannot call set on a read only HAMT") + data: bytes + if skip_encode: + data = val # type: ignore let users get an exception if they pass in a non bytes when they want to skip encoding + else: + data = dag_cbor.encode(val) + + pointer = await self.store.save(data, codec="raw") + await self._set_pointer(key, pointer) + + async def _set_pointer(self, key: str, val_ptr: IPLDKind): async with self.lock: node_stack: list[tuple[IPLDKind, Node]] = [] root_node = await self.node_store.load(self.root_node_id) @@ -486,7 +457,8 @@ async def _set_pointer(self, key: str, val_ptr: IPLDKind): continue # The current key is not in the bucket and the bucket is too full, so empty KVs from the bucket and restart insertion - for k, v_ptr in bucket: + for k in bucket: + v_ptr = bucket[k] kvs_queue.append((k, v_ptr)) # Create a new link to a new node so that we can reflow these KVs into a new subtree @@ -543,71 +515,100 @@ async def delete(self, key: str): # If we didn't make a change, then this key must not exist within the HAMT raise KeyError - async def get(self, key: str) -> IPLDKind: - pointer: IPLDKind = await self._get_pointer(key) - return dag_cbor.decode(await self.store.load(pointer)) + # include option to skip decode if the user knows that the value inside is also going to be a bytes object + async def get(self, key: str, skip_decode=False) -> IPLDKind: + # If read only, no need to acquire a lock + pointer: IPLDKind + if self.read_only: + pointer = await self._get_pointer(key) + else: + async with self.lock: + pointer = await self._get_pointer(key) + data = await self.store.load(pointer) + if skip_decode: + return data + else: + return dag_cbor.decode(data) + + # Callers MUST handle acquiring a lock async def _get_pointer(self, key: str) -> IPLDKind: - async with self.lock: - raw_hash = self.hash_fn(key.encode()) + raw_hash = self.hash_fn(key.encode()) - current_id = self.root_node_id - current_depth = 0 + current_id = self.root_node_id + current_depth = 0 - # Don't check if result is none but use a boolean to indicate finding something, this is because None is a possible value of IPLDKind - result_ptr: IPLDKind = None - found_a_result: bool = False - while True: - top_id = current_id - top_node = await self.node_store.load(top_id) - map_key = extract_bits(raw_hash, current_depth, 8) + # Don't check if result is none but use a boolean to indicate finding something, this is because None is a possible value of IPLDKind + result_ptr: IPLDKind = None + found_a_result: bool = False + while True: + top_id = current_id + top_node = await self.node_store.load(top_id) + map_key = extract_bits(raw_hash, current_depth, 8) - # Check if this key is in one of the buckets - item = top_node.data[map_key] - if isinstance(item, dict): - bucket = item - if key in bucket: - result_ptr = bucket[key] - found_a_result = True - break + # Check if this key is in one of the buckets + item = top_node.data[map_key] + if isinstance(item, dict): + bucket = item + if key in bucket: + result_ptr = bucket[key] + found_a_result = True + break - if isinstance(item, list): - link = item[0] - current_id = link - current_depth += 1 - continue + if isinstance(item, list): + link = item[0] + current_id = link + current_depth += 1 + continue - # Nowhere left to go, stop walking down the tree - break + # Nowhere left to go, stop walking down the tree + break - if isinstance(self.node_store, InMemoryTreeStore): - await self.node_store.flush_buffer() + if isinstance(self.node_store, InMemoryTreeStore): + await self.node_store.flush_buffer() - if not found_a_result: - raise KeyError + if not found_a_result: + raise KeyError - return result_ptr + return result_ptr + # Callers MUST handle locking or not on their own async def _iter_nodes(self) -> AsyncIterator[tuple[IPLDKind, Node]]: - async with self.lock: - node_id_stack = [self.root_node_id] - while len(node_id_stack) > 0: - top_id = node_id_stack.pop() - node = await self.node_store.load(top_id) - yield (top_id, node) - node_id_stack.extend(list(node.iter_links())) - - # TODO documentation warning that iterating does not lock the HAMT so be careful, but this choice was made to allow for getting keys in the middle of iteration, otherwise you'd have to wait for the whole thing to finish + node_id_stack = [self.root_node_id] + while len(node_id_stack) > 0: + top_id = node_id_stack.pop() + node = await self.node_store.load(top_id) + yield (top_id, node) + node_id_stack.extend(list(node.iter_links())) + async def keys(self) -> AsyncIterator[str]: + """ + AsyncIterator returning all keys in the HAMT. + + When the HAMT is write enabled, to maintain strong consistency this will obtain a lock and not a llow any other operations to proceed. For example, if you are inside of a for loop using this iterator, you cannot also get a value at the same time until iteration is completely done. If you try to get in fact, you will run into deadlock. + + In read only mode however, this can be run concurrently with get operations. + """ + if self.read_only: + async for k in self._keys_no_locking(): + yield k + else: + async with self.lock: + async for k in self._keys_no_locking(): + yield k + + async def _keys_no_locking(self) -> AsyncIterator[str]: async for _, node in self._iter_nodes(): - for bucket_index in node.iter_bucket_indices(): - bucket: dict[str, IPLDKind] = node.data[bucket_index] # type: ignore + for bucket in node.iter_buckets(): for key in bucket: yield key - # TODO similar documentation warning that iterating does not lock the HAMT so don't modify the HAMT in the middle of this thing running or you will get incorrect results async def len(self) -> int: - """Return the number of key value mappings in this HAMT.""" + """ + Return the number of key value mappings in this HAMT. + + When the HAMT is write enabled, to maintain strong consistency it will acquire a lock and thus not allow any other operations to proceed until the length is fully done being calculated. If read only, then this can be run concurrently with other operations. + """ count = 0 async for _ in self.keys(): count += 1 From 465935615dfacfa54427fd8b94b50a4b040cbe88 Mon Sep 17 00:00:00 2001 From: Abid Sikder <41392423+abidsikder@users.noreply.github.com> Date: Mon, 12 May 2025 14:13:49 -0400 Subject: [PATCH 022/118] more bug fixes, large portion of test coverage --- py_hamt/hamt.py | 24 +++++--- tests/test_hamt.py | 144 +++++++++++++++++++++++---------------------- 2 files changed, 90 insertions(+), 78 deletions(-) diff --git a/py_hamt/hamt.py b/py_hamt/hamt.py index 5299e07..970f72a 100644 --- a/py_hamt/hamt.py +++ b/py_hamt/hamt.py @@ -131,11 +131,11 @@ def deserialize(cls, data: bytes) -> "Node": class NodeStore(ABC): @abstractmethod async def save(self, original_id: IPLDKind, node: Node) -> IPLDKind: - pass + """Save nodes to the store""" @abstractmethod async def load(self, id: IPLDKind) -> Node: - pass + """Load nodes from the store""" class ReadCacheStore(NodeStore): @@ -198,14 +198,14 @@ def needs_flushing(self) -> bool: # TODO, reimplement without treating the root node specially, but do assume that the root node is always in the in memory buffer since it will always be called first in any operations doing tree traversal async def flush_buffer(self, flush_everything: bool = False): - if ( - (not self.needs_flushing()) - and (not flush_everything) - or len(self.buffer) == 0 - ): + if not self.needs_flushing() and not flush_everything: return - # Start by removing completely empty nodes, which will end up being unreferencing by anything else, but which will still be inside the buffer since this in memory tree assigns unique IDs to every node unlike a normal content-addressed system + if len(self.buffer) == 0: + return + + + # Start by removing completely empty nodes, which will be unreferenced by other nodes but will still be inside the buffer since this in memory tree assigns unique IDs to every node, unlike a normal content-addressed system which would have consolidated all the empty nodes empty_node_buffer_ids: list[ int ] = [] # we can't modify a dictionary while iterating so do the deletion in a separate step @@ -216,9 +216,11 @@ async def flush_buffer(self, flush_everything: bool = False): node = self.buffer[buffer_id] if node.is_empty(): empty_node_buffer_ids.append(buffer_id) + for buffer_id in empty_node_buffer_ids: del self.buffer[buffer_id] + # Start with the root node's children, which should always be in the in memory buffer if there's anything there # there is an implicit assumption that the entire continuous line of branches up to an ancestor in the memory buffer, which will happen because of the DFS style traversal in all HAMT operations # node stack is a list of tuples that look like (parent_id, self_id, node) @@ -347,6 +349,7 @@ def __init__( self.node_store: NodeStore if read_only: self.node_store = ReadCacheStore(self) + else: self.node_store = InMemoryTreeStore(self) @classmethod @@ -368,8 +371,13 @@ async def make_read_only(self): async def enable_write(self): async with self.lock: + # Get the root node right before we clear out the cache store + root_node = await self.node_store.load(self.root_node_id) + self.read_only = False self.node_store = InMemoryTreeStore(self) + # Make sure the root node is in memory, we can't modify the originating root node otherwise when loading things in + self.root_node_id = await self.node_store.save(self.root_node_id, root_node) async def _reserialize_and_link(self, node_stack: list[tuple[Link, Node]]): """ diff --git a/tests/test_hamt.py b/tests/test_hamt.py index 74c8f51..55b12c8 100644 --- a/tests/test_hamt.py +++ b/tests/test_hamt.py @@ -1,4 +1,4 @@ -from copy import deepcopy +import asyncio import random from collections.abc import MutableMapping @@ -17,74 +17,79 @@ @pytest.mark.asyncio @given(key_value_list) async def test_fuzz(kvs: list[tuple[str, IPLDKind]]): +# async def test_fuzz(): store = DictStore() hamt = await HAMT.build(store=store) - # The HAMT should be able to withstand its bucket size changing in between operations + # Sequential setting and getting, while randomly changing the bucket size which the HAMT should be able to withstand for key, value in kvs: hamt.max_bucket_size = random.randint(1, 10) await hamt.set(key, value) assert (await hamt.get(key)) == value - assert (await hamt.len()) == len(kvs) - assert len([key async for key in hamt.keys()]) == (await hamt.len()) + + assert len([key async for key in hamt.keys()]) == (await hamt.len()) == len(kvs) + await asyncio.gather(*[hamt.delete(k) for k, _ in kvs]) # delete everything + assert len([key async for key in hamt.keys()]) == (await hamt.len()) == 0 + + # Set entirely concurrently thus with unpredictable order + await asyncio.gather(*[hamt.set(k, v) for k, v in kvs]) + + # Switching this one and off should not cause any problems + await hamt.make_read_only() + await hamt.enable_write() + await hamt.make_read_only() + + # Verify completely concurrently + async def verify(k, v): + assert (await hamt.get(k)) == v + + await asyncio.gather(*[verify(k, v) for k, v in kvs]) + + await hamt.enable_write() + # Delete and empty it out again + await asyncio.gather(*[hamt.delete(k) for k, _ in kvs]) + assert len([key async for key in hamt.keys()]) == (await hamt.len()) == 0 + + # Re insert all items but now with a bucket size that forces linking, which actually runs the link following code branches, otherwise we would miss 100% code coverage + hamt.max_bucket_size = 1 + await asyncio.gather(*[hamt.set(k, v) for k, v in kvs]) + assert len([key async for key in hamt.keys()]) == (await hamt.len()) == len(kvs) + + # HAMT should be throwing errors on keys that do not exist + ks = [k for k, _ in kvs] + key_that_cannot_exist = "".join(ks).join( + "string to account for empty string key case" + ) + with pytest.raises(KeyError): + await hamt.get(key_that_cannot_exist) + with pytest.raises(KeyError): + await hamt.delete(key_that_cannot_exist) + + hamt_keys = [key async for key in hamt.keys()] + hamt_key_set = set(hamt_keys) + keys_set = set() for key, _ in kvs: - await hamt.delete(key) - assert (await hamt.len()) == 0 - # assert len(list(hamt)) == len(hamt) - # # Re insert all items but now with a bucket size that forces linking, which actually runs the link following code branches, otherwise we would miss 100% code coverage - # hamt.max_bucket_size = 1 - # for key, value in kvs: - # hamt[key] = value - # assert hamt[key] == value - # assert len(hamt) == len(kvs) - # assert len(list(hamt)) == len(hamt) - - # ks = [k for k, _ in kvs] - # key_that_cannot_exist = "".join(ks).join( - # "string to account for empty string key case" - # ) - # with pytest.raises(KeyError): - # hamt[key_that_cannot_exist] - # with pytest.raises(KeyError): - # del hamt[key_that_cannot_exist] - - # for key, value in kvs: - # assert hamt[key] == value - - # assert len(hamt) == len(kvs) - # assert len(list(hamt)) == len(kvs) - - # hamt_keys = list(hamt) - # hamt_key_set = set(hamt_keys) - # keys_set = set() - # for key, _ in kvs: - # keys_set.add(key) - - # assert hamt_key_set == keys_set - - # # Make sure all ids actually exist in the store, this should not raies any exceptions - # store_ids: list[bytes] = list(hamt.ids()) # type: ignore - # for id in store_ids: - # store.load(id) - - # hamt.make_read_only() - # with pytest.raises(Exception, match="Cannot call set on a read only HAMT"): - # hamt["foo"] = b"bar" - # with pytest.raises(Exception, match="Cannot call delete on a read only HAMT"): - # del hamt["foo"] - # hamt.enable_write() - - # copy_hamt = deepcopy(hamt) - - # # Modify our current hamt and since the copy is a deep copy, they should be different - # for key, _ in kvs: - # del hamt[key] - # assert len(hamt) == 0 - # assert len(copy_hamt) == len(kvs) - - # # Test that when a hamt has its root manually initialized by a user, that the key count is accurate - # hamt_re_initialized = HAMT(store=store, root_node_id=copy_hamt.root_node_id) - # assert len(hamt_re_initialized) == len(kvs) + keys_set.add(key) + + assert hamt_key_set == keys_set + + # Make sure all pointers actually exist in the store, this should not raise any exceptions + for k,_ in kvs: + # Callers must handle acquiring a lock themselves, so do these entirely sequentially + pointer: bytes = await hamt._get_pointer(k) # type: ignore we know that DictStore only returns bytes for its Link type + await store.load(pointer) + + await hamt.make_read_only() + with pytest.raises(Exception, match="Cannot call set on a read only HAMT"): + await hamt.set("foo", "bar") + with pytest.raises(Exception, match="Cannot call delete on a read only HAMT"): + await hamt.delete("foo") + + + # Test that when a hamt has its root manually initialized by a user, that the key count is accurate + # We can only get the root node id here since hamt is in read mode and thus the in memory tree has been entirely flushed + new_hamt = await HAMT.build(store=store, root_node_id=hamt.root_node_id) + assert len([key async for key in new_hamt.keys()]) == (await new_hamt.len()) == len(kvs) # Mostly for complete code coverage's sake @@ -137,24 +142,23 @@ def test_key_rewrite(): def test_cache_clear(): - hamt = HAMT(store=DictStore(), max_cache_size_bytes=1000) + hamt = HAMT(store=DictStore(), read_cache_limit=1000) for key_int in range(50): hamt[str(key_int)] = key_int # Test that is guaranteed to induce overfull buckets that then requires our hamt to follow deeper into the tree to do insertions -def test_link_following(): - store = DictStore() - hamt = HAMT(store=store) +async def test_link_following(): + hamt = HAMT(store=DictStore()) hamt.max_bucket_size = 1 - # The first byte of the blake3 hash of each of these is 0b10110011 + # The first byte of the blake3 hash of each of these is the same, 10110011 kvs = [(str(5), b""), (str(15), b""), (str(123), b"")] for k, v in kvs: - hamt[k] = v - assert len(hamt) == 3 + await hamt.set(k, v) + assert (await hamt.len()) == 3 for k, _ in kvs: - del hamt[k] - assert len(hamt) == 0 + await hamt.delete(k) + assert (await hamt.len()) == 0 # Run this with varying cache sizes to see the impact on performance of the cache when using IPFSStore() From 2e3fe03cd6cc3aea37d867510db76e74840e2508 Mon Sep 17 00:00:00 2001 From: Abid Sikder <41392423+abidsikder@users.noreply.github.com> Date: Mon, 12 May 2025 15:13:22 -0400 Subject: [PATCH 023/118] Fix bug with flushing in memory tree when there are internally unlinked nodes --- py_hamt/hamt.py | 21 +++++++++++---------- tests/test_hamt.py | 2 ++ 2 files changed, 13 insertions(+), 10 deletions(-) diff --git a/py_hamt/hamt.py b/py_hamt/hamt.py index 970f72a..1850d13 100644 --- a/py_hamt/hamt.py +++ b/py_hamt/hamt.py @@ -196,9 +196,8 @@ def has_children_in_memory(self, node: Node) -> bool: def needs_flushing(self) -> bool: return getsizeof(self.buffer) > self.hamt.inmemory_tree_limit - # TODO, reimplement without treating the root node specially, but do assume that the root node is always in the in memory buffer since it will always be called first in any operations doing tree traversal async def flush_buffer(self, flush_everything: bool = False): - if not self.needs_flushing() and not flush_everything: + if not (self.needs_flushing() or flush_everything): return if len(self.buffer) == 0: @@ -258,19 +257,22 @@ async def flush_buffer(self, flush_everything: bool = False): del self.buffer[top_buffer_id] node_stack.pop() - # Only flush the root node if our size limits are still too big, or we've been instructed to remove everything. Always keeping the root node is important for performance - if self.needs_flushing() or flush_everything: + # Flush out the root node along before we do everything else as well + if (self.needs_flushing() or flush_everything) and self.is_buffer_id(self.hamt.root_node_id): + root_node: Node = self.buffer[self.hamt.root_node_id] # type: ignore del self.buffer[self.hamt.root_node_id] # type: ignore self.hamt.root_node_id = await self.hamt.store.save( root_node.serialize(), codec="dag-cbor" ) + # If the in memory tree is used for only read purposes, then we will have a bunch of nodes that seem "unlinked" to anything else, since Links used within the Nodes will reference the real underlying store + # For this case, just clear everything, nothing inside is linked to anything else anyhow + if self.needs_flushing() or flush_everything: + self.buffer = dict() + assert not self.is_buffer_id(self.hamt.root_node_id) + if flush_everything: assert len(self.buffer) == 0 - if self.needs_flushing(): - raise Exception( - "Could not flush in memory tree buffer enough to reach limit, consider raising limit to accomodate for python empty object overheads" - ) async def add_to_buffer(self, node: Node) -> IPLDKind: # This is IPLDKind type, but not dag_cbor serializable due to int limits so this will throw errors early if the tree is written with the buffer_ids still in there @@ -376,7 +378,7 @@ async def enable_write(self): self.read_only = False self.node_store = InMemoryTreeStore(self) - # Make sure the root node is in memory, we can't modify the originating root node otherwise when loading things in + # Guarantee the root node is in the inmemory tree, we can't modify the originating root node otherwise when loading things in if the user is quickly switching between enabling write and making it read only without using any other operations self.root_node_id = await self.node_store.save(self.root_node_id, root_node) async def _reserialize_and_link(self, node_stack: list[tuple[Link, Node]]): @@ -477,7 +479,6 @@ async def _set_pointer(self, key: str, val_ptr: IPLDKind): # Finally, reserialize and fix all links, deleting empty nodes as needed await self._reserialize_and_link(node_stack) - self.root_node_id = node_stack[0][0] # This needs to be called after the root node is set from the node stack, since this may change the root node if the memory buffer is too small to hold the root node if isinstance(self.node_store, InMemoryTreeStore): await self.node_store.flush_buffer() diff --git a/tests/test_hamt.py b/tests/test_hamt.py index 55b12c8..744e20c 100644 --- a/tests/test_hamt.py +++ b/tests/test_hamt.py @@ -53,7 +53,9 @@ async def verify(k, v): # Re insert all items but now with a bucket size that forces linking, which actually runs the link following code branches, otherwise we would miss 100% code coverage hamt.max_bucket_size = 1 await asyncio.gather(*[hamt.set(k, v) for k, v in kvs]) + await hamt.make_read_only() # cover code branch in keys() that does not need to acquire lock for read only mode assert len([key async for key in hamt.keys()]) == (await hamt.len()) == len(kvs) + await hamt.enable_write() # HAMT should be throwing errors on keys that do not exist ks = [k for k, _ in kvs] From cd2334a960aca17536a5eba6481084def4595b14 Mon Sep 17 00:00:00 2001 From: Abid Sikder <41392423+abidsikder@users.noreply.github.com> Date: Tue, 13 May 2025 17:02:33 -0400 Subject: [PATCH 024/118] misc design and documentation changes, no regressions demonstrated with testing --- py_hamt/hamt.py | 62 ++++++++---------- tests/test_hamt.py | 157 +++++++++++++++++++++++++-------------------- 2 files changed, 115 insertions(+), 104 deletions(-) diff --git a/py_hamt/hamt.py b/py_hamt/hamt.py index 1850d13..bc3d33f 100644 --- a/py_hamt/hamt.py +++ b/py_hamt/hamt.py @@ -13,16 +13,14 @@ def extract_bits(hash_bytes: bytes, depth: int, nbits: int) -> int: - """Extract `nbits` bits from `hash_bytes`, beginning at position `depth * nbits`, - and convert them into an unsigned integer value. + """ + Extract `nbits` bits from `hash_bytes`, beginning at position `depth * nbits`, and convert them into an unsigned integer value. - Args: - hash_bytes (bytes): binary hash to extract bit sequence from - depth (int): depth of the node containing the hash - nbits (int): bit width of hash + hash_bytes: binary hash to extract bit sequence from + depth: depth of the node containing the hash + nbits: bit width of hash - Returns: - int: An unsigned integer version of the bit sequence + returns an unsigned integer version of the bit sequence """ # This is needed since int.bit_length on a integer representation of a bytes object ignores leading 0s hash_bit_length = len(hash_bytes) * 8 @@ -46,9 +44,9 @@ def extract_bits(hash_bytes: bytes, depth: int, nbits: int) -> int: def blake3_hashfn(input_bytes: bytes) -> bytes: """ - This is provided as a default recommended hash function by py-hamt. It uses the blake3 hash function and uses 32 bytes as the hash size. + This is the default hash function used for . It uses the blake3 hash function and uses 32 bytes as the hash size. - To bring your own hash function, just create a function that takes in bytes and returns the hash bytes, and use that in the HAMT init method. + To provide your own hash function, create a function that takes in arbitrarily long bytes and returns the hash bytes. It's important to note that the resulting hash must must always be a multiple of 8 bits since python bytes object can only represent in segments of bytes, and thus 8 bits. """ @@ -57,33 +55,28 @@ def blake3_hashfn(input_bytes: bytes) -> bytes: raw_bytes = b3.unwrap(digest) return raw_bytes - -# Used for readability, since a HAMT also stores IPLDKind objects -# Store IDs are also IPLDKind, which makes the code harder to read if only using IPLDKind rather than this type alias -type Link = IPLDKind -type StoreID = IPLDKind - - class Node: + """ + The Node class encapsulates + """ def __init__(self): self.data: list[IPLDKind] = [dict() for _ in range(0, 256)] # empty dicts represent empty buckets, lists with one element are links, with the internal element being a link def iter_buckets(self) -> Iterator[dict]: - for i in range(len(self.data)): - item = self.data[i] + for item in self.data: if isinstance(item, dict): yield item def iter_link_indices(self) -> Iterator[int]: - """Return the list indices where there are links.""" for i in range(len(self.data)): if isinstance(self.data[i], list): yield i def iter_links(self) -> Iterator[IPLDKind]: - for i in self.iter_link_indices(): - yield self.get_link(i) + for item in self.data: + if isinstance(item, list): + yield item[0] def get_link(self, index: int) -> IPLDKind: link_wrapper: list[IPLDKind] = self.data[index] # type: ignore @@ -119,12 +112,11 @@ def deserialize(cls, data: bytes) -> "Node": raise Exception( "Invalid dag-cbor encoded data from the store was attempted to be decoded" ) - if isinstance(decoded_data, list) and len(decoded_data) == 256: - node = cls() - node.data = decoded_data - return node - else: - raise ValueError("Data does not contain a valid Node") + + # Don't do any further checks for speed purposes + node = cls() + node.data = decoded_data # type: ignore + return node # For HAMT internal use for increaing performance with nodes @@ -324,11 +316,13 @@ def __init__( max_bucket_size: int = 4, inmemory_tree_limit: int = 10_000_000, # 10 MB default read_cache_limit: int = 10_000_000, # 10 MB default + values_are_bytes: bool = False ): self.store = store self.hash_fn = hash_fn self.lock = asyncio.Lock() self.read_only = read_only + self.values_are_bytes = values_are_bytes if max_bucket_size < 1: raise ValueError("Bucket size maximum must be a positive integer") @@ -381,7 +375,7 @@ async def enable_write(self): # Guarantee the root node is in the inmemory tree, we can't modify the originating root node otherwise when loading things in if the user is quickly switching between enabling write and making it read only without using any other operations self.root_node_id = await self.node_store.save(self.root_node_id, root_node) - async def _reserialize_and_link(self, node_stack: list[tuple[Link, Node]]): + async def _reserialize_and_link(self, node_stack: list[tuple[IPLDKind, Node]]): """ This function starts from the node at the end of the list and reserializes so that each node holds valid new IDs after insertion into the store Takes a stack of nodes, we represent a stack with a list where the first element is the root element and the last element is the top of the stack @@ -420,13 +414,13 @@ async def _reserialize_and_link(self, node_stack: list[tuple[Link, Node]]): prev_node.replace_link(old_id, new_store_id) # automatically skip encoding if the value provided is of the bytes variety - async def set(self, key: str, val: IPLDKind, skip_encode=False): + async def set(self, key: str, val: IPLDKind): """TODO add something about how skip encoding can make large bytes setting much more efficient""" if self.read_only: raise Exception("Cannot call set on a read only HAMT") data: bytes - if skip_encode: + if self.values_are_bytes: data = val # type: ignore let users get an exception if they pass in a non bytes when they want to skip encoding else: data = dag_cbor.encode(val) @@ -524,8 +518,8 @@ async def delete(self, key: str): # If we didn't make a change, then this key must not exist within the HAMT raise KeyError - # include option to skip decode if the user knows that the value inside is also going to be a bytes object - async def get(self, key: str, skip_decode=False) -> IPLDKind: + # TODO document option to skip decode if the user knows that the value inside is also going to be a bytes object + async def get(self, key: str) -> IPLDKind: # If read only, no need to acquire a lock pointer: IPLDKind if self.read_only: @@ -535,7 +529,7 @@ async def get(self, key: str, skip_decode=False) -> IPLDKind: pointer = await self._get_pointer(key) data = await self.store.load(pointer) - if skip_decode: + if self.values_are_bytes: return data else: return dag_cbor.decode(data) diff --git a/tests/test_hamt.py b/tests/test_hamt.py index 744e20c..12417fa 100644 --- a/tests/test_hamt.py +++ b/tests/test_hamt.py @@ -6,6 +6,7 @@ from dag_cbor import IPLDKind from multiformats import CID from hypothesis import given +from hypothesis import strategies as st import pytest from py_hamt import HAMT, DictStore @@ -13,11 +14,9 @@ from testing_utils import key_value_list - @pytest.mark.asyncio @given(key_value_list) async def test_fuzz(kvs: list[tuple[str, IPLDKind]]): -# async def test_fuzz(): store = DictStore() hamt = await HAMT.build(store=store) @@ -33,8 +32,6 @@ async def test_fuzz(kvs: list[tuple[str, IPLDKind]]): # Set entirely concurrently thus with unpredictable order await asyncio.gather(*[hamt.set(k, v) for k, v in kvs]) - - # Switching this one and off should not cause any problems await hamt.make_read_only() await hamt.enable_write() await hamt.make_read_only() @@ -87,80 +84,100 @@ async def verify(k, v): with pytest.raises(Exception, match="Cannot call delete on a read only HAMT"): await hamt.delete("foo") - # Test that when a hamt has its root manually initialized by a user, that the key count is accurate # We can only get the root node id here since hamt is in read mode and thus the in memory tree has been entirely flushed new_hamt = await HAMT.build(store=store, root_node_id=hamt.root_node_id) assert len([key async for key in new_hamt.keys()]) == (await new_hamt.len()) == len(kvs) +key_bytes_list = st.lists( + st.tuples(st.text(), st.binary()), + min_size=0, + max_size=10000, + unique_by=lambda x: x[ + 0 + ], # ensure unique keys, otherwise we can't do the length and size checks when using these KVs for the HAMT +) -# Mostly for complete code coverage's sake -def test_remaining_exceptions(): - memory_store = DictStore() - with pytest.raises(Exception, match="ID not found in store"): - memory_store.load(b"foo") +@pytest.mark.asyncio +@given(kvs=key_bytes_list) +async def test_values_are_bytes(kvs: list[tuple[str, bytes]]): + store = DictStore() + hamt = await HAMT.build(store=store, values_are_bytes=True) - with pytest.raises(ValueError, match="Data not a valid Node serialization"): - bad_serialization = dag_cbor.encode([]) - Node.deserialize(bad_serialization) + await asyncio.gather(*[hamt.set(k, v) for k, v in kvs]) + for k,v in kvs: + value = await hamt.get(k) + assert value == v + assert len([key async for key in hamt.keys()]) == (await hamt.len()) == len(kvs) + await asyncio.gather(*[hamt.delete(k) for k, _ in kvs]) # delete everything + assert len([key async for key in hamt.keys()]) == (await hamt.len()) == 0 - hamt = HAMT( - store=memory_store, - ) - root_node = Node.deserialize(memory_store.load(hamt.root_node_id)) # type: ignore - buckets = root_node.get_buckets() - links = root_node.get_links() - # 4 is the map key for the string "foo" - buckets["4"] = [] - links["4"] = b"bar" - bad_node_id = memory_store.save(root_node.serialize()) - bad_hamt = HAMT(store=memory_store, root_node_id=bad_node_id) - - with pytest.raises( - Exception, - match="Key in both buckets and links of the node, invariant violated", - ): - bad_hamt["foo"] = b"bar2" - - with pytest.raises( - Exception, - match="Key in both buckets and links of the node, invariant violated", - ): - del bad_hamt["foo"] - - -def test_key_rewrite(): - hamt = HAMT(store=DictStore()) - hamt["foo"] = b"bar" - assert b"bar" == hamt["foo"] - assert len(hamt) == 1 - - hamt["foo"] = bytes("something else", "utf-8") - assert len(hamt) == 1 - assert b"something else" == hamt["foo"] - - hamt["foo"] = CID("base32", 1, "dag-cbor", ("blake3", bytes(32))) - assert len(hamt) == 1 - - -def test_cache_clear(): - hamt = HAMT(store=DictStore(), read_cache_limit=1000) - for key_int in range(50): - hamt[str(key_int)] = key_int - - -# Test that is guaranteed to induce overfull buckets that then requires our hamt to follow deeper into the tree to do insertions -async def test_link_following(): - hamt = HAMT(store=DictStore()) - hamt.max_bucket_size = 1 - # The first byte of the blake3 hash of each of these is the same, 10110011 - kvs = [(str(5), b""), (str(15), b""), (str(123), b"")] - for k, v in kvs: - await hamt.set(k, v) - assert (await hamt.len()) == 3 - for k, _ in kvs: - await hamt.delete(k) - assert (await hamt.len()) == 0 +# # Mostly for complete code coverage's sake +# def test_remaining_exceptions(): +# memory_store = DictStore() +# with pytest.raises(Exception, match="ID not found in store"): +# memory_store.load(b"foo") + +# with pytest.raises(ValueError, match="Data not a valid Node serialization"): +# bad_serialization = dag_cbor.encode([]) +# Node.deserialize(bad_serialization) + +# hamt = HAMT( +# store=memory_store, +# ) +# root_node = Node.deserialize(memory_store.load(hamt.root_node_id)) # type: ignore +# buckets = root_node.get_buckets() +# links = root_node.get_links() +# # 4 is the map key for the string "foo" +# buckets["4"] = [] +# links["4"] = b"bar" +# bad_node_id = memory_store.save(root_node.serialize()) +# bad_hamt = HAMT(store=memory_store, root_node_id=bad_node_id) + +# with pytest.raises( +# Exception, +# match="Key in both buckets and links of the node, invariant violated", +# ): +# bad_hamt["foo"] = b"bar2" + +# with pytest.raises( +# Exception, +# match="Key in both buckets and links of the node, invariant violated", +# ): +# del bad_hamt["foo"] + + +# def test_key_rewrite(): +# hamt = HAMT(store=DictStore()) +# hamt["foo"] = b"bar" +# assert b"bar" == hamt["foo"] +# assert len(hamt) == 1 + +# hamt["foo"] = bytes("something else", "utf-8") +# assert len(hamt) == 1 +# assert b"something else" == hamt["foo"] + +# hamt["foo"] = CID("base32", 1, "dag-cbor", ("blake3", bytes(32))) +# assert len(hamt) == 1 + + +# async def test_cache_clear(): +# hamt = await HAMT.build(store=DictStore(), read_cache_limit=10000) +# await asyncio.gather(*[hamt.set(str(key_int), key_int) for key_int in range(50)]) + + +# # Test that is guaranteed to induce overfull buckets that then requires our hamt to follow deeper into the tree to do insertions +# async def test_link_following(): +# hamt = await HAMT.build(store=DictStore()) +# hamt.max_bucket_size = 1 +# # The first byte of the blake3 hash of each of these is the same, 10110011 +# kvs = [(str(5), b""), (str(15), b""), (str(123), b"")] +# for k, v in kvs: +# await hamt.set(k, v) +# assert (await hamt.len()) == 3 +# for k, _ in kvs: +# await hamt.delete(k) +# assert (await hamt.len()) == 0 # Run this with varying cache sizes to see the impact on performance of the cache when using IPFSStore() From 6607848e981b0d372d10a9b662f46a7f86c779a4 Mon Sep 17 00:00:00 2001 From: Abid Sikder <41392423+abidsikder@users.noreply.github.com> Date: Tue, 13 May 2025 17:17:22 -0400 Subject: [PATCH 025/118] 100% test coverage for stores --- py_hamt/store.py | 26 +++++++++++----- tests/test_ipfsstore.py | 28 ----------------- tests/test_stores.py | 68 +++++++++++++++++++++++++++++++++++++++++ 3 files changed, 87 insertions(+), 35 deletions(-) delete mode 100644 tests/test_ipfsstore.py create mode 100644 tests/test_stores.py diff --git a/py_hamt/store.py b/py_hamt/store.py index eeeb31c..a86049a 100644 --- a/py_hamt/store.py +++ b/py_hamt/store.py @@ -12,6 +12,9 @@ type CodecInput = Literal["raw", "dag-cbor"] +# TODO add Store documentation note about not supporting Stores that use null as a valid ID, since the HAMT uses this as a way to indicate null for its root node in its constructor + + class Store(ABC): """Abstract class that represents a storage mechanism the HAMT can use for keeping data. @@ -50,8 +53,8 @@ async def save(self, data: bytes, codec: CodecInput) -> bytes: async def load(self, id: bytes) -> bytes: # type: ignore since bytes is a subset of the IPLDKind type if id in self.store: return self.store[id] - else: - raise Exception("ID not found in store") + + raise KeyError class IPFSStore(Store): @@ -102,8 +105,9 @@ async def save(self, data: bytes, codec: CodecInput) -> CID: base_url=IPFSStore.KUBO_DEFAULT_LOCAL_RPC_BASE_URL ) - async with self.rpc_session.request( - method="POST", url=self.rpc_url, data={"file": io.BytesIO(data)} + async with self.rpc_session.post( + url=self.rpc_url, + data={"file": io.BytesIO(data)}, ) as response: response.raise_for_status() json_bytes = await response.read() @@ -124,8 +128,16 @@ async def load( # type: ignore CID is definitely in the IPLDKind type base_url=IPFSStore.KUBO_DEFAULT_LOCAL_GATEWAY_BASE_URL ) - async with self.gateway_session.request( - method="GET", url=f"/ipfs/{str(id)}" - ) as response: + async with self.gateway_session.get(url=f"/ipfs/{str(id)}") as response: response.raise_for_status() return await response.read() + + async def close_sessions(self): + # TODO write about no-oping when sessions are closed but they either don't exist or were already closed + if self.rpc_session is not None: + await self.rpc_session.close() + self.rpc_session = None + + if self.gateway_session is not None: + await self.gateway_session.close() + self.gateway_session = None diff --git a/tests/test_ipfsstore.py b/tests/test_ipfsstore.py deleted file mode 100644 index 177a17f..0000000 --- a/tests/test_ipfsstore.py +++ /dev/null @@ -1,28 +0,0 @@ -import aiohttp -import dag_cbor -from dag_cbor import IPLDKind -from hypothesis import given -import pytest - -from py_hamt import IPFSStore - -from testing_utils import ipld_strategy, create_ipfs # noqa - - -@pytest.mark.asyncio -@given(data=ipld_strategy()) -async def test_ipfsstore(create_ipfs, data: IPLDKind): # noqa - rpc_uri_stem, gateway_uri_stem = create_ipfs - gateway_session = aiohttp.ClientSession(base_url=gateway_uri_stem) - rpc_session = aiohttp.ClientSession(base_url=rpc_uri_stem) - - try: - ipfsstore = IPFSStore(rpc_session=rpc_session, gateway_session=gateway_session) - - for codec in ["raw", "dag-cbor"]: - cid = await ipfsstore.save(dag_cbor.encode(data), codec=codec) # type: ignore - result = dag_cbor.decode(await ipfsstore.load(cid)) - assert data == result - finally: - await rpc_session.close() - await gateway_session.close() diff --git a/tests/test_stores.py b/tests/test_stores.py new file mode 100644 index 0000000..f4fcdd3 --- /dev/null +++ b/tests/test_stores.py @@ -0,0 +1,68 @@ +import aiohttp +import dag_cbor +from dag_cbor import IPLDKind +from hypothesis import given +import pytest + +from py_hamt import IPFSStore + +from py_hamt.store import DictStore +from testing_utils import ipld_strategy, create_ipfs # noqa + +# Just to cover this one case that isn't covered within test_hamt +@pytest.mark.asyncio +async def test_memory_store_exception(): + s = DictStore() + with pytest.raises(KeyError): + await s.load(bytes()) + +@pytest.mark.asyncio +@given(data=ipld_strategy()) +async def test_ipfsstore_default_urls(data: IPLDKind): + ipfsstore = IPFSStore() + # test that ipfs store close session when both are already missing is a no-op + await ipfsstore.close_sessions() + cids = [] + try: + for codec in ["raw", "dag-cbor"]: + cid = await ipfsstore.save(dag_cbor.encode(data), codec=codec) # type: ignore + cids.append(cid) + result = dag_cbor.decode(await ipfsstore.load(cid)) + assert data == result + # We should be able to close right after every result and it will remake its sessions if it needs to + await ipfsstore.close_sessions() + finally: + await ipfsstore.close_sessions() + # test that it's a no-op again + await ipfsstore.close_sessions() + + # Now do it but with only loading data, which will be a common use pattern for HAMT readers + try: + for cid in cids: + for codec in ["raw", "dag-cbor"]: + result = dag_cbor.decode(await ipfsstore.load(cid)) + assert data == result + await ipfsstore.close_sessions() + finally: + await ipfsstore.close_sessions() + await ipfsstore.close_sessions() + + + +@pytest.mark.asyncio +@given(data=ipld_strategy()) +async def test_ipfsstore(create_ipfs, data: IPLDKind): # noqa + rpc_uri_stem, gateway_uri_stem = create_ipfs + gateway_session = aiohttp.ClientSession(base_url=gateway_uri_stem) + rpc_session = aiohttp.ClientSession(base_url=rpc_uri_stem) + + try: + ipfsstore = IPFSStore(rpc_session=rpc_session, gateway_session=gateway_session) + + for codec in ["raw", "dag-cbor"]: + cid = await ipfsstore.save(dag_cbor.encode(data), codec=codec) # type: ignore + result = dag_cbor.decode(await ipfsstore.load(cid)) + assert data == result + finally: + await rpc_session.close() + await gateway_session.close() From cda896b01657f469ab2b08b76738aeecf81b4c6c Mon Sep 17 00:00:00 2001 From: Abid Sikder <41392423+abidsikder@users.noreply.github.com> Date: Tue, 13 May 2025 17:44:28 -0400 Subject: [PATCH 026/118] remove need to constantly initialize with the root node for in memory store --- py_hamt/hamt.py | 90 ++++++++++++++++++++-------------------------- tests/test_hamt.py | 26 ++++++++++++-- 2 files changed, 62 insertions(+), 54 deletions(-) diff --git a/py_hamt/hamt.py b/py_hamt/hamt.py index bc3d33f..c741f6a 100644 --- a/py_hamt/hamt.py +++ b/py_hamt/hamt.py @@ -195,7 +195,6 @@ async def flush_buffer(self, flush_everything: bool = False): if len(self.buffer) == 0: return - # Start by removing completely empty nodes, which will be unreferenced by other nodes but will still be inside the buffer since this in memory tree assigns unique IDs to every node, unlike a normal content-addressed system which would have consolidated all the empty nodes empty_node_buffer_ids: list[ int @@ -211,45 +210,46 @@ async def flush_buffer(self, flush_everything: bool = False): for buffer_id in empty_node_buffer_ids: del self.buffer[buffer_id] - - # Start with the root node's children, which should always be in the in memory buffer if there's anything there - # there is an implicit assumption that the entire continuous line of branches up to an ancestor in the memory buffer, which will happen because of the DFS style traversal in all HAMT operations - # node stack is a list of tuples that look like (parent_id, self_id, node) - node_stack: list[tuple[int, int, Node]] = [] - root_node: Node = self.buffer[self.hamt.root_node_id] # type: ignore - for child_buffer_id in self.children_in_memory(root_node): - child_node = self.buffer[child_buffer_id] - node_stack.append((self.hamt.root_node_id, child_buffer_id, child_node)) # type: ignore - - shuffle(node_stack) # avoid always recursing down the rightmost branch - - while len(node_stack) > 0 and (self.needs_flushing() or flush_everything): - parent_buffer_id, top_buffer_id, top_node = node_stack[-1] - new_nodes_on_stack = [] - if self.has_children_in_memory(top_node): - for child_buffer_id in self.children_in_memory(top_node): - child_node = self.buffer[child_buffer_id] - new_nodes_on_stack.append( - (top_buffer_id, child_buffer_id, child_node) + # The root node may not be in the buffer, e.g. this is freshly created + if self.is_buffer_id(self.hamt.root_node_id): + # Start with the root node's children, which should always be in the in memory buffer if there's anything there + # there is an implicit assumption that the entire continuous line of branches up to an ancestor in the memory buffer, which will happen because of the DFS style traversal in all HAMT operations + # node stack is a list of tuples that look like (parent_id, self_id, node) + node_stack: list[tuple[int, int, Node]] = [] + root_node: Node = self.buffer[self.hamt.root_node_id] # type: ignore + for child_buffer_id in self.children_in_memory(root_node): + child_node = self.buffer[child_buffer_id] + node_stack.append((self.hamt.root_node_id, child_buffer_id, child_node)) # type: ignore + + shuffle(node_stack) # avoid always recursing down the rightmost branch + + while len(node_stack) > 0 and (self.needs_flushing() or flush_everything): + parent_buffer_id, top_buffer_id, top_node = node_stack[-1] + new_nodes_on_stack = [] + if self.has_children_in_memory(top_node): + for child_buffer_id in self.children_in_memory(top_node): + child_node = self.buffer[child_buffer_id] + new_nodes_on_stack.append( + (top_buffer_id, child_buffer_id, child_node) + ) + + shuffle( + new_nodes_on_stack + ) # avoid always recursing down the rightmost branch + node_stack.extend(new_nodes_on_stack) + else: + # We can flush this one completely since it has no children in memory, we'll just have to edit its parent after serializing it + old_id = top_buffer_id + new_id = await self.hamt.store.save( + top_node.serialize(), codec="dag-cbor" ) + parent_node = self.buffer[parent_buffer_id] + parent_node.replace_link(old_id, new_id) - shuffle( - new_nodes_on_stack - ) # avoid always recursing down the rightmost branch - node_stack.extend(new_nodes_on_stack) - else: - # We can flush this one completely since it has no children in memory, we'll just have to edit its parent after serializing it - old_id = top_buffer_id - new_id = await self.hamt.store.save( - top_node.serialize(), codec="dag-cbor" - ) - parent_node = self.buffer[parent_buffer_id] - parent_node.replace_link(old_id, new_id) - - del self.buffer[top_buffer_id] - node_stack.pop() - - # Flush out the root node along before we do everything else as well + del self.buffer[top_buffer_id] + node_stack.pop() + + # Flush out the root node before we do everything else as well if (self.needs_flushing() or flush_everything) and self.is_buffer_id(self.hamt.root_node_id): root_node: Node = self.buffer[self.hamt.root_node_id] # type: ignore del self.buffer[self.hamt.root_node_id] # type: ignore @@ -328,14 +328,7 @@ def __init__( raise ValueError("Bucket size maximum must be a positive integer") self.max_bucket_size = max_bucket_size - # TODO add documentation about buffer limit and cache limit minimums being 10 KB, to avoid strange boundary cases in the algorithms due to python object overhead meaning that an in memory buffer should just never be used - # Add documentation about how its values should not be positive, otherwise the HAMT will not work - # Specify a minimum size of a couple hundred bytes, since just an empty dict will consume some memory - - if read_cache_limit < 10_000: - raise ValueError("Cache limit too small, less than 10 KB") - if inmemory_tree_limit < 10_000: - raise ValueError("In memory tree limit too small, less than 10 KB") + # TODO add documentation about buffer limit and cache limit minimums and how if they are set to a really low limit they'll effectively constantly flush self.inmemory_tree_limit = inmemory_tree_limit self.read_cache_limit = read_cache_limit @@ -367,13 +360,8 @@ async def make_read_only(self): async def enable_write(self): async with self.lock: - # Get the root node right before we clear out the cache store - root_node = await self.node_store.load(self.root_node_id) - self.read_only = False self.node_store = InMemoryTreeStore(self) - # Guarantee the root node is in the inmemory tree, we can't modify the originating root node otherwise when loading things in if the user is quickly switching between enabling write and making it read only without using any other operations - self.root_node_id = await self.node_store.save(self.root_node_id, root_node) async def _reserialize_and_link(self, node_stack: list[tuple[IPLDKind, Node]]): """ diff --git a/tests/test_hamt.py b/tests/test_hamt.py index 12417fa..8d14fa2 100644 --- a/tests/test_hamt.py +++ b/tests/test_hamt.py @@ -17,6 +17,8 @@ @pytest.mark.asyncio @given(key_value_list) async def test_fuzz(kvs: list[tuple[str, IPLDKind]]): +# async def test_fuzz(): +# kvs=[('', None), ('0', None)] store = DictStore() hamt = await HAMT.build(store=store) @@ -84,10 +86,22 @@ async def verify(k, v): with pytest.raises(Exception, match="Cannot call delete on a read only HAMT"): await hamt.delete("foo") + async def verify_kvs_and_len(h: HAMT): + for k,v in kvs: + assert (await h.get(k)) == v + assert len([key async for key in h.keys()]) == (await h.len()) == len(kvs) + # Test that when a hamt has its root manually initialized by a user, that the key count is accurate # We can only get the root node id here since hamt is in read mode and thus the in memory tree has been entirely flushed - new_hamt = await HAMT.build(store=store, root_node_id=hamt.root_node_id) - assert len([key async for key in new_hamt.keys()]) == (await new_hamt.len()) == len(kvs) + new_hamt = await HAMT.build(store=store, root_node_id=hamt.root_node_id, read_only=True) + await verify_kvs_and_len(new_hamt) + + # Test a hamt with too small of a read cache + hamt_no_read_cache = await HAMT.build(store=store, root_node_id=hamt.root_node_id, read_only=True, read_cache_limit=0) + await verify_kvs_and_len(hamt_no_read_cache) + + hamt_no_memory_tree = await HAMT.build(store=store, root_node_id=hamt.root_node_id, inmemory_tree_limit = 0) + await verify_kvs_and_len(hamt_no_memory_tree) key_bytes_list = st.lists( st.tuples(st.text(), st.binary()), @@ -112,7 +126,13 @@ async def test_values_are_bytes(kvs: list[tuple[str, bytes]]): await asyncio.gather(*[hamt.delete(k) for k, _ in kvs]) # delete everything assert len([key async for key in hamt.keys()]) == (await hamt.len()) == 0 -# # Mostly for complete code coverage's sake +@pytest.mark.asyncio +async def test_invalid_node(): + memory_store = DictStore() + with pytest.raises(Exception, match="Invalid dag-cbor encoded data from the store was attempted to be decoded"): + Node.deserialize(bytes()) + + # def test_remaining_exceptions(): # memory_store = DictStore() # with pytest.raises(Exception, match="ID not found in store"): From 0ac1d3a0d1bb4800110626bdda3773b5a9559b02 Mon Sep 17 00:00:00 2001 From: Abid Sikder <41392423+abidsikder@users.noreply.github.com> Date: Tue, 13 May 2025 18:12:09 -0400 Subject: [PATCH 027/118] fix bug with not setting root node after reserializing in set_pointer --- py_hamt/hamt.py | 1 + 1 file changed, 1 insertion(+) diff --git a/py_hamt/hamt.py b/py_hamt/hamt.py index c741f6a..7d67860 100644 --- a/py_hamt/hamt.py +++ b/py_hamt/hamt.py @@ -461,6 +461,7 @@ async def _set_pointer(self, key: str, val_ptr: IPLDKind): # Finally, reserialize and fix all links, deleting empty nodes as needed await self._reserialize_and_link(node_stack) + self.root_node_id = node_stack[0][0] # This needs to be called after the root node is set from the node stack, since this may change the root node if the memory buffer is too small to hold the root node if isinstance(self.node_store, InMemoryTreeStore): await self.node_store.flush_buffer() From a030c3a94357512c9b0dcb9d5d4601ba0776f80f Mon Sep 17 00:00:00 2001 From: Abid Sikder <41392423+abidsikder@users.noreply.github.com> Date: Wed, 14 May 2025 16:00:35 -0400 Subject: [PATCH 028/118] simplify cache eviction calling and in memory flushing algorithm --- py_hamt/hamt.py | 178 ++++++++++++++++++----------------------- tests/test_hamt.py | 195 ++++++++++++++++++++++++--------------------- 2 files changed, 181 insertions(+), 192 deletions(-) diff --git a/py_hamt/hamt.py b/py_hamt/hamt.py index 7d67860..b081253 100644 --- a/py_hamt/hamt.py +++ b/py_hamt/hamt.py @@ -1,6 +1,5 @@ from abc import ABC, abstractmethod -from sys import getsizeof -from typing import Callable, Iterator, AsyncIterator, Literal +from typing import Callable, Iterator, AsyncIterator import uuid from random import shuffle import asyncio @@ -55,10 +54,13 @@ def blake3_hashfn(input_bytes: bytes) -> bytes: raw_bytes = b3.unwrap(digest) return raw_bytes + class Node: """ + TODO The Node class encapsulates """ + def __init__(self): self.data: list[IPLDKind] = [dict() for _ in range(0, 256)] # empty dicts represent empty buckets, lists with one element are links, with the internal element being a link @@ -115,7 +117,7 @@ def deserialize(cls, data: bytes) -> "Node": # Don't do any further checks for speed purposes node = cls() - node.data = decoded_data # type: ignore + node.data = decoded_data # type: ignore return node @@ -129,19 +131,21 @@ async def save(self, original_id: IPLDKind, node: Node) -> IPLDKind: async def load(self, id: IPLDKind) -> Node: """Load nodes from the store""" + @abstractmethod + def size(self) -> int: + """Calculate the size of all internal Nodes in memory. Should not include the overhead in python of the dict or all the keys, which will be negligible compared to the Node sizes.""" + + # Async because the in memory tree has async calls + @abstractmethod + async def vacate(self): + """Remove everything from the cache.""" + class ReadCacheStore(NodeStore): def __init__(self, hamt: "HAMT"): self.hamt = hamt self.cache: dict[IPLDKind, Node] = dict() - def cache_eviction_lru(self): - while getsizeof(self.cache) > self.hamt.read_cache_limit: - if len(self.cache) == 0: - return - stalest_node_id = next(iter(self.cache.keys())) - del self.cache[stalest_node_id] - async def save(self, original_id: IPLDKind, node: Node) -> IPLDKind: raise Exception( "Save called in virtual store ReadCacheStore, only supposed to be used for reading" @@ -160,9 +164,18 @@ async def load(self, id: IPLDKind) -> Node: # Cache Miss node = Node.deserialize(await self.hamt.store.load(id)) self.cache[id] = node - self.cache_eviction_lru() return node + def size(self): + total = 0 + for k in self.cache: + node = self.cache[k] + total += len(node.serialize()) + return total + + async def vacate(self): + self.cache = dict() + class InMemoryTreeStore(NodeStore): # Add note about how this initiates by adding the HAMT's root node to the in memory tree buffer @@ -185,86 +198,63 @@ def has_children_in_memory(self, node: Node) -> bool: return True return False - def needs_flushing(self) -> bool: - return getsizeof(self.buffer) > self.hamt.inmemory_tree_limit - - async def flush_buffer(self, flush_everything: bool = False): - if not (self.needs_flushing() or flush_everything): - return - - if len(self.buffer) == 0: - return - - # Start by removing completely empty nodes, which will be unreferenced by other nodes but will still be inside the buffer since this in memory tree assigns unique IDs to every node, unlike a normal content-addressed system which would have consolidated all the empty nodes - empty_node_buffer_ids: list[ - int - ] = [] # we can't modify a dictionary while iterating so do the deletion in a separate step - for buffer_id in self.buffer: - # Just don't delete an empty root node - if buffer_id == self.hamt.root_node_id: - continue - node = self.buffer[buffer_id] - if node.is_empty(): - empty_node_buffer_ids.append(buffer_id) - - for buffer_id in empty_node_buffer_ids: - del self.buffer[buffer_id] - - # The root node may not be in the buffer, e.g. this is freshly created + # Callers must acquire a lock/stop operations to ensure an accurate calculation! + def size(self) -> int: + total = 0 + for k in self.buffer: + node = self.buffer[k] + total += len(node.serialize()) + return total + + # The HAMT must properly acquire a lock for this to run successfully! This is not async or thread safe + # This algorithm has an implicit assumption that the entire continuous line of branches up to an ancestor is in the memory buffer, which will happen because of the DFS style traversal in all HAMT operations + async def vacate(self): + # node stack is a list of tuples that look like (parent_id, self_id, node) + node_stack: list[tuple[int | None, int, Node]] = [] + # The root node may not be in the buffer, e.g. this is HAMT initialized with a specific root node id if self.is_buffer_id(self.hamt.root_node_id): - # Start with the root node's children, which should always be in the in memory buffer if there's anything there - # there is an implicit assumption that the entire continuous line of branches up to an ancestor in the memory buffer, which will happen because of the DFS style traversal in all HAMT operations - # node stack is a list of tuples that look like (parent_id, self_id, node) - node_stack: list[tuple[int, int, Node]] = [] root_node: Node = self.buffer[self.hamt.root_node_id] # type: ignore - for child_buffer_id in self.children_in_memory(root_node): + node_stack.append((None, self.hamt.root_node_id, root_node)) # type: ignore + + while len(node_stack) > 0: + parent_buffer_id, top_buffer_id, top_node = node_stack[-1] + new_nodes_on_stack = [] + for child_buffer_id in self.children_in_memory(top_node): child_node = self.buffer[child_buffer_id] - node_stack.append((self.hamt.root_node_id, child_buffer_id, child_node)) # type: ignore - - shuffle(node_stack) # avoid always recursing down the rightmost branch - - while len(node_stack) > 0 and (self.needs_flushing() or flush_everything): - parent_buffer_id, top_buffer_id, top_node = node_stack[-1] - new_nodes_on_stack = [] - if self.has_children_in_memory(top_node): - for child_buffer_id in self.children_in_memory(top_node): - child_node = self.buffer[child_buffer_id] - new_nodes_on_stack.append( - (top_buffer_id, child_buffer_id, child_node) - ) - - shuffle( - new_nodes_on_stack - ) # avoid always recursing down the rightmost branch - node_stack.extend(new_nodes_on_stack) + new_nodes_on_stack.append((top_buffer_id, child_buffer_id, child_node)) + + no_children_in_memory = len(new_nodes_on_stack) == 0 + # We can flush this node out and relink as necessary + if no_children_in_memory: + # We can flush this one completely since it has no children in memory + is_root = parent_buffer_id is None + old_id = top_buffer_id + new_id = await self.hamt.store.save( + top_node.serialize(), codec="dag-cbor" + ) + del self.buffer[old_id] + node_stack.pop() + + # If it's the root, we need to set the hamt's root node id once this is done sending to the backing store + if is_root: + self.hamt.root_node_id = new_id + # Edit the parent if this is not the root else: - # We can flush this one completely since it has no children in memory, we'll just have to edit its parent after serializing it - old_id = top_buffer_id - new_id = await self.hamt.store.save( - top_node.serialize(), codec="dag-cbor" - ) parent_node = self.buffer[parent_buffer_id] parent_node.replace_link(old_id, new_id) + # Continue recursing down the tree + else: + shuffle( + new_nodes_on_stack + ) # avoids always recursing down the rightmost branch - del self.buffer[top_buffer_id] - node_stack.pop() - - # Flush out the root node before we do everything else as well - if (self.needs_flushing() or flush_everything) and self.is_buffer_id(self.hamt.root_node_id): - root_node: Node = self.buffer[self.hamt.root_node_id] # type: ignore - del self.buffer[self.hamt.root_node_id] # type: ignore - self.hamt.root_node_id = await self.hamt.store.save( - root_node.serialize(), codec="dag-cbor" - ) - - # If the in memory tree is used for only read purposes, then we will have a bunch of nodes that seem "unlinked" to anything else, since Links used within the Nodes will reference the real underlying store - # For this case, just clear everything, nothing inside is linked to anything else anyhow - if self.needs_flushing() or flush_everything: - self.buffer = dict() - assert not self.is_buffer_id(self.hamt.root_node_id) + node_stack.extend(new_nodes_on_stack) - if flush_everything: - assert len(self.buffer) == 0 + # There are only two types of nodes left in the buffer: + # 1. A bunch of nodes that seem "unlinked" to anything else, since Links used within the Nodes will reference the real underlying store + # 2. A bunch of empty nodes leftover if the key values they contain are deleted, these would normally be consolidated by a content addressed system but will be remaining here + # We can ignore those when clearing out everything else, nothing inside is linked to anything else anyhow + self.buffer = dict() async def add_to_buffer(self, node: Node) -> IPLDKind: # This is IPLDKind type, but not dag_cbor serializable due to int limits so this will throw errors early if the tree is written with the buffer_ids still in there @@ -316,7 +306,7 @@ def __init__( max_bucket_size: int = 4, inmemory_tree_limit: int = 10_000_000, # 10 MB default read_cache_limit: int = 10_000_000, # 10 MB default - values_are_bytes: bool = False + values_are_bytes: bool = False, ): self.store = store self.hash_fn = hash_fn @@ -328,10 +318,7 @@ def __init__( raise ValueError("Bucket size maximum must be a positive integer") self.max_bucket_size = max_bucket_size - # TODO add documentation about buffer limit and cache limit minimums and how if they are set to a really low limit they'll effectively constantly flush - - self.inmemory_tree_limit = inmemory_tree_limit - self.read_cache_limit = read_cache_limit + # TODO add documentation about how to manage cache memories increasing self.root_node_id = root_node_id @@ -351,15 +338,15 @@ async def build(cls, *args, **kwargs) -> "HAMT": # This is typically a massive blocking operation, you dont want to be running this concurrently with a bunch of other operations, so it's ok to have it not be async async def make_read_only(self): async with self.lock: - self.read_only = True - inmemory_tree: InMemoryTreeStore = self.node_store # type: ignore - await inmemory_tree.flush_buffer(flush_everything=True) + await inmemory_tree.vacate() + self.read_only = True self.node_store = ReadCacheStore(self) async def enable_write(self): async with self.lock: + # The read cache has no writes that need to be sent upstream so we can remove it without vacating self.read_only = False self.node_store = InMemoryTreeStore(self) @@ -462,9 +449,6 @@ async def _set_pointer(self, key: str, val_ptr: IPLDKind): # Finally, reserialize and fix all links, deleting empty nodes as needed await self._reserialize_and_link(node_stack) self.root_node_id = node_stack[0][0] - # This needs to be called after the root node is set from the node stack, since this may change the root node if the memory buffer is too small to hold the root node - if isinstance(self.node_store, InMemoryTreeStore): - await self.node_store.flush_buffer() async def delete(self, key: str): # Also deletes the pointer at the same time so this doesn't have a _delete_pointer duo @@ -500,9 +484,6 @@ async def delete(self, key: str): if created_change: await self._reserialize_and_link(node_stack) self.root_node_id = node_stack[0][0] - # This needs to be called after the root node is set from the node stack, since this may change the root node if the memory buffer is too small to hold the root node - if isinstance(self.node_store, InMemoryTreeStore): - await self.node_store.flush_buffer() else: # If we didn't make a change, then this key must not exist within the HAMT raise KeyError @@ -556,9 +537,6 @@ async def _get_pointer(self, key: str) -> IPLDKind: # Nowhere left to go, stop walking down the tree break - if isinstance(self.node_store, InMemoryTreeStore): - await self.node_store.flush_buffer() - if not found_a_result: raise KeyError diff --git a/tests/test_hamt.py b/tests/test_hamt.py index 8d14fa2..c479cb6 100644 --- a/tests/test_hamt.py +++ b/tests/test_hamt.py @@ -1,11 +1,9 @@ import asyncio import random -from collections.abc import MutableMapping -import dag_cbor from dag_cbor import IPLDKind from multiformats import CID -from hypothesis import given +from hypothesis import given, settings, HealthCheck from hypothesis import strategies as st import pytest @@ -14,11 +12,12 @@ from testing_utils import key_value_list + @pytest.mark.asyncio @given(key_value_list) async def test_fuzz(kvs: list[tuple[str, IPLDKind]]): -# async def test_fuzz(): -# kvs=[('', None), ('0', None)] + # async def test_fuzz(): + # kvs=[('', None), ('0', None)] store = DictStore() hamt = await HAMT.build(store=store) @@ -29,7 +28,7 @@ async def test_fuzz(kvs: list[tuple[str, IPLDKind]]): assert (await hamt.get(key)) == value assert len([key async for key in hamt.keys()]) == (await hamt.len()) == len(kvs) - await asyncio.gather(*[hamt.delete(k) for k, _ in kvs]) # delete everything + await asyncio.gather(*[hamt.delete(k) for k, _ in kvs]) # delete everything assert len([key async for key in hamt.keys()]) == (await hamt.len()) == 0 # Set entirely concurrently thus with unpredictable order @@ -52,7 +51,7 @@ async def verify(k, v): # Re insert all items but now with a bucket size that forces linking, which actually runs the link following code branches, otherwise we would miss 100% code coverage hamt.max_bucket_size = 1 await asyncio.gather(*[hamt.set(k, v) for k, v in kvs]) - await hamt.make_read_only() # cover code branch in keys() that does not need to acquire lock for read only mode + await hamt.make_read_only() # cover code branch in keys() that does not need to acquire lock for read only mode assert len([key async for key in hamt.keys()]) == (await hamt.len()) == len(kvs) await hamt.enable_write() @@ -75,9 +74,9 @@ async def verify(k, v): assert hamt_key_set == keys_set # Make sure all pointers actually exist in the store, this should not raise any exceptions - for k,_ in kvs: + for k, _ in kvs: # Callers must handle acquiring a lock themselves, so do these entirely sequentially - pointer: bytes = await hamt._get_pointer(k) # type: ignore we know that DictStore only returns bytes for its Link type + pointer: bytes = await hamt._get_pointer(k) # type: ignore we know that DictStore only returns bytes for its Link type await store.load(pointer) await hamt.make_read_only() @@ -87,118 +86,130 @@ async def verify(k, v): await hamt.delete("foo") async def verify_kvs_and_len(h: HAMT): - for k,v in kvs: + for k, v in kvs: assert (await h.get(k)) == v assert len([key async for key in h.keys()]) == (await h.len()) == len(kvs) # Test that when a hamt has its root manually initialized by a user, that the key count is accurate # We can only get the root node id here since hamt is in read mode and thus the in memory tree has been entirely flushed - new_hamt = await HAMT.build(store=store, root_node_id=hamt.root_node_id, read_only=True) + new_hamt = await HAMT.build( + store=store, root_node_id=hamt.root_node_id, read_only=True + ) await verify_kvs_and_len(new_hamt) - # Test a hamt with too small of a read cache - hamt_no_read_cache = await HAMT.build(store=store, root_node_id=hamt.root_node_id, read_only=True, read_cache_limit=0) - await verify_kvs_and_len(hamt_no_read_cache) + # Most for code coverage's sake + with pytest.raises( + Exception, + match="Save called in virtual store ReadCacheStore, only supposed to be used for reading", + ): + await new_hamt.node_store.save(bytes(), Node()) - hamt_no_memory_tree = await HAMT.build(store=store, root_node_id=hamt.root_node_id, inmemory_tree_limit = 0) + hamt_no_memory_tree = await HAMT.build( + store=store, root_node_id=hamt.root_node_id, inmemory_tree_limit=0 + ) await verify_kvs_and_len(hamt_no_memory_tree) -key_bytes_list = st.lists( - st.tuples(st.text(), st.binary()), - min_size=0, - max_size=10000, - unique_by=lambda x: x[ - 0 - ], # ensure unique keys, otherwise we can't do the length and size checks when using these KVs for the HAMT + # TODO + # None of the keys should be in a new hamt using the same store but with a fresh root node + + # invalid bucket size + with pytest.raises( + ValueError, match="Bucket size maximum must be a positive integer" + ): + await HAMT.build(store=store, max_bucket_size=-1) + + +# The code branches for flushing children of children of the root node rarely run in test_fuzz, this forces them to run and rigorously +# Use st.binary for the values, otherwise hypothesis will take too long to run +@pytest.mark.asyncio +@settings(suppress_health_check=[HealthCheck.data_too_large]) +@given( + st.lists( + st.binary(), # just do bytes for faster test case generation in hypothesis + min_size=100, # test with a large number of elements to force children + max_size=100000, + ) ) +async def test_tree_flushing_children(vs: list[bytes]): + store = DictStore() + hamt = await HAMT.build( + store=store, + inmemory_tree_limit=100000, + max_bucket_size=1, + values_are_bytes=True, + ) + await asyncio.gather(*[hamt.set(str(k_int), vs[k_int]) for k_int in range(len(vs))]) + for k_int in range(len(vs)): + k = str(k_int) + v = vs[k_int] + assert (await hamt.get(k)) == v + @pytest.mark.asyncio -@given(kvs=key_bytes_list) +# This is a list of keys to arbitrary bytes +@given( + kvs=st.lists( + st.tuples(st.text(), st.binary()), + min_size=0, + max_size=10000, + unique_by=lambda x: x[ + 0 + ], # ensure unique keys, otherwise we can't do the length and size checks when using these KVs for the HAMT + ) +) async def test_values_are_bytes(kvs: list[tuple[str, bytes]]): store = DictStore() hamt = await HAMT.build(store=store, values_are_bytes=True) await asyncio.gather(*[hamt.set(k, v) for k, v in kvs]) - for k,v in kvs: + for k, v in kvs: value = await hamt.get(k) assert value == v assert len([key async for key in hamt.keys()]) == (await hamt.len()) == len(kvs) - await asyncio.gather(*[hamt.delete(k) for k, _ in kvs]) # delete everything + await asyncio.gather(*[hamt.delete(k) for k, _ in kvs]) # delete everything assert len([key async for key in hamt.keys()]) == (await hamt.len()) == 0 + @pytest.mark.asyncio async def test_invalid_node(): - memory_store = DictStore() - with pytest.raises(Exception, match="Invalid dag-cbor encoded data from the store was attempted to be decoded"): + with pytest.raises( + Exception, + match="Invalid dag-cbor encoded data from the store was attempted to be decoded", + ): Node.deserialize(bytes()) -# def test_remaining_exceptions(): -# memory_store = DictStore() -# with pytest.raises(Exception, match="ID not found in store"): -# memory_store.load(b"foo") - -# with pytest.raises(ValueError, match="Data not a valid Node serialization"): -# bad_serialization = dag_cbor.encode([]) -# Node.deserialize(bad_serialization) - -# hamt = HAMT( -# store=memory_store, -# ) -# root_node = Node.deserialize(memory_store.load(hamt.root_node_id)) # type: ignore -# buckets = root_node.get_buckets() -# links = root_node.get_links() -# # 4 is the map key for the string "foo" -# buckets["4"] = [] -# links["4"] = b"bar" -# bad_node_id = memory_store.save(root_node.serialize()) -# bad_hamt = HAMT(store=memory_store, root_node_id=bad_node_id) - -# with pytest.raises( -# Exception, -# match="Key in both buckets and links of the node, invariant violated", -# ): -# bad_hamt["foo"] = b"bar2" - -# with pytest.raises( -# Exception, -# match="Key in both buckets and links of the node, invariant violated", -# ): -# del bad_hamt["foo"] - - -# def test_key_rewrite(): -# hamt = HAMT(store=DictStore()) -# hamt["foo"] = b"bar" -# assert b"bar" == hamt["foo"] -# assert len(hamt) == 1 - -# hamt["foo"] = bytes("something else", "utf-8") -# assert len(hamt) == 1 -# assert b"something else" == hamt["foo"] - -# hamt["foo"] = CID("base32", 1, "dag-cbor", ("blake3", bytes(32))) -# assert len(hamt) == 1 - - -# async def test_cache_clear(): -# hamt = await HAMT.build(store=DictStore(), read_cache_limit=10000) -# await asyncio.gather(*[hamt.set(str(key_int), key_int) for key_int in range(50)]) - - -# # Test that is guaranteed to induce overfull buckets that then requires our hamt to follow deeper into the tree to do insertions -# async def test_link_following(): -# hamt = await HAMT.build(store=DictStore()) -# hamt.max_bucket_size = 1 -# # The first byte of the blake3 hash of each of these is the same, 10110011 -# kvs = [(str(5), b""), (str(15), b""), (str(123), b"")] -# for k, v in kvs: -# await hamt.set(k, v) -# assert (await hamt.len()) == 3 -# for k, _ in kvs: -# await hamt.delete(k) -# assert (await hamt.len()) == 0 +@pytest.mark.asyncio +async def test_key_rewrite(): + hamt = await HAMT.build(store=DictStore()) + await hamt.set("foo", b"bar") + assert b"bar" == await hamt.get("foo") + assert (await hamt.len()) == 1 + + await hamt.set("foo", bytes("something else", "utf-8")) + assert (await hamt.len()) == 1 + assert b"something else" == (await hamt.get("foo")) + + await hamt.set("foo", CID("base32", 1, "dag-cbor", ("blake3", bytes(32)))) + assert (await hamt.len()) == 1 + + +# Test that is guaranteed to induce overfull buckets that then requires our hamt to follow deeper into the tree to do insertions +@pytest.mark.asyncio +async def test_link_following(): + hamt = await HAMT.build(store=DictStore()) + hamt.max_bucket_size = 1 + # The first byte of the blake3 hash of each of these is the same, 10110011 + kvs = [(str(5), b""), (str(15), b""), (str(123), b"")] + for k, v in kvs: + await hamt.set(k, v) + assert (await hamt.len()) == 3 + for k, _ in kvs: + await hamt.delete(k) + assert (await hamt.len()) == 0 + +# The below 2 commented out tests are from HAMT version 2, if using keep in mind to update them with the new API (and adjust this comment accordingly) # Run this with varying cache sizes to see the impact on performance of the cache when using IPFSStore() # Commented out since this increases test time a lot From adeff28459167eff6d30b49caa7699bf86928cd9 Mon Sep 17 00:00:00 2001 From: Abid Sikder <41392423+abidsikder@users.noreply.github.com> Date: Wed, 14 May 2025 16:02:39 -0400 Subject: [PATCH 029/118] remove unused method --- py_hamt/hamt.py | 5 ----- 1 file changed, 5 deletions(-) diff --git a/py_hamt/hamt.py b/py_hamt/hamt.py index b081253..d9b1d74 100644 --- a/py_hamt/hamt.py +++ b/py_hamt/hamt.py @@ -193,11 +193,6 @@ def children_in_memory(self, node: Node) -> Iterator[int]: if self.is_buffer_id(link): yield link # type: ignore we know for sure this is an int if it's a buffer id - def has_children_in_memory(self, node: Node) -> bool: - for _ in self.children_in_memory(node): - return True - return False - # Callers must acquire a lock/stop operations to ensure an accurate calculation! def size(self) -> int: total = 0 From d956a5cc46db23178399dc9e8ea27ca0bff83dbe Mon Sep 17 00:00:00 2001 From: Abid Sikder <41392423+abidsikder@users.noreply.github.com> Date: Wed, 14 May 2025 16:26:47 -0400 Subject: [PATCH 030/118] first 100% code coverage on core files --- py_hamt/hamt.py | 31 ++++++++++++++++++++++- tests/test_hamt.py | 58 ++++++++++++++++++++++---------------------- tests/test_stores.py | 3 ++- 3 files changed, 61 insertions(+), 31 deletions(-) diff --git a/py_hamt/hamt.py b/py_hamt/hamt.py index d9b1d74..2d33104 100644 --- a/py_hamt/hamt.py +++ b/py_hamt/hamt.py @@ -3,6 +3,7 @@ import uuid from random import shuffle import asyncio +from copy import deepcopy import dag_cbor from dag_cbor.ipld import IPLDKind @@ -96,6 +97,11 @@ def replace_link(self, old_link: IPLDKind, new_link: IPLDKind): self.set_link(link_index, new_link) return + def __deepcopy__(self, memo) -> "Node": + new_node = Node() + new_node.data = deepcopy(self.data) + return new_node + def is_empty(self) -> bool: for i in range(len(self.data)): item = self.data[i] @@ -193,12 +199,21 @@ def children_in_memory(self, node: Node) -> Iterator[int]: if self.is_buffer_id(link): yield link # type: ignore we know for sure this is an int if it's a buffer id + _replaced_id_marker = bytes(64) + # Callers must acquire a lock/stop operations to ensure an accurate calculation! def size(self) -> int: + # This is more difficult than normal links are intentionally unencodable in dag-cbor as the UUIDv4 128-bit integer IDs do not fit + # So before serializing, make a copy of the node, replace all of those integer links with zeroed out 64 byte marker which should be close to most IDs returned by backing stores total = 0 for k in self.buffer: node = self.buffer[k] - total += len(node.serialize()) + copied = deepcopy(node) + for link_index in copied.iter_link_indices(): + if self.is_buffer_id(copied.get_link(link_index)): + copied.set_link(link_index, InMemoryTreeStore._replaced_id_marker) + total += len(copied.serialize()) + return total # The HAMT must properly acquire a lock for this to run successfully! This is not async or thread safe @@ -345,6 +360,20 @@ async def enable_write(self): self.read_only = False self.node_store = InMemoryTreeStore(self) + # TODO specify in documentation that this is async concurrency safe + async def cache_size(self) -> int: + if self.read_only: + return self.node_store.size() + async with self.lock: + return self.node_store.size() + + # TODO documentation + async def cache_vacate(self): + if self.read_only: + await self.node_store.vacate() + async with self.lock: + await self.node_store.vacate() + async def _reserialize_and_link(self, node_stack: list[tuple[IPLDKind, Node]]): """ This function starts from the node at the end of the list and reserializes so that each node holds valid new IDs after insertion into the store diff --git a/tests/test_hamt.py b/tests/test_hamt.py index c479cb6..e242442 100644 --- a/tests/test_hamt.py +++ b/tests/test_hamt.py @@ -104,13 +104,12 @@ async def verify_kvs_and_len(h: HAMT): ): await new_hamt.node_store.save(bytes(), Node()) - hamt_no_memory_tree = await HAMT.build( - store=store, root_node_id=hamt.root_node_id, inmemory_tree_limit=0 - ) - await verify_kvs_and_len(hamt_no_memory_tree) - - # TODO # None of the keys should be in a new hamt using the same store but with a fresh root node + empty_hamt = await HAMT.build(store=store) + for k, _ in kvs: + with pytest.raises(KeyError): + await empty_hamt.get(k) + assert len([key async for key in empty_hamt.keys()]) == (await empty_hamt.len()) == 0 # invalid bucket size with pytest.raises( @@ -119,30 +118,31 @@ async def verify_kvs_and_len(h: HAMT): await HAMT.build(store=store, max_bucket_size=-1) -# The code branches for flushing children of children of the root node rarely run in test_fuzz, this forces them to run and rigorously -# Use st.binary for the values, otherwise hypothesis will take too long to run -@pytest.mark.asyncio -@settings(suppress_health_check=[HealthCheck.data_too_large]) -@given( - st.lists( - st.binary(), # just do bytes for faster test case generation in hypothesis - min_size=100, # test with a large number of elements to force children - max_size=100000, - ) -) -async def test_tree_flushing_children(vs: list[bytes]): - store = DictStore() - hamt = await HAMT.build( - store=store, - inmemory_tree_limit=100000, - max_bucket_size=1, - values_are_bytes=True, - ) - await asyncio.gather(*[hamt.set(str(k_int), vs[k_int]) for k_int in range(len(vs))]) - for k_int in range(len(vs)): - k = str(k_int) - v = vs[k_int] + # Cache size management code branches coverage, do it all in async concurrency + + small_cache_size_bytes = 1000 + # Read cache + read_hamt = await HAMT.build(store=store, root_node_id=hamt.root_node_id) + async def get_and_vacate(k,v): assert (await hamt.get(k)) == v + if (await hamt.cache_size()) > small_cache_size_bytes: + await hamt.cache_vacate() + assert (await hamt.cache_size()) == 0 + + await asyncio.gather(*[get_and_vacate(k,v) for k,v in kvs]) + + # In memory tree while writing + # set small max bucket size to force more linking and more nodes + small_memory_tree = await HAMT.build(store=store, max_bucket_size=1) + async def set_and_vacate(k,v): + await small_memory_tree.set(k, v) + assert (await small_memory_tree.get(k)) == v + if (await small_memory_tree.cache_size()) > small_cache_size_bytes: + await small_memory_tree.cache_vacate() + assert (await small_memory_tree.cache_size()) == 0 + assert (await small_memory_tree.get(k)) == v + + await asyncio.gather(*[set_and_vacate(k,v) for k,v in kvs]) @pytest.mark.asyncio diff --git a/tests/test_stores.py b/tests/test_stores.py index f4fcdd3..8ef12e1 100644 --- a/tests/test_stores.py +++ b/tests/test_stores.py @@ -9,6 +9,7 @@ from py_hamt.store import DictStore from testing_utils import ipld_strategy, create_ipfs # noqa + # Just to cover this one case that isn't covered within test_hamt @pytest.mark.asyncio async def test_memory_store_exception(): @@ -16,6 +17,7 @@ async def test_memory_store_exception(): with pytest.raises(KeyError): await s.load(bytes()) + @pytest.mark.asyncio @given(data=ipld_strategy()) async def test_ipfsstore_default_urls(data: IPLDKind): @@ -48,7 +50,6 @@ async def test_ipfsstore_default_urls(data: IPLDKind): await ipfsstore.close_sessions() - @pytest.mark.asyncio @given(data=ipld_strategy()) async def test_ipfsstore(create_ipfs, data: IPLDKind): # noqa From 9328add052d5eab29bc33f62c0b1c77fd47cb43d Mon Sep 17 00:00:00 2001 From: Abid Sikder <41392423+abidsikder@users.noreply.github.com> Date: Thu, 15 May 2025 14:05:11 -0400 Subject: [PATCH 031/118] remove remnants of lru cache insertion order manipulation --- py_hamt/hamt.py | 4 ---- 1 file changed, 4 deletions(-) diff --git a/py_hamt/hamt.py b/py_hamt/hamt.py index 2d33104..ae52e52 100644 --- a/py_hamt/hamt.py +++ b/py_hamt/hamt.py @@ -160,11 +160,7 @@ async def save(self, original_id: IPLDKind, node: Node) -> IPLDKind: async def load(self, id: IPLDKind) -> Node: # Cache Hit if id in self.cache: - # Reinsert to put this key as the most recently used and last in the dict insertion order node = self.cache[id] - del self.cache[id] - self.cache[id] = node - return node # Cache Miss From f7f3f7267bc6dd8bb2884bd5be13cf904acbf8ae Mon Sep 17 00:00:00 2001 From: Abid Sikder <41392423+abidsikder@users.noreply.github.com> Date: Fri, 16 May 2025 16:33:36 -0400 Subject: [PATCH 032/118] remove extraneous performance testing file --- performance_tests/cache_with_ipfsstore.py | 24 ----------------------- 1 file changed, 24 deletions(-) delete mode 100644 performance_tests/cache_with_ipfsstore.py diff --git a/performance_tests/cache_with_ipfsstore.py b/performance_tests/cache_with_ipfsstore.py deleted file mode 100644 index a5c0d75..0000000 --- a/performance_tests/cache_with_ipfsstore.py +++ /dev/null @@ -1,24 +0,0 @@ -from py_hamt import HAMT, IPFSStore -import time - - -# Run this with varying cache sizes to see the impact on performance of the cache when using IPFSStore() -def test_and_print_perf(): - # usual cache size - hamt = HAMT(store=IPFSStore()) - start_time = time.perf_counter() - num_ops = 50 - for key_int in range(num_ops): - hamt[str(key_int)] = key_int - end_time = time.perf_counter() - cache_time = end_time - start_time - - # no cache - hamt = HAMT(store=IPFSStore(), max_cache_size_bytes=0) - start_time = time.perf_counter() - for key_int in range(num_ops): - hamt[str(key_int)] = key_int - end_time = time.perf_counter() - no_cache_time = end_time - start_time - - print(f"Improvement of {(1 - cache_time / no_cache_time) * 100:.2f}%") From 7d798450766efc5586c839be4ecefadde68bb936 Mon Sep 17 00:00:00 2001 From: Abid Sikder <41392423+abidsikder@users.noreply.github.com> Date: Mon, 19 May 2025 16:32:49 -0400 Subject: [PATCH 033/118] remove nginx since no ipfsstore internal auth, change tags to hashes --- .github/workflows/run-checks.yaml | 75 +++---------------------------- 1 file changed, 6 insertions(+), 69 deletions(-) diff --git a/.github/workflows/run-checks.yaml b/.github/workflows/run-checks.yaml index 1782271..4264c39 100644 --- a/.github/workflows/run-checks.yaml +++ b/.github/workflows/run-checks.yaml @@ -10,91 +10,28 @@ jobs: steps: - name: Checkout repo - uses: actions/checkout@v4 + uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2 - name: Install uv - uses: astral-sh/setup-uv@v3 + uses: astral-sh/setup-uv@6b9c6063abd6010835644d4c2e1bef4cf5cd0fca # v6 + with: + version: "latest" - name: Create project environment run: uv sync - name: Install IPFS - uses: ibnesayeed/setup-ipfs@master + uses: ibnesayeed/setup-ipfs@e183d0d2538b866dc30d8850883bd4cd4f8ab431 # v0.6.0 with: ipfs_version: "0.34.1" run_daemon: true id: ipfs_setup - - name: Install and configure Nginx - run: | - # Install Nginx - sudo apt-get update - sudo apt-get install -y nginx - - # Create Nginx config for reverse proxy with auth - cat < Date: Mon, 19 May 2025 16:33:00 -0400 Subject: [PATCH 034/118] change all tags to hashes in action --- .github/workflows/pages-main.yaml | 16 +++++++++++++++- 1 file changed, 15 insertions(+), 1 deletion(-) diff --git a/.github/workflows/pages-main.yaml b/.github/workflows/pages-main.yaml index 02384c0..83de431 100644 --- a/.github/workflows/pages-main.yaml +++ b/.github/workflows/pages-main.yaml @@ -1,35 +1,49 @@ name: Deploy static site generated by pdoc to GitHub Pages + on: push: branches: ["main"] + permissions: contents: read pages: write id-token: write + jobs: build: environment: name: github-pages url: ${{ steps.deployment.outputs.page_url }} + permissions: contents: read pages: write id-token: write + runs-on: ubuntu-latest + steps: - name: Checkout uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 + - name: Setup Pages uses: actions/configure-pages@983d7736d9b0ae728b81ab479565c72886d7745b # v5 + - name: Install uv - uses: astral-sh/setup-uv@v3 + uses: astral-sh/setup-uv@6b9c6063abd6010835644d4c2e1bef4cf5cd0fca # v6 + with: + version: "latest" + - name: Create project environment run: uv sync + - name: Build with pdoc run: uv run pdoc py_hamt -o ./_site + - name: Upload artifact # Automatically uploads an artifact from the './_site' directory by default uses: actions/upload-pages-artifact@56afc609e74202658d3ffba0e8f6dda462b719fa # v3 + - name: Deploy to GitHub Pages id: deployment uses: actions/deploy-pages@d6db90164ac5ed86f2b6aed7e0febac5b3c0c03e # v4 From a11cdbcb37341f08f187a486da56298e8fbe853d Mon Sep 17 00:00:00 2001 From: Abid Sikder <41392423+abidsikder@users.noreply.github.com> Date: Mon, 19 May 2025 16:36:08 -0400 Subject: [PATCH 035/118] add xarray complete, refresh ruff version --- py_hamt/hamt.py | 22 +- py_hamt/zarr_hamt_store.py | 145 ++++ pyproject.toml | 8 +- uv.lock | 1306 +++++++++++++++++++++++++++--------- 4 files changed, 1147 insertions(+), 334 deletions(-) create mode 100644 py_hamt/zarr_hamt_store.py diff --git a/py_hamt/hamt.py b/py_hamt/hamt.py index ae52e52..97ac26a 100644 --- a/py_hamt/hamt.py +++ b/py_hamt/hamt.py @@ -314,18 +314,21 @@ def __init__( read_cache_limit: int = 10_000_000, # 10 MB default values_are_bytes: bool = False, ): + # TODO add documentation about how to manage cache memories increasing + # TODO add notice about calling build if needing to initialize a completely empty HAMT + # rename store to cas to point out the Content Addressed Store nature of it self.store = store self.hash_fn = hash_fn self.lock = asyncio.Lock() self.read_only = read_only self.values_are_bytes = values_are_bytes + # TODO Say that values are bytes are safe to change in between operations, so put a hypothetical example of toggling it when its in read only mode and back in write for a completely safe toggle. + self.total = 0 if max_bucket_size < 1: raise ValueError("Bucket size maximum must be a positive integer") self.max_bucket_size = max_bucket_size - # TODO add documentation about how to manage cache memories increasing - self.root_node_id = root_node_id self.node_store: NodeStore @@ -336,6 +339,7 @@ def __init__( @classmethod async def build(cls, *args, **kwargs) -> "HAMT": + # TODO add notice about referring to the init but this is what needs to actually get called, if you are initializing a completely new empty HAMT hamt = cls(*args, **kwargs) if hamt.root_node_id is None: hamt.root_node_id = await hamt.node_store.save(None, Node()) @@ -414,6 +418,7 @@ async def set(self, key: str, val: IPLDKind): if self.read_only: raise Exception("Cannot call set on a read only HAMT") + # print(f"setting {key}") data: bytes if self.values_are_bytes: data = val # type: ignore let users get an exception if they pass in a non bytes when they want to skip encoding @@ -421,7 +426,11 @@ async def set(self, key: str, val: IPLDKind): data = dag_cbor.encode(val) pointer = await self.store.save(data, codec="raw") + start = time.perf_counter() await self._set_pointer(key, pointer) + end = time.perf_counter() + elapsed = end - start + self.total += elapsed async def _set_pointer(self, key: str, val_ptr: IPLDKind): async with self.lock: @@ -511,12 +520,18 @@ async def delete(self, key: str): # TODO document option to skip decode if the user knows that the value inside is also going to be a bytes object async def get(self, key: str) -> IPLDKind: # If read only, no need to acquire a lock + start = time.perf_counter() pointer: IPLDKind if self.read_only: pointer = await self._get_pointer(key) else: async with self.lock: pointer = await self._get_pointer(key) + end = time.perf_counter() + elapsed = end - start + self.total += elapsed + + # print(f"getting {key}") data = await self.store.load(pointer) if self.values_are_bytes: @@ -575,7 +590,8 @@ async def keys(self) -> AsyncIterator[str]: """ AsyncIterator returning all keys in the HAMT. - When the HAMT is write enabled, to maintain strong consistency this will obtain a lock and not a llow any other operations to proceed. For example, if you are inside of a for loop using this iterator, you cannot also get a value at the same time until iteration is completely done. If you try to get in fact, you will run into deadlock. + TODO clean up this paragraph's language + When the HAMT is write enabled, to maintain strong consistency this will obtain a lock and not a llow any other operations to proceed. For example, if you are inside of a for loop using this iterator, you cannot also get a value at the same time until iteration is completely done. If you try you will run into deadlock. In read only mode however, this can be run concurrently with get operations. """ diff --git a/py_hamt/zarr_hamt_store.py b/py_hamt/zarr_hamt_store.py new file mode 100644 index 0000000..c0f17fd --- /dev/null +++ b/py_hamt/zarr_hamt_store.py @@ -0,0 +1,145 @@ +from collections.abc import AsyncIterator, Iterable +import zarr.abc.store +import zarr.core.buffer +from zarr.core.common import BytesLike + +from py_hamt.hamt import HAMT + + +class ZarrHAMTStore(zarr.abc.store.Store): + """ + Write and read Zarr v3s with a HAMT. + + TODO write about reinitializing if the hamt's read only mode changes to take advantage of performance, or if the separator has changed. Put some example code to show a sample usage of using xarray to put some into a HAMT + """ + + def __init__(self, hamt: HAMT, read_only: bool = False) -> None: + """ + ### `hamt` and `read_only` + You need to make sure the following two things are true: + + 1. The HAMT is in the same read only mode that you are passing into the Zarr store. This means that `hamt.read_only == read_only`. This is because making a HAMT read only automatically requires async operations, but `__init__` cannot be async. + 2. The HAMT has `hamt.values_are_bytes == True`. This improves efficiency with Zarr v3 operations. + + ##### A note about the zarr chunk separator, "/" vs "." + While Zarr v2 used periods by default, Zarr v3 uses forward slashes, and that is assumed here as well. + """ + super().__init__(read_only=read_only) + + assert hamt.read_only == read_only + assert hamt.values_are_bytes + self.hamt = hamt + """ + The internal HAMT. + Once done with write operations, the hamt can be set to read only mode as usual to get your root node ID. + """ + + @property + def read_only(self) -> bool: + """@private""" + return self.hamt.read_only + + def __eq__(self, other: object) -> bool: + """@private""" + if not isinstance(other, ZarrHAMTStore): + return False + return self.hamt.root_node_id == other.hamt.root_node_id + + async def get( + self, + key: str, + prototype: zarr.core.buffer.BufferPrototype, + byte_range: zarr.abc.store.ByteRequest | None = None, + ) -> zarr.core.buffer.Buffer | None: + """@private""" + try: + val: bytes = await self.hamt.get(key) # type: ignore We know values received will always be bytes since we only store bytes in the HAMT + return prototype.buffer.from_bytes(val) + except KeyError: + # Sometimes zarr queries keys that don't exist anymore, just return nothing on those cases + return + + async def get_partial_values( + self, + prototype: zarr.core.buffer.BufferPrototype, + key_ranges: Iterable[tuple[str, zarr.abc.store.ByteRequest | None]], + ) -> list[zarr.core.buffer.Buffer | None]: + """@private""" + raise NotImplementedError + + async def exists(self, key: str) -> bool: + """@private""" + try: + await self.hamt.get(key) + return True + except KeyError: + return False + + @property + def supports_writes(self) -> bool: + """@private""" + return not self.hamt.read_only + + @property + def supports_partial_writes(self) -> bool: + """@private""" + return False + + async def set(self, key: str, value: zarr.core.buffer.Buffer) -> None: + """@private""" + await self.hamt.set(key, value.to_bytes()) + + async def set_if_not_exists(self, key: str, value: zarr.core.buffer.Buffer) -> None: + """@private""" + if not (await self.exists(key)): + await self.set(key, value) + + async def set_partial_values( + self, key_start_values: Iterable[tuple[str, int, BytesLike]] + ) -> None: + """@private""" + raise NotImplementedError + + @property + def supports_deletes(self) -> bool: + """@private""" + return not self.hamt.read_only + + async def delete(self, key: str) -> None: + """@private""" + try: + await self.hamt.delete(key) + # It's fine if the key was not in the HAMT + # Sometimes zarr v3 calls deletes on keys that don't exist (or have already been deleted) for some reason, probably concurrency issues + except KeyError: + return + + @property + def supports_listing(self) -> bool: + """@private""" + return True + + async def list(self) -> AsyncIterator[str]: + """@private""" + async for key in self.hamt.keys(): + yield key + + async def list_prefix(self, prefix: str) -> AsyncIterator: + """@private""" + async for key in self.hamt.keys(): + if key.startswith(prefix): + yield key + + async def list_dir(self, prefix: str) -> AsyncIterator: + """ + @private + """ + async for key in self.hamt.keys(): + if key.startswith(prefix): + suffix = key[len(prefix) :] + first_slash = suffix.find("/") + if first_slash == -1: + yield suffix + else: + name = suffix[0:first_slash] + yield name diff --git a/pyproject.toml b/pyproject.toml index 0acbf65..328402f 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,14 +1,14 @@ [project] name = "py-hamt" -version = "2.4.1" -description = "HAMT implementation for an abstract backing store" +version = "3.0.0rc1" +description = "HAMT implementation for a content-addressed storage system." readme = "README.md" requires-python = ">=3.12" dependencies = [ - "aiohttp>=3.11.18", "dag-cbor>=0.3.3", "msgspec>=0.18.6", "multiformats[full]>=0.3.1.post4", + "requests>=2.32.3", "zarr>=3.0.6", ] @@ -28,5 +28,5 @@ dev = [ 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<41392423+abidsikder@users.noreply.github.com> Date: Mon, 19 May 2025 16:36:32 -0400 Subject: [PATCH 037/118] remove old ipfszarrr3 file --- py_hamt/ipfszarr3.py | 147 ------------------------------------------- 1 file changed, 147 deletions(-) delete mode 100644 py_hamt/ipfszarr3.py diff --git a/py_hamt/ipfszarr3.py b/py_hamt/ipfszarr3.py deleted file mode 100644 index 2480d8e..0000000 --- a/py_hamt/ipfszarr3.py +++ /dev/null @@ -1,147 +0,0 @@ -from collections.abc import AsyncIterator, Iterable -import zarr.abc.store -import zarr.core.buffer -from zarr.core.common import BytesLike - -from py_hamt.hamt import HAMT - - -class IPFSZarr3(zarr.abc.store.Store): - """ - While Zarr v2 can use a generic key-value map (MutableMapping) that HAMT already conforms to, Zarr v3s require storage classes to conform to a new abstract class. IPFSZarr3 just wraps over a HAMT to provide this compatibility. - - An example of how to write and read a zarr, using xarray, is provided below. - # Write and get CID - ```python - import xarray as xr - from py_hamt import IPFSStore, HAMT, IPFSZarr3 - - ds = ... # some xarray Dataset - ipfszarr3 = IPFSZarr3(HAMT(store=IPFSStore())) - xr.to_zarr(store=ipfszarr3) - print(ipfszarr3.hamt.root_node_id) # The CID of the root, which is used for reading - ``` - - # Read from CID - ```python - import xarray as xr - from multiformats import CID - from py_hamt import IPFSStore, HAMT, IPFSZarr3 - - cid = CID.decode("...") # the CID for the HAMT root - ipfszarr3 = IPFSZarr3(HAMT(store=IPFSStore(), root_node_id=cid), read_only=True) - ds = xr.open_zarr(store=ipfszarr3) - print(ds) - ``` - """ - - hamt: HAMT - """The internal HAMT. Safe to read the CID from, if done doing operations.""" - - def __init__(self, hamt: HAMT, read_only: bool = False) -> None: - super().__init__(read_only=read_only) - self.hamt = hamt - if read_only: - self.hamt.make_read_only() - else: - self.hamt.enable_write() - - @property - def read_only(self) -> bool: - return self.hamt.read_only - - def __eq__(self, val: object) -> bool: - if not isinstance(val, IPFSZarr3): - return False - return self.hamt.root_node_id == val.hamt.root_node_id - - async def get( - self, - key: str, - prototype: zarr.core.buffer.BufferPrototype, - byte_range: zarr.abc.store.ByteRequest | None = None, - ) -> zarr.core.buffer.Buffer | None: - if key not in self.hamt: - return - # We know this value will always be bytes since we only store bytes in the HAMT - val: bytes = self.hamt[key] # type: ignore - return prototype.buffer.from_bytes(val) - - # Hypothetical code for supporting partial writes, but there is not much point since IPFS itself doesn't support partial write and reads - # Untested! If for some reason this is being uncommented and then used in the future, this needs to be tested - # subset: bytes - # match byte_range: - # case None: - # subset = val - # case zarr.abc.store.RangeByteRequest: - # subset = val[byte_range.start : byte_range.end] - # case zarr.abc.store.OffsetByteRequest: - # subset = val[byte_range.offset :] - # case zarr.abc.store.SuffixByteRequest: - # subset = val[-byte_range.suffix :] - - async def get_partial_values( - self, - prototype: zarr.core.buffer.BufferPrototype, - key_ranges: Iterable[tuple[str, zarr.abc.store.ByteRequest | None]], - ) -> list[zarr.core.buffer.Buffer | None]: - raise NotImplementedError - - async def exists(self, key: str) -> bool: - return key in self.hamt - - @property - def supports_writes(self) -> bool: - return not self.hamt.read_only - - @property - def supports_partial_writes(self) -> bool: - return False - - async def set(self, key: str, value: zarr.core.buffer.Buffer) -> None: - self.hamt[key] = value.to_bytes() - - async def set_if_not_exists(self, key: str, value: zarr.core.buffer.Buffer) -> None: - if key not in self.hamt: - await self.set(key, value) - - async def set_partial_values( - self, key_start_values: Iterable[tuple[str, int, BytesLike]] - ) -> None: - raise NotImplementedError - - @property - def supports_deletes(self) -> bool: - return not self.hamt.read_only - - async def delete(self, key: str) -> None: - try: - del self.hamt[key] - # It's fine if the key was not in the HAMT - # Sometimes zarr v3 calls deletes on keys that don't exist (or have already been deleted) for some reason - except KeyError: - return - - @property - def supports_listing(self) -> bool: - return True - - async def list(self) -> AsyncIterator[str]: - for key in self.hamt: - yield key - - async def list_prefix(self, prefix: str) -> AsyncIterator: - for key in self.hamt: - if key.startswith(prefix): - yield key - - async def list_dir(self, prefix: str) -> AsyncIterator: - for key in self.hamt: - if key.startswith(prefix): - suffix = key[len(prefix) :] - first_slash = suffix.find("/") - if first_slash == -1: - yield suffix - else: - name = suffix[0:first_slash] - yield name From eff2af5f5f05b63e9e04e1cbd74535055db2745f Mon Sep 17 00:00:00 2001 From: Abid Sikder <41392423+abidsikder@users.noreply.github.com> Date: Mon, 19 May 2025 16:40:43 -0400 Subject: [PATCH 038/118] Finish ZarrHAMTStore documentation --- py_hamt/zarr_hamt_store.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/py_hamt/zarr_hamt_store.py b/py_hamt/zarr_hamt_store.py index c0f17fd..f75b83a 100644 --- a/py_hamt/zarr_hamt_store.py +++ b/py_hamt/zarr_hamt_store.py @@ -10,7 +10,8 @@ class ZarrHAMTStore(zarr.abc.store.Store): """ Write and read Zarr v3s with a HAMT. - TODO write about reinitializing if the hamt's read only mode changes to take advantage of performance, or if the separator has changed. Put some example code to show a sample usage of using xarray to put some into a HAMT + #### A note about using the same `ZarrHAMTStore` for writing and then reading again + If you write a Zarr to a HAMT, and then change it to read only mode, it's best to reinitialize a new ZarrHAMTStore with the proper read only setting. This is because this class, to err on the safe side, will not touch its super class's settings. """ def __init__(self, hamt: HAMT, read_only: bool = False) -> None: From 91506f26ca40e0f94068ec052c55f2c330b0a304 Mon Sep 17 00:00:00 2001 From: Abid Sikder <41392423+abidsikder@users.noreply.github.com> Date: Mon, 19 May 2025 16:41:38 -0400 Subject: [PATCH 039/118] finish store documentation --- py_hamt/store.py | 151 +++++++++++++++++++++-------------------------- 1 file changed, 67 insertions(+), 84 deletions(-) diff --git a/py_hamt/store.py b/py_hamt/store.py index a86049a..59818b2 100644 --- a/py_hamt/store.py +++ b/py_hamt/store.py @@ -1,4 +1,3 @@ -import io from typing import Literal from abc import ABC, abstractmethod from dag_cbor.ipld import IPLDKind @@ -6,50 +5,49 @@ from multiformats import multihash from multiformats import CID from multiformats.multihash import Multihash +import requests -import aiohttp - -type CodecInput = Literal["raw", "dag-cbor"] - - -# TODO add Store documentation note about not supporting Stores that use null as a valid ID, since the HAMT uses this as a way to indicate null for its root node in its constructor +class ContentAddressedStore(ABC): + """ + Abstract class that represents a content addressed storage that the `HAMT` can use for keeping data. -class Store(ABC): - """Abstract class that represents a storage mechanism the HAMT can use for keeping data. + Note that the return type of save and input to load is really type `IPLDKind`, but the documentation generator pdoc mangles it unfortunately. - The return type of save and input to load is really type IPLDKind, but the documentation generates something a bit strange since IPLDKind is a type union. + #### A note on the IPLDKind return types + Save and load return the type IPLDKind and not just a CID. As long as python regards the underlying type as immutable it can be used, allowing for more flexibility. There are two exceptions: + 1. No lists or dicts, since python does not classify these as immutable. + 2. No `None` values since this is used in HAMT's `__init__` to indicate that an empty HAMT needs to be initialized. """ + type CodecInput = Literal["raw", "dag-cbor"] + @abstractmethod async def save(self, data: bytes, codec: CodecInput) -> IPLDKind: - """Take any set of bytes, save it to the storage mechanism, and reutrn an ID in the type of IPLDKind which can be used to retrieve those bytes later. This also includes extra information in `codec` on whether to mark this data as special linked data.""" - # TODO add bit about its important that dag-cbor is only called for an internal data structure node, and ONLY that type + """Save data to a storage mechanism, and return an ID for the data in the IPLDKind type. + + `codec` will be set to "dag-cbor" if this data should be marked as special linked data a la IPLD data model.""" @abstractmethod async def load(self, id: IPLDKind) -> bytes: - """Retrieve the bytes based on an ID returned earlier by the save function.""" + """Retrieve data.""" -# Inspired by https://github.com/rvagg/iamap/blob/master/examples/memory-backed.js -class DictStore(Store): - """A basic implementation of a backing store, mostly for demonstration and testing purposes. It hashes all inputs and uses that as a key to an in-memory python dict. The hash bytes are the ID that `save` returns and `load` takes in.""" +class InMemoryCAS(ContentAddressedStore): + """Used mostly for faster testing, this is why this is not exported. It hashes all inputs and uses that as a key to an in-memory python dict, mimicking a content addressed storage system. The hash bytes are the ID that `save` returns and `load` takes in.""" store: dict[bytes, bytes] - """@private""" hash_alg: Multihash - """@private""" def __init__(self): self.store = dict() self.hash_alg = multihash.get("blake3") - async def save(self, data: bytes, codec: CodecInput) -> bytes: + async def save(self, data: bytes, codec: ContentAddressedStore.CodecInput) -> bytes: hash = self.hash_alg.digest(data, size=32) self.store[hash] = data return hash - # Ignore the type error since bytes is in the IPLDKind type async def load(self, id: bytes) -> bytes: # type: ignore since bytes is a subset of the IPLDKind type if id in self.store: return self.store[id] @@ -57,87 +55,72 @@ async def load(self, id: bytes) -> bytes: # type: ignore since bytes is a subse raise KeyError -class IPFSStore(Store): +class KuboCAS(ContentAddressedStore): """ - Use IPFS as a backing store for a HAMT. The IDs returned from save and used by load are IPFS CIDs. + Talks to a kubo daemon. The IDs in save and load are IPLD CIDs. - Save methods use the RPC API but `load` uses the HTTP Gateway, so read-only HAMTs will only access the HTTP Gateway. This allows for connection to remote gateways as well. - - You can write to an authenticated IPFS node by providing credentials in the constructor. The following authentication methods are supported: - - Basic Authentication: Provide a tuple of (username, password) to the `basic_auth` parameter. - - Bearer Token: Provide a bearer token to the `bearer_token` parameter. - - API Key: Provide an API key to the `api_key` parameter. You can customize the header name for the API key by setting the `api_key_header` parameter. + `save` uses the RPC API and `load` uses the HTTP Gateway. This means that read-only HAMTs will only access the HTTP Gateway, so no RPC endpoint is required for use. """ KUBO_DEFAULT_LOCAL_GATEWAY_BASE_URL = "http://127.0.0.1:8080" KUBO_DEFAULT_LOCAL_RPC_BASE_URL = "http://127.0.0.1:5001" + DAG_PB_MARKER = 0x70 + """@private""" + # Take in a aiohttp session that can be reused across POSTs and GETs to a specific ipfs daemon, also allow for not doing that and creating our own single request lifetime session instead def __init__( self, - gateway_session: aiohttp.ClientSession | None = None, - rpc_session: aiohttp.ClientSession | None = None, hasher: str = "blake3", + requests_session: requests.Session | None = None, + rpc_base_url=KUBO_DEFAULT_LOCAL_RPC_BASE_URL, + gateway_base_url=KUBO_DEFAULT_LOCAL_GATEWAY_BASE_URL, ): """ - TODO write about user needing to close the aiohttp session at the end of IPFSStore's use if this thing is being used in a long running program + ### `requests.Session` Management + If `requests_session` is not provided, it will be automatically initialized. It is the responsibility of the user to close this at an appropriate time, as a class instance cannot know when it will no longer be in use. + + ### Authenticated RPC/Gateway Access + Users can set whatever headers and auth credentials they need if they are connecting to an authenticated kubo instance by setting them in their own `requests.Session` and then passing that in. + + ### RPC and HTTP Gateway Base URLs + These are the first part of the url, defaults that refer to the default that kubo launches with on a local machine are provided. """ - # Don't initialize a self-managed ClientSession here, so that they are only created when needed, a lot of clients will only ever read from IPFS - self.gateway_session = gateway_session - self.rpc_session = rpc_session self.hasher = hasher - """The hash function to send to IPFS when storing bytes.""" - - self.rpc_url = f"/api/v0/add?hash={self.hasher}&pin=false" - - # TODO make this a future feature for IPFSStore after all the HAMT stuff is already done - # self.debug: bool = debug - # """If true, this records the total number of bytes sent in and out of IPFSStore to the network. You can access this information in `total_sent` and `total_received`. Bytes are counted in terms of either how much was sent to IPFS to store a CID, or how much data was inside of a retrieved IPFS block. This does not include the overhead of the HTTP requests themselves.""" - # self.total_sent: None | int = 0 if debug else None - # """Total bytes sent to IPFS. Used for debugging purposes.""" - # self.total_received: None | int = 0 if debug else None - # """Total bytes in responses from IPFS for blocks. Used for debugging purposes.""" - - async def save(self, data: bytes, codec: CodecInput) -> CID: - if self.rpc_session is None: - self.rpc_session = aiohttp.ClientSession( - base_url=IPFSStore.KUBO_DEFAULT_LOCAL_RPC_BASE_URL - ) - - async with self.rpc_session.post( - url=self.rpc_url, - data={"file": io.BytesIO(data)}, - ) as response: - response.raise_for_status() - json_bytes = await response.read() - cid_str: str = json.decode(json_bytes)["Hash"] - cid = CID.decode(cid_str) - # If it's dag-pb it means we should not reset the cid codec, since this is a UnixFS entry for a large amount of data that thus had to be sharded - # 0x70 means dag-pb - if cid.codec.code != 0x70: - cid = cid.set(codec=codec) - - return cid + """The hash function to send to IPFS when storing bytes. Cannot be changed after initialization. The default blake3 follows the default hashing algorithm used by HAMT.""" + + self.rpc_url = f"{rpc_base_url}/api/v0/add?hash={self.hasher}&pin=false" + """@private""" + self.gateway_base_url = gateway_base_url + "/ipfs/" + """@private""" + + self.requests_session: requests.Session + """@private""" + if requests_session is None: + self.requests_session = requests.Session() + else: + self.requests_session = requests_session + + async def save(self, data: bytes, codec: ContentAddressedStore.CodecInput) -> CID: + """@private""" + response = self.requests_session.post(self.rpc_url, files={"file": data}) + response.raise_for_status() + + cid_str: str = json.decode(response.content)["Hash"] # type: ignore + cid = CID.decode(cid_str) + + # If it's dag-pb it means we should not reset the cid codec, kubo shards large data into a UnixFS structure + if cid.codec.code != KuboCAS.DAG_PB_MARKER: + cid = cid.set(codec=codec) + + return cid async def load( # type: ignore CID is definitely in the IPLDKind type self, id: CID ) -> bytes: - if self.gateway_session is None: - self.gateway_session = aiohttp.ClientSession( - base_url=IPFSStore.KUBO_DEFAULT_LOCAL_GATEWAY_BASE_URL - ) - - async with self.gateway_session.get(url=f"/ipfs/{str(id)}") as response: - response.raise_for_status() - return await response.read() - - async def close_sessions(self): - # TODO write about no-oping when sessions are closed but they either don't exist or were already closed - if self.rpc_session is not None: - await self.rpc_session.close() - self.rpc_session = None - - if self.gateway_session is not None: - await self.gateway_session.close() - self.gateway_session = None + """@private""" + url = self.gateway_base_url + str(id) + response = self.requests_session.get(url) + response.raise_for_status() + return response.content From d453781bd43c6a96e9bd357c2b18d059a69444bd Mon Sep 17 00:00:00 2001 From: Abid Sikder <41392423+abidsikder@users.noreply.github.com> Date: Mon, 19 May 2025 17:25:55 -0400 Subject: [PATCH 040/118] sample code in documentation --- py_hamt/zarr_hamt_store.py | 20 ++++++++++++++++++++ 1 file changed, 20 insertions(+) diff --git a/py_hamt/zarr_hamt_store.py b/py_hamt/zarr_hamt_store.py index f75b83a..a86d34e 100644 --- a/py_hamt/zarr_hamt_store.py +++ b/py_hamt/zarr_hamt_store.py @@ -12,6 +12,26 @@ class ZarrHAMTStore(zarr.abc.store.Store): #### A note about using the same `ZarrHAMTStore` for writing and then reading again If you write a Zarr to a HAMT, and then change it to read only mode, it's best to reinitialize a new ZarrHAMTStore with the proper read only setting. This is because this class, to err on the safe side, will not touch its super class's settings. + + #### Sample Code + ```python + # Write + ds: xarray.Dataset = # ... + cas: ContentAddressedStore = # ... + hamt: HAMT = # ... make sure values_are_bytes is True and read_only is False to enable writes + zhs = ZarrHAMTStore(hamt, False) + xarray.to_zarr(store=zhs) + await hamt.make_read_only() + root_node_id = hamt.root_node_id + print(root_node_id) + + # Read + hamt_read = HAMT(cas=cas, root_node_id=root_node_id, read_only=True, values_are_bytes=True) + zhs_read = ZarrHAMTStore(hamt, True) + ds_read = xarray.open_zarr(store=zhs_read) + print(ds_read) + xarray.testing.assert_identical(ds, ds_read) + ``` """ def __init__(self, hamt: HAMT, read_only: bool = False) -> None: From ad30213ccbc32d58c78a3b5c1f53c2a1fa16cb77 Mon Sep 17 00:00:00 2001 From: Abid Sikder <41392423+abidsikder@users.noreply.github.com> Date: Mon, 19 May 2025 17:41:15 -0400 Subject: [PATCH 041/118] update readme --- README.md | 77 ++++++++++--------------------------------------------- 1 file changed, 13 insertions(+), 64 deletions(-) diff --git a/README.md b/README.md index a0754e3..2750cf9 100644 --- a/README.md +++ b/README.md @@ -4,13 +4,15 @@

-[![codecov](https://codecov.io/gh/dClimate/py-hamt/graph/badge.svg?token=M6Y4D19Y38)](https://codecov.io/gh/dClimate/py-hamt) # py-hamt +[![codecov](https://codecov.io/gh/dClimate/py-hamt/graph/badge.svg?token=M6Y4D19Y38)](https://codecov.io/gh/dClimate/py-hamt) + This is a python implementation of a HAMT, inspired by [rvagg's IAMap project written in JavaScript](https://github.com/rvagg/iamap). -Like IAMap, py-hamt abstracts over a content-addressed storage system, something that can keep arbitrary values but will return its own key, like IPFS. -dClimate primarily created this for storing [zarr](https://zarr.dev/) on IPFS. To see this in action, see our [data ETLs](https://github.com/dClimate/etl-scripts). +py-hamt provides efficient storage and retrieval of large sets of key-value mappings in a content-addressed storage system. The main target is IPFS, and the data model used is IPLD. + +dClimate primarily created this for storing large [zarrs](https://zarr.dev/) on IPFS. To see this in action, see our [data ETLs](https://github.com/dClimate/etl-scripts). # Installation and Usage To install, since we do not publish this package to PyPI, add this library to your project directly from git. @@ -18,63 +20,9 @@ To install, since we do not publish this package to PyPI, add this library to yo pip install 'git+https://github.com/dClimate/py-hamt' ``` -Below are some examples, but for more information see the [API documentation](https://dclimate.github.io/py-hamt/py_hamt.html). Each major item has example code. You can also see this library used in [Jupyter notebooks for data analysis](https://github.com/dClimate/jupyter-notebooks). - -## Basic Writing/Reading -A HAMT allows for generic key-value storage. -```python -from py_hamt import HAMT, IPFSStore - -# Setup a HAMT and connect it to your local ipfs node -hamt = HAMT(store=IPFSStore()) - -# Set and get one value -hamt["foo"] = "bar" -assert "bar" == hamt["foo"] -assert len(hamt) == 1 - -# Set and get multiple values -hamt["foo"] = "bar1" -hamt["foo2"] = 2 -assert 2 == hamt["foo2"] -assert len(hamt) == 2 - -# Iterate over keys -for key in hamt: - print(key) -print (list(hamt)) # [foo, foo2], order depends on the hash function used - -# Delete a value -del hamt["foo"] -assert len(hamt) == 1 - -# Print CID of the HAMT -print(hamt.root_node_id) -``` - -## Reading a CID from IPFS -```python -from py_hamt import HAMT, IPFSStore -from multiformats import CID - -# A CID for data you wish to read, from a blog post, a smart contract, or a friend -dataset_cid = "baf..." - -# Use the multiformats library to decode the CID into an object -root_cid = CID.decode(dataset_cid) - -# Create HAMT instance using the IPFSStore connecting to your locally -# running IPFS Gateway from your local running IPFS Node, If you wish -# you can change the default IPFS gateway -hamt = HAMT(store=IPFSStore(), root_node_id=root_cid) # You can optionally pass your own gateway instead of defaults with the argument gateway_uri_stem="http://:", - -# Do something with the hamt key/values -... -``` - -For an example on how to read and write Zarr v3, check the API documentation and look at the `IPFSZarr3` class. +For usage information, take a look at our [API documentation](https://dclimate.github.io/py-hamt/py_hamt.html), major items have example code. -For how to create partially encrypted zarrs, check the API documentation's `create_zarr_encryption_transformers` section. +You can also see this library used in either our [data ETLs](https://github.com/dClimate/etl-scripts) or [Jupyter notebooks for data analysis](https://github.com/dClimate/jupyter-notebooks). # Development Guide ## Setting Up @@ -86,18 +34,19 @@ uv sync to create the project virtual environment at `.venv`. Don't worry about activating this virtual environment to run tests or formatting and linting, uv will automatically take care of that. ## Run tests, formatting, linting -First, make sure you have the ipfs kubo daemon installed so that you can run the tests that utilize IPFS as a backing store. e.g. `ipfs daemon`. If needed, configure the test with your custom HTTP gateway and RPC API endpoints. Then run the script +First, make sure you have the ipfs kubo daemon installed and running with the default endpoints open. Then run the script ```sh bash run-checks.sh ``` -This will run tests with code coverage information, and then check formatting and linting. +This will run tests with code coverage, and check formatting and linting. We use `pytest` with 100% code coverage, and with test inputs that are both handwritten as well as generated by `hypothesis`. This allows us to try out millions of randomized inputs to create a more robust library. -Note that due to the randomized inputs, it is possible sometimes to get 99% or lower test coverage by pure chance. Rerun the tests to get back complete code coverage. If this happens on a GitHub action, try rerunning the action. +> [!NOTE] +> Due to the randomized test inputs, it is possible sometimes to get 99% or lower test coverage by pure chance. Rerun the tests to get back complete code coverage. If this happens on a GitHub action, try rerunning the action. ## CPU and Memory Profiling -We use python's native `cProfile` for running CPU profiles and snakeviz visualization the profile. We use `memray` for the memory profiling. We run the profile on the test suite, since the tests are supposed have complete code coverage anyhow. +We use python's native `cProfile` for running CPU profiles and snakeviz for visualizing the profile. We use `memray` for the memory profiling. We will walk through using the profiling tools on the test suite. Creating the CPU and memory profile requires manual activation of the virtual environment. ```sh @@ -114,7 +63,7 @@ uv run memray flamegraph # e.g. = memray-pytest. ``` ## Generating documentation -`py-hamt` uses [pdoc](https://pdoc.dev/) for its ease of use. To see a live documentation preview on your local machine, run +`py-hamt` uses [pdoc](https://pdoc.dev/). To see a live documentation preview on your local machine, run ```sh uv run pdoc py_hamt ``` From c78f260b9222555c3edef2c000215478d883d1ff Mon Sep 17 00:00:00 2001 From: Abid Sikder <41392423+abidsikder@users.noreply.github.com> Date: Mon, 19 May 2025 17:41:31 -0400 Subject: [PATCH 042/118] change from release candidate to major --- pyproject.toml | 2 +- uv.lock | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 328402f..c8abae9 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [project] name = "py-hamt" -version = "3.0.0rc1" +version = "3.0.0" description = "HAMT implementation for a content-addressed storage system." readme = "README.md" requires-python = ">=3.12" diff --git a/uv.lock b/uv.lock index c27ff8f..f216ce9 100644 --- a/uv.lock +++ b/uv.lock @@ -1263,7 +1263,7 @@ wheels = [ [[package]] name = "py-hamt" -version = "3.0.0rc1" +version = "3.0.0" source = { editable = "." } dependencies = [ { name = "dag-cbor" }, From 1938f7f0e573e375220082b1b07767cb5c95ed52 Mon Sep 17 00:00:00 2001 From: Abid Sikder <41392423+abidsikder@users.noreply.github.com> Date: Mon, 19 May 2025 17:51:08 -0400 Subject: [PATCH 043/118] finish documentation --- py_hamt/hamt.py | 195 ++++++++++++++++++++++++++++-------------------- 1 file changed, 114 insertions(+), 81 deletions(-) diff --git a/py_hamt/hamt.py b/py_hamt/hamt.py index 97ac26a..f3528b6 100644 --- a/py_hamt/hamt.py +++ b/py_hamt/hamt.py @@ -1,7 +1,6 @@ from abc import ABC, abstractmethod from typing import Callable, Iterator, AsyncIterator import uuid -from random import shuffle import asyncio from copy import deepcopy @@ -9,7 +8,7 @@ from dag_cbor.ipld import IPLDKind from multiformats import multihash -from .store import Store +from .store import ContentAddressedStore def extract_bits(hash_bytes: bytes, depth: int, nbits: int) -> int: @@ -44,11 +43,8 @@ def extract_bits(hash_bytes: bytes, depth: int, nbits: int) -> int: def blake3_hashfn(input_bytes: bytes) -> bytes: """ - This is the default hash function used for . It uses the blake3 hash function and uses 32 bytes as the hash size. + This is the default blake3 hash function used for the `HAMT`, with a 32 byte hash size. - To provide your own hash function, create a function that takes in arbitrarily long bytes and returns the hash bytes. - - It's important to note that the resulting hash must must always be a multiple of 8 bits since python bytes object can only represent in segments of bytes, and thus 8 bits. """ # 32 bytes is the recommended byte size for blake3 and the default, but multihash forces us to explicitly specify digest = b3.digest(input_bytes, size=32) @@ -57,14 +53,10 @@ def blake3_hashfn(input_bytes: bytes) -> bytes: class Node: - """ - TODO - The Node class encapsulates - """ - def __init__(self): self.data: list[IPLDKind] = [dict() for _ in range(0, 256)] - # empty dicts represent empty buckets, lists with one element are links, with the internal element being a link + # empty dicts represent empty buckets + # lists with one element are links, where list[0] is the real link def iter_buckets(self) -> Iterator[dict]: for item in self.data: @@ -121,27 +113,25 @@ def deserialize(cls, data: bytes) -> "Node": "Invalid dag-cbor encoded data from the store was attempted to be decoded" ) - # Don't do any further checks for speed purposes node = cls() node.data = decoded_data # type: ignore return node -# For HAMT internal use for increaing performance with nodes class NodeStore(ABC): @abstractmethod async def save(self, original_id: IPLDKind, node: Node) -> IPLDKind: - """Save nodes to the store""" + pass @abstractmethod async def load(self, id: IPLDKind) -> Node: - """Load nodes from the store""" + pass @abstractmethod def size(self) -> int: """Calculate the size of all internal Nodes in memory. Should not include the overhead in python of the dict or all the keys, which will be negligible compared to the Node sizes.""" - # Async because the in memory tree has async calls + # Async only because the in memory tree has to make async calls when flushing out @abstractmethod async def vacate(self): """Remove everything from the cache.""" @@ -153,9 +143,7 @@ def __init__(self, hamt: "HAMT"): self.cache: dict[IPLDKind, Node] = dict() async def save(self, original_id: IPLDKind, node: Node) -> IPLDKind: - raise Exception( - "Save called in virtual store ReadCacheStore, only supposed to be used for reading" - ) + raise Exception("Node was attempted to be written to the read cache") async def load(self, id: IPLDKind) -> Node: # Cache Hit @@ -164,7 +152,7 @@ async def load(self, id: IPLDKind) -> Node: return node # Cache Miss - node = Node.deserialize(await self.hamt.store.load(id)) + node = Node.deserialize(await self.hamt.cas.load(id)) self.cache[id] = node return node @@ -180,11 +168,9 @@ async def vacate(self): class InMemoryTreeStore(NodeStore): - # Add note about how this initiates by adding the HAMT's root node to the in memory tree buffer - # TODO add notice about how flushing needs to be handled by the HAMT internally and called after every operation is finished def __init__(self, hamt: "HAMT"): self.hamt = hamt - # This buffer goes from the node's virtual store uuid to a tuple of (original store id, Node), we can return the original node + # The integer key is a uuidv4 128-bit integer, for (almost perfectly) guaranteeing uniqueness self.buffer: dict[int, Node] = dict() def is_buffer_id(self, id: IPLDKind) -> bool: @@ -200,7 +186,7 @@ def children_in_memory(self, node: Node) -> Iterator[int]: # Callers must acquire a lock/stop operations to ensure an accurate calculation! def size(self) -> int: # This is more difficult than normal links are intentionally unencodable in dag-cbor as the UUIDv4 128-bit integer IDs do not fit - # So before serializing, make a copy of the node, replace all of those integer links with zeroed out 64 byte marker which should be close to most IDs returned by backing stores + # So before serializing, make a copy of the node, replace all of those integer links with zeroed out 64 byte marker. 64 bytes is a conservative estimate for most IDs returned by CASes total = 0 for k in self.buffer: node = self.buffer[k] @@ -230,12 +216,11 @@ async def vacate(self): new_nodes_on_stack.append((top_buffer_id, child_buffer_id, child_node)) no_children_in_memory = len(new_nodes_on_stack) == 0 - # We can flush this node out and relink as necessary + # Flush this node out and relink the rest of the tree if no_children_in_memory: - # We can flush this one completely since it has no children in memory is_root = parent_buffer_id is None old_id = top_buffer_id - new_id = await self.hamt.store.save( + new_id = await self.hamt.cas.save( top_node.serialize(), codec="dag-cbor" ) del self.buffer[old_id] @@ -244,28 +229,23 @@ async def vacate(self): # If it's the root, we need to set the hamt's root node id once this is done sending to the backing store if is_root: self.hamt.root_node_id = new_id - # Edit the parent if this is not the root + # Edit and properly relink the parent if this is not the root else: parent_node = self.buffer[parent_buffer_id] parent_node.replace_link(old_id, new_id) # Continue recursing down the tree else: - shuffle( - new_nodes_on_stack - ) # avoids always recursing down the rightmost branch - node_stack.extend(new_nodes_on_stack) # There are only two types of nodes left in the buffer: - # 1. A bunch of nodes that seem "unlinked" to anything else, since Links used within the Nodes will reference the real underlying store - # 2. A bunch of empty nodes leftover if the key values they contain are deleted, these would normally be consolidated by a content addressed system but will be remaining here - # We can ignore those when clearing out everything else, nothing inside is linked to anything else anyhow + # 1. A bunch of nodes that seem "unlinked" to anything else, since Links used within the Nodes will reference the real underlying CAS + # 2. A bunch of empty nodes leftover if the key values they contain are deleted, these would normally be consolidated by a content addressed system but will be leftover in the buffer + # So we can just clear out everything since these nodes are not used by the rest of the tree self.buffer = dict() async def add_to_buffer(self, node: Node) -> IPLDKind: - # This is IPLDKind type, but not dag_cbor serializable due to int limits so this will throw errors early if the tree is written with the buffer_ids still in there + # This buffer_id is IPLDKind type since technically it's an int, but it's not dag_cbor serializable since that library can only do up to 64-bit ints. Thus this will throw errors early if a node is written with buffer_ids still in there buffer_id = uuid.uuid4().int - # Returns the virtual store ID that was generated for this node self.buffer[buffer_id] = node return buffer_id @@ -281,57 +261,103 @@ async def save(self, original_id: IPLDKind, node: Node) -> IPLDKind: async def load(self, id: IPLDKind) -> Node: # Hit for something already in the in memory tree if self.is_buffer_id(id): - node: Node = self.buffer[id] # type: ignore + node: Node = self.buffer[id] # type: ignore we know all buffer ids are ints return node - # Miss, something that isn't in the in memory tree, add it - node = Node.deserialize(await self.hamt.store.load(id)) + # Something that isn't in the in memory tree, add it + node = Node.deserialize(await self.hamt.cas.load(id)) await self.add_to_buffer(node) return node class HAMT: - store: Store + """ + An implementation of a Hash Array Mapped Trie for an arbitrary Content Addressed Storage (CAS) system, e.g. IPFS. This uses the IPLD data model. - # Every call of this will look like self.hash_fn() and so the first argument will always take a self argument - hash_fn: Callable[[bytes], bytes] + Use this to store arbitrarily large key-value mappings in your CAS of choice. - # Only important for writing, when reading this will use buckets even if they are overly big - max_bucket_size: int + #### A note about memory management, read/write and read-only modes + The HAMT can be in either read/write mode or read-only mode. For either of these modes, the HAMT has some internal performance optimizations. - root_node_id: IPLDKind + If in read/write, you should use `make_read_only()` to convert to read only mode to get a valid root node id. - lock: asyncio.Lock + These optimizations also trade off performance for memory use. Use `cache_size` to monitor the approximate memory usage. Be warned that for large key-value mapping sets this may take a bit to run. Use `cache_vacate` if you are over your memory limits for the HAMT. + + #### IPFS HAMT Sample Code + ```python + kubo_cas = KuboCAS() # connects to a local kubo node with the default endpoints + hamt = await HAMT.build(cas=kubo_cas) + await hamt.set("foo", "bar") + assert (await hamt.get("foo")) == "bar" + await hamt.make_read_only() + cid = hamt.root_node_id # our root node CID + print(cid) + ``` + """ def __init__( self, - store: Store, + cas: ContentAddressedStore, hash_fn: Callable[[bytes], bytes] = blake3_hashfn, root_node_id: IPLDKind = None, read_only: bool = False, max_bucket_size: int = 4, - inmemory_tree_limit: int = 10_000_000, # 10 MB default - read_cache_limit: int = 10_000_000, # 10 MB default values_are_bytes: bool = False, ): - # TODO add documentation about how to manage cache memories increasing - # TODO add notice about calling build if needing to initialize a completely empty HAMT - # rename store to cas to point out the Content Addressed Store nature of it - self.store = store - self.hash_fn = hash_fn + """ + Use `build` if you need to create a completely empty HAMT, as this requires some async operations with the CAS. For what each of the constructor input variables refer to, check the documentation with the matching names below. + """ + + self.cas: ContentAddressedStore = cas + """The backing storage system. py-hamt provides an implementation `KuboCAS` for IPFS.""" + + self.hash_fn: Callable[[bytes], bytes] = hash_fn + """ + This is the hash function used to place a key-value within the HAMT. + + To provide your own hash function, create a function that takes in arbitrarily long bytes and returns the hash bytes. + + It's important to note that the resulting hash must must always be a multiple of 8 bits since python bytes object can only represent in segments of bytes, and thus 8 bits. + + Theoretically your hash size must only be a minimum of 1 byte, and there can be less than or the same number of hash collisions as the bucket size. Any more and the HAMT will most likely throw errors. + """ + self.lock = asyncio.Lock() - self.read_only = read_only - self.values_are_bytes = values_are_bytes - # TODO Say that values are bytes are safe to change in between operations, so put a hypothetical example of toggling it when its in read only mode and back in write for a completely safe toggle. - self.total = 0 + """@private""" + + self.values_are_bytes: bool = values_are_bytes + """Set this to true if you are only going to be storing python bytes objects into the hamt. This will improve performance by skipping a serialization step from IPLDKind. + + This is theoretically safe to change in between operations, but this has not been verified in testing, so only do this at your own risk. + """ if max_bucket_size < 1: raise ValueError("Bucket size maximum must be a positive integer") self.max_bucket_size = max_bucket_size + """ + This is only important for tuning performance when writing! For reading a HAMT that was written with a different max bucket size, this does not need to match and can be left unprovided. + + This is an internal detail that has been exposed for performance tuning. The HAMT handles large key-value mapping sets even on a content addressed system by essentially sharding all the mappings across many smaller Nodes. The memory footprint of each of these Nodes footprint is a linear function of the maximum bucket size. Larger bucket sizes will result in larger Nodes, but more time taken to retrieve and decode these nodes from your backing CAS. + + This must be a positive integer with a minimum of 1. + """ self.root_node_id = root_node_id + """ + This is type IPLDKind but the documentation generator pdoc mangles it a bit. + + Read from this only when in read mode to get something valid! + """ + + self.read_only: bool = read_only + """Clients should NOT modify this. + This is here for checking whether the HAMT is in read only or read/write mode. + + The distinction is made for performance and correctness reasons. In read only mode, the HAMT has an internal read cache that can speed up operations. In read/write mode, for reads the HAMT maintains strong consistency for reads by using async locks, and for writes the HAMT writes to an in memory buffer rather than performing (possibly) network calls to the underlying CAS. + """ self.node_store: NodeStore + """@private""" if read_only: self.node_store = ReadCacheStore(self) else: @@ -339,7 +365,11 @@ def __init__( @classmethod async def build(cls, *args, **kwargs) -> "HAMT": - # TODO add notice about referring to the init but this is what needs to actually get called, if you are initializing a completely new empty HAMT + """ + Use this if you are initializing a completely empty HAMT! That means passing in None for the root_node_id. Method arguments are the exact same as `__init__`. If the root_node_id is not None, this will have no difference than creating a HAMT instance with __init__. + + This separate async method is required since initializing an empty HAMT means sending some internal objects to the underlying CAS, which requires async operations. python does not allow for an async __init__, so this method is separately provided. + """ hamt = cls(*args, **kwargs) if hamt.root_node_id is None: hamt.root_node_id = await hamt.node_store.save(None, Node()) @@ -360,15 +390,29 @@ async def enable_write(self): self.read_only = False self.node_store = InMemoryTreeStore(self) - # TODO specify in documentation that this is async concurrency safe async def cache_size(self) -> int: + """ + Returns the memory used by some internal performance optimization tools in bytes. + + This is async concurrency safe, so call it whenever. This does mean it will block and wait for other writes to finish however. + + Be warned that this may take a while to run for large HAMTs. + + For more on memory management, see the `HAMT` class documentation. + """ if self.read_only: return self.node_store.size() async with self.lock: return self.node_store.size() - # TODO documentation async def cache_vacate(self): + """ + Vacate and completely empty out the internal read/write cache. + + Be warned that this may take a while if there have been a lot of write operations. + + For more on memory management, see the `HAMT` class documentation. + """ if self.read_only: await self.node_store.vacate() async with self.lock: @@ -414,23 +458,18 @@ async def _reserialize_and_link(self, node_stack: list[tuple[IPLDKind, Node]]): # automatically skip encoding if the value provided is of the bytes variety async def set(self, key: str, val: IPLDKind): - """TODO add something about how skip encoding can make large bytes setting much more efficient""" + """Write a key-value mapping.""" if self.read_only: raise Exception("Cannot call set on a read only HAMT") - # print(f"setting {key}") data: bytes if self.values_are_bytes: data = val # type: ignore let users get an exception if they pass in a non bytes when they want to skip encoding else: data = dag_cbor.encode(val) - pointer = await self.store.save(data, codec="raw") - start = time.perf_counter() + pointer = await self.cas.save(data, codec="raw") await self._set_pointer(key, pointer) - end = time.perf_counter() - elapsed = end - start - self.total += elapsed async def _set_pointer(self, key: str, val_ptr: IPLDKind): async with self.lock: @@ -480,6 +519,8 @@ async def _set_pointer(self, key: str, val_ptr: IPLDKind): self.root_node_id = node_stack[0][0] async def delete(self, key: str): + """Delete a key-value mapping.""" + # Also deletes the pointer at the same time so this doesn't have a _delete_pointer duo if self.read_only: raise Exception("Cannot call delete on a read only HAMT") @@ -517,23 +558,16 @@ async def delete(self, key: str): # If we didn't make a change, then this key must not exist within the HAMT raise KeyError - # TODO document option to skip decode if the user knows that the value inside is also going to be a bytes object async def get(self, key: str) -> IPLDKind: # If read only, no need to acquire a lock - start = time.perf_counter() pointer: IPLDKind if self.read_only: pointer = await self._get_pointer(key) else: async with self.lock: pointer = await self._get_pointer(key) - end = time.perf_counter() - elapsed = end - start - self.total += elapsed - - # print(f"getting {key}") - data = await self.store.load(pointer) + data = await self.cas.load(pointer) if self.values_are_bytes: return data else: @@ -590,10 +624,9 @@ async def keys(self) -> AsyncIterator[str]: """ AsyncIterator returning all keys in the HAMT. - TODO clean up this paragraph's language - When the HAMT is write enabled, to maintain strong consistency this will obtain a lock and not a llow any other operations to proceed. For example, if you are inside of a for loop using this iterator, you cannot also get a value at the same time until iteration is completely done. If you try you will run into deadlock. + If the HAMT is write enabled, to maintain strong consistency this will obtain an async lock and not allow any other operations to proceed. - In read only mode however, this can be run concurrently with get operations. + When the HAMT is in read only mode however, this can be run concurrently with get operations. """ if self.read_only: async for k in self._keys_no_locking(): From c3203d4ef4e485e9493edbaf428cc2bafee9c038 Mon Sep 17 00:00:00 2001 From: Abid Sikder <41392423+abidsikder@users.noreply.github.com> Date: Mon, 19 May 2025 18:03:56 -0400 Subject: [PATCH 044/118] fix hamt tests with the store -> cas renaming --- tests/test_hamt.py | 51 ++++++++++++++++++++++++---------------------- 1 file changed, 27 insertions(+), 24 deletions(-) diff --git a/tests/test_hamt.py b/tests/test_hamt.py index e242442..8c6cd06 100644 --- a/tests/test_hamt.py +++ b/tests/test_hamt.py @@ -3,12 +3,12 @@ from dag_cbor import IPLDKind from multiformats import CID -from hypothesis import given, settings, HealthCheck +from hypothesis import given from hypothesis import strategies as st import pytest -from py_hamt import HAMT, DictStore -from py_hamt.hamt import Node +from py_hamt.hamt import HAMT, Node +from py_hamt.store import InMemoryCAS from testing_utils import key_value_list @@ -16,10 +16,8 @@ @pytest.mark.asyncio @given(key_value_list) async def test_fuzz(kvs: list[tuple[str, IPLDKind]]): - # async def test_fuzz(): - # kvs=[('', None), ('0', None)] - store = DictStore() - hamt = await HAMT.build(store=store) + cas= InMemoryCAS() + hamt = await HAMT.build(cas=cas) # Sequential setting and getting, while randomly changing the bucket size which the HAMT should be able to withstand for key, value in kvs: @@ -77,7 +75,7 @@ async def verify(k, v): for k, _ in kvs: # Callers must handle acquiring a lock themselves, so do these entirely sequentially pointer: bytes = await hamt._get_pointer(k) # type: ignore we know that DictStore only returns bytes for its Link type - await store.load(pointer) + await cas.load(pointer) await hamt.make_read_only() with pytest.raises(Exception, match="Cannot call set on a read only HAMT"): @@ -93,48 +91,53 @@ async def verify_kvs_and_len(h: HAMT): # Test that when a hamt has its root manually initialized by a user, that the key count is accurate # We can only get the root node id here since hamt is in read mode and thus the in memory tree has been entirely flushed new_hamt = await HAMT.build( - store=store, root_node_id=hamt.root_node_id, read_only=True + cas=cas, root_node_id=hamt.root_node_id, read_only=True ) await verify_kvs_and_len(new_hamt) # Most for code coverage's sake with pytest.raises( Exception, - match="Save called in virtual store ReadCacheStore, only supposed to be used for reading", + match="Node was attempted to be written to the read cache", ): await new_hamt.node_store.save(bytes(), Node()) # None of the keys should be in a new hamt using the same store but with a fresh root node - empty_hamt = await HAMT.build(store=store) + empty_hamt = await HAMT.build(cas=cas) for k, _ in kvs: with pytest.raises(KeyError): await empty_hamt.get(k) - assert len([key async for key in empty_hamt.keys()]) == (await empty_hamt.len()) == 0 + assert ( + len([key async for key in empty_hamt.keys()]) + == (await empty_hamt.len()) + == 0 + ) # invalid bucket size with pytest.raises( ValueError, match="Bucket size maximum must be a positive integer" ): - await HAMT.build(store=store, max_bucket_size=-1) - + await HAMT.build(cas=cas, max_bucket_size=-1) # Cache size management code branches coverage, do it all in async concurrency small_cache_size_bytes = 1000 # Read cache - read_hamt = await HAMT.build(store=store, root_node_id=hamt.root_node_id) - async def get_and_vacate(k,v): + read_hamt = await HAMT.build(cas=cas, root_node_id=hamt.root_node_id) + + async def get_and_vacate(k, v): assert (await hamt.get(k)) == v if (await hamt.cache_size()) > small_cache_size_bytes: await hamt.cache_vacate() assert (await hamt.cache_size()) == 0 - await asyncio.gather(*[get_and_vacate(k,v) for k,v in kvs]) + await asyncio.gather(*[get_and_vacate(k, v) for k, v in kvs]) # In memory tree while writing # set small max bucket size to force more linking and more nodes - small_memory_tree = await HAMT.build(store=store, max_bucket_size=1) - async def set_and_vacate(k,v): + small_memory_tree = await HAMT.build(cas=cas, max_bucket_size=1) + + async def set_and_vacate(k, v): await small_memory_tree.set(k, v) assert (await small_memory_tree.get(k)) == v if (await small_memory_tree.cache_size()) > small_cache_size_bytes: @@ -142,7 +145,7 @@ async def set_and_vacate(k,v): assert (await small_memory_tree.cache_size()) == 0 assert (await small_memory_tree.get(k)) == v - await asyncio.gather(*[set_and_vacate(k,v) for k,v in kvs]) + await asyncio.gather(*[set_and_vacate(k, v) for k, v in kvs]) @pytest.mark.asyncio @@ -158,8 +161,8 @@ async def set_and_vacate(k,v): ) ) async def test_values_are_bytes(kvs: list[tuple[str, bytes]]): - store = DictStore() - hamt = await HAMT.build(store=store, values_are_bytes=True) + cas = InMemoryCAS() + hamt = await HAMT.build(cas=cas, values_are_bytes=True) await asyncio.gather(*[hamt.set(k, v) for k, v in kvs]) for k, v in kvs: @@ -181,7 +184,7 @@ async def test_invalid_node(): @pytest.mark.asyncio async def test_key_rewrite(): - hamt = await HAMT.build(store=DictStore()) + hamt = await HAMT.build(cas=InMemoryCAS()) await hamt.set("foo", b"bar") assert b"bar" == await hamt.get("foo") assert (await hamt.len()) == 1 @@ -197,7 +200,7 @@ async def test_key_rewrite(): # Test that is guaranteed to induce overfull buckets that then requires our hamt to follow deeper into the tree to do insertions @pytest.mark.asyncio async def test_link_following(): - hamt = await HAMT.build(store=DictStore()) + hamt = await HAMT.build(cas=InMemoryCAS()) hamt.max_bucket_size = 1 # The first byte of the blake3 hash of each of these is the same, 10110011 kvs = [(str(5), b""), (str(15), b""), (str(123), b"")] From 98ee8083a079a5b306258bd6569e3c6960812984 Mon Sep 17 00:00:00 2001 From: Abid Sikder <41392423+abidsikder@users.noreply.github.com> Date: Mon, 19 May 2025 18:12:03 -0400 Subject: [PATCH 045/118] complete hamt and stores code coverage --- py_hamt/hamt.py | 4 +-- tests/test_kubo_cas.py | 44 +++++++++++++++++++++++++++ tests/test_stores.py | 69 ------------------------------------------ 3 files changed, 46 insertions(+), 71 deletions(-) create mode 100644 tests/test_kubo_cas.py delete mode 100644 tests/test_stores.py diff --git a/py_hamt/hamt.py b/py_hamt/hamt.py index f3528b6..3f5ec6c 100644 --- a/py_hamt/hamt.py +++ b/py_hamt/hamt.py @@ -121,11 +121,11 @@ def deserialize(cls, data: bytes) -> "Node": class NodeStore(ABC): @abstractmethod async def save(self, original_id: IPLDKind, node: Node) -> IPLDKind: - pass + """""" @abstractmethod async def load(self, id: IPLDKind) -> Node: - pass + """""" @abstractmethod def size(self) -> int: diff --git a/tests/test_kubo_cas.py b/tests/test_kubo_cas.py new file mode 100644 index 0000000..12c1806 --- /dev/null +++ b/tests/test_kubo_cas.py @@ -0,0 +1,44 @@ +import dag_cbor +from dag_cbor import IPLDKind +from hypothesis import given +import pytest +import requests + +from py_hamt import KuboCAS + +from py_hamt.store import InMemoryCAS +from testing_utils import ipld_strategy, create_ipfs # noqa + + +# Just to cover this one case that isn't covered within test_hamt +@pytest.mark.asyncio +async def test_memory_store_exception(): + s = InMemoryCAS() + with pytest.raises(KeyError): + await s.load(bytes()) + + +@pytest.mark.asyncio +@given(data=ipld_strategy()) +async def test_kubo_default_urls(data: IPLDKind): + kubo_cas = KuboCAS() + cids = [] + for codec in ["raw", "dag-cbor"]: + cid = await kubo_cas.save(dag_cbor.encode(data), codec=codec) # type: ignore + cids.append(cid) + result = dag_cbor.decode(await kubo_cas.load(cid)) + assert data == result + + +@pytest.mark.asyncio +@given(data=ipld_strategy()) +async def test_kubo_cas(create_ipfs, data: IPLDKind): # noqa + rpc_base_url, gateway_base_url = create_ipfs + + # Provide our own requests Session, for complete code coverage + kubo_cas = KuboCAS(rpc_base_url=rpc_base_url, gateway_base_url=gateway_base_url, requests_session=requests.Session()) + + for codec in ["raw", "dag-cbor"]: + cid = await kubo_cas.save(dag_cbor.encode(data), codec=codec) # type: ignore + result = dag_cbor.decode(await kubo_cas.load(cid)) + assert data == result diff --git a/tests/test_stores.py b/tests/test_stores.py deleted file mode 100644 index 8ef12e1..0000000 --- a/tests/test_stores.py +++ /dev/null @@ -1,69 +0,0 @@ -import aiohttp -import dag_cbor -from dag_cbor import IPLDKind -from hypothesis import given -import pytest - -from py_hamt import IPFSStore - -from py_hamt.store import DictStore -from testing_utils import ipld_strategy, create_ipfs # noqa - - -# Just to cover this one case that isn't covered within test_hamt -@pytest.mark.asyncio -async def test_memory_store_exception(): - s = DictStore() - with pytest.raises(KeyError): - await s.load(bytes()) - - -@pytest.mark.asyncio -@given(data=ipld_strategy()) -async def test_ipfsstore_default_urls(data: IPLDKind): - ipfsstore = IPFSStore() - # test that ipfs store close session when both are already missing is a no-op - await ipfsstore.close_sessions() - cids = [] - try: - for codec in ["raw", "dag-cbor"]: - cid = await ipfsstore.save(dag_cbor.encode(data), codec=codec) # type: ignore - cids.append(cid) - result = dag_cbor.decode(await ipfsstore.load(cid)) - assert data == result - # We should be able to close right after every result and it will remake its sessions if it needs to - await ipfsstore.close_sessions() - finally: - await ipfsstore.close_sessions() - # test that it's a no-op again - await ipfsstore.close_sessions() - - # Now do it but with only loading data, which will be a common use pattern for HAMT readers - try: - for cid in cids: - for codec in ["raw", "dag-cbor"]: - result = dag_cbor.decode(await ipfsstore.load(cid)) - assert data == result - await ipfsstore.close_sessions() - finally: - await ipfsstore.close_sessions() - await ipfsstore.close_sessions() - - -@pytest.mark.asyncio -@given(data=ipld_strategy()) -async def test_ipfsstore(create_ipfs, data: IPLDKind): # noqa - rpc_uri_stem, gateway_uri_stem = create_ipfs - gateway_session = aiohttp.ClientSession(base_url=gateway_uri_stem) - rpc_session = aiohttp.ClientSession(base_url=rpc_uri_stem) - - try: - ipfsstore = IPFSStore(rpc_session=rpc_session, gateway_session=gateway_session) - - for codec in ["raw", "dag-cbor"]: - cid = await ipfsstore.save(dag_cbor.encode(data), codec=codec) # type: ignore - result = dag_cbor.decode(await ipfsstore.load(cid)) - assert data == result - finally: - await rpc_session.close() - await gateway_session.close() From 2a10acd1f8d56567d11fe9c61bd62cb394c69909 Mon Sep 17 00:00:00 2001 From: Abid Sikder <41392423+abidsikder@users.noreply.github.com> Date: Mon, 19 May 2025 18:18:55 -0400 Subject: [PATCH 046/118] finish tests with complete code coverage --- tests/test_zarr_ipfs.py | 250 ++++++++++------------------------------ 1 file changed, 64 insertions(+), 186 deletions(-) diff --git a/tests/test_zarr_ipfs.py b/tests/test_zarr_ipfs.py index c8fd7f2..f782aa2 100644 --- a/tests/test_zarr_ipfs.py +++ b/tests/test_zarr_ipfs.py @@ -1,20 +1,16 @@ -import json -import os -import shutil -import socket -import subprocess -import tempfile import time -from pathlib import Path import numpy as np import pandas as pd -import requests import xarray as xr import pytest +import zarr import zarr.core.buffer -from py_hamt import HAMT, IPFSStore, IPFSZarr3, create_zarr_encryption_transformers +from py_hamt import HAMT, KuboCAS + +from py_hamt.zarr_hamt_store import ZarrHAMTStore +from testing_utils import create_ipfs # noqa pytest detects by name but this shows up as unused import error @pytest.fixture(scope="module") @@ -62,41 +58,35 @@ def random_zarr_dataset(): # This test also collects miscellaneous statistics about performance, run with pytest -s to see these statistics being printed out @pytest.mark.asyncio -async def test_write_read(create_ipfs, random_zarr_dataset: xr.Dataset): - rpc_uri_stem, gateway_uri_stem = create_ipfs +async def test_write_read(create_ipfs, random_zarr_dataset: xr.Dataset): # noqa for fixture which is imported above but then "redefined" + rpc_base_url, gateway_base_url= create_ipfs test_ds = random_zarr_dataset print("=== Writing this xarray Dataset to a Zarr v3 on IPFS ===") print(test_ds) - ipfsstore = IPFSStore( - debug=True, rpc_uri_stem=rpc_uri_stem, gateway_uri_stem=gateway_uri_stem - ) - hamt = HAMT(store=ipfsstore) - ipfszarr3 = IPFSZarr3(hamt) - assert ipfszarr3.supports_writes + kubo_cas = KuboCAS(rpc_base_url=rpc_base_url, gateway_base_url=gateway_base_url) + hamt = await HAMT.build(cas=kubo_cas, values_are_bytes=True) + zhs = ZarrHAMTStore(hamt) + assert zhs.supports_writes start = time.perf_counter() - # Do an initial write along with an append - test_ds.to_zarr(store=ipfszarr3) # type: ignore - test_ds.to_zarr(store=ipfszarr3, mode="a", append_dim="time") # type: ignore + # Do an initial write along with an append which is a common xarray/zarr operation + test_ds.to_zarr(store=zhs) # type: ignore + test_ds.to_zarr(store=zhs, mode="a", append_dim="time") # type: ignore end = time.perf_counter() elapsed = end - start print("=== Write Stats") print(f"Total time in seconds: {elapsed:.2f}") - print(f"Sent bytes: {ipfsstore.total_sent}") - print(f"Received bytes: {ipfsstore.total_received}") print("=== Root CID") + await hamt.make_read_only() cid = hamt.root_node_id print(cid) print("=== Reading data back in and checking if identical") - ipfsstore = IPFSStore( - debug=True, rpc_uri_stem=rpc_uri_stem, gateway_uri_stem=gateway_uri_stem - ) - hamt = HAMT(store=ipfsstore, root_node_id=cid) + hamt = await HAMT.build(cas=kubo_cas, root_node_id=cid, values_are_bytes=True, read_only=True) start = time.perf_counter() ipfs_ds: xr.Dataset - ipfszarr3 = IPFSZarr3(hamt, read_only=True) - ipfs_ds = xr.open_zarr(store=ipfszarr3) + zhs = ZarrHAMTStore(hamt, read_only=True) + ipfs_ds = xr.open_zarr(store=zhs) print(ipfs_ds) # Check both halves, since each are an identical copy @@ -110,186 +100,74 @@ async def test_write_read(create_ipfs, random_zarr_dataset: xr.Dataset): elapsed = end - start print("=== Read Stats") print(f"Total time in seconds: {elapsed:.2f}") - print(f"Sent bytes: {ipfsstore.total_sent}") - print(f"Received bytes: {ipfsstore.total_received}") # Tests for code coverage's sake - assert await ipfszarr3.exists("zarr.json") + assert await zhs.exists("zarr.json") # __eq__ - assert ipfszarr3 == ipfszarr3 - assert ipfszarr3 != hamt - assert not ipfszarr3.supports_writes - assert not ipfszarr3.supports_partial_writes - assert not ipfszarr3.supports_deletes - - hamt_keys = set(ipfszarr3.hamt.keys()) - ipfszarr3_keys: set[str] = set() - async for k in ipfszarr3.list(): - ipfszarr3_keys.add(k) - assert hamt_keys == ipfszarr3_keys - - ipfszarr3_keys: set[str] = set() - async for k in ipfszarr3.list(): - ipfszarr3_keys.add(k) - assert hamt_keys == ipfszarr3_keys - - ipfszarr3_keys: set[str] = set() - async for k in ipfszarr3.list_prefix(""): - ipfszarr3_keys.add(k) - assert hamt_keys == ipfszarr3_keys + assert zhs == zhs + assert zhs != hamt + assert not zhs.supports_writes + assert not zhs.supports_partial_writes + assert not zhs.supports_deletes + + hamt_keys = set() + async for k in zhs.hamt.keys(): + hamt_keys.add(k) + + zhs_keys: set[str] = set() + async for k in zhs.list(): + zhs_keys.add(k) + assert hamt_keys == zhs_keys + + zhs_keys: set[str] = set() + async for k in zhs.list(): + zhs_keys.add(k) + assert hamt_keys == zhs_keys + + zhs_keys: set[str] = set() + async for k in zhs.list_prefix(""): + zhs_keys.add(k) + assert hamt_keys == zhs_keys with pytest.raises(NotImplementedError): - await ipfszarr3.set_partial_values([]) + await zhs.set_partial_values([]) with pytest.raises(NotImplementedError): - await ipfszarr3.get_partial_values( + await zhs.get_partial_values( zarr.core.buffer.default_buffer_prototype(), [] ) - previous_zarr_json = await ipfszarr3.get( + previous_zarr_json = await zhs.get( "zarr.json", zarr.core.buffer.default_buffer_prototype() ) assert previous_zarr_json is not None # Setting a metadata file that should always exist should not change anything - await ipfszarr3.set_if_not_exists("zarr.json", np.array([b"a"], dtype=np.bytes_)) # type: ignore np.arrays, if dtype is bytes, is usable as a zarr buffer - zarr_json_now = await ipfszarr3.get( + await zhs.set_if_not_exists( + "zarr.json", np.array([b"a"], dtype=np.bytes_) + ) # type: ignore np.arrays, if dtype is bytes, is usable as a zarr buffer + zarr_json_now = await zhs.get( "zarr.json", zarr.core.buffer.default_buffer_prototype() ) assert zarr_json_now is not None assert previous_zarr_json.to_bytes() == zarr_json_now.to_bytes() # now remove that metadata file and then add it back - ipfszarr3 = IPFSZarr3(ipfszarr3.hamt, read_only=False) # make a writable version - await ipfszarr3.delete("zarr.json") + await zhs.hamt.enable_write() + zhs = ZarrHAMTStore( + zhs.hamt, read_only=False + ) # make a writable version + await zhs.delete("zarr.json") # doing a duplicate delete should not result in an error - await ipfszarr3.delete("zarr.json") - ipfszarr3_keys: set[str] = set() - async for k in ipfszarr3.list(): - ipfszarr3_keys.add(k) - assert hamt_keys != ipfszarr3_keys - assert "zarr.json" not in ipfszarr3_keys - - await ipfszarr3.set_if_not_exists("zarr.json", previous_zarr_json) - zarr_json_now = await ipfszarr3.get( + await zhs.delete("zarr.json") + zhs_keys: set[str] = set() + async for k in zhs.list(): + zhs_keys.add(k) + assert hamt_keys != zhs_keys + assert "zarr.json" not in zhs_keys + + await zhs.set_if_not_exists("zarr.json", previous_zarr_json) + zarr_json_now = await zhs.get( "zarr.json", zarr.core.buffer.default_buffer_prototype() ) assert zarr_json_now is not None assert previous_zarr_json.to_bytes() == zarr_json_now.to_bytes() - - -def test_encryption(create_ipfs, random_zarr_dataset: xr.Dataset): - rpc_uri_stem, gateway_uri_stem = create_ipfs - test_ds = random_zarr_dataset - - with pytest.raises(ValueError, match="Encryption key is not 32 bytes"): - create_zarr_encryption_transformers(bytes(), bytes()) - - encryption_key = bytes(32) - # Encrypt only precipitation, not temperature or the coordinate variables - encrypt, decrypt = create_zarr_encryption_transformers( - encryption_key, - header="sample-header".encode(), - exclude_vars=["temp"], - detect_exclude=test_ds, - ) - hamt = HAMT( - store=IPFSStore(rpc_uri_stem=rpc_uri_stem, gateway_uri_stem=gateway_uri_stem), - transformer_encode=encrypt, - transformer_decode=decrypt, - ) - ipfszarr3 = IPFSZarr3(hamt) - test_ds.to_zarr(store=ipfszarr3) # type: ignore - - ipfszarr3 = IPFSZarr3(ipfszarr3.hamt, read_only=True) - ipfs_ds = xr.open_zarr(store=ipfszarr3) - xr.testing.assert_identical(ipfs_ds, test_ds) - - # Now trying to load without a decryptor, xarray should be able to read the metadata and still perform operations on the unencrypted variable - print("=== Attempting to read and print metadata of partially encrypted zarr") - - bad_key = bytes([0xAA]) * 32 - bad_header = "".encode() - bad_encrypt, auto_detecting_decrypt = create_zarr_encryption_transformers( - bad_key, - bad_header, - ) - ds = xr.open_zarr( - store=IPFSZarr3( - HAMT( - store=IPFSStore( - rpc_uri_stem=rpc_uri_stem, gateway_uri_stem=gateway_uri_stem - ), - root_node_id=ipfszarr3.hamt.root_node_id, - transformer_encode=bad_encrypt, - transformer_decode=auto_detecting_decrypt, - ), - read_only=True, - ) - ) - print(ds) - assert ds.temp.sum() == test_ds.temp.sum() # type: ignore - # We should be unable to read precipitation values which are still encrypted - with pytest.raises(Exception): - ds.precip.sum() - - # For code coverage's sake - # Don't auto detect, and thus encounter an error when trying to read back an unencrypted variable with the wrong encryption key and header - bad_encrypt, bad_decrypt = create_zarr_encryption_transformers( - bad_key, bad_header, detect_exclude=False - ) - with pytest.raises(Exception): - ds = xr.open_zarr( - store=IPFSZarr3( - HAMT( - store=IPFSStore( - rpc_uri_stem=rpc_uri_stem, gateway_uri_stem=gateway_uri_stem - ), - root_node_id=ipfszarr3.hamt.root_node_id, - transformer_encode=bad_encrypt, - transformer_decode=bad_decrypt, - ), - read_only=True, - ) - ) - assert ds.temp.sum() == test_ds.temp.sum() - - -# This test assumes the other zarr ipfs tests are working fine, so if other things are breaking check those first -def test_authenticated_gateway(random_zarr_dataset: xr.Dataset): - test_ds = random_zarr_dataset - - def write_and_check(store: IPFSStore) -> bool: - try: - store.rpc_uri_stem = "http://127.0.0.1:5002" # 5002 is the port configured in the run-checks.yaml actions file for nginx to serve the proxy on - hamt = HAMT(store=store) - ipfszarr3 = IPFSZarr3(hamt) - test_ds.to_zarr(store=ipfszarr3, mode="w") # type: ignore - loaded_ds = xr.open_zarr(store=ipfszarr3) - xr.testing.assert_identical(test_ds, loaded_ds) - return True - except Exception as _: - return False - - # Test with API Key - api_key_store = IPFSStore(api_key="test") - assert write_and_check(api_key_store) - - # Test that wrong API Key fails - bad_api_key_store = IPFSStore(api_key="badKey") - assert not write_and_check(bad_api_key_store) - - # Test just bearer token - bearer_ipfs_store = IPFSStore(bearer_token="test") - assert write_and_check(bearer_ipfs_store) - - # Test with wrong bearer - bad_bearer_store = IPFSStore(bearer_token="wrongBearer") - assert not write_and_check(bad_bearer_store) - - # Test with just basic auth - basic_auth_store = IPFSStore(basic_auth=("test", "test")) - assert write_and_check(basic_auth_store) - - # Test with wrong basic auth - bad_basic_auth_store = IPFSStore(basic_auth=("wrong", "wrong")) - assert not write_and_check(bad_basic_auth_store) From f6953ef2c2413860b54e7cc2498ecb83ba937e4f Mon Sep 17 00:00:00 2001 From: Abid Sikder <41392423+abidsikder@users.noreply.github.com> Date: Mon, 19 May 2025 18:19:30 -0400 Subject: [PATCH 047/118] ignore type error --- tests/test_zarr_ipfs.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/test_zarr_ipfs.py b/tests/test_zarr_ipfs.py index f782aa2..6c3961e 100644 --- a/tests/test_zarr_ipfs.py +++ b/tests/test_zarr_ipfs.py @@ -143,7 +143,7 @@ async def test_write_read(create_ipfs, random_zarr_dataset: xr.Dataset): # noqa assert previous_zarr_json is not None # Setting a metadata file that should always exist should not change anything await zhs.set_if_not_exists( - "zarr.json", np.array([b"a"], dtype=np.bytes_) + "zarr.json", np.array([b"a"], dtype=np.bytes_) # type: ignore ) # type: ignore np.arrays, if dtype is bytes, is usable as a zarr buffer zarr_json_now = await zhs.get( "zarr.json", zarr.core.buffer.default_buffer_prototype() From b0bb6ae31958bd041e7f6207d792dd05df3c2b62 Mon Sep 17 00:00:00 2001 From: Abid Sikder <41392423+abidsikder@users.noreply.github.com> Date: Mon, 19 May 2025 18:28:48 -0400 Subject: [PATCH 048/118] update ipfs setup action used --- .github/workflows/run-checks.yaml | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/.github/workflows/run-checks.yaml b/.github/workflows/run-checks.yaml index 4264c39..4d399f7 100644 --- a/.github/workflows/run-checks.yaml +++ b/.github/workflows/run-checks.yaml @@ -21,11 +21,10 @@ jobs: run: uv sync - name: Install IPFS - uses: ibnesayeed/setup-ipfs@e183d0d2538b866dc30d8850883bd4cd4f8ab431 # v0.6.0 + uses: oduwsdl/setup-ipfs@e92fedca9f61ab9184cb74940254859f4d7af4d9 # v0.6.3 with: ipfs_version: "0.34.1" run_daemon: true - id: ipfs_setup - name: Run pytest with coverage run: uv run pytest --cov=py_hamt tests/ --cov-report=xml From aaf722a818a0aabf7395ed1f8bae1f260b724576 Mon Sep 17 00:00:00 2001 From: Abid Sikder <41392423+abidsikder@users.noreply.github.com> Date: Mon, 19 May 2025 18:28:54 -0400 Subject: [PATCH 049/118] ruff format --- tests/test_hamt.py | 6 ++---- tests/test_kubo_cas.py | 6 +++++- tests/test_zarr_ipfs.py | 17 ++++++++--------- 3 files changed, 15 insertions(+), 14 deletions(-) diff --git a/tests/test_hamt.py b/tests/test_hamt.py index 8c6cd06..ebafd4c 100644 --- a/tests/test_hamt.py +++ b/tests/test_hamt.py @@ -16,7 +16,7 @@ @pytest.mark.asyncio @given(key_value_list) async def test_fuzz(kvs: list[tuple[str, IPLDKind]]): - cas= InMemoryCAS() + cas = InMemoryCAS() hamt = await HAMT.build(cas=cas) # Sequential setting and getting, while randomly changing the bucket size which the HAMT should be able to withstand @@ -90,9 +90,7 @@ async def verify_kvs_and_len(h: HAMT): # Test that when a hamt has its root manually initialized by a user, that the key count is accurate # We can only get the root node id here since hamt is in read mode and thus the in memory tree has been entirely flushed - new_hamt = await HAMT.build( - cas=cas, root_node_id=hamt.root_node_id, read_only=True - ) + new_hamt = await HAMT.build(cas=cas, root_node_id=hamt.root_node_id, read_only=True) await verify_kvs_and_len(new_hamt) # Most for code coverage's sake diff --git a/tests/test_kubo_cas.py b/tests/test_kubo_cas.py index 12c1806..65da3a6 100644 --- a/tests/test_kubo_cas.py +++ b/tests/test_kubo_cas.py @@ -36,7 +36,11 @@ async def test_kubo_cas(create_ipfs, data: IPLDKind): # noqa rpc_base_url, gateway_base_url = create_ipfs # Provide our own requests Session, for complete code coverage - kubo_cas = KuboCAS(rpc_base_url=rpc_base_url, gateway_base_url=gateway_base_url, requests_session=requests.Session()) + kubo_cas = KuboCAS( + rpc_base_url=rpc_base_url, + gateway_base_url=gateway_base_url, + requests_session=requests.Session(), + ) for codec in ["raw", "dag-cbor"]: cid = await kubo_cas.save(dag_cbor.encode(data), codec=codec) # type: ignore diff --git a/tests/test_zarr_ipfs.py b/tests/test_zarr_ipfs.py index 6c3961e..75ba40f 100644 --- a/tests/test_zarr_ipfs.py +++ b/tests/test_zarr_ipfs.py @@ -59,7 +59,7 @@ def random_zarr_dataset(): # This test also collects miscellaneous statistics about performance, run with pytest -s to see these statistics being printed out @pytest.mark.asyncio async def test_write_read(create_ipfs, random_zarr_dataset: xr.Dataset): # noqa for fixture which is imported above but then "redefined" - rpc_base_url, gateway_base_url= create_ipfs + rpc_base_url, gateway_base_url = create_ipfs test_ds = random_zarr_dataset print("=== Writing this xarray Dataset to a Zarr v3 on IPFS ===") print(test_ds) @@ -82,7 +82,9 @@ async def test_write_read(create_ipfs, random_zarr_dataset: xr.Dataset): # noqa print(cid) print("=== Reading data back in and checking if identical") - hamt = await HAMT.build(cas=kubo_cas, root_node_id=cid, values_are_bytes=True, read_only=True) + hamt = await HAMT.build( + cas=kubo_cas, root_node_id=cid, values_are_bytes=True, read_only=True + ) start = time.perf_counter() ipfs_ds: xr.Dataset zhs = ZarrHAMTStore(hamt, read_only=True) @@ -133,9 +135,7 @@ async def test_write_read(create_ipfs, random_zarr_dataset: xr.Dataset): # noqa await zhs.set_partial_values([]) with pytest.raises(NotImplementedError): - await zhs.get_partial_values( - zarr.core.buffer.default_buffer_prototype(), [] - ) + await zhs.get_partial_values(zarr.core.buffer.default_buffer_prototype(), []) previous_zarr_json = await zhs.get( "zarr.json", zarr.core.buffer.default_buffer_prototype() @@ -143,7 +143,8 @@ async def test_write_read(create_ipfs, random_zarr_dataset: xr.Dataset): # noqa assert previous_zarr_json is not None # Setting a metadata file that should always exist should not change anything await zhs.set_if_not_exists( - "zarr.json", np.array([b"a"], dtype=np.bytes_) # type: ignore + "zarr.json", + np.array([b"a"], dtype=np.bytes_), # type: ignore ) # type: ignore np.arrays, if dtype is bytes, is usable as a zarr buffer zarr_json_now = await zhs.get( "zarr.json", zarr.core.buffer.default_buffer_prototype() @@ -153,9 +154,7 @@ async def test_write_read(create_ipfs, random_zarr_dataset: xr.Dataset): # noqa # now remove that metadata file and then add it back await zhs.hamt.enable_write() - zhs = ZarrHAMTStore( - zhs.hamt, read_only=False - ) # make a writable version + zhs = ZarrHAMTStore(zhs.hamt, read_only=False) # make a writable version await zhs.delete("zarr.json") # doing a duplicate delete should not result in an error await zhs.delete("zarr.json") From 81aad06c27d8689f0ff7deb5353786bfd8294ce1 Mon Sep 17 00:00:00 2001 From: Abid Sikder <41392423+abidsikder@users.noreply.github.com> Date: Mon, 19 May 2025 18:33:36 -0400 Subject: [PATCH 050/118] restore 100% code coverage --- tests/test_hamt.py | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/tests/test_hamt.py b/tests/test_hamt.py index ebafd4c..82ccf6c 100644 --- a/tests/test_hamt.py +++ b/tests/test_hamt.py @@ -121,13 +121,13 @@ async def verify_kvs_and_len(h: HAMT): small_cache_size_bytes = 1000 # Read cache - read_hamt = await HAMT.build(cas=cas, root_node_id=hamt.root_node_id) + read_hamt = await HAMT.build(cas=cas, root_node_id=hamt.root_node_id, read_only=True) async def get_and_vacate(k, v): - assert (await hamt.get(k)) == v - if (await hamt.cache_size()) > small_cache_size_bytes: - await hamt.cache_vacate() - assert (await hamt.cache_size()) == 0 + assert (await read_hamt.get(k)) == v + if (await read_hamt.cache_size()) > small_cache_size_bytes: + await read_hamt.cache_vacate() + assert (await read_hamt.cache_size()) == 0 await asyncio.gather(*[get_and_vacate(k, v) for k, v in kvs]) From 9c95b62a68359bdbf0d4bfb3813ce85ea89400fe Mon Sep 17 00:00:00 2001 From: Abid Sikder <41392423+abidsikder@users.noreply.github.com> Date: Mon, 19 May 2025 18:34:30 -0400 Subject: [PATCH 051/118] ruff format --- tests/test_hamt.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/tests/test_hamt.py b/tests/test_hamt.py index 82ccf6c..5fc1338 100644 --- a/tests/test_hamt.py +++ b/tests/test_hamt.py @@ -121,7 +121,9 @@ async def verify_kvs_and_len(h: HAMT): small_cache_size_bytes = 1000 # Read cache - read_hamt = await HAMT.build(cas=cas, root_node_id=hamt.root_node_id, read_only=True) + read_hamt = await HAMT.build( + cas=cas, root_node_id=hamt.root_node_id, read_only=True + ) async def get_and_vacate(k, v): assert (await read_hamt.get(k)) == v From 1684803990f33ba0be32a156cd26ca6e2536dfc4 Mon Sep 17 00:00:00 2001 From: Abid Sikder <41392423+abidsikder@users.noreply.github.com> Date: Mon, 19 May 2025 18:35:22 -0400 Subject: [PATCH 052/118] add note about async/thread safety --- py_hamt/hamt.py | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/py_hamt/hamt.py b/py_hamt/hamt.py index 3f5ec6c..f1e9431 100644 --- a/py_hamt/hamt.py +++ b/py_hamt/hamt.py @@ -276,6 +276,10 @@ class HAMT: Use this to store arbitrarily large key-value mappings in your CAS of choice. + For writing, this HAMT is async safe but NOT thread safe. Only write in an async event loop within the same thread. + + When in read-only mode, the HAMT is both async and thread safe. + #### A note about memory management, read/write and read-only modes The HAMT can be in either read/write mode or read-only mode. For either of these modes, the HAMT has some internal performance optimizations. From b3fbbc535a72b3d3571fb6677089416e45a0a31b Mon Sep 17 00:00:00 2001 From: Abid Sikder <41392423+abidsikder@users.noreply.github.com> Date: Tue, 20 May 2025 10:45:07 -0400 Subject: [PATCH 053/118] remove old unnecessary commented out tests --- tests/test_hamt.py | 39 --------------------------------------- 1 file changed, 39 deletions(-) diff --git a/tests/test_hamt.py b/tests/test_hamt.py index 5fc1338..88f954b 100644 --- a/tests/test_hamt.py +++ b/tests/test_hamt.py @@ -210,42 +210,3 @@ async def test_link_following(): for k, _ in kvs: await hamt.delete(k) assert (await hamt.len()) == 0 - - -# The below 2 commented out tests are from HAMT version 2, if using keep in mind to update them with the new API (and adjust this comment accordingly) - -# Run this with varying cache sizes to see the impact on performance of the cache when using IPFSStore() -# Commented out since this increases test time a lot -# def test_and_print_perf(): -# import time -# num_ops = 50 -# # usual cache size -# hamt = HAMT(store=IPFSStore()) -# start_time = time.time() -# for key_int in range(num_ops): -# hamt[str(key_int)] = key_int -# end_time = time.time() -# op_avg_cache = (end_time - start_time) / 100 -# # no cache -# hamt = HAMT(store=IPFSStore(), max_cache_size_bytes=0) -# start_time = time.time() -# for key_int in range(num_ops): -# hamt[str(key_int)] = key_int -# end_time = time.time() -# op_avg_no_cache = (end_time - start_time) / 100 -# print(f"Improvement of {(1 - op_avg_cache / op_avg_no_cache) * 100:.2f}%") - - -# Sometimes useful to lace throughout the test lines when debugging cache problems -# def find_cache_incosistency(hamt: HAMT): -# for id in hamt.cache: -# cache_node = hamt.cache[id] -# store_node = Node.deserialize(hamt.store.load(id)) -# if cache_node.data != store_node.data: -# print("*** Inconsistency found") -# print(f"Cache Node: {cache_node.data}") -# print(f"Store Node: {store_node.data}") -# print(f"HAMT cache: {hamt.cache}") -# print(f"HAMT id_to_time: {hamt.id_to_time}") -# print(f"HAMT last accessed time: {hamt.last_accessed_times}") -# raise Exception("Cache inconsistency") From c428c530511c78808bc9fe4af7de10b71cea0aa0 Mon Sep 17 00:00:00 2001 From: Abid Sikder <41392423+abidsikder@users.noreply.github.com> Date: Tue, 20 May 2025 10:53:14 -0400 Subject: [PATCH 054/118] add large kv set performance test --- tests/performance_tests.py | 38 ++++++++++++++++++++++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 tests/performance_tests.py diff --git a/tests/performance_tests.py b/tests/performance_tests.py new file mode 100644 index 0000000..41bfc61 --- /dev/null +++ b/tests/performance_tests.py @@ -0,0 +1,38 @@ +""" +This file can be run by pytest, but is not automatically included since it includes some tests that may run for a long time, and are not useful for verifying the HAMT's correctness properties. + +This test suite contains various performance tests, which are meant to be run individually. +""" + +import pytest +import time +import asyncio + +from py_hamt import HAMT +from py_hamt.store import InMemoryCAS + + +@pytest.mark.asyncio +async def test_large_kv_set(): + """This test is meant for finding whether the HAMT performance scales linearly with increasing set size, an issue with HAMT v2. + Feel free to tune and run the LARGE_KV_SET_SIZE variable as needed for gathering the different timepoints. + """ + LARGE_KV_SET_SIZE = 1_000_000 + + cas = InMemoryCAS() + hamt = await HAMT.build(cas=cas) + start = time.perf_counter() + await asyncio.gather( + *[hamt.set(str(k_int), k_int) for k_int in range(LARGE_KV_SET_SIZE)] + ) + await hamt.make_read_only() + end = time.perf_counter() + elapsed = end - start + print(f"Took {elapsed:.2f} seconds") + assert ( + len([key async for key in hamt.keys()]) + == (await hamt.len()) + == LARGE_KV_SET_SIZE + ) + for k_int in range(LARGE_KV_SET_SIZE): + assert (await hamt.get(str(k_int))) == k_int From 26f9bfc4de0f9a2bddf96c48f21864fde9723b2f Mon Sep 17 00:00:00 2001 From: Abid Sikder <41392423+abidsikder@users.noreply.github.com> Date: Tue, 20 May 2025 13:43:56 -0400 Subject: [PATCH 055/118] github ci hypothesis test limit increase --- tests/test_hamt.py | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/tests/test_hamt.py b/tests/test_hamt.py index 88f954b..e4b9e7a 100644 --- a/tests/test_hamt.py +++ b/tests/test_hamt.py @@ -3,7 +3,7 @@ from dag_cbor import IPLDKind from multiformats import CID -from hypothesis import given +from hypothesis import given, settings from hypothesis import strategies as st import pytest @@ -15,6 +15,9 @@ @pytest.mark.asyncio @given(key_value_list) +@settings( + deadline=500 +) # increase for github CI which sometimes takees longer than the default 250 ms async def test_fuzz(kvs: list[tuple[str, IPLDKind]]): cas = InMemoryCAS() hamt = await HAMT.build(cas=cas) From c99a55c47b98d33b02f066e7477fbc38e1c52f9f Mon Sep 17 00:00:00 2001 From: Abid Sikder <41392423+abidsikder@users.noreply.github.com> Date: Wed, 21 May 2025 12:34:24 -0400 Subject: [PATCH 056/118] fix duplicate node store vacate if write-enabled --- py_hamt/hamt.py | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/py_hamt/hamt.py b/py_hamt/hamt.py index f1e9431..198028e 100644 --- a/py_hamt/hamt.py +++ b/py_hamt/hamt.py @@ -419,8 +419,9 @@ async def cache_vacate(self): """ if self.read_only: await self.node_store.vacate() - async with self.lock: - await self.node_store.vacate() + else: + async with self.lock: + await self.node_store.vacate() async def _reserialize_and_link(self, node_stack: list[tuple[IPLDKind, Node]]): """ From 9865565d2464c42cdede700a085b15cd18bec50e Mon Sep 17 00:00:00 2001 From: Abid Sikder <41392423+abidsikder@users.noreply.github.com> Date: Wed, 21 May 2025 12:35:01 -0400 Subject: [PATCH 057/118] allow None to specify the default as well for base urls --- py_hamt/store.py | 11 +++++++++-- tests/test_kubo_cas.py | 8 ++++++++ 2 files changed, 17 insertions(+), 2 deletions(-) diff --git a/py_hamt/store.py b/py_hamt/store.py index 59818b2..43b886a 100644 --- a/py_hamt/store.py +++ b/py_hamt/store.py @@ -73,10 +73,12 @@ def __init__( self, hasher: str = "blake3", requests_session: requests.Session | None = None, - rpc_base_url=KUBO_DEFAULT_LOCAL_RPC_BASE_URL, - gateway_base_url=KUBO_DEFAULT_LOCAL_GATEWAY_BASE_URL, + rpc_base_url: str | None = KUBO_DEFAULT_LOCAL_RPC_BASE_URL, + gateway_base_url: str | None = KUBO_DEFAULT_LOCAL_GATEWAY_BASE_URL, ): """ + If None is passed into the rpc or gateway base url, then the default for kubo local daemons will be used. The default local values will also be used if nothing is passed in at all. + ### `requests.Session` Management If `requests_session` is not provided, it will be automatically initialized. It is the responsibility of the user to close this at an appropriate time, as a class instance cannot know when it will no longer be in use. @@ -90,6 +92,11 @@ def __init__( self.hasher = hasher """The hash function to send to IPFS when storing bytes. Cannot be changed after initialization. The default blake3 follows the default hashing algorithm used by HAMT.""" + if rpc_base_url is None: + rpc_base_url = KuboCAS.KUBO_DEFAULT_LOCAL_RPC_BASE_URL + if gateway_base_url is None: + gateway_base_url = KuboCAS.KUBO_DEFAULT_LOCAL_GATEWAY_BASE_URL + self.rpc_url = f"{rpc_base_url}/api/v0/add?hash={self.hasher}&pin=false" """@private""" self.gateway_base_url = gateway_base_url + "/ipfs/" diff --git a/tests/test_kubo_cas.py b/tests/test_kubo_cas.py index 65da3a6..66ea177 100644 --- a/tests/test_kubo_cas.py +++ b/tests/test_kubo_cas.py @@ -29,6 +29,14 @@ async def test_kubo_default_urls(data: IPLDKind): result = dag_cbor.decode(await kubo_cas.load(cid)) assert data == result + kubo_cas = KuboCAS(gateway_base_url=None, rpc_base_url=None) + cids = [] + for codec in ["raw", "dag-cbor"]: + cid = await kubo_cas.save(dag_cbor.encode(data), codec=codec) # type: ignore + cids.append(cid) + result = dag_cbor.decode(await kubo_cas.load(cid)) + assert data == result + @pytest.mark.asyncio @given(data=ipld_strategy()) From 3a5c198a5e031fc7d69caa840ce54fe14d8edf88 Mon Sep 17 00:00:00 2001 From: Abid Sikder <41392423+abidsikder@users.noreply.github.com> Date: Wed, 21 May 2025 12:35:18 -0400 Subject: [PATCH 058/118] send blocking requests actions to separate thread --- py_hamt/store.py | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/py_hamt/store.py b/py_hamt/store.py index 43b886a..aeb8a9e 100644 --- a/py_hamt/store.py +++ b/py_hamt/store.py @@ -1,3 +1,4 @@ +import asyncio from typing import Literal from abc import ABC, abstractmethod from dag_cbor.ipld import IPLDKind @@ -111,7 +112,9 @@ def __init__( async def save(self, data: bytes, codec: ContentAddressedStore.CodecInput) -> CID: """@private""" - response = self.requests_session.post(self.rpc_url, files={"file": data}) + response = await asyncio.to_thread( + self.requests_session.post, self.rpc_url, files={"file": data} + ) response.raise_for_status() cid_str: str = json.decode(response.content)["Hash"] # type: ignore @@ -128,6 +131,6 @@ async def load( # type: ignore CID is definitely in the IPLDKind type ) -> bytes: """@private""" url = self.gateway_base_url + str(id) - response = self.requests_session.get(url) + response = await asyncio.to_thread(self.requests_session.get, url) response.raise_for_status() return response.content From 2552c00ceda84d4b883c334c43ffa6f23b251e16 Mon Sep 17 00:00:00 2001 From: Abid Sikder <41392423+abidsikder@users.noreply.github.com> Date: Wed, 21 May 2025 15:33:47 -0400 Subject: [PATCH 059/118] hypothesis test deadline increase --- tests/test_kubo_cas.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/tests/test_kubo_cas.py b/tests/test_kubo_cas.py index 66ea177..2d5b596 100644 --- a/tests/test_kubo_cas.py +++ b/tests/test_kubo_cas.py @@ -1,6 +1,6 @@ import dag_cbor from dag_cbor import IPLDKind -from hypothesis import given +from hypothesis import given, settings import pytest import requests @@ -20,6 +20,7 @@ async def test_memory_store_exception(): @pytest.mark.asyncio @given(data=ipld_strategy()) +@settings(deadline=500) # this sometimes takes longer than the default 250 ms async def test_kubo_default_urls(data: IPLDKind): kubo_cas = KuboCAS() cids = [] From ec7d71276c3f4d843cfd086d35ef9c2684ba47d9 Mon Sep 17 00:00:00 2001 From: Abid Sikder <41392423+abidsikder@users.noreply.github.com> Date: Wed, 21 May 2025 15:34:03 -0400 Subject: [PATCH 060/118] fix typo --- tests/test_hamt.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/test_hamt.py b/tests/test_hamt.py index e4b9e7a..2a654d2 100644 --- a/tests/test_hamt.py +++ b/tests/test_hamt.py @@ -17,7 +17,7 @@ @given(key_value_list) @settings( deadline=500 -) # increase for github CI which sometimes takees longer than the default 250 ms +) # increase for github CI which sometimes takes longer than the default 250 ms async def test_fuzz(kvs: list[tuple[str, IPLDKind]]): cas = InMemoryCAS() hamt = await HAMT.build(cas=cas) From 0c42c78105a2b39fe27aefa5d950a376b1edd65c Mon Sep 17 00:00:00 2001 From: Abid Sikder <41392423+abidsikder@users.noreply.github.com> Date: Wed, 21 May 2025 15:34:39 -0400 Subject: [PATCH 061/118] docs --- py_hamt/hamt.py | 16 ++++++++++++---- 1 file changed, 12 insertions(+), 4 deletions(-) diff --git a/py_hamt/hamt.py b/py_hamt/hamt.py index 198028e..978159c 100644 --- a/py_hamt/hamt.py +++ b/py_hamt/hamt.py @@ -280,12 +280,12 @@ class HAMT: When in read-only mode, the HAMT is both async and thread safe. - #### A note about memory management, read/write and read-only modes - The HAMT can be in either read/write mode or read-only mode. For either of these modes, the HAMT has some internal performance optimizations. + #### A note about memory management, read+write and read-only modes + The HAMT can be in either read+write mode or read-only mode. For either of these modes, the HAMT has some internal performance optimizations. - If in read/write, you should use `make_read_only()` to convert to read only mode to get a valid root node id. + Note that in read+write, the real root node id IS NOT VALID. You should call `make_read_only()` to convert to read only mode and then read `root_node_id`. - These optimizations also trade off performance for memory use. Use `cache_size` to monitor the approximate memory usage. Be warned that for large key-value mapping sets this may take a bit to run. Use `cache_vacate` if you are over your memory limits for the HAMT. + These optimizations also trade off performance for memory use. Use `cache_size` to monitor the approximate memory usage. Be warned that for large key-value mapping sets this may take a bit to run. Use `cache_vacate` if you are over your memory limits. #### IPFS HAMT Sample Code ```python @@ -381,6 +381,11 @@ async def build(cls, *args, **kwargs) -> "HAMT": # This is typically a massive blocking operation, you dont want to be running this concurrently with a bunch of other operations, so it's ok to have it not be async async def make_read_only(self): + """ + Makes the HAMT read only, which allows for more parallel read operations. The HAMT also needs to be in read only mode to get the real root node ID. + + In read+write mode, the HAMT normally has to block separate get calls to enable strong consistency in case a set/delete operation falls in between. + """ async with self.lock: inmemory_tree: InMemoryTreeStore = self.node_store # type: ignore await inmemory_tree.vacate() @@ -389,6 +394,9 @@ async def make_read_only(self): self.node_store = ReadCacheStore(self) async def enable_write(self): + """ + Enable both reads and writes. This creates an internal structure for performance optimizations which will result in the root node ID no longer being valid, in order to read that at the end of your operations you must first use `make_read_only`. + """ async with self.lock: # The read cache has no writes that need to be sent upstream so we can remove it without vacating self.read_only = False From 2905bed4cac66c487465cb757f9e3fb34db98c31 Mon Sep 17 00:00:00 2001 From: Abid Sikder <41392423+abidsikder@users.noreply.github.com> Date: Wed, 21 May 2025 15:34:59 -0400 Subject: [PATCH 062/118] add get_pointer and implement metadata read cache for ZHS --- py_hamt/hamt.py | 20 +++++++++++++++----- py_hamt/zarr_hamt_store.py | 23 ++++++++++++++++++++++- tests/test_hamt.py | 2 +- 3 files changed, 38 insertions(+), 7 deletions(-) diff --git a/py_hamt/hamt.py b/py_hamt/hamt.py index 978159c..ad867c2 100644 --- a/py_hamt/hamt.py +++ b/py_hamt/hamt.py @@ -572,6 +572,20 @@ async def delete(self, key: str): raise KeyError async def get(self, key: str) -> IPLDKind: + """Get a value.""" + pointer = await self.get_pointer(key) + data = await self.cas.load(pointer) + if self.values_are_bytes: + return data + else: + return dag_cbor.decode(data) + + async def get_pointer(self, key: str) -> IPLDKind: + """ + Get a store ID that points to the value for this key. + + This is useful for some applications that want to implement a read cache. Due to the restrictions of `ContentAddressedStore` on IDs, pointers are regarded as immutable by python so they can be easily used as IDs for read caches. This is utilized in `ZarrHAMTStore` for example. + """ # If read only, no need to acquire a lock pointer: IPLDKind if self.read_only: @@ -580,11 +594,7 @@ async def get(self, key: str) -> IPLDKind: async with self.lock: pointer = await self._get_pointer(key) - data = await self.cas.load(pointer) - if self.values_are_bytes: - return data - else: - return dag_cbor.decode(data) + return pointer # Callers MUST handle acquiring a lock async def _get_pointer(self, key: str) -> IPLDKind: diff --git a/py_hamt/zarr_hamt_store.py b/py_hamt/zarr_hamt_store.py index a86d34e..cab9cbb 100644 --- a/py_hamt/zarr_hamt_store.py +++ b/py_hamt/zarr_hamt_store.py @@ -1,4 +1,5 @@ from collections.abc import AsyncIterator, Iterable +from dag_cbor import IPLDKind import zarr.abc.store import zarr.core.buffer from zarr.core.common import BytesLike @@ -44,6 +45,9 @@ def __init__(self, hamt: HAMT, read_only: bool = False) -> None: ##### A note about the zarr chunk separator, "/" vs "." While Zarr v2 used periods by default, Zarr v3 uses forward slashes, and that is assumed here as well. + + #### Metadata Read Cache + `ZarrHAMTStore` has an internal read cache for metadata. In practice metadata "zarr.json" files are very very frequently and duplicately requested compared to all other keys, and there are significant speed improvements gotten by implementing this cache. In terms of memory management, in practice this cache does not need an eviction step since "zarr.json" files are much smaller than the memory requirement of the zarr data. """ super().__init__(read_only=read_only) @@ -55,6 +59,9 @@ def __init__(self, hamt: HAMT, read_only: bool = False) -> None: Once done with write operations, the hamt can be set to read only mode as usual to get your root node ID. """ + self.metadata_read_cache: dict[IPLDKind, bytes] = dict() + """@private""" + @property def read_only(self) -> bool: """@private""" @@ -74,7 +81,21 @@ async def get( ) -> zarr.core.buffer.Buffer | None: """@private""" try: - val: bytes = await self.hamt.get(key) # type: ignore We know values received will always be bytes since we only store bytes in the HAMT + val: bytes + val_ptr: IPLDKind = await self.hamt.get_pointer(key) + if val_ptr in self.metadata_read_cache: + val = self.metadata_read_cache[val_ptr] + else: + val = await self.hamt.get(key) # type: ignore We know values received will always be bytes since we only store bytes in the HAMT + + # do len check to avoid indexing into overly short strings, 3.12 does not throw errors but we dont know if others will + is_metadata = ( + len(key) >= 9 and key[-9:] == "zarr.json" + ) # if path ends with zarr.json + + if is_metadata and val_ptr not in self.metadata_read_cache: + self.metadata_read_cache[val_ptr] = val + return prototype.buffer.from_bytes(val) except KeyError: # Sometimes zarr queries keys that don't exist anymore, just return nothing on those cases diff --git a/tests/test_hamt.py b/tests/test_hamt.py index 2a654d2..cb4846d 100644 --- a/tests/test_hamt.py +++ b/tests/test_hamt.py @@ -77,7 +77,7 @@ async def verify(k, v): # Make sure all pointers actually exist in the store, this should not raise any exceptions for k, _ in kvs: # Callers must handle acquiring a lock themselves, so do these entirely sequentially - pointer: bytes = await hamt._get_pointer(k) # type: ignore we know that DictStore only returns bytes for its Link type + pointer: bytes = await hamt.get_pointer(k) # type: ignore we know that DictStore only returns bytes for its Link type await cas.load(pointer) await hamt.make_read_only() From 3cf5c151deb6cede7bec30eeb9c8a45e24f20839 Mon Sep 17 00:00:00 2001 From: Abid Sikder <41392423+abidsikder@users.noreply.github.com> Date: Wed, 21 May 2025 15:36:33 -0400 Subject: [PATCH 063/118] increase test deadline --- tests/test_kubo_cas.py | 3 +++ 1 file changed, 3 insertions(+) diff --git a/tests/test_kubo_cas.py b/tests/test_kubo_cas.py index 2d5b596..f1177e5 100644 --- a/tests/test_kubo_cas.py +++ b/tests/test_kubo_cas.py @@ -41,6 +41,9 @@ async def test_kubo_default_urls(data: IPLDKind): @pytest.mark.asyncio @given(data=ipld_strategy()) +@settings( + deadline=500 +) # this sometimes takes longer than the default 250 ms in GitHub CI async def test_kubo_cas(create_ipfs, data: IPLDKind): # noqa rpc_base_url, gateway_base_url = create_ipfs From a550d39c2306fb86430bc264a0a6fbd35de429db Mon Sep 17 00:00:00 2001 From: Abid Sikder <41392423+abidsikder@users.noreply.github.com> Date: Wed, 21 May 2025 16:13:26 -0400 Subject: [PATCH 064/118] add even faster zhs metadata cache --- py_hamt/zarr_hamt_store.py | 24 +++++++++++++----------- tests/test_zarr_ipfs.py | 2 +- 2 files changed, 14 insertions(+), 12 deletions(-) diff --git a/py_hamt/zarr_hamt_store.py b/py_hamt/zarr_hamt_store.py index cab9cbb..f5c5dbb 100644 --- a/py_hamt/zarr_hamt_store.py +++ b/py_hamt/zarr_hamt_store.py @@ -1,5 +1,4 @@ from collections.abc import AsyncIterator, Iterable -from dag_cbor import IPLDKind import zarr.abc.store import zarr.core.buffer from zarr.core.common import BytesLike @@ -59,7 +58,7 @@ def __init__(self, hamt: HAMT, read_only: bool = False) -> None: Once done with write operations, the hamt can be set to read only mode as usual to get your root node ID. """ - self.metadata_read_cache: dict[IPLDKind, bytes] = dict() + self.metadata_read_cache: dict[str, bytes] = dict() """@private""" @property @@ -82,19 +81,17 @@ async def get( """@private""" try: val: bytes - val_ptr: IPLDKind = await self.hamt.get_pointer(key) - if val_ptr in self.metadata_read_cache: - val = self.metadata_read_cache[val_ptr] - else: - val = await self.hamt.get(key) # type: ignore We know values received will always be bytes since we only store bytes in the HAMT - - # do len check to avoid indexing into overly short strings, 3.12 does not throw errors but we dont know if others will + # do len check to avoid indexing into overly short strings, 3.12 does not throw errors but we dont know if other versions will is_metadata = ( len(key) >= 9 and key[-9:] == "zarr.json" ) # if path ends with zarr.json - if is_metadata and val_ptr not in self.metadata_read_cache: - self.metadata_read_cache[val_ptr] = val + if is_metadata and key in self.metadata_read_cache: + val = self.metadata_read_cache[key] + else: + val = await self.hamt.get(key) # type: ignore We know values received will always be bytes since we only store bytes in the HAMT + if is_metadata: + self.metadata_read_cache[key] = val return prototype.buffer.from_bytes(val) except KeyError: @@ -129,6 +126,8 @@ def supports_partial_writes(self) -> bool: async def set(self, key: str, value: zarr.core.buffer.Buffer) -> None: """@private""" + if key in self.metadata_read_cache: + self.metadata_read_cache[key] = value.to_bytes() await self.hamt.set(key, value.to_bytes()) async def set_if_not_exists(self, key: str, value: zarr.core.buffer.Buffer) -> None: @@ -151,6 +150,9 @@ async def delete(self, key: str) -> None: """@private""" try: await self.hamt.delete(key) + # In practice these lines never seem to be needed, creating and appending data are the only operations most zarrs actually undergo + # if key in self.metadata_read_cache: + # del self.metadata_read_cache[key] # It's fine if the key was not in the HAMT # Sometimes zarr v3 calls deletes on keys that don't exist (or have already been deleted) for some reason, probably concurrency issues except KeyError: diff --git a/tests/test_zarr_ipfs.py b/tests/test_zarr_ipfs.py index 75ba40f..f03981f 100644 --- a/tests/test_zarr_ipfs.py +++ b/tests/test_zarr_ipfs.py @@ -71,7 +71,7 @@ async def test_write_read(create_ipfs, random_zarr_dataset: xr.Dataset): # noqa start = time.perf_counter() # Do an initial write along with an append which is a common xarray/zarr operation test_ds.to_zarr(store=zhs) # type: ignore - test_ds.to_zarr(store=zhs, mode="a", append_dim="time") # type: ignore + test_ds.to_zarr(store=zhs, mode="a", append_dim="time", zarr_format=3) # type: ignore end = time.perf_counter() elapsed = end - start print("=== Write Stats") From f2cbe62d478e87906276422aea53127c91057a57 Mon Sep 17 00:00:00 2001 From: Abid Sikder <41392423+abidsikder@users.noreply.github.com> Date: Wed, 21 May 2025 16:15:11 -0400 Subject: [PATCH 065/118] remove extraneous comment --- tests/test_hamt.py | 1 - 1 file changed, 1 deletion(-) diff --git a/tests/test_hamt.py b/tests/test_hamt.py index cb4846d..1be57d8 100644 --- a/tests/test_hamt.py +++ b/tests/test_hamt.py @@ -76,7 +76,6 @@ async def verify(k, v): # Make sure all pointers actually exist in the store, this should not raise any exceptions for k, _ in kvs: - # Callers must handle acquiring a lock themselves, so do these entirely sequentially pointer: bytes = await hamt.get_pointer(k) # type: ignore we know that DictStore only returns bytes for its Link type await cas.load(pointer) From ef180270a6b4bd3002e6483886d09e01f27d37c8 Mon Sep 17 00:00:00 2001 From: Abid Sikder <41392423+abidsikder@users.noreply.github.com> Date: Wed, 21 May 2025 16:50:15 -0400 Subject: [PATCH 066/118] docs note about exceeded test deadlines --- README.md | 3 +++ 1 file changed, 3 insertions(+) diff --git a/README.md b/README.md index 2750cf9..e443d7a 100644 --- a/README.md +++ b/README.md @@ -45,6 +45,9 @@ We use `pytest` with 100% code coverage, and with test inputs that are both hand > [!NOTE] > Due to the randomized test inputs, it is possible sometimes to get 99% or lower test coverage by pure chance. Rerun the tests to get back complete code coverage. If this happens on a GitHub action, try rerunning the action. +> [!NOTE] +> Due to the restricted performance on GitHub actions runners, you may also sometimes see hypothesis tests running with errors because they exceeded test deadlines. Rerun the action if this happens. + ## CPU and Memory Profiling We use python's native `cProfile` for running CPU profiles and snakeviz for visualizing the profile. We use `memray` for the memory profiling. We will walk through using the profiling tools on the test suite. From e2cf99cde8a599e224b7be3aa70401dc5b215598 Mon Sep 17 00:00:00 2001 From: Abid Sikder <41392423+abidsikder@users.noreply.github.com> Date: Wed, 21 May 2025 16:50:46 -0400 Subject: [PATCH 067/118] fix reference to old class in comment --- tests/test_hamt.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/test_hamt.py b/tests/test_hamt.py index 1be57d8..17de49e 100644 --- a/tests/test_hamt.py +++ b/tests/test_hamt.py @@ -76,7 +76,7 @@ async def verify(k, v): # Make sure all pointers actually exist in the store, this should not raise any exceptions for k, _ in kvs: - pointer: bytes = await hamt.get_pointer(k) # type: ignore we know that DictStore only returns bytes for its Link type + pointer: bytes = await hamt.get_pointer(k) # type: ignore we know that InMemoryCAS only returns bytes for its IDs await cas.load(pointer) await hamt.make_read_only() From a958246dc7060f6e07cf247e86810795baab1ba0 Mon Sep 17 00:00:00 2001 From: Faolain Date: Thu, 22 May 2025 12:37:05 -0400 Subject: [PATCH 068/118] refactor: replace requests with aiohttp --- py_hamt/store.py | 81 +- pyproject.toml | 1 + tests/test_kubo_cas.py | 24 +- uv.lock | 2056 +++++++++++++++++++++++----------------- 4 files changed, 1259 insertions(+), 903 deletions(-) diff --git a/py_hamt/store.py b/py_hamt/store.py index aeb8a9e..074349c 100644 --- a/py_hamt/store.py +++ b/py_hamt/store.py @@ -1,4 +1,6 @@ import asyncio +import aiohttp +import weakref from typing import Literal from abc import ABC, abstractmethod from dag_cbor.ipld import IPLDKind @@ -27,7 +29,8 @@ class ContentAddressedStore(ABC): async def save(self, data: bytes, codec: CodecInput) -> IPLDKind: """Save data to a storage mechanism, and return an ID for the data in the IPLDKind type. - `codec` will be set to "dag-cbor" if this data should be marked as special linked data a la IPLD data model.""" + `codec` will be set to "dag-cbor" if this data should be marked as special linked data a la IPLD data model. + """ @abstractmethod async def load(self, id: IPLDKind) -> bytes: @@ -73,7 +76,7 @@ class KuboCAS(ContentAddressedStore): def __init__( self, hasher: str = "blake3", - requests_session: requests.Session | None = None, + session: aiohttp.ClientSession | None = None, rpc_base_url: str | None = KUBO_DEFAULT_LOCAL_RPC_BASE_URL, gateway_base_url: str | None = KUBO_DEFAULT_LOCAL_GATEWAY_BASE_URL, ): @@ -103,34 +106,70 @@ def __init__( self.gateway_base_url = gateway_base_url + "/ipfs/" """@private""" - self.requests_session: requests.Session - """@private""" - if requests_session is None: - self.requests_session = requests.Session() - else: - self.requests_session = requests_session + concurrency = 32 + self._session = session or aiohttp.ClientSession() + self._sem = asyncio.Semaphore(concurrency) + self._external_session = session + self._sessions: "weakref.WeakKeyDictionary[asyncio.AbstractEventLoop, aiohttp.ClientSession]" = (weakref.WeakKeyDictionary()) + # """@private""" + # if requests_session is None: + # self.requests_session = requests.Session() + # else: + # self.requests_session = requests_session + + async def _loop_session(self) -> aiohttp.ClientSession: + """Return a ClientSession bound to *this* loop, lazily creating one.""" + loop = asyncio.get_running_loop() + if self._external_session is not None: + # caller manages lifetime; just return it + return self._external_session # caller manages it + try: + return self._sessions[loop] # reuse if we made one + except KeyError: + sess = aiohttp.ClientSession() + self._sessions[loop] = sess + return sess + + async def aclose(self): + if self._external_session is None: + await asyncio.gather(*[s.close() for s in self._sessions.values()]) + + async def __aenter__(self): + return self + + async def __aexit__(self, *exc): + await self.aclose() async def save(self, data: bytes, codec: ContentAddressedStore.CodecInput) -> CID: """@private""" - response = await asyncio.to_thread( - self.requests_session.post, self.rpc_url, files={"file": data} - ) - response.raise_for_status() + async with self._sem: # throttle RPC calls if needed + session = await self._loop_session() # your loop-local helper + form = aiohttp.FormData() + # field-name MUST be "file", filename can be anything + form.add_field( + "file", data, filename="blob", content_type="application/octet-stream" + ) - cid_str: str = json.decode(response.content)["Hash"] # type: ignore - cid = CID.decode(cid_str) + async with session.post(self.rpc_url, data=form) as resp: + resp.raise_for_status() # no more 400s + cid_str = (await resp.json())["Hash"] - # If it's dag-pb it means we should not reset the cid codec, kubo shards large data into a UnixFS structure - if cid.codec.code != KuboCAS.DAG_PB_MARKER: - cid = cid.set(codec=codec) + cid = CID.decode(cid_str) + if cid.codec.code != self.DAG_PB_MARKER: + cid = cid.set(codec=codec) - return cid + return cid async def load( # type: ignore CID is definitely in the IPLDKind type self, id: CID ) -> bytes: """@private""" url = self.gateway_base_url + str(id) - response = await asyncio.to_thread(self.requests_session.get, url) - response.raise_for_status() - return response.content + # If this coroutine is running inside an event loop, # + # off-load the *blocking* requests call to a worker thread. # + async with self._sem: # throttle gateway + async with (await self._loop_session()).get( + self.gateway_base_url + str(id) + ) as r: + r.raise_for_status() + return await r.read() diff --git a/pyproject.toml b/pyproject.toml index c8abae9..2ccd16a 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -5,6 +5,7 @@ description = "HAMT implementation for a content-addressed storage system." readme = "README.md" requires-python = ">=3.12" dependencies = [ + "aiohttp>=3.11.18", "dag-cbor>=0.3.3", "msgspec>=0.18.6", "multiformats[full]>=0.3.1.post4", diff --git a/tests/test_kubo_cas.py b/tests/test_kubo_cas.py index f1177e5..278b8ff 100644 --- a/tests/test_kubo_cas.py +++ b/tests/test_kubo_cas.py @@ -1,3 +1,4 @@ +import aiohttp import dag_cbor from dag_cbor import IPLDKind from hypothesis import given, settings @@ -47,14 +48,15 @@ async def test_kubo_default_urls(data: IPLDKind): async def test_kubo_cas(create_ipfs, data: IPLDKind): # noqa rpc_base_url, gateway_base_url = create_ipfs - # Provide our own requests Session, for complete code coverage - kubo_cas = KuboCAS( - rpc_base_url=rpc_base_url, - gateway_base_url=gateway_base_url, - requests_session=requests.Session(), - ) - - for codec in ["raw", "dag-cbor"]: - cid = await kubo_cas.save(dag_cbor.encode(data), codec=codec) # type: ignore - result = dag_cbor.decode(await kubo_cas.load(cid)) - assert data == result + # Provide our own async Session, for complete code coverage + async with aiohttp.ClientSession() as session: + kubo_cas = KuboCAS( + rpc_base_url=rpc_base_url, + gateway_base_url=gateway_base_url, + session=session, + ) + + for codec in ["raw", "dag-cbor"]: + cid = await 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++--- pyproject.toml | 4 + pytest.ini | 4 + tests/test_hamt.py | 2 +- tests/test_kubo_cas.py | 45 +++-- tests/test_zarr_ipfs.py | 353 ++++++++++++++++++++-------------------- 6 files changed, 224 insertions(+), 226 deletions(-) create mode 100644 pytest.ini diff --git a/py_hamt/store.py b/py_hamt/store.py index 074349c..797eb8a 100644 --- a/py_hamt/store.py +++ b/py_hamt/store.py @@ -106,33 +106,18 @@ def __init__( self.gateway_base_url = gateway_base_url + "/ipfs/" """@private""" - concurrency = 32 - self._session = session or aiohttp.ClientSession() - self._sem = asyncio.Semaphore(concurrency) - self._external_session = session - self._sessions: "weakref.WeakKeyDictionary[asyncio.AbstractEventLoop, aiohttp.ClientSession]" = (weakref.WeakKeyDictionary()) - # """@private""" - # if requests_session is None: - # self.requests_session = requests.Session() - # else: - # self.requests_session = requests_session - - async def _loop_session(self) -> aiohttp.ClientSession: - """Return a ClientSession bound to *this* loop, lazily creating one.""" - loop = asyncio.get_running_loop() - if self._external_session is not None: - # caller manages lifetime; just return it - return self._external_session # caller manages it - try: - return self._sessions[loop] # reuse if we made one - except KeyError: - sess = aiohttp.ClientSession() - self._sessions[loop] = sess - return sess + # One shared session per KuboCAS instance. + self._session = session or aiohttp.ClientSession( + timeout=aiohttp.ClientTimeout(total=60), + connector=aiohttp.TCPConnector(limit=64, limit_per_host=32), + ) + self._owns_session = session is None + self._sem = asyncio.Semaphore(64) async def aclose(self): - if self._external_session is None: - await asyncio.gather(*[s.close() for s in self._sessions.values()]) + """Close our connector if we created it.""" + if self._owns_session and not self._session.closed: + await self._session.close() async def __aenter__(self): return self @@ -143,14 +128,13 @@ async def __aexit__(self, *exc): async def save(self, data: bytes, codec: ContentAddressedStore.CodecInput) -> CID: """@private""" async with self._sem: # throttle RPC calls if needed - session = await self._loop_session() # your loop-local helper form = aiohttp.FormData() # field-name MUST be "file", filename can be anything form.add_field( "file", data, filename="blob", content_type="application/octet-stream" ) - async with session.post(self.rpc_url, data=form) as resp: + async with self._session.post(self.rpc_url, data=form) as resp: resp.raise_for_status() # no more 400s cid_str = (await resp.json())["Hash"] @@ -168,8 +152,6 @@ async def load( # type: ignore CID is definitely in the IPLDKind type # If this coroutine is running inside an event loop, # # off-load the *blocking* requests call to a worker thread. # async with self._sem: # throttle gateway - async with (await self._loop_session()).get( - self.gateway_base_url + str(id) - ) as r: + async with self._session.get(url) as r: r.raise_for_status() return await r.read() diff --git a/pyproject.toml b/pyproject.toml index 2ccd16a..25f2822 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -31,3 +31,7 @@ dev = [ "pytest-asyncio>=0.25.3", "xarray[complete]>=2025.3.0", ] + +[pytest] +asyncio_mode = "auto" +asyncio_default_fixture_loop_scope = "function" diff --git a/pytest.ini b/pytest.ini new file mode 100644 index 0000000..4f243a2 --- /dev/null +++ b/pytest.ini @@ -0,0 +1,4 @@ +# pytest.ini +[pytest] +asyncio_mode = auto +asyncio_default_fixture_loop_scope = function \ No newline at end of file diff --git a/tests/test_hamt.py b/tests/test_hamt.py index 17de49e..5ccd752 100644 --- a/tests/test_hamt.py +++ b/tests/test_hamt.py @@ -16,7 +16,7 @@ @pytest.mark.asyncio @given(key_value_list) @settings( - deadline=500 + deadline=1000 ) # increase for github CI which sometimes takes longer than the default 250 ms async def test_fuzz(kvs: list[tuple[str, IPLDKind]]): cas = InMemoryCAS() diff --git a/tests/test_kubo_cas.py b/tests/test_kubo_cas.py index 278b8ff..c8dc204 100644 --- a/tests/test_kubo_cas.py +++ b/tests/test_kubo_cas.py @@ -21,23 +21,23 @@ async def test_memory_store_exception(): @pytest.mark.asyncio @given(data=ipld_strategy()) -@settings(deadline=500) # this sometimes takes longer than the default 250 ms +@settings(deadline=1000) # this sometimes takes longer than the default 250 ms async def test_kubo_default_urls(data: IPLDKind): - kubo_cas = KuboCAS() - cids = [] - for codec in ["raw", "dag-cbor"]: - cid = await kubo_cas.save(dag_cbor.encode(data), codec=codec) # type: ignore - cids.append(cid) - result = dag_cbor.decode(await kubo_cas.load(cid)) - assert data == result - - kubo_cas = KuboCAS(gateway_base_url=None, rpc_base_url=None) - cids = [] - for codec in ["raw", "dag-cbor"]: - cid = await kubo_cas.save(dag_cbor.encode(data), codec=codec) # type: ignore - cids.append(cid) - result = dag_cbor.decode(await kubo_cas.load(cid)) - assert data == result + async with KuboCAS() as kubo_cas: + cids = [] + for codec in ["raw", "dag-cbor"]: + cid = await kubo_cas.save(dag_cbor.encode(data), codec=codec) # type: ignore + cids.append(cid) + result = dag_cbor.decode(await kubo_cas.load(cid)) + assert data == result + + async with KuboCAS(gateway_base_url=None, rpc_base_url=None) as kubo_cas: + cids = [] + for codec in ["raw", "dag-cbor"]: + cid = await kubo_cas.save(dag_cbor.encode(data), codec=codec) # type: ignore + cids.append(cid) + result = dag_cbor.decode(await kubo_cas.load(cid)) + assert data == result @pytest.mark.asyncio @@ -50,13 +50,12 @@ async def test_kubo_cas(create_ipfs, data: IPLDKind): # noqa # Provide our own async Session, for complete code coverage async with aiohttp.ClientSession() as session: - kubo_cas = KuboCAS( + async with KuboCAS( rpc_base_url=rpc_base_url, gateway_base_url=gateway_base_url, session=session, - ) - - for codec in ["raw", "dag-cbor"]: - cid = await kubo_cas.save(dag_cbor.encode(data), codec=codec) - result = dag_cbor.decode(await kubo_cas.load(cid)) - assert data == result + ) as kubo_cas: + for codec in ["raw", "dag-cbor"]: + cid = await kubo_cas.save(dag_cbor.encode(data), codec=codec) + result = dag_cbor.decode(await kubo_cas.load(cid)) + assert data == result diff --git a/tests/test_zarr_ipfs.py b/tests/test_zarr_ipfs.py index f03981f..41be546 100644 --- a/tests/test_zarr_ipfs.py +++ b/tests/test_zarr_ipfs.py @@ -1,172 +1,181 @@ -import time - -import numpy as np -import pandas as pd -import xarray as xr -import pytest -import zarr -import zarr.core.buffer - -from py_hamt import HAMT, KuboCAS - -from py_hamt.zarr_hamt_store import ZarrHAMTStore -from testing_utils import create_ipfs # noqa pytest detects by name but this shows up as unused import error - - -@pytest.fixture(scope="module") -def random_zarr_dataset(): - """Creates a random xarray Dataset. - - Returns: - tuple: (dataset_path, expected_data) - - dataset_path: Path to the zarr store - - expected_data: The original xarray Dataset for comparison - """ - # Coordinates of the random data - times = pd.date_range("2024-01-01", periods=100) - lats = np.linspace(-90, 90, 18) - lons = np.linspace(-180, 180, 36) - - # Create random variables with different shapes - temp = np.random.randn(len(times), len(lats), len(lons)) - precip = np.random.gamma(2, 0.5, size=(len(times), len(lats), len(lons))) - - # Create the dataset - ds = xr.Dataset( - { - "temp": ( - ["time", "lat", "lon"], - temp, - {"units": "celsius", "long_name": "Surface Temperature"}, - ), - "precip": ( - ["time", "lat", "lon"], - precip, - {"units": "mm/day", "long_name": "Daily Precipitation"}, - ), - }, - coords={ - "time": times, - "lat": ("lat", lats, {"units": "degrees_north"}), - "lon": ("lon", lons, {"units": "degrees_east"}), - }, - attrs={"description": "Test dataset with random weather data"}, - ) - - yield ds - - -# This test also collects miscellaneous statistics about performance, run with pytest -s to see these statistics being printed out -@pytest.mark.asyncio -async def test_write_read(create_ipfs, random_zarr_dataset: xr.Dataset): # noqa for fixture which is imported above but then "redefined" - rpc_base_url, gateway_base_url = create_ipfs - test_ds = random_zarr_dataset - print("=== Writing this xarray Dataset to a Zarr v3 on IPFS ===") - print(test_ds) - - kubo_cas = KuboCAS(rpc_base_url=rpc_base_url, gateway_base_url=gateway_base_url) - hamt = await HAMT.build(cas=kubo_cas, values_are_bytes=True) - zhs = ZarrHAMTStore(hamt) - assert zhs.supports_writes - start = time.perf_counter() - # Do an initial write along with an append which is a common xarray/zarr operation - test_ds.to_zarr(store=zhs) # type: ignore - test_ds.to_zarr(store=zhs, mode="a", append_dim="time", zarr_format=3) # type: ignore - end = time.perf_counter() - elapsed = end - start - print("=== Write Stats") - print(f"Total time in seconds: {elapsed:.2f}") - print("=== Root CID") - await hamt.make_read_only() - cid = hamt.root_node_id - print(cid) - - print("=== Reading data back in and checking if identical") - hamt = await HAMT.build( - cas=kubo_cas, root_node_id=cid, values_are_bytes=True, read_only=True - ) - start = time.perf_counter() - ipfs_ds: xr.Dataset - zhs = ZarrHAMTStore(hamt, read_only=True) - ipfs_ds = xr.open_zarr(store=zhs) - print(ipfs_ds) - - # Check both halves, since each are an identical copy - ds1 = ipfs_ds.isel(time=slice(0, len(ipfs_ds.time) // 2)) - ds2 = ipfs_ds.isel(time=slice(len(ipfs_ds.time) // 2, len(ipfs_ds.time))) - xr.testing.assert_identical(ds1, ds2) - xr.testing.assert_identical(test_ds, ds1) - xr.testing.assert_identical(test_ds, ds2) - - end = time.perf_counter() - elapsed = end - start - print("=== Read Stats") - print(f"Total time in seconds: {elapsed:.2f}") - - # Tests for code coverage's sake - assert await zhs.exists("zarr.json") - # __eq__ - assert zhs == zhs - assert zhs != hamt - assert not zhs.supports_writes - assert not zhs.supports_partial_writes - assert not zhs.supports_deletes - - hamt_keys = set() - async for k in zhs.hamt.keys(): - hamt_keys.add(k) - - zhs_keys: set[str] = set() - async for k in zhs.list(): - zhs_keys.add(k) - assert hamt_keys == zhs_keys - - zhs_keys: set[str] = set() - async for k in zhs.list(): - zhs_keys.add(k) - assert hamt_keys == zhs_keys - - zhs_keys: set[str] = set() - async for k in zhs.list_prefix(""): - zhs_keys.add(k) - assert hamt_keys == zhs_keys - - with pytest.raises(NotImplementedError): - await zhs.set_partial_values([]) - - with pytest.raises(NotImplementedError): - await zhs.get_partial_values(zarr.core.buffer.default_buffer_prototype(), []) - - previous_zarr_json = await zhs.get( - "zarr.json", zarr.core.buffer.default_buffer_prototype() - ) - assert previous_zarr_json is not None - # Setting a metadata file that should always exist should not change anything - await zhs.set_if_not_exists( - "zarr.json", - np.array([b"a"], dtype=np.bytes_), # type: ignore - ) # type: ignore np.arrays, if dtype is bytes, is usable as a zarr buffer - zarr_json_now = await zhs.get( - "zarr.json", zarr.core.buffer.default_buffer_prototype() - ) - assert zarr_json_now is not None - assert previous_zarr_json.to_bytes() == zarr_json_now.to_bytes() - - # now remove that metadata file and then add it back - await zhs.hamt.enable_write() - zhs = ZarrHAMTStore(zhs.hamt, read_only=False) # make a writable version - await zhs.delete("zarr.json") - # doing a duplicate delete should not result in an error - await zhs.delete("zarr.json") - zhs_keys: set[str] = set() - async for k in zhs.list(): - zhs_keys.add(k) - assert hamt_keys != zhs_keys - assert "zarr.json" not in zhs_keys - - await zhs.set_if_not_exists("zarr.json", previous_zarr_json) - zarr_json_now = await zhs.get( - "zarr.json", zarr.core.buffer.default_buffer_prototype() - ) - assert zarr_json_now is not None - assert previous_zarr_json.to_bytes() == zarr_json_now.to_bytes() +# import time + +# import numpy as np +# import pandas as pd +# import xarray as xr +# import pytest +# import zarr +# import zarr.core.buffer + +# from py_hamt import HAMT, KuboCAS + +# from py_hamt.zarr_hamt_store import ZarrHAMTStore +# from testing_utils import ( +# create_ipfs, +# ) # noqa pytest detects by name but this shows up as unused import error + + +# @pytest.fixture(scope="module") +# def random_zarr_dataset(): +# """Creates a random xarray Dataset. + +# Returns: +# tuple: (dataset_path, expected_data) +# - dataset_path: Path to the zarr store +# - expected_data: The original xarray Dataset for comparison +# """ +# # Coordinates of the random data +# times = pd.date_range("2024-01-01", periods=100) +# lats = np.linspace(-90, 90, 18) +# lons = np.linspace(-180, 180, 36) + +# # Create random variables with different shapes +# temp = np.random.randn(len(times), len(lats), len(lons)) +# precip = np.random.gamma(2, 0.5, size=(len(times), len(lats), len(lons))) + +# # Create the dataset +# ds = xr.Dataset( +# { +# "temp": ( +# ["time", "lat", "lon"], +# temp, +# {"units": "celsius", "long_name": "Surface Temperature"}, +# ), +# "precip": ( +# ["time", "lat", "lon"], +# precip, +# {"units": "mm/day", "long_name": "Daily Precipitation"}, +# ), +# }, +# coords={ +# "time": times, +# "lat": ("lat", lats, {"units": "degrees_north"}), +# "lon": ("lon", lons, {"units": "degrees_east"}), +# }, +# attrs={"description": "Test dataset with random weather data"}, +# ) + +# yield ds + + +# # This test also collects miscellaneous statistics about performance, run with pytest -s to see these statistics being printed out +# @pytest.mark.asyncio +# async def test_write_read( +# create_ipfs, random_zarr_dataset: xr.Dataset +# ): # noqa for fixture which is imported above but then "redefined" +# rpc_base_url, gateway_base_url = create_ipfs +# test_ds = random_zarr_dataset +# print("=== Writing this xarray Dataset to a Zarr v3 on IPFS ===") +# print(test_ds) + +# async with KuboCAS( # <-- own and auto-close session +# rpc_base_url=rpc_base_url, +# gateway_base_url=gateway_base_url, +# ) as kubo_cas: +# hamt = await HAMT.build(cas=kubo_cas, values_are_bytes=True) +# zhs = ZarrHAMTStore(hamt) +# assert zhs.supports_writes +# start = time.perf_counter() +# # Do an initial write along with an append which is a common xarray/zarr operation +# test_ds.to_zarr(store=zhs) # type: ignore +# test_ds.to_zarr(store=zhs, mode="a", append_dim="time", zarr_format=3) # type: ignore +# end = time.perf_counter() +# elapsed = end - start +# print("=== Write Stats") +# print(f"Total time in seconds: {elapsed:.2f}") +# print("=== Root CID") +# await hamt.make_read_only() +# cid = hamt.root_node_id +# print(cid) + +# print("=== Reading data back in and checking if identical") +# hamt = await HAMT.build( +# cas=kubo_cas, root_node_id=cid, values_are_bytes=True, read_only=True +# ) +# start = time.perf_counter() +# ipfs_ds: xr.Dataset +# zhs = ZarrHAMTStore(hamt, read_only=True) +# ipfs_ds = xr.open_zarr(store=zhs) +# print(ipfs_ds) + +# # Check both halves, since each are an identical copy +# ds1 = ipfs_ds.isel(time=slice(0, len(ipfs_ds.time) // 2)) +# ds2 = ipfs_ds.isel(time=slice(len(ipfs_ds.time) // 2, len(ipfs_ds.time))) +# xr.testing.assert_identical(ds1, ds2) +# xr.testing.assert_identical(test_ds, ds1) +# xr.testing.assert_identical(test_ds, ds2) + +# end = time.perf_counter() +# elapsed = end - start +# print("=== Read Stats") +# print(f"Total time in seconds: {elapsed:.2f}") + +# # Tests for code coverage's sake +# assert await zhs.exists("zarr.json") +# # __eq__ +# assert zhs == zhs +# assert zhs != hamt +# assert not zhs.supports_writes +# assert not zhs.supports_partial_writes +# assert not zhs.supports_deletes + +# hamt_keys = set() +# async for k in zhs.hamt.keys(): +# hamt_keys.add(k) + +# zhs_keys: set[str] = set() +# async for k in zhs.list(): +# zhs_keys.add(k) +# assert hamt_keys == zhs_keys + +# zhs_keys: set[str] = set() +# async for k in zhs.list(): +# zhs_keys.add(k) +# assert hamt_keys == zhs_keys + +# zhs_keys: set[str] = set() +# async for k in zhs.list_prefix(""): +# zhs_keys.add(k) +# assert hamt_keys == zhs_keys + +# with pytest.raises(NotImplementedError): +# await zhs.set_partial_values([]) + +# with pytest.raises(NotImplementedError): +# await zhs.get_partial_values( +# zarr.core.buffer.default_buffer_prototype(), [] +# ) + +# previous_zarr_json = await zhs.get( +# "zarr.json", zarr.core.buffer.default_buffer_prototype() +# ) +# assert previous_zarr_json is not None +# # Setting a metadata file that should always exist should not change anything +# await zhs.set_if_not_exists( +# "zarr.json", +# np.array([b"a"], dtype=np.bytes_), # type: ignore +# ) # type: ignore np.arrays, if dtype is bytes, is usable as a zarr buffer +# zarr_json_now = await zhs.get( +# "zarr.json", zarr.core.buffer.default_buffer_prototype() +# ) +# assert zarr_json_now is not None +# assert previous_zarr_json.to_bytes() == zarr_json_now.to_bytes() + +# # now remove that metadata file and then add it back +# await zhs.hamt.enable_write() +# zhs = ZarrHAMTStore(zhs.hamt, read_only=False) # make a writable version +# await zhs.delete("zarr.json") +# # doing a duplicate delete should not result in an error +# await zhs.delete("zarr.json") +# zhs_keys: set[str] = set() +# async for k in zhs.list(): +# zhs_keys.add(k) +# assert hamt_keys != zhs_keys +# assert "zarr.json" not in zhs_keys + +# await zhs.set_if_not_exists("zarr.json", previous_zarr_json) +# zarr_json_now = await zhs.get( +# "zarr.json", zarr.core.buffer.default_buffer_prototype() +# ) +# assert zarr_json_now is not None +# assert previous_zarr_json.to_bytes() == zarr_json_now.to_bytes() From bc4c42f7ba53ef7ad93d38abf0c43f19634160ab Mon Sep 17 00:00:00 2001 From: Faolain Date: Mon, 26 May 2025 01:44:12 -0400 Subject: [PATCH 070/118] refactor: ensure tests pass with new architecture --- pytest.ini | 2 +- tests/conftest.py | 13 ++ tests/test_kubo_cas.py | 90 ++++++++-- tests/test_zarr_ipfs.py | 362 ++++++++++++++++++++-------------------- tests/testing_utils.py | 3 + 5 files changed, 273 insertions(+), 197 deletions(-) create mode 100644 tests/conftest.py diff --git a/pytest.ini b/pytest.ini index 4f243a2..54942c0 100644 --- a/pytest.ini +++ b/pytest.ini @@ -1,4 +1,4 @@ # pytest.ini [pytest] asyncio_mode = auto -asyncio_default_fixture_loop_scope = function \ No newline at end of file +asyncio_default_fixture_loop_scope = session diff --git a/tests/conftest.py b/tests/conftest.py new file mode 100644 index 0000000..0951b74 --- /dev/null +++ b/tests/conftest.py @@ -0,0 +1,13 @@ +import aiohttp +import pytest + +# re-export helpers so existing imports keep working (optional) +from testing_utils import ipld_strategy, create_ipfs # noqa: F401 + + +@pytest.fixture(scope="session") +async def global_client_session(): + """One aiohttp.ClientSession shared by the whole test run.""" + async with aiohttp.ClientSession() as session: + yield session + # aiohttp’s async context manager awaits session.close() for us diff --git a/tests/test_kubo_cas.py b/tests/test_kubo_cas.py index c8dc204..1f6a09b 100644 --- a/tests/test_kubo_cas.py +++ b/tests/test_kubo_cas.py @@ -19,25 +19,85 @@ async def test_memory_store_exception(): await s.load(bytes()) -@pytest.mark.asyncio +@pytest.mark.asyncio(loop_scope="session") @given(data=ipld_strategy()) -@settings(deadline=1000) # this sometimes takes longer than the default 250 ms -async def test_kubo_default_urls(data: IPLDKind): - async with KuboCAS() as kubo_cas: - cids = [] +@settings( + deadline=1000, print_blob=True +) # Increased deadline, print_blob for debugging +async def test_kubo_default_urls( + global_client_session, data: IPLDKind +): # Inject the session fixture + """ + Tests KuboCAS using its default URLs and when None is passed for URLs, + leveraging a globally managed aiohttp.ClientSession. + """ + # Test Case 1: KuboCAS instantiated without explicit URLs (should use its defaults) + # We pass the managed global_client_session to it. + # KuboCAS itself is responsible for having default URLs if none are provided. + async with KuboCAS(session=global_client_session) as kubo_cas_default: + # print(f"Testing with default URLs: RPC={kubo_cas_default.rpc_base_url}, Gateway={kubo_cas_default.gateway_base_url}") + encoded_data = dag_cbor.encode(data) for codec in ["raw", "dag-cbor"]: - cid = await kubo_cas.save(dag_cbor.encode(data), codec=codec) # type: ignore - cids.append(cid) - result = dag_cbor.decode(await kubo_cas.load(cid)) - assert data == result + # print(f"Saving with codec: {codec}, data: {data}") + try: + cid = await kubo_cas_default.save(encoded_data, codec=codec) + # print(f"Saved. CID: {cid}") + loaded_encoded_data = await kubo_cas_default.load(cid) + # print(f"Loaded encoded data length: {len(loaded_encoded_data)}") + result = dag_cbor.decode(loaded_encoded_data) + # print(f"Decoded result: {result}") + assert ( + data == result + ), f"Data mismatch for codec {codec} with default URLs" + except Exception as e: + pytest.fail( + f"Error during KuboCAS default URL test (codec: {codec}): {e}" + ) - async with KuboCAS(gateway_base_url=None, rpc_base_url=None) as kubo_cas: - cids = [] + # Test Case 2: KuboCAS instantiated with None for URLs (should also use its defaults) + # We pass the managed global_client_session to it. + async with KuboCAS( + rpc_base_url=None, gateway_base_url=None, session=global_client_session + ) as kubo_cas_none_urls: + # print(f"Testing with None URLs: RPC={kubo_cas_none_urls.rpc_base_url}, Gateway={kubo_cas_none_urls.gateway_base_url}") + encoded_data = dag_cbor.encode( + data + ) # Re-encode just in case, though it's the same data for codec in ["raw", "dag-cbor"]: - cid = await kubo_cas.save(dag_cbor.encode(data), codec=codec) # type: ignore - cids.append(cid) - result = dag_cbor.decode(await kubo_cas.load(cid)) - assert data == result + # print(f"Saving with codec: {codec}, data: {data}") + try: + cid = await kubo_cas_none_urls.save(encoded_data, codec=codec) + # print(f"Saved. CID: {cid}") + loaded_encoded_data = await kubo_cas_none_urls.load(cid) + # print(f"Loaded encoded data length: {len(loaded_encoded_data)}") + result = dag_cbor.decode(loaded_encoded_data) + # print(f"Decoded result: {result}") + assert data == result, f"Data mismatch for codec {codec} with None URLs" + except Exception as e: + pytest.fail(f"Error during KuboCAS None URL test (codec: {codec}): {e}") + + +# @given(data=ipld_strategy()) +# @settings(deadline=1000) +# @pytest.mark.asyncio +# async def test_kubo_default_urls(data: IPLDKind): +# try: +# async with KuboCAS() as kubo_cas: +# for codec in ("raw", "dag-cbor"): +# cid = await kubo_cas.save(dag_cbor.encode(data), codec=codec) +# result = dag_cbor.decode(await kubo_cas.load(cid)) +# assert data == result + +# async with KuboCAS(gateway_base_url=None, rpc_base_url=None) as kubo_cas: +# for codec in ("raw", "dag-cbor"): +# cid = await kubo_cas.save(dag_cbor.encode(data), codec=codec) +# result = dag_cbor.decode(await kubo_cas.load(cid)) +# assert data == result +# finally: +# # if Hypothesis cancels early, make sure every open CAS is closed +# for obj in list(globals().values()): +# if isinstance(obj, KuboCAS): +# await obj.aclose() @pytest.mark.asyncio diff --git a/tests/test_zarr_ipfs.py b/tests/test_zarr_ipfs.py index 41be546..e322f1b 100644 --- a/tests/test_zarr_ipfs.py +++ b/tests/test_zarr_ipfs.py @@ -1,181 +1,181 @@ -# import time - -# import numpy as np -# import pandas as pd -# import xarray as xr -# import pytest -# import zarr -# import zarr.core.buffer - -# from py_hamt import HAMT, KuboCAS - -# from py_hamt.zarr_hamt_store import ZarrHAMTStore -# from testing_utils import ( -# create_ipfs, -# ) # noqa pytest detects by name but this shows up as unused import error - - -# @pytest.fixture(scope="module") -# def random_zarr_dataset(): -# """Creates a random xarray Dataset. - -# Returns: -# tuple: (dataset_path, expected_data) -# - dataset_path: Path to the zarr store -# - expected_data: The original xarray Dataset for comparison -# """ -# # Coordinates of the random data -# times = pd.date_range("2024-01-01", periods=100) -# lats = np.linspace(-90, 90, 18) -# lons = np.linspace(-180, 180, 36) - -# # Create random variables with different shapes -# temp = np.random.randn(len(times), len(lats), len(lons)) -# precip = np.random.gamma(2, 0.5, size=(len(times), len(lats), len(lons))) - -# # Create the dataset -# ds = xr.Dataset( -# { -# "temp": ( -# ["time", "lat", "lon"], -# temp, -# {"units": "celsius", "long_name": "Surface Temperature"}, -# ), -# "precip": ( -# ["time", "lat", "lon"], -# precip, -# {"units": "mm/day", "long_name": "Daily Precipitation"}, -# ), -# }, -# coords={ -# "time": times, -# "lat": ("lat", lats, {"units": "degrees_north"}), -# "lon": ("lon", lons, {"units": "degrees_east"}), -# }, -# attrs={"description": "Test dataset with random weather data"}, -# ) - -# yield ds - - -# # This test also collects miscellaneous statistics about performance, run with pytest -s to see these statistics being printed out -# @pytest.mark.asyncio -# async def test_write_read( -# create_ipfs, random_zarr_dataset: xr.Dataset -# ): # noqa for fixture which is imported above but then "redefined" -# rpc_base_url, gateway_base_url = create_ipfs -# test_ds = random_zarr_dataset -# print("=== Writing this xarray Dataset to a Zarr v3 on IPFS ===") -# print(test_ds) - -# async with KuboCAS( # <-- own and auto-close session -# rpc_base_url=rpc_base_url, -# gateway_base_url=gateway_base_url, -# ) as kubo_cas: -# hamt = await HAMT.build(cas=kubo_cas, values_are_bytes=True) -# zhs = ZarrHAMTStore(hamt) -# assert zhs.supports_writes -# start = time.perf_counter() -# # Do an initial write along with an append which is a common xarray/zarr operation -# test_ds.to_zarr(store=zhs) # type: ignore -# test_ds.to_zarr(store=zhs, mode="a", append_dim="time", zarr_format=3) # type: ignore -# end = time.perf_counter() -# elapsed = end - start -# print("=== Write Stats") -# print(f"Total time in seconds: {elapsed:.2f}") -# print("=== Root CID") -# await hamt.make_read_only() -# cid = hamt.root_node_id -# print(cid) - -# print("=== Reading data back in and checking if identical") -# hamt = await HAMT.build( -# cas=kubo_cas, root_node_id=cid, values_are_bytes=True, read_only=True -# ) -# start = time.perf_counter() -# ipfs_ds: xr.Dataset -# zhs = ZarrHAMTStore(hamt, read_only=True) -# ipfs_ds = xr.open_zarr(store=zhs) -# print(ipfs_ds) - -# # Check both halves, since each are an identical copy -# ds1 = ipfs_ds.isel(time=slice(0, len(ipfs_ds.time) // 2)) -# ds2 = ipfs_ds.isel(time=slice(len(ipfs_ds.time) // 2, len(ipfs_ds.time))) -# xr.testing.assert_identical(ds1, ds2) -# xr.testing.assert_identical(test_ds, ds1) -# xr.testing.assert_identical(test_ds, ds2) - -# end = time.perf_counter() -# elapsed = end - start -# print("=== Read Stats") -# print(f"Total time in seconds: {elapsed:.2f}") - -# # Tests for code coverage's sake -# assert await zhs.exists("zarr.json") -# # __eq__ -# assert zhs == zhs -# assert zhs != hamt -# assert not zhs.supports_writes -# assert not zhs.supports_partial_writes -# assert not zhs.supports_deletes - -# hamt_keys = set() -# async for k in zhs.hamt.keys(): -# hamt_keys.add(k) - -# zhs_keys: set[str] = set() -# async for k in zhs.list(): -# zhs_keys.add(k) -# assert hamt_keys == zhs_keys - -# zhs_keys: set[str] = set() -# async for k in zhs.list(): -# zhs_keys.add(k) -# assert hamt_keys == zhs_keys - -# zhs_keys: set[str] = set() -# async for k in zhs.list_prefix(""): -# zhs_keys.add(k) -# assert hamt_keys == zhs_keys - -# with pytest.raises(NotImplementedError): -# await zhs.set_partial_values([]) - -# with pytest.raises(NotImplementedError): -# await zhs.get_partial_values( -# zarr.core.buffer.default_buffer_prototype(), [] -# ) - -# previous_zarr_json = await zhs.get( -# "zarr.json", zarr.core.buffer.default_buffer_prototype() -# ) -# assert previous_zarr_json is not None -# # Setting a metadata file that should always exist should not change anything -# await zhs.set_if_not_exists( -# "zarr.json", -# np.array([b"a"], dtype=np.bytes_), # type: ignore -# ) # type: ignore np.arrays, if dtype is bytes, is usable as a zarr buffer -# zarr_json_now = await zhs.get( -# "zarr.json", zarr.core.buffer.default_buffer_prototype() -# ) -# assert zarr_json_now is not None -# assert previous_zarr_json.to_bytes() == zarr_json_now.to_bytes() - -# # now remove that metadata file and then add it back -# await zhs.hamt.enable_write() -# zhs = ZarrHAMTStore(zhs.hamt, read_only=False) # make a writable version -# await zhs.delete("zarr.json") -# # doing a duplicate delete should not result in an error -# await zhs.delete("zarr.json") -# zhs_keys: set[str] = set() -# async for k in zhs.list(): -# zhs_keys.add(k) -# assert hamt_keys != zhs_keys -# assert "zarr.json" not in zhs_keys - -# await zhs.set_if_not_exists("zarr.json", previous_zarr_json) -# zarr_json_now = await zhs.get( -# "zarr.json", zarr.core.buffer.default_buffer_prototype() -# ) -# assert zarr_json_now is not None -# assert previous_zarr_json.to_bytes() == zarr_json_now.to_bytes() +import time + +import numpy as np +import pandas as pd +import xarray as xr +import pytest +import zarr +import zarr.core.buffer + +from py_hamt import HAMT, KuboCAS + +from py_hamt.zarr_hamt_store import ZarrHAMTStore +from testing_utils import ( + create_ipfs, +) # noqa pytest detects by name but this shows up as unused import error + + +@pytest.fixture(scope="module") +def random_zarr_dataset(): + """Creates a random xarray Dataset. + + Returns: + tuple: (dataset_path, expected_data) + - dataset_path: Path to the zarr store + - expected_data: The original xarray Dataset for comparison + """ + # Coordinates of the random data + times = pd.date_range("2024-01-01", periods=100) + lats = np.linspace(-90, 90, 18) + lons = np.linspace(-180, 180, 36) + + # Create random variables with different shapes + temp = np.random.randn(len(times), len(lats), len(lons)) + precip = np.random.gamma(2, 0.5, size=(len(times), len(lats), len(lons))) + + # Create the dataset + ds = xr.Dataset( + { + "temp": ( + ["time", "lat", "lon"], + temp, + {"units": "celsius", "long_name": "Surface Temperature"}, + ), + "precip": ( + ["time", "lat", "lon"], + precip, + {"units": "mm/day", "long_name": "Daily Precipitation"}, + ), + }, + coords={ + "time": times, + "lat": ("lat", lats, {"units": "degrees_north"}), + "lon": ("lon", lons, {"units": "degrees_east"}), + }, + attrs={"description": "Test dataset with random weather data"}, + ) + + yield ds + + +# This test also collects miscellaneous statistics about performance, run with pytest -s to see these statistics being printed out +@pytest.mark.asyncio(loop_scope="session") # ← match the loop of the fixture +async def test_write_read( + create_ipfs, + random_zarr_dataset: xr.Dataset, +): # noqa for fixture which is imported above but then "redefined" + rpc_base_url, gateway_base_url = create_ipfs + test_ds = random_zarr_dataset + print("=== Writing this xarray Dataset to a Zarr v3 on IPFS ===") + print(test_ds) + + async with KuboCAS( # <-- own and auto-close session + rpc_base_url=rpc_base_url, gateway_base_url=gateway_base_url + ) as kubo_cas: + hamt = await HAMT.build(cas=kubo_cas, values_are_bytes=True) + zhs = ZarrHAMTStore(hamt) + assert zhs.supports_writes + start = time.perf_counter() + # Do an initial write along with an append which is a common xarray/zarr operation + test_ds.to_zarr(store=zhs) # type: ignore + test_ds.to_zarr(store=zhs, mode="a", append_dim="time", zarr_format=3) # type: ignore + end = time.perf_counter() + elapsed = end - start + print("=== Write Stats") + print(f"Total time in seconds: {elapsed:.2f}") + print("=== Root CID") + await hamt.make_read_only() + cid = hamt.root_node_id + print(cid) + + print("=== Reading data back in and checking if identical") + hamt = await HAMT.build( + cas=kubo_cas, root_node_id=cid, values_are_bytes=True, read_only=True + ) + start = time.perf_counter() + ipfs_ds: xr.Dataset + zhs = ZarrHAMTStore(hamt, read_only=True) + ipfs_ds = xr.open_zarr(store=zhs) + print(ipfs_ds) + + # Check both halves, since each are an identical copy + ds1 = ipfs_ds.isel(time=slice(0, len(ipfs_ds.time) // 2)) + ds2 = ipfs_ds.isel(time=slice(len(ipfs_ds.time) // 2, len(ipfs_ds.time))) + xr.testing.assert_identical(ds1, ds2) + xr.testing.assert_identical(test_ds, ds1) + xr.testing.assert_identical(test_ds, ds2) + + end = time.perf_counter() + elapsed = end - start + print("=== Read Stats") + print(f"Total time in seconds: {elapsed:.2f}") + + # Tests for code coverage's sake + assert await zhs.exists("zarr.json") + # __eq__ + assert zhs == zhs + assert zhs != hamt + assert not zhs.supports_writes + assert not zhs.supports_partial_writes + assert not zhs.supports_deletes + + hamt_keys = set() + async for k in zhs.hamt.keys(): + hamt_keys.add(k) + + zhs_keys: set[str] = set() + async for k in zhs.list(): + zhs_keys.add(k) + assert hamt_keys == zhs_keys + + zhs_keys: set[str] = set() + async for k in zhs.list(): + zhs_keys.add(k) + assert hamt_keys == zhs_keys + + zhs_keys: set[str] = set() + async for k in zhs.list_prefix(""): + zhs_keys.add(k) + assert hamt_keys == zhs_keys + + with pytest.raises(NotImplementedError): + await zhs.set_partial_values([]) + + with pytest.raises(NotImplementedError): + await zhs.get_partial_values( + zarr.core.buffer.default_buffer_prototype(), [] + ) + + previous_zarr_json = await zhs.get( + "zarr.json", zarr.core.buffer.default_buffer_prototype() + ) + assert previous_zarr_json is not None + # Setting a metadata file that should always exist should not change anything + await zhs.set_if_not_exists( + "zarr.json", + np.array([b"a"], dtype=np.bytes_), # type: ignore + ) # type: ignore np.arrays, if dtype is bytes, is usable as a zarr buffer + zarr_json_now = await zhs.get( + "zarr.json", zarr.core.buffer.default_buffer_prototype() + ) + assert zarr_json_now is not None + assert previous_zarr_json.to_bytes() == zarr_json_now.to_bytes() + + # now remove that metadata file and then add it back + await zhs.hamt.enable_write() + zhs = ZarrHAMTStore(zhs.hamt, read_only=False) # make a writable version + await zhs.delete("zarr.json") + # doing a duplicate delete should not result in an error + await zhs.delete("zarr.json") + zhs_keys: set[str] = set() + async for k in zhs.list(): + zhs_keys.add(k) + assert hamt_keys != zhs_keys + assert "zarr.json" not in zhs_keys + + await zhs.set_if_not_exists("zarr.json", previous_zarr_json) + zarr_json_now = await zhs.get( + "zarr.json", zarr.core.buffer.default_buffer_prototype() + ) + assert zarr_json_now is not None + assert previous_zarr_json.to_bytes() == zarr_json_now.to_bytes() diff --git a/tests/testing_utils.py b/tests/testing_utils.py index 5975a7b..bb9ac41 100644 --- a/tests/testing_utils.py +++ b/tests/testing_utils.py @@ -12,6 +12,9 @@ from hypothesis.strategies import SearchStrategy from multiformats import CID +import aiohttp +from py_hamt.store import KuboCAS # Your KuboCAS import + def cid_strategy() -> SearchStrategy: """Generate random CIDs for testing.""" From 20cdf920e8963830a3156bed8ff02b7e7af65f06 Mon Sep 17 00:00:00 2001 From: Faolain Date: Mon, 26 May 2025 01:57:15 -0400 Subject: [PATCH 071/118] refactor: event loop on linux issues --- py_hamt/store.py | 81 ++++++++++++++++++++++++++++++++++-------------- 1 file changed, 58 insertions(+), 23 deletions(-) diff --git a/py_hamt/store.py b/py_hamt/store.py index 797eb8a..d12e0da 100644 --- a/py_hamt/store.py +++ b/py_hamt/store.py @@ -111,13 +111,50 @@ def __init__( timeout=aiohttp.ClientTimeout(total=60), connector=aiohttp.TCPConnector(limit=64, limit_per_host=32), ) - self._owns_session = session is None + self._session_per_loop: dict[asyncio.AbstractEventLoop, aiohttp.ClientSession] = {} + + if session is not None: + # user supplied → bind it to *their* current loop + self._session_per_loop[asyncio.get_running_loop()] = session + self._owns_session = False + else: + self._owns_session = True # we’ll create sessions lazily + self._sem = asyncio.Semaphore(64) + # --------------------------------------------------------------------- # + # helper: get or create the session bound to the current running loop # + # --------------------------------------------------------------------- # + def _session(self) -> aiohttp.ClientSession: + loop = asyncio.get_running_loop() + try: + return self._session_per_loop[loop] + except KeyError: + sess = aiohttp.ClientSession( + timeout=aiohttp.ClientTimeout(total=60), + connector=aiohttp.TCPConnector(limit=64, limit_per_host=32), + ) + self._session_per_loop[loop] = sess + return sess + # ---------- internal helper ---------- + def _get_session_for_current_loop(self) -> aiohttp.ClientSession: + loop = asyncio.get_running_loop() + sess = self._session_per_loop.get(loop) + if sess is None: + sess = aiohttp.ClientSession( + timeout=aiohttp.ClientTimeout(total=60), + connector=aiohttp.TCPConnector(limit=64, limit_per_host=32), + ) + self._session_per_loop[loop] = sess + return sess +# --------------------------------------------------------------------- # + # graceful shutdown: close **all** sessions we own # + # --------------------------------------------------------------------- # async def aclose(self): - """Close our connector if we created it.""" - if self._owns_session and not self._session.closed: - await self._session.close() + if self._owns_session: + for sess in list(self._session_per_loop.values()): + if not sess.closed: + await sess.close() async def __aenter__(self): return self @@ -125,33 +162,31 @@ async def __aenter__(self): async def __aexit__(self, *exc): await self.aclose() - async def save(self, data: bytes, codec: ContentAddressedStore.CodecInput) -> CID: - """@private""" - async with self._sem: # throttle RPC calls if needed + # --------------------------------------------------------------------- # + # save() – now uses the per-loop session # + # --------------------------------------------------------------------- # + async def save(self, data: bytes, codec: ContentAddressedStore.CodecInput) -> CID: + async with self._sem: # throttle RPC form = aiohttp.FormData() - # field-name MUST be "file", filename can be anything - form.add_field( - "file", data, filename="blob", content_type="application/octet-stream" - ) + form.add_field("file", data, + filename="blob", + content_type="application/octet-stream") - async with self._session.post(self.rpc_url, data=form) as resp: - resp.raise_for_status() # no more 400s + async with self._session().post(self.rpc_url, data=form) as resp: + resp.raise_for_status() cid_str = (await resp.json())["Hash"] - cid = CID.decode(cid_str) - if cid.codec.code != self.DAG_PB_MARKER: - cid = cid.set(codec=codec) - - return cid + cid = CID.decode(cid_str) + if cid.codec.code != self.DAG_PB_MARKER: + cid = cid.set(codec=codec) + return cid async def load( # type: ignore CID is definitely in the IPLDKind type self, id: CID ) -> bytes: """@private""" url = self.gateway_base_url + str(id) - # If this coroutine is running inside an event loop, # - # off-load the *blocking* requests call to a worker thread. # async with self._sem: # throttle gateway - async with self._session.get(url) as r: - r.raise_for_status() - return await r.read() + async with self._session().get(url) as resp: + resp.raise_for_status() + return await resp.read() From 77ab5940f4308106f6353cbdaadf50ea5dc5665d Mon Sep 17 00:00:00 2001 From: Faolain Date: Mon, 26 May 2025 02:00:13 -0400 Subject: [PATCH 072/118] fix: identation --- py_hamt/store.py | 20 ++++++++++++-------- 1 file changed, 12 insertions(+), 8 deletions(-) diff --git a/py_hamt/store.py b/py_hamt/store.py index d12e0da..69a6d39 100644 --- a/py_hamt/store.py +++ b/py_hamt/store.py @@ -111,16 +111,19 @@ def __init__( timeout=aiohttp.ClientTimeout(total=60), connector=aiohttp.TCPConnector(limit=64, limit_per_host=32), ) - self._session_per_loop: dict[asyncio.AbstractEventLoop, aiohttp.ClientSession] = {} + self._session_per_loop: dict[ + asyncio.AbstractEventLoop, aiohttp.ClientSession + ] = {} if session is not None: # user supplied → bind it to *their* current loop self._session_per_loop[asyncio.get_running_loop()] = session self._owns_session = False else: - self._owns_session = True # we’ll create sessions lazily + self._owns_session = True # we’ll create sessions lazily self._sem = asyncio.Semaphore(64) + # --------------------------------------------------------------------- # # helper: get or create the session bound to the current running loop # # --------------------------------------------------------------------- # @@ -135,6 +138,7 @@ def _session(self) -> aiohttp.ClientSession: ) self._session_per_loop[loop] = sess return sess + # ---------- internal helper ---------- def _get_session_for_current_loop(self) -> aiohttp.ClientSession: loop = asyncio.get_running_loop() @@ -147,7 +151,7 @@ def _get_session_for_current_loop(self) -> aiohttp.ClientSession: self._session_per_loop[loop] = sess return sess -# --------------------------------------------------------------------- # + # --------------------------------------------------------------------- # # graceful shutdown: close **all** sessions we own # # --------------------------------------------------------------------- # async def aclose(self): @@ -165,12 +169,12 @@ async def __aexit__(self, *exc): # --------------------------------------------------------------------- # # save() – now uses the per-loop session # # --------------------------------------------------------------------- # - async def save(self, data: bytes, codec: ContentAddressedStore.CodecInput) -> CID: - async with self._sem: # throttle RPC + async def save(self, data: bytes, codec: ContentAddressedStore.CodecInput) -> CID: + async with self._sem: # throttle RPC form = aiohttp.FormData() - form.add_field("file", data, - filename="blob", - content_type="application/octet-stream") + form.add_field( + "file", data, filename="blob", content_type="application/octet-stream" + ) async with self._session().post(self.rpc_url, data=form) as resp: resp.raise_for_status() From 21b8f349235cd847e11a3629a1de24ca111cdf1b Mon Sep 17 00:00:00 2001 From: Faolain Date: Mon, 26 May 2025 02:09:17 -0400 Subject: [PATCH 073/118] fix: session errors --- py_hamt/store.py | 11 +++-------- 1 file changed, 3 insertions(+), 8 deletions(-) diff --git a/py_hamt/store.py b/py_hamt/store.py index 69a6d39..8ddafd9 100644 --- a/py_hamt/store.py +++ b/py_hamt/store.py @@ -106,11 +106,6 @@ def __init__( self.gateway_base_url = gateway_base_url + "/ipfs/" """@private""" - # One shared session per KuboCAS instance. - self._session = session or aiohttp.ClientSession( - timeout=aiohttp.ClientTimeout(total=60), - connector=aiohttp.TCPConnector(limit=64, limit_per_host=32), - ) self._session_per_loop: dict[ asyncio.AbstractEventLoop, aiohttp.ClientSession ] = {} @@ -127,7 +122,7 @@ def __init__( # --------------------------------------------------------------------- # # helper: get or create the session bound to the current running loop # # --------------------------------------------------------------------- # - def _session(self) -> aiohttp.ClientSession: + def _loop_session(self) -> aiohttp.ClientSession: loop = asyncio.get_running_loop() try: return self._session_per_loop[loop] @@ -176,7 +171,7 @@ async def save(self, data: bytes, codec: ContentAddressedStore.CodecInput) -> CI "file", data, filename="blob", content_type="application/octet-stream" ) - async with self._session().post(self.rpc_url, data=form) as resp: + async with self._loop_session().post(self.rpc_url, data=form) as resp: resp.raise_for_status() cid_str = (await resp.json())["Hash"] @@ -191,6 +186,6 @@ async def load( # type: ignore CID is definitely in the IPLDKind type """@private""" url = self.gateway_base_url + str(id) async with self._sem: # throttle gateway - async with self._session().get(url) as resp: + async with self._loop_session().get(url) as resp: resp.raise_for_status() return await resp.read() From 27d56e7b97e4b65550f2cb6cb86eb05844519363 Mon Sep 17 00:00:00 2001 From: Faolain Date: Mon, 26 May 2025 02:10:55 -0400 Subject: [PATCH 074/118] fix: indent --- py_hamt/store.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/py_hamt/store.py b/py_hamt/store.py index 8ddafd9..c9f80c1 100644 --- a/py_hamt/store.py +++ b/py_hamt/store.py @@ -171,7 +171,7 @@ async def save(self, data: bytes, codec: ContentAddressedStore.CodecInput) -> CI "file", data, filename="blob", content_type="application/octet-stream" ) - async with self._loop_session().post(self.rpc_url, data=form) as resp: + async with self._loop_session().post(self.rpc_url, data=form) as resp: resp.raise_for_status() cid_str = (await resp.json())["Hash"] From 5703750a1f871c97694e7166c54c1a82e050434d Mon Sep 17 00:00:00 2001 From: Faolain Date: Mon, 26 May 2025 02:44:49 -0400 Subject: [PATCH 075/118] fix: tests --- py_hamt/store.py | 12 ---- tests/test_kubocas_session.py | 103 ++++++++++++++++++++++++++++++++++ 2 files changed, 103 insertions(+), 12 deletions(-) create mode 100644 tests/test_kubocas_session.py diff --git a/py_hamt/store.py b/py_hamt/store.py index c9f80c1..9aa2301 100644 --- a/py_hamt/store.py +++ b/py_hamt/store.py @@ -134,18 +134,6 @@ def _loop_session(self) -> aiohttp.ClientSession: self._session_per_loop[loop] = sess return sess - # ---------- internal helper ---------- - def _get_session_for_current_loop(self) -> aiohttp.ClientSession: - loop = asyncio.get_running_loop() - sess = self._session_per_loop.get(loop) - if sess is None: - sess = aiohttp.ClientSession( - timeout=aiohttp.ClientTimeout(total=60), - connector=aiohttp.TCPConnector(limit=64, limit_per_host=32), - ) - self._session_per_loop[loop] = sess - return sess - # --------------------------------------------------------------------- # # graceful shutdown: close **all** sessions we own # # --------------------------------------------------------------------- # diff --git a/tests/test_kubocas_session.py b/tests/test_kubocas_session.py new file mode 100644 index 0000000..c836d6a --- /dev/null +++ b/tests/test_kubocas_session.py @@ -0,0 +1,103 @@ +import asyncio +import inspect +from threading import Thread, Event + +import aiohttp +import pytest + +from py_hamt.store import KuboCAS + + +async def _maybe_await(value): + """Helper that awaits *value* if it is awaitable, otherwise returns it as‑is.""" + if inspect.isawaitable(value): + return await value + return value + + +@pytest.mark.asyncio +async def test_get_session_same_instance_same_loop(): + """Two successive calls in the same event loop must hand back the *same* + ClientSession instance and `aclose()` should close the session when the + store owns it.""" + kubo = KuboCAS( + rpc_base_url="http://127.0.0.1:5001", gateway_base_url="http://127.0.0.1:8080" + ) + + sess1 = await _maybe_await(kubo._loop_session()) + sess2 = await _maybe_await(kubo._loop_session()) + + assert sess1 is sess2 # no churn + + # the implementation is free to keep its internal mapping private. + # We only guarantee behavioural semantics (same object, still open, closes via aclose). + assert not sess1.closed + + await kubo.aclose() + assert sess1.closed + + +@pytest.mark.asyncio +async def test_get_session_respects_user_supplied_session(global_client_session): + """A pre‑created session passed to the constructor must always be reused + and never closed by `aclose()`.""" + kubo = KuboCAS( + session=global_client_session, + rpc_base_url="http://127.0.0.1:5001", + gateway_base_url="http://127.0.0.1:8080", + ) + + sess = await _maybe_await(kubo._loop_session()) + assert sess is global_client_session + + await kubo.aclose() # should *not* close the external session + assert not global_client_session.closed + + +async def _session_in_new_loop(kubo: KuboCAS): + """Spawn a *separate* thread with its own event loop, obtain a session for + that loop and hand both the session and the thread‑local loop object + back to the caller.""" + ready = Event() + container: list = [] # will receive (session, loop) + + def _worker(): + new_loop = asyncio.new_event_loop() + asyncio.set_event_loop(new_loop) + + async def _get(): + return await _maybe_await(kubo._loop_session()) + + try: + session = new_loop.run_until_complete(_get()) + container.append((session, new_loop)) + finally: + ready.set() + + t = Thread(target=_worker, daemon=True) + t.start() + ready.wait() + return container[0] + + +@pytest.mark.asyncio +async def test_distinct_loops_get_distinct_sessions(): + """Different event loops must receive distinct `ClientSession` objects and + both must be tracked in `_session_per_loop`.""" + kubo = KuboCAS( + rpc_base_url="http://127.0.0.1:5001", gateway_base_url="http://127.0.0.1:8080" + ) + + primary_session = await _maybe_await(kubo._loop_session()) + + secondary_session, secondary_loop = await _session_in_new_loop(kubo) + + assert primary_session is not secondary_session + assert len(kubo._session_per_loop) == 2 + assert kubo._session_per_loop[asyncio.get_running_loop()] is primary_session + assert kubo._session_per_loop[secondary_loop] is secondary_session + + # Clean‑up + await kubo.aclose() + if not secondary_session.closed: + await asyncio.to_thread(secondary_session.close) From 652693bb1d399b89e0e5a992cba9108b1f27cec6 Mon Sep 17 00:00:00 2001 From: Faolain Date: Mon, 26 May 2025 02:52:44 -0400 Subject: [PATCH 076/118] lint(ruff): remove unused imports --- py_hamt/store.py | 3 --- tests/test_kubo_cas.py | 1 - tests/test_kubocas_session.py | 1 - tests/test_zarr_ipfs.py | 3 --- tests/testing_utils.py | 3 --- 5 files changed, 11 deletions(-) diff --git a/py_hamt/store.py b/py_hamt/store.py index 9aa2301..0fbe62e 100644 --- a/py_hamt/store.py +++ b/py_hamt/store.py @@ -1,14 +1,11 @@ import asyncio import aiohttp -import weakref from typing import Literal from abc import ABC, abstractmethod from dag_cbor.ipld import IPLDKind -from msgspec import json from multiformats import multihash from multiformats import CID from multiformats.multihash import Multihash -import requests class ContentAddressedStore(ABC): diff --git a/tests/test_kubo_cas.py b/tests/test_kubo_cas.py index 1f6a09b..a430b6e 100644 --- a/tests/test_kubo_cas.py +++ b/tests/test_kubo_cas.py @@ -3,7 +3,6 @@ from dag_cbor import IPLDKind from hypothesis import given, settings import pytest -import requests from py_hamt import KuboCAS diff --git a/tests/test_kubocas_session.py b/tests/test_kubocas_session.py index c836d6a..b9d1054 100644 --- a/tests/test_kubocas_session.py +++ b/tests/test_kubocas_session.py @@ -2,7 +2,6 @@ import inspect from threading import Thread, Event -import aiohttp import pytest from py_hamt.store import KuboCAS diff --git a/tests/test_zarr_ipfs.py b/tests/test_zarr_ipfs.py index e322f1b..46248cb 100644 --- a/tests/test_zarr_ipfs.py +++ b/tests/test_zarr_ipfs.py @@ -10,9 +10,6 @@ from py_hamt import HAMT, KuboCAS from py_hamt.zarr_hamt_store import ZarrHAMTStore -from testing_utils import ( - create_ipfs, -) # noqa pytest detects by name but this shows up as unused import error @pytest.fixture(scope="module") diff --git a/tests/testing_utils.py b/tests/testing_utils.py index bb9ac41..5975a7b 100644 --- a/tests/testing_utils.py +++ b/tests/testing_utils.py @@ -12,9 +12,6 @@ from hypothesis.strategies import SearchStrategy from multiformats import CID -import aiohttp -from py_hamt.store import KuboCAS # Your KuboCAS import - def cid_strategy() -> SearchStrategy: """Generate random CIDs for testing.""" From 1b9cce10aab3e27dc8d5e5ba5d3a65deb57b96b2 Mon Sep 17 00:00:00 2001 From: Faolain Date: Mon, 26 May 2025 02:54:38 -0400 Subject: [PATCH 077/118] lint(ruff): format with ruff --- tests/test_kubo_cas.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/tests/test_kubo_cas.py b/tests/test_kubo_cas.py index a430b6e..956c404 100644 --- a/tests/test_kubo_cas.py +++ b/tests/test_kubo_cas.py @@ -45,9 +45,9 @@ async def test_kubo_default_urls( # print(f"Loaded encoded data length: {len(loaded_encoded_data)}") result = dag_cbor.decode(loaded_encoded_data) # print(f"Decoded result: {result}") - assert ( - data == result - ), f"Data mismatch for codec {codec} with default URLs" + assert data == result, ( + f"Data mismatch for codec {codec} with default URLs" + ) except Exception as e: pytest.fail( f"Error during KuboCAS default URL test (codec: {codec}): {e}" From c55fd4a0d3fa3d9b9ecbe14128cda34ff45fbcc6 Mon Sep 17 00:00:00 2001 From: Faolain Date: Wed, 28 May 2025 01:17:05 -0400 Subject: [PATCH 078/118] ci: replace manual checks with pre-commit gha and local --- .github/workflows/run-checks.yaml | 39 +++++++++++++++++++++---------- .pre-commit-config.yaml | 28 ++++++++++++++++++++++ pyproject.toml | 4 ---- 3 files changed, 55 insertions(+), 16 deletions(-) create mode 100644 .pre-commit-config.yaml diff --git a/.github/workflows/run-checks.yaml b/.github/workflows/run-checks.yaml index 4d399f7..e5c0a77 100644 --- a/.github/workflows/run-checks.yaml +++ b/.github/workflows/run-checks.yaml @@ -1,16 +1,37 @@ name: Run checks run-name: Triggered on push from ${{ github.actor }} to branch/tag ${{ github.ref_name }} on: push -# Should be the same as py-hamt/run-checks.sh jobs: - run_checks: + validate: + needs: check-changes + runs-on: ubuntu-latest + env: + SETUPTOOLS_USE_DISTUTILS: stdlib + steps: + - uses: actions/checkout@v4 + - uses: actions/setup-python@v5 + with: + python-version: "3.12" + - name: Install base libraries + run: pip install nodeenv cython setuptools pip --upgrade --quiet --user + - uses: pre-commit/action@v3.0.1 + test: name: Create project environment, run all checks + needs: + - validate runs-on: ubuntu-latest - + strategy: + fail-fast: true + matrix: + python-version: ["3.12"] steps: - - name: Checkout repo - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2 + - name: Check out repository + uses: actions/checkout@v4 + - name: Set up python ${{ matrix.python-version }} + uses: actions/setup-python@v5 + with: + python-version: ${{ matrix.python-version }} - name: Install uv uses: astral-sh/setup-uv@6b9c6063abd6010835644d4c2e1bef4cf5cd0fca # v6 @@ -23,7 +44,7 @@ jobs: - name: Install IPFS uses: oduwsdl/setup-ipfs@e92fedca9f61ab9184cb74940254859f4d7af4d9 # v0.6.3 with: - ipfs_version: "0.34.1" + ipfs_version: "0.35.0" run_daemon: true - name: Run pytest with coverage @@ -36,9 +57,3 @@ jobs: - name: Check coverage run: uv run coverage report --fail-under=100 --show-missing - - - name: Check linting with ruff - run: uv run ruff check - - - name: Check formatting with ruff - run: uv run ruff format --check diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml new file mode 100644 index 0000000..75f6546 --- /dev/null +++ b/.pre-commit-config.yaml @@ -0,0 +1,28 @@ +repos: + - repo: https://github.com/compilerla/conventional-pre-commit + rev: v4.0.0 + hooks: + - id: conventional-pre-commit + stages: [commit-msg] + - repo: https://github.com/pre-commit/pre-commit-hooks + rev: v5.0.0 + hooks: + - id: check-ast + - id: check-case-conflict + - id: check-merge-conflict + - id: check-toml + - id: debug-statements + - id: end-of-file-fixer + - id: mixed-line-ending + - id: trailing-whitespace + - repo: https://github.com/charliermarsh/ruff-pre-commit + rev: v0.11.11 + hooks: + - id: ruff-check + - id: ruff-format + - repo: https://github.com/ariebovenberg/slotscheck + rev: v0.17.1 + hooks: + - id: slotscheck + name: slotscheck + entry: bash -c 'env PYTHONPATH=src slotscheck' diff --git a/pyproject.toml b/pyproject.toml index 25f2822..2ccd16a 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -31,7 +31,3 @@ dev = [ "pytest-asyncio>=0.25.3", "xarray[complete]>=2025.3.0", ] - -[pytest] -asyncio_mode = "auto" -asyncio_default_fixture_loop_scope = "function" From 37c8924d1f9d1dea67ca5da975d91499f96208e3 Mon Sep 17 00:00:00 2001 From: Faolain Date: Wed, 28 May 2025 01:23:42 -0400 Subject: [PATCH 079/118] ci: remove extraneous installs for gha --- .github/workflows/run-checks.yaml | 5 ----- 1 file changed, 5 deletions(-) diff --git a/.github/workflows/run-checks.yaml b/.github/workflows/run-checks.yaml index e5c0a77..112fd93 100644 --- a/.github/workflows/run-checks.yaml +++ b/.github/workflows/run-checks.yaml @@ -4,17 +4,12 @@ on: push jobs: validate: - needs: check-changes runs-on: ubuntu-latest - env: - SETUPTOOLS_USE_DISTUTILS: stdlib steps: - uses: actions/checkout@v4 - uses: actions/setup-python@v5 with: python-version: "3.12" - - name: Install base libraries - run: pip install nodeenv cython setuptools pip --upgrade --quiet --user - uses: pre-commit/action@v3.0.1 test: name: Create project environment, run all checks From 0ca66516fdf7bfd326bac82fd1a469051f24d9d5 Mon Sep 17 00:00:00 2001 From: Faolain Date: Wed, 28 May 2025 02:13:33 -0400 Subject: [PATCH 080/118] deps: upgrade zarr, uv warning that zarr.load deleted data --- pyproject.toml | 2 +- uv.lock | 8 ++++---- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 2ccd16a..6d19866 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -10,7 +10,7 @@ dependencies = [ "msgspec>=0.18.6", "multiformats[full]>=0.3.1.post4", "requests>=2.32.3", - "zarr>=3.0.6", + "zarr>=3.0.8", ] [build-system] diff --git a/uv.lock b/uv.lock index 01b9548..e14c0e7 100644 --- a/uv.lock +++ b/uv.lock @@ -1543,7 +1543,7 @@ requires-dist = [ { name = "msgspec", specifier = ">=0.18.6" }, { name = "multiformats", extras = ["full"], specifier = ">=0.3.1.post4" }, { name = "requests", specifier = ">=2.32.3" }, - { name = "zarr", specifier = ">=3.0.6" }, + { name = "zarr", specifier = ">=3.0.8" }, ] [package.metadata.requires-dev] @@ -2194,7 +2194,7 @@ wheels = [ [[package]] name = "zarr" -version = "3.0.6" +version = "3.0.8" source = { registry = "https://pypi.org/simple" } dependencies = [ { name = "donfig" }, @@ -2203,9 +2203,9 @@ dependencies = [ { name = "packaging" }, { name = "typing-extensions" }, ] -sdist = { url = "https://files.pythonhosted.org/packages/6f/bf/2820e8ad5f086ea5cd4c4d65eb5e0113f98145ddf5810cec1c75fb10fb98/zarr-3.0.6.tar.gz", hash = "sha256:6ef23c740e34917a2a1099471361537732942e49f0cabe95c9b7124cd0d6d84f", size = 240812 } +sdist = { url = "https://files.pythonhosted.org/packages/52/60/9652fd0536fbaca8d08cbc1a5572c52e0ce01773297df75da8bb47e45907/zarr-3.0.8.tar.gz", hash = "sha256:88505d095af899a88ae8ac4db02f4650ef0801d2ff6f65b6d1f0a45dcf760a6d", size = 256825 } wheels = [ - { url = "https://files.pythonhosted.org/packages/fb/38/56a1c129577d20dc975a934ccc3f7f16276eab04ff0ffbe02ea348407a37/zarr-3.0.6-py3-none-any.whl", hash = "sha256:dba078726b6e4defb0ae6a852b7e7035ce163d89d485961681ece49191dcce82", size = 196357 }, + { url = "https://files.pythonhosted.org/packages/00/3b/e20bdf84088c11f2c396d034506cbffadd53e024111c1aa4585c2aba1523/zarr-3.0.8-py3-none-any.whl", hash = "sha256:7f81e7aec086437d98882aa432209107114bd7f3a9f4958b2af9c6b5928a70a7", size = 205364 }, ] [[package]] From b7be57a573ec3b539eb8340eee5c1c9d2e3c7e1e Mon Sep 17 00:00:00 2001 From: Faolain Date: Wed, 28 May 2025 03:48:46 -0400 Subject: [PATCH 081/118] refactor: add mypy to hamt --- py_hamt/hamt.py | 206 +++++++++++++++++++++++++++--------------------- pyproject.toml | 1 + uv.lock | 36 +++++++++ 3 files changed, 151 insertions(+), 92 deletions(-) diff --git a/py_hamt/hamt.py b/py_hamt/hamt.py index ad867c2..8304096 100644 --- a/py_hamt/hamt.py +++ b/py_hamt/hamt.py @@ -1,5 +1,16 @@ from abc import ABC, abstractmethod -from typing import Callable, Iterator, AsyncIterator +from typing import ( + Callable, + Iterator, + AsyncIterator, + Any, + Optional, + Union, + cast, + Dict, + List, + Tuple, +) import uuid import asyncio from copy import deepcopy @@ -22,18 +33,18 @@ def extract_bits(hash_bytes: bytes, depth: int, nbits: int) -> int: returns an unsigned integer version of the bit sequence """ # This is needed since int.bit_length on a integer representation of a bytes object ignores leading 0s - hash_bit_length = len(hash_bytes) * 8 + hash_bit_length: int = len(hash_bytes) * 8 - start_bit_index = depth * nbits + start_bit_index: int = depth * nbits if hash_bit_length - start_bit_index < nbits: raise IndexError("Arguments extract more bits than remain in the hash bits") - mask = (0b1 << (hash_bit_length - start_bit_index)) - 1 - n_chop_off_at_end = int.bit_length(mask) - nbits + mask: int = (0b1 << (hash_bit_length - start_bit_index)) - 1 + n_chop_off_at_end: int = int.bit_length(mask) - nbits - hash_as_int = int.from_bytes(hash_bytes) - result = (hash_as_int & mask) >> n_chop_off_at_end + hash_as_int: int = int.from_bytes(hash_bytes) + result: int = (hash_as_int & mask) >> n_chop_off_at_end return result @@ -47,21 +58,21 @@ def blake3_hashfn(input_bytes: bytes) -> bytes: """ # 32 bytes is the recommended byte size for blake3 and the default, but multihash forces us to explicitly specify - digest = b3.digest(input_bytes, size=32) - raw_bytes = b3.unwrap(digest) + digest: bytes = b3.digest(input_bytes, size=32) + raw_bytes: bytes = b3.unwrap(digest) return raw_bytes class Node: def __init__(self): - self.data: list[IPLDKind] = [dict() for _ in range(0, 256)] + self.data: List[IPLDKind] = [{} for _ in range(0, 256)] # empty dicts represent empty buckets # lists with one element are links, where list[0] is the real link - def iter_buckets(self) -> Iterator[dict]: + def iter_buckets(self) -> Iterator[Dict[str, IPLDKind]]: for item in self.data: if isinstance(item, dict): - yield item + yield cast(Dict[str, IPLDKind], item) def iter_link_indices(self) -> Iterator[int]: for i in range(len(self.data)): @@ -71,32 +82,32 @@ def iter_link_indices(self) -> Iterator[int]: def iter_links(self) -> Iterator[IPLDKind]: for item in self.data: if isinstance(item, list): - yield item[0] + yield cast(List[IPLDKind], item)[0] def get_link(self, index: int) -> IPLDKind: - link_wrapper: list[IPLDKind] = self.data[index] # type: ignore + link_wrapper: List[IPLDKind] = cast(List[IPLDKind], self.data[index]) return link_wrapper[0] def set_link(self, index: int, link: IPLDKind): - wrapped = [link] + wrapped: List[IPLDKind] = [link] self.data[index] = wrapped # This assumes that there is only one unique link matching the old link, which is valid since we prune empty Nodes when reserializing and relinking - def replace_link(self, old_link: IPLDKind, new_link: IPLDKind): + def replace_link(self, old_link: IPLDKind, new_link: IPLDKind) -> None: for link_index in self.iter_link_indices(): link = self.get_link(link_index) if link == old_link: self.set_link(link_index, new_link) return - def __deepcopy__(self, memo) -> "Node": + def __deepcopy__(self, memo: Dict[int, Any]) -> "Node": new_node = Node() new_node.data = deepcopy(self.data) return new_node def is_empty(self) -> bool: for i in range(len(self.data)): - item = self.data[i] + item: IPLDKind = self.data[i] if (isinstance(item, dict) and len(item) > 0) or isinstance(item, list): return False return True @@ -107,7 +118,10 @@ def serialize(self) -> bytes: @classmethod def deserialize(cls, data: bytes) -> "Node": try: - decoded_data = dag_cbor.decode(data) + # dag_cbor.decode() returns a union of many IPLD kinds. + # We know a serialised Node is always a *list* of IPLDKinds, + # so narrow the type for mypy. + decoded_data = cast(List[IPLDKind], dag_cbor.decode(data)) except: # noqa: E722 raise Exception( "Invalid dag-cbor encoded data from the store was attempted to be decoded" @@ -138,9 +152,9 @@ async def vacate(self): class ReadCacheStore(NodeStore): - def __init__(self, hamt: "HAMT"): - self.hamt = hamt - self.cache: dict[IPLDKind, Node] = dict() + def __init__(self, hamt: "HAMT") -> None: + self.hamt: HAMT = hamt + self.cache: Dict[IPLDKind, Node] = {} async def save(self, original_id: IPLDKind, node: Node) -> IPLDKind: raise Exception("Node was attempted to be written to the read cache") @@ -148,7 +162,7 @@ async def save(self, original_id: IPLDKind, node: Node) -> IPLDKind: async def load(self, id: IPLDKind) -> Node: # Cache Hit if id in self.cache: - node = self.cache[id] + node: Node = self.cache[id] return node # Cache Miss @@ -156,22 +170,22 @@ async def load(self, id: IPLDKind) -> Node: self.cache[id] = node return node - def size(self): - total = 0 + def size(self) -> int: + total: int = 0 for k in self.cache: - node = self.cache[k] + node: Node = self.cache[k] total += len(node.serialize()) return total async def vacate(self): - self.cache = dict() + self.cache = {} class InMemoryTreeStore(NodeStore): - def __init__(self, hamt: "HAMT"): - self.hamt = hamt + def __init__(self, hamt: "HAMT") -> None: + self.hamt: HAMT = hamt # The integer key is a uuidv4 128-bit integer, for (almost perfectly) guaranteeing uniqueness - self.buffer: dict[int, Node] = dict() + self.buffer: Dict[int, Node] = {} def is_buffer_id(self, id: IPLDKind) -> bool: return id in self.buffer @@ -179,18 +193,20 @@ def is_buffer_id(self, id: IPLDKind) -> bool: def children_in_memory(self, node: Node) -> Iterator[int]: for link in node.iter_links(): if self.is_buffer_id(link): - yield link # type: ignore we know for sure this is an int if it's a buffer id + yield cast( + int, link + ) # we know for sure this is an int if it's a buffer id - _replaced_id_marker = bytes(64) + _replaced_id_marker: bytes = bytes(64) # Callers must acquire a lock/stop operations to ensure an accurate calculation! def size(self) -> int: # This is more difficult than normal links are intentionally unencodable in dag-cbor as the UUIDv4 128-bit integer IDs do not fit # So before serializing, make a copy of the node, replace all of those integer links with zeroed out 64 byte marker. 64 bytes is a conservative estimate for most IDs returned by CASes - total = 0 + total: int = 0 for k in self.buffer: - node = self.buffer[k] - copied = deepcopy(node) + node: Node = self.buffer[k] + copied: Node = deepcopy(node) for link_index in copied.iter_link_indices(): if self.is_buffer_id(copied.get_link(link_index)): copied.set_link(link_index, InMemoryTreeStore._replaced_id_marker) @@ -200,27 +216,27 @@ def size(self) -> int: # The HAMT must properly acquire a lock for this to run successfully! This is not async or thread safe # This algorithm has an implicit assumption that the entire continuous line of branches up to an ancestor is in the memory buffer, which will happen because of the DFS style traversal in all HAMT operations - async def vacate(self): + async def vacate(self) -> None: # node stack is a list of tuples that look like (parent_id, self_id, node) - node_stack: list[tuple[int | None, int, Node]] = [] + node_stack: List[Tuple[Optional[int], int, Node]] = [] # The root node may not be in the buffer, e.g. this is HAMT initialized with a specific root node id if self.is_buffer_id(self.hamt.root_node_id): - root_node: Node = self.buffer[self.hamt.root_node_id] # type: ignore - node_stack.append((None, self.hamt.root_node_id, root_node)) # type: ignore + root_node: Node = self.buffer[cast(int, self.hamt.root_node_id)] + node_stack.append((None, cast(int, self.hamt.root_node_id), root_node)) while len(node_stack) > 0: parent_buffer_id, top_buffer_id, top_node = node_stack[-1] - new_nodes_on_stack = [] + new_nodes_on_stack: List[Tuple[int, int, Node]] = [] for child_buffer_id in self.children_in_memory(top_node): - child_node = self.buffer[child_buffer_id] + child_node: Node = self.buffer[child_buffer_id] new_nodes_on_stack.append((top_buffer_id, child_buffer_id, child_node)) - no_children_in_memory = len(new_nodes_on_stack) == 0 + no_children_in_memory: bool = len(new_nodes_on_stack) == 0 # Flush this node out and relink the rest of the tree if no_children_in_memory: - is_root = parent_buffer_id is None - old_id = top_buffer_id - new_id = await self.hamt.cas.save( + is_root: bool = parent_buffer_id is None + old_id: int = top_buffer_id + new_id: IPLDKind = await self.hamt.cas.save( top_node.serialize(), codec="dag-cbor" ) del self.buffer[old_id] @@ -231,7 +247,9 @@ async def vacate(self): self.hamt.root_node_id = new_id # Edit and properly relink the parent if this is not the root else: - parent_node = self.buffer[parent_buffer_id] + # parent_buffer_id is never None in this branch + assert parent_buffer_id is not None + parent_node: Node = self.buffer[parent_buffer_id] parent_node.replace_link(old_id, new_id) # Continue recursing down the tree else: @@ -241,11 +259,11 @@ async def vacate(self): # 1. A bunch of nodes that seem "unlinked" to anything else, since Links used within the Nodes will reference the real underlying CAS # 2. A bunch of empty nodes leftover if the key values they contain are deleted, these would normally be consolidated by a content addressed system but will be leftover in the buffer # So we can just clear out everything since these nodes are not used by the rest of the tree - self.buffer = dict() + self.buffer = {} async def add_to_buffer(self, node: Node) -> IPLDKind: # This buffer_id is IPLDKind type since technically it's an int, but it's not dag_cbor serializable since that library can only do up to 64-bit ints. Thus this will throw errors early if a node is written with buffer_ids still in there - buffer_id = uuid.uuid4().int + buffer_id: int = uuid.uuid4().int self.buffer[buffer_id] = node return buffer_id @@ -255,13 +273,13 @@ async def save(self, original_id: IPLDKind, node: Node) -> IPLDKind: return original_id # This node was not in the buffer, don't save it to the backing store but rather add to it to the in memory buffer - buffer_id = await self.add_to_buffer(node) + buffer_id: IPLDKind = await self.add_to_buffer(node) return buffer_id async def load(self, id: IPLDKind) -> Node: # Hit for something already in the in memory tree if self.is_buffer_id(id): - node: Node = self.buffer[id] # type: ignore we know all buffer ids are ints + node: Node = self.buffer[cast(int, id)] # we know all buffer ids are ints return node # Something that isn't in the in memory tree, add it @@ -303,7 +321,7 @@ def __init__( self, cas: ContentAddressedStore, hash_fn: Callable[[bytes], bytes] = blake3_hashfn, - root_node_id: IPLDKind = None, + root_node_id: Optional[IPLDKind] = None, read_only: bool = False, max_bucket_size: int = 4, values_are_bytes: bool = False, @@ -326,7 +344,7 @@ def __init__( Theoretically your hash size must only be a minimum of 1 byte, and there can be less than or the same number of hash collisions as the bucket size. Any more and the HAMT will most likely throw errors. """ - self.lock = asyncio.Lock() + self.lock: asyncio.Lock = asyncio.Lock() """@private""" self.values_are_bytes: bool = values_are_bytes @@ -337,7 +355,7 @@ def __init__( if max_bucket_size < 1: raise ValueError("Bucket size maximum must be a positive integer") - self.max_bucket_size = max_bucket_size + self.max_bucket_size: int = max_bucket_size """ This is only important for tuning performance when writing! For reading a HAMT that was written with a different max bucket size, this does not need to match and can be left unprovided. @@ -346,7 +364,7 @@ def __init__( This must be a positive integer with a minimum of 1. """ - self.root_node_id = root_node_id + self.root_node_id: IPLDKind = root_node_id """ This is type IPLDKind but the documentation generator pdoc mangles it a bit. @@ -368,7 +386,7 @@ def __init__( self.node_store = InMemoryTreeStore(self) @classmethod - async def build(cls, *args, **kwargs) -> "HAMT": + async def build(cls, *args: Any, **kwargs: Any) -> "HAMT": """ Use this if you are initializing a completely empty HAMT! That means passing in None for the root_node_id. Method arguments are the exact same as `__init__`. If the root_node_id is not None, this will have no difference than creating a HAMT instance with __init__. @@ -380,20 +398,20 @@ async def build(cls, *args, **kwargs) -> "HAMT": return hamt # This is typically a massive blocking operation, you dont want to be running this concurrently with a bunch of other operations, so it's ok to have it not be async - async def make_read_only(self): + async def make_read_only(self) -> None: """ Makes the HAMT read only, which allows for more parallel read operations. The HAMT also needs to be in read only mode to get the real root node ID. In read+write mode, the HAMT normally has to block separate get calls to enable strong consistency in case a set/delete operation falls in between. """ async with self.lock: - inmemory_tree: InMemoryTreeStore = self.node_store # type: ignore + inmemory_tree: InMemoryTreeStore = cast(InMemoryTreeStore, self.node_store) await inmemory_tree.vacate() self.read_only = True self.node_store = ReadCacheStore(self) - async def enable_write(self): + async def enable_write(self) -> None: """ Enable both reads and writes. This creates an internal structure for performance optimizations which will result in the root node ID no longer being valid, in order to read that at the end of your operations you must first use `make_read_only`. """ @@ -417,7 +435,7 @@ async def cache_size(self) -> int: async with self.lock: return self.node_store.size() - async def cache_vacate(self): + async def cache_vacate(self) -> None: """ Vacate and completely empty out the internal read/write cache. @@ -431,7 +449,9 @@ async def cache_vacate(self): async with self.lock: await self.node_store.vacate() - async def _reserialize_and_link(self, node_stack: list[tuple[IPLDKind, Node]]): + async def _reserialize_and_link( + self, node_stack: List[Tuple[IPLDKind, Node]] + ) -> None: """ This function starts from the node at the end of the list and reserializes so that each node holds valid new IDs after insertion into the store Takes a stack of nodes, we represent a stack with a list where the first element is the root element and the last element is the top of the stack @@ -444,7 +464,7 @@ async def _reserialize_and_link(self, node_stack: list[tuple[IPLDKind, Node]]): old_id, node = node_stack[stack_index] # If this node is empty, and it's not the root node, then we can delete it entirely from the list - is_root = stack_index == 0 + is_root: bool = stack_index == 0 if node.is_empty() and not is_root: # Unlink from the rest of the tree _, prev_node = node_stack[stack_index - 1] @@ -453,7 +473,7 @@ async def _reserialize_and_link(self, node_stack: list[tuple[IPLDKind, Node]]): link = prev_node.get_link(link_index) if link == old_id: # Delete the link by making it an empty bucket - prev_node.data[link_index] = dict() + prev_node.data[link_index] = {} break # Remove from our stack, continue reserializing up the tree @@ -461,7 +481,7 @@ async def _reserialize_and_link(self, node_stack: list[tuple[IPLDKind, Node]]): continue # If not an empty node, just reserialize like normal and replace this one - new_store_id = await self.node_store.save(old_id, node) + new_store_id: IPLDKind = await self.node_store.save(old_id, node) node_stack[stack_index] = (new_store_id, node) # If this is not the last i.e. root node, we need to change the linking of the node prior in the list since we just reserialized @@ -470,45 +490,47 @@ async def _reserialize_and_link(self, node_stack: list[tuple[IPLDKind, Node]]): prev_node.replace_link(old_id, new_store_id) # automatically skip encoding if the value provided is of the bytes variety - async def set(self, key: str, val: IPLDKind): + async def set(self, key: str, val: IPLDKind) -> None: """Write a key-value mapping.""" if self.read_only: raise Exception("Cannot call set on a read only HAMT") data: bytes if self.values_are_bytes: - data = val # type: ignore let users get an exception if they pass in a non bytes when they want to skip encoding + data = cast( + bytes, val + ) # let users get an exception if they pass in a non bytes when they want to skip encoding else: data = dag_cbor.encode(val) - pointer = await self.cas.save(data, codec="raw") + pointer: IPLDKind = await self.cas.save(data, codec="raw") await self._set_pointer(key, pointer) - async def _set_pointer(self, key: str, val_ptr: IPLDKind): + async def _set_pointer(self, key: str, val_ptr: IPLDKind) -> None: async with self.lock: - node_stack: list[tuple[IPLDKind, Node]] = [] - root_node = await self.node_store.load(self.root_node_id) + node_stack: List[Tuple[IPLDKind, Node]] = [] + root_node: Node = await self.node_store.load(self.root_node_id) node_stack.append((self.root_node_id, root_node)) # FIFO queue to keep track of all the KVs we need to insert # This is needed if any buckets overflow and so we need to reinsert all those KVs - kvs_queue: list[tuple[str, IPLDKind]] = [] + kvs_queue: List[Tuple[str, IPLDKind]] = [] kvs_queue.append((key, val_ptr)) while len(kvs_queue) > 0: _, top_node = node_stack[-1] curr_key, curr_val_ptr = kvs_queue[0] - raw_hash = self.hash_fn(curr_key.encode()) - map_key = extract_bits(raw_hash, len(node_stack) - 1, 8) + raw_hash: bytes = self.hash_fn(curr_key.encode()) + map_key: int = extract_bits(raw_hash, len(node_stack) - 1, 8) item = top_node.data[map_key] if isinstance(item, list): - next_node_id = item[0] - next_node = await self.node_store.load(next_node_id) + next_node_id: IPLDKind = item[0] + next_node: Node = await self.node_store.load(next_node_id) node_stack.append((next_node_id, next_node)) elif isinstance(item, dict): - bucket: dict[str, IPLDKind] = item + bucket: Dict[str, IPLDKind] = item # If this bucket already has this same key, or has space, just rewrite the value and then go work on the others in the queue if curr_key in bucket or len(bucket) < self.max_bucket_size: @@ -523,15 +545,15 @@ async def _set_pointer(self, key: str, val_ptr: IPLDKind): # Create a new link to a new node so that we can reflow these KVs into a new subtree new_node = Node() - new_node_id = await self.node_store.save(None, new_node) - link = [new_node_id] + new_node_id: IPLDKind = await self.node_store.save(None, new_node) + link: List[IPLDKind] = [new_node_id] top_node.data[map_key] = link # Finally, reserialize and fix all links, deleting empty nodes as needed await self._reserialize_and_link(node_stack) self.root_node_id = node_stack[0][0] - async def delete(self, key: str): + async def delete(self, key: str) -> None: """Delete a key-value mapping.""" # Also deletes the pointer at the same time so this doesn't have a _delete_pointer duo @@ -539,16 +561,16 @@ async def delete(self, key: str): raise Exception("Cannot call delete on a read only HAMT") async with self.lock: - raw_hash = self.hash_fn(key.encode()) + raw_hash: bytes = self.hash_fn(key.encode()) - node_stack: list[tuple[IPLDKind, Node]] = [] - root_node = await self.node_store.load(self.root_node_id) + node_stack: List[Tuple[IPLDKind, Node]] = [] + root_node: Node = await self.node_store.load(self.root_node_id) node_stack.append((self.root_node_id, root_node)) - created_change = False + created_change: bool = False while True: _, top_node = node_stack[-1] - map_key = extract_bits(raw_hash, len(node_stack) - 1, 8) + map_key: int = extract_bits(raw_hash, len(node_stack) - 1, 8) item = top_node.data[map_key] if isinstance(item, dict): @@ -559,8 +581,8 @@ async def delete(self, key: str): # Break out since whether or not the key is in the bucket, it should have been here so either now reserialize or raise a KeyError break elif isinstance(item, list): - link = item[0] - next_node = await self.node_store.load(link) + link: IPLDKind = item[0] + next_node: Node = await self.node_store.load(link) node_stack.append((link, next_node)) # Finally, reserialize and fix all links, deleting empty nodes as needed @@ -573,8 +595,8 @@ async def delete(self, key: str): async def get(self, key: str) -> IPLDKind: """Get a value.""" - pointer = await self.get_pointer(key) - data = await self.cas.load(pointer) + pointer: IPLDKind = await self.get_pointer(key) + data: bytes = await self.cas.load(pointer) if self.values_are_bytes: return data else: @@ -598,18 +620,18 @@ async def get_pointer(self, key: str) -> IPLDKind: # Callers MUST handle acquiring a lock async def _get_pointer(self, key: str) -> IPLDKind: - raw_hash = self.hash_fn(key.encode()) + raw_hash: bytes = self.hash_fn(key.encode()) - current_id = self.root_node_id + current_id: IPLDKind = self.root_node_id current_depth = 0 # Don't check if result is none but use a boolean to indicate finding something, this is because None is a possible value of IPLDKind result_ptr: IPLDKind = None found_a_result: bool = False while True: - top_id = current_id - top_node = await self.node_store.load(top_id) - map_key = extract_bits(raw_hash, current_depth, 8) + top_id: IPLDKind = current_id + top_node: Node = await self.node_store.load(top_id) + map_key: int = extract_bits(raw_hash, current_depth, 8) # Check if this key is in one of the buckets item = top_node.data[map_key] diff --git a/pyproject.toml b/pyproject.toml index 6d19866..177e6b9 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -30,4 +30,5 @@ dev = [ "numpy>=2.1.3", "pytest-asyncio>=0.25.3", "xarray[complete]>=2025.3.0", + "mypy>=1.15.0", 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py_hamt/store.py | 41 +++++++++++++++++++------------------- py_hamt/zarr_hamt_store.py | 23 +++++++++++---------- pyproject.toml | 1 + tests/test_zarr_ipfs.py | 26 ++++++++++++------------ uv.lock | 24 ++++++++++++++++++++++ 6 files changed, 77 insertions(+), 50 deletions(-) diff --git a/py_hamt/hamt.py b/py_hamt/hamt.py index 8304096..0371cb4 100644 --- a/py_hamt/hamt.py +++ b/py_hamt/hamt.py @@ -623,7 +623,7 @@ async def _get_pointer(self, key: str) -> IPLDKind: raw_hash: bytes = self.hash_fn(key.encode()) current_id: IPLDKind = self.root_node_id - current_depth = 0 + current_depth: int = 0 # Don't check if result is none but use a boolean to indicate finding something, this is because None is a possible value of IPLDKind result_ptr: IPLDKind = None @@ -643,7 +643,7 @@ async def _get_pointer(self, key: str) -> IPLDKind: break if isinstance(item, list): - link = item[0] + link: IPLDKind = item[0] current_id = link current_depth += 1 continue @@ -658,10 +658,10 @@ async def _get_pointer(self, key: str) -> IPLDKind: # Callers MUST handle locking or not on their own async def _iter_nodes(self) -> AsyncIterator[tuple[IPLDKind, Node]]: - node_id_stack = [self.root_node_id] + node_id_stack: List[IPLDKind] = [self.root_node_id] while len(node_id_stack) > 0: - top_id = node_id_stack.pop() - node = await self.node_store.load(top_id) + top_id: IPLDKind = node_id_stack.pop() + node: Node = await self.node_store.load(top_id) yield (top_id, node) node_id_stack.extend(list(node.iter_links())) @@ -693,7 +693,7 @@ async def len(self) -> int: When the HAMT is write enabled, to maintain strong consistency it will acquire a lock and thus not allow any other operations to proceed until the length is fully done being calculated. If read only, then this can be run concurrently with other operations. """ - count = 0 + count: int = 0 async for _ in self.keys(): count += 1 diff --git a/py_hamt/store.py b/py_hamt/store.py index 0fbe62e..cc8096a 100644 --- a/py_hamt/store.py +++ b/py_hamt/store.py @@ -1,6 +1,6 @@ import asyncio import aiohttp -from typing import Literal +from typing import Literal, Optional, Dict, cast, Any from abc import ABC, abstractmethod from dag_cbor.ipld import IPLDKind from multiformats import multihash @@ -37,7 +37,7 @@ async def load(self, id: IPLDKind) -> bytes: class InMemoryCAS(ContentAddressedStore): """Used mostly for faster testing, this is why this is not exported. It hashes all inputs and uses that as a key to an in-memory python dict, mimicking a content addressed storage system. The hash bytes are the ID that `save` returns and `load` takes in.""" - store: dict[bytes, bytes] + store: Dict[bytes, bytes] hash_alg: Multihash def __init__(self): @@ -45,7 +45,7 @@ def __init__(self): self.hash_alg = multihash.get("blake3") async def save(self, data: bytes, codec: ContentAddressedStore.CodecInput) -> bytes: - hash = self.hash_alg.digest(data, size=32) + hash: bytes = self.hash_alg.digest(data, size=32) self.store[hash] = data return hash @@ -63,10 +63,10 @@ class KuboCAS(ContentAddressedStore): `save` uses the RPC API and `load` uses the HTTP Gateway. This means that read-only HAMTs will only access the HTTP Gateway, so no RPC endpoint is required for use. """ - KUBO_DEFAULT_LOCAL_GATEWAY_BASE_URL = "http://127.0.0.1:8080" - KUBO_DEFAULT_LOCAL_RPC_BASE_URL = "http://127.0.0.1:5001" + KUBO_DEFAULT_LOCAL_GATEWAY_BASE_URL: str = "http://127.0.0.1:8080" + KUBO_DEFAULT_LOCAL_RPC_BASE_URL: str = "http://127.0.0.1:5001" - DAG_PB_MARKER = 0x70 + DAG_PB_MARKER: int = 0x70 """@private""" # Take in a aiohttp session that can be reused across POSTs and GETs to a specific ipfs daemon, also allow for not doing that and creating our own single request lifetime session instead @@ -90,7 +90,7 @@ def __init__( These are the first part of the url, defaults that refer to the default that kubo launches with on a local machine are provided. """ - self.hasher = hasher + self.hasher: str = hasher """The hash function to send to IPFS when storing bytes. Cannot be changed after initialization. The default blake3 follows the default hashing algorithm used by HAMT.""" if rpc_base_url is None: @@ -98,9 +98,9 @@ def __init__( if gateway_base_url is None: gateway_base_url = KuboCAS.KUBO_DEFAULT_LOCAL_GATEWAY_BASE_URL - self.rpc_url = f"{rpc_base_url}/api/v0/add?hash={self.hasher}&pin=false" + self.rpc_url: str = f"{rpc_base_url}/api/v0/add?hash={self.hasher}&pin=false" """@private""" - self.gateway_base_url = gateway_base_url + "/ipfs/" + self.gateway_base_url: str = f"{gateway_base_url}/ipfs/" """@private""" self._session_per_loop: dict[ @@ -110,17 +110,17 @@ def __init__( if session is not None: # user supplied → bind it to *their* current loop self._session_per_loop[asyncio.get_running_loop()] = session - self._owns_session = False + self._owns_session: bool = False else: self._owns_session = True # we’ll create sessions lazily - self._sem = asyncio.Semaphore(64) + self._sem: asyncio.Semaphore = asyncio.Semaphore(64) # --------------------------------------------------------------------- # # helper: get or create the session bound to the current running loop # # --------------------------------------------------------------------- # def _loop_session(self) -> aiohttp.ClientSession: - loop = asyncio.get_running_loop() + loop: asyncio.AbstractEventLoop = asyncio.get_running_loop() try: return self._session_per_loop[loop] except KeyError: @@ -134,16 +134,16 @@ def _loop_session(self) -> aiohttp.ClientSession: # --------------------------------------------------------------------- # # graceful shutdown: close **all** sessions we own # # --------------------------------------------------------------------- # - async def aclose(self): + async def aclose(self) -> None: if self._owns_session: for sess in list(self._session_per_loop.values()): if not sess.closed: await sess.close() - async def __aenter__(self): + async def __aenter__(self) -> "KuboCAS": return self - async def __aexit__(self, *exc): + async def __aexit__(self, *exc: Any) -> None: await self.aclose() # --------------------------------------------------------------------- # @@ -158,18 +158,17 @@ async def save(self, data: bytes, codec: ContentAddressedStore.CodecInput) -> CI async with self._loop_session().post(self.rpc_url, data=form) as resp: resp.raise_for_status() - cid_str = (await resp.json())["Hash"] + cid_str: str = (await resp.json())["Hash"] - cid = CID.decode(cid_str) + cid: CID = CID.decode(cid_str) if cid.codec.code != self.DAG_PB_MARKER: cid = cid.set(codec=codec) return cid - async def load( # type: ignore CID is definitely in the IPLDKind type - self, id: CID - ) -> bytes: + async def load(self, id: IPLDKind) -> bytes: """@private""" - url = self.gateway_base_url + str(id) + cid = cast(CID, id) # CID is definitely in the IPLDKind type + url: str = self.gateway_base_url + str(cid) async with self._sem: # throttle gateway async with self._loop_session().get(url) as resp: resp.raise_for_status() diff --git a/py_hamt/zarr_hamt_store.py b/py_hamt/zarr_hamt_store.py index f5c5dbb..a1a3e1b 100644 --- a/py_hamt/zarr_hamt_store.py +++ b/py_hamt/zarr_hamt_store.py @@ -1,4 +1,5 @@ from collections.abc import AsyncIterator, Iterable +from typing import Optional, Dict, List, Tuple, cast import zarr.abc.store import zarr.core.buffer from zarr.core.common import BytesLike @@ -52,13 +53,13 @@ def __init__(self, hamt: HAMT, read_only: bool = False) -> None: assert hamt.read_only == read_only assert hamt.values_are_bytes - self.hamt = hamt + self.hamt: HAMT = hamt """ The internal HAMT. Once done with write operations, the hamt can be set to read only mode as usual to get your root node ID. """ - self.metadata_read_cache: dict[str, bytes] = dict() + self.metadata_read_cache: dict[str, bytes] = {} """@private""" @property @@ -82,21 +83,23 @@ async def get( try: val: bytes # do len check to avoid indexing into overly short strings, 3.12 does not throw errors but we dont know if other versions will - is_metadata = ( + is_metadata: bool = ( len(key) >= 9 and key[-9:] == "zarr.json" ) # if path ends with zarr.json if is_metadata and key in self.metadata_read_cache: val = self.metadata_read_cache[key] else: - val = await self.hamt.get(key) # type: ignore We know values received will always be bytes since we only store bytes in the HAMT + val = cast( + bytes, await self.hamt.get(key) + ) # We know values received will always be bytes since we only store bytes in the HAMT if is_metadata: self.metadata_read_cache[key] = val return prototype.buffer.from_bytes(val) except KeyError: # Sometimes zarr queries keys that don't exist anymore, just return nothing on those cases - return + return None async def get_partial_values( self, @@ -168,22 +171,22 @@ async def list(self) -> AsyncIterator[str]: async for key in self.hamt.keys(): yield key - async def list_prefix(self, prefix: str) -> AsyncIterator: + async def list_prefix(self, prefix: str) -> AsyncIterator[str]: """@private""" async for key in self.hamt.keys(): if key.startswith(prefix): yield key - async def list_dir(self, prefix: str) -> AsyncIterator: + async def list_dir(self, prefix: str) -> AsyncIterator[str]: """ @private """ async for key in self.hamt.keys(): if key.startswith(prefix): - suffix = key[len(prefix) :] - first_slash = suffix.find("/") + suffix: str = key[len(prefix) :] + first_slash: int = suffix.find("/") if first_slash == -1: yield suffix else: - name = suffix[0:first_slash] + name: str = suffix[0:first_slash] yield name diff --git a/pyproject.toml b/pyproject.toml index 177e6b9..612ed14 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -31,4 +31,5 @@ dev = [ "pytest-asyncio>=0.25.3", "xarray[complete]>=2025.3.0", "mypy>=1.15.0", + "pandas-stubs>=2.2.3.250527", ] diff --git a/tests/test_zarr_ipfs.py b/tests/test_zarr_ipfs.py index 46248cb..9b3bf35 100644 --- a/tests/test_zarr_ipfs.py +++ b/tests/test_zarr_ipfs.py @@ -120,20 +120,20 @@ async def test_write_read( async for k in zhs.hamt.keys(): hamt_keys.add(k) - zhs_keys: set[str] = set() + zhs_keys_1: set[str] = set() async for k in zhs.list(): - zhs_keys.add(k) - assert hamt_keys == zhs_keys + zhs_keys_1.add(k) + assert hamt_keys == zhs_keys_1 - zhs_keys: set[str] = set() + zhs_keys_2: set[str] = set() async for k in zhs.list(): - zhs_keys.add(k) - assert hamt_keys == zhs_keys + zhs_keys_2.add(k) + assert hamt_keys == zhs_keys_2 - zhs_keys: set[str] = set() + zhs_keys_3: set[str] = set() async for k in zhs.list_prefix(""): - zhs_keys.add(k) - assert hamt_keys == zhs_keys + zhs_keys_3.add(k) + assert hamt_keys == zhs_keys_3 with pytest.raises(NotImplementedError): await zhs.set_partial_values([]) @@ -164,11 +164,11 @@ async def test_write_read( await zhs.delete("zarr.json") # doing a duplicate delete should not result in an error await zhs.delete("zarr.json") - zhs_keys: set[str] = set() + zhs_keys_4: set[str] = set() async for k in zhs.list(): - zhs_keys.add(k) - assert hamt_keys != zhs_keys - assert "zarr.json" not in zhs_keys + zhs_keys_4.add(k) + assert hamt_keys != zhs_keys_4 + assert "zarr.json" not in zhs_keys_4 await zhs.set_if_not_exists("zarr.json", previous_zarr_json) zarr_json_now = await zhs.get( diff --git a/uv.lock b/uv.lock index 3a36bf9..b29e1a7 100644 --- a/uv.lock +++ b/uv.lock @@ -1370,6 +1370,19 @@ wheels = [ { url = "https://files.pythonhosted.org/packages/ab/5f/b38085618b950b79d2d9164a711c52b10aefc0ae6833b96f626b7021b2ed/pandas-2.2.3-cp313-cp313t-musllinux_1_2_x86_64.whl", hash = "sha256:ad5b65698ab28ed8d7f18790a0dc58005c7629f227be9ecc1072aa74c0c1d43a", size = 13098436 }, ] +[[package]] +name = "pandas-stubs" +version = "2.2.3.250527" +source = { registry = "https://pypi.org/simple" } +dependencies = [ + { name = "numpy" }, + { name = "types-pytz" }, +] +sdist = { url = "https://files.pythonhosted.org/packages/5f/0d/5fe7f7f3596eb1c2526fea151e9470f86b379183d8b9debe44b2098651ca/pandas_stubs-2.2.3.250527.tar.gz", hash = "sha256:e2d694c4e72106055295ad143664e5c99e5815b07190d1ff85b73b13ff019e63", size = 106312 } +wheels = [ + { url = "https://files.pythonhosted.org/packages/ec/f8/46141ba8c9d7064dc5008bfb4a6ae5bd3c30e4c61c28b5c5ed485bf358ba/pandas_stubs-2.2.3.250527-py3-none-any.whl", hash = "sha256:cd0a49a95b8c5f944e605be711042a4dd8550e2c559b43d70ba2c4b524b66163", size = 159683 }, +] + [[package]] name = "partd" version = "1.4.2" @@ -1562,6 +1575,7 @@ dev = [ { name = "mypy" }, { name = "numpy" }, { name = "pandas" }, + { name = "pandas-stubs" }, { name = "pdoc" }, { name = "pytest" }, { name = "pytest-asyncio" }, @@ -1588,6 +1602,7 @@ dev = [ { name = "mypy", specifier = ">=1.15.0" }, { name = "numpy", specifier = ">=2.1.3" }, { name = 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"https://files.pythonhosted.org/packages/c1/ba/e205cd11c1c7183b23c97e4bcd1de7bc0633e2e867601c32ecfc6ad42675/types_pytz-2025.2.0.20250516-py3-none-any.whl", hash = "sha256:e0e0c8a57e2791c19f718ed99ab2ba623856b11620cb6b637e5f62ce285a7451", size = 10136 }, +] + [[package]] name = "typing-extensions" version = "4.12.2" From 9560c26e3cad0830b6258301170306c124c2c3df Mon Sep 17 00:00:00 2001 From: TheGreatAlgo <37487508+TheGreatAlgo@users.noreply.github.com> Date: Wed, 28 May 2025 11:27:35 -0400 Subject: [PATCH 083/118] fix: simple encrypted zarr --- py_hamt/__init__.py | 2 + py_hamt/encryption_hamt_store.py | 165 ++ pyproject.toml | 1 + tests/test_zarr_ipfs_encrypted.py | 152 ++ uv.lock | 2423 +++++++++++++++-------------- 5 files changed, 1550 insertions(+), 1193 deletions(-) create mode 100644 py_hamt/encryption_hamt_store.py create mode 100644 tests/test_zarr_ipfs_encrypted.py diff --git a/py_hamt/__init__.py b/py_hamt/__init__.py index 2d420b1..6098400 100644 --- a/py_hamt/__init__.py +++ b/py_hamt/__init__.py @@ -1,6 +1,7 @@ from .hamt import HAMT, blake3_hashfn from .store import ContentAddressedStore, KuboCAS from .zarr_hamt_store import ZarrHAMTStore +from .encryption_hamt_store import SimpleEncryptedZarrHAMTStore __all__ = [ "blake3_hashfn", @@ -8,4 +9,5 @@ "ContentAddressedStore", "KuboCAS", "ZarrHAMTStore", + "SimpleEncryptedZarrHAMTStore", ] diff --git a/py_hamt/encryption_hamt_store.py b/py_hamt/encryption_hamt_store.py new file mode 100644 index 0000000..6d75f05 --- /dev/null +++ b/py_hamt/encryption_hamt_store.py @@ -0,0 +1,165 @@ +from collections.abc import AsyncIterator, Iterable +import zarr.abc.store +import zarr.core.buffer +from zarr.core.common import BytesLike +from py_hamt.hamt import HAMT +from Crypto.Cipher import ChaCha20_Poly1305 +from Crypto.Random import get_random_bytes +from py_hamt.zarr_hamt_store import ZarrHAMTStore + +class SimpleEncryptedZarrHAMTStore(ZarrHAMTStore): + """ + Write and read Zarr v3s with a HAMT, encrypting *everything* for maximum privacy. + + This store uses ChaCha20-Poly1305 to encrypt every single key-value pair + stored in the Zarr, including all metadata (`zarr.json`, `.zarray`, etc.) + and data chunks. This provides strong privacy but means the Zarr store is + completely opaque and unusable without the correct encryption key and header. + + #### Encryption Details + - Uses XChaCha20_Poly1305 (via pycryptodome's ChaCha20_Poly1305 with a 24-byte nonce). + - Requires a 32-byte encryption key and a header. + - Each encrypted value includes a 24-byte nonce and a 16-byte tag. + + #### Important Considerations + - Since metadata is encrypted, standard Zarr tools cannot inspect the + dataset without prior decryption using this store class. + - There is no support for partial encryption or excluding variables. + - There is no metadata caching. + + #### Sample Code + ```python + import xarray + from py_hamt import HAMT, IPFSStore # Assuming an IPFSStore or similar + from Crypto.Random import get_random_bytes + import numpy as np + + # Setup + ds = xarray.Dataset( + {"data": (("y", "x"), np.arange(12).reshape(3, 4))}, + coords={"y": [1, 2, 3], "x": [10, 20, 30, 40]} + ) + cas = IPFSStore() # Example ContentAddressedStore + encryption_key = get_random_bytes(32) + header = b"fully-encrypted-zarr" + + # --- Write --- + hamt_write = HAMT(cas=cas, values_are_bytes=True, read_only=False) + ezhs_write = SimpleEncryptedZarrHAMTStore( + hamt_write, False, encryption_key, header + ) + print("Writing fully encrypted Zarr...") + ds.to_zarr(store=ezhs_write, mode="w") + await hamt_write.make_read_only() + root_node_id = hamt_write.root_node_id + print(f"Wrote Zarr with root: {root_node_id}") + + # --- Read --- + hamt_read = HAMT(cas=cas, root_node_id=root_node_id, read_only=True, values_are_bytes=True) + ezhs_read = SimpleEncryptedZarrHAMTStore( + hamt_read, True, encryption_key, header + ) + print("\nReading fully encrypted Zarr...") + ds_read = xarray.open_zarr(store=ezhs_read) + print("Read back dataset:") + print(ds_read) + xarray.testing.assert_identical(ds, ds_read) + print("Read successful and data verified.") + + # --- Read with wrong key (demonstrates failure) --- + wrong_key = get_random_bytes(32) + hamt_bad = HAMT(cas=cas, root_node_id=root_node_id, read_only=True, values_are_bytes=True) + ezhs_bad = SimpleEncryptedZarrHAMTStore( + hamt_bad, True, wrong_key, header + ) + print("\nAttempting to read with wrong key...") + try: + ds_bad = xarray.open_zarr(store=ezhs_bad) + print(ds_bad) + except Exception as e: + print(f"Failed to read as expected: {type(e).__name__} - {e}") + ``` + """ + + def __init__( + self, hamt: HAMT, read_only: bool, encryption_key: bytes, header: bytes + ) -> None: + """ + Initializes the SimpleEncryptedZarrHAMTStore. + + Args: + hamt: The HAMT instance for storage. Must have `values_are_bytes=True`. + Its `read_only` status must match the `read_only` argument. + read_only: If True, the store is in read-only mode. + encryption_key: A 32-byte key for ChaCha20-Poly1305. + header: A header (bytes) used as associated data in encryption. + """ + super().__init__(hamt, read_only=read_only) + + if len(encryption_key) != 32: + raise ValueError("Encryption key must be exactly 32 bytes long.") + self.encryption_key = encryption_key + self.header = header + + def _encrypt(self, val: bytes) -> bytes: + """Encrypts data using ChaCha20-Poly1305.""" + nonce = get_random_bytes(24) # XChaCha20 uses a 24-byte nonce + cipher = ChaCha20_Poly1305.new(key=self.encryption_key, nonce=nonce) + cipher.update(self.header) + ciphertext, tag = cipher.encrypt_and_digest(val) + return nonce + tag + ciphertext + + def _decrypt(self, val: bytes) -> bytes: + """Decrypts data using ChaCha20-Poly1305.""" + try: + # Extract nonce (24), tag (16), and ciphertext + nonce, tag, ciphertext = val[:24], val[24:40], val[40:] + cipher = ChaCha20_Poly1305.new(key=self.encryption_key, nonce=nonce) + cipher.update(self.header) + plaintext = cipher.decrypt_and_verify(ciphertext, tag) + return plaintext + except Exception as e: + # Catching a broad exception as various issues (key, tag, length) can occur. + raise ValueError( + "Decryption failed. Check key, header, or data integrity." + ) from e + + def __eq__(self, other: object) -> bool: + """@private""" + if not isinstance(other, SimpleEncryptedZarrHAMTStore): + return False + return ( + self.hamt.root_node_id == other.hamt.root_node_id + and self.encryption_key == other.encryption_key + and self.header == other.header + ) + + async def get( + self, + key: str, + prototype: zarr.core.buffer.BufferPrototype, + byte_range: zarr.abc.store.ByteRequest | None = None, + ) -> zarr.core.buffer.Buffer | None: + """@private""" + if byte_range is not None: + raise NotImplementedError( + "Byte range requests are not supported by SimpleEncryptedZarrHAMTStore." + ) + try: + # Fetch raw (encrypted) value from HAMT + raw_val = await self.hamt.get(key) # type: ignore + # Decrypt it + decrypted_val = self._decrypt(raw_val) + return prototype.buffer.from_bytes(decrypted_val) + except KeyError: + return None + + async def set(self, key: str, value: zarr.core.buffer.Buffer) -> None: + """@private""" + if self.read_only: + raise Exception("Cannot write to a read-only store.") + + raw_bytes = value.to_bytes() + # Encrypt it + encrypted_bytes = self._encrypt(raw_bytes) + await self.hamt.set(key, encrypted_bytes) \ No newline at end of file diff --git a/pyproject.toml b/pyproject.toml index 6d19866..68dea62 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -11,6 +11,7 @@ dependencies = [ "multiformats[full]>=0.3.1.post4", "requests>=2.32.3", "zarr>=3.0.8", + "pycryptodome>=3.21.0", ] [build-system] diff --git a/tests/test_zarr_ipfs_encrypted.py b/tests/test_zarr_ipfs_encrypted.py new file mode 100644 index 0000000..a610e31 --- /dev/null +++ b/tests/test_zarr_ipfs_encrypted.py @@ -0,0 +1,152 @@ +import json +import numpy as np +import pandas as pd +import xarray as xr +import pytest +import zarr +import zarr.core.buffer +from Crypto.Random import get_random_bytes +from py_hamt import HAMT, KuboCAS, SimpleEncryptedZarrHAMTStore +from py_hamt.zarr_hamt_store import ZarrHAMTStore + + +@pytest.fixture(scope="module") +def random_zarr_dataset(): + """Creates a random xarray Dataset.""" + times = pd.date_range("2024-01-01", periods=10) # Reduced size for faster tests + lats = np.linspace(-90, 90, 5) + lons = np.linspace(-180, 180, 10) + temp = np.random.randn(len(times), len(lats), len(lons)) + ds = xr.Dataset( + {"temp": (["time", "lat", "lon"], temp)}, + coords={"time": times, "lat": lats, "lon": lons}, + attrs={"description": "Test dataset"}, + ) + yield ds + + +# Assume create_ipfs fixture exists and provides (rpc_base_url, gateway_base_url) +# You might need to add: @pytest.mark.asyncio(loop_scope="session") +@pytest.mark.asyncio +async def test_encrypted_write_read( + create_ipfs, # This fixture needs to be available in your conftest.py + random_zarr_dataset: xr.Dataset, +): + """ + Tests writing and reading a Zarr dataset using SimpleEncryptedZarrHAMTStore. + It covers successful reads, reads with incorrect keys, and reads + attempted without decryption. + """ + rpc_base_url, gateway_base_url = create_ipfs + test_ds = random_zarr_dataset + + # --- Setup Encryption --- + correct_key = get_random_bytes(32) + wrong_key = get_random_bytes(32) + header = b"test-encryption-header" + + root_cid = None + + # --- Write Phase --- + async with KuboCAS( + rpc_base_url=rpc_base_url, gateway_base_url=gateway_base_url + ) as kubo_cas: + print("\n--- Writing Encrypted Zarr ---") + hamt_write = await HAMT.build(cas=kubo_cas, values_are_bytes=True) + ezhs_write = SimpleEncryptedZarrHAMTStore( + hamt_write, False, correct_key, header + ) + + assert ezhs_write.supports_writes + test_ds.to_zarr(store=ezhs_write, mode="w", zarr_format=3) # Use mode='w' + + await hamt_write.make_read_only() + root_cid = hamt_write.root_node_id + print(f"Encrypted Root CID: {root_cid}") + assert root_cid is not None + + # --- Read Phase --- + async with KuboCAS( + rpc_base_url=rpc_base_url, gateway_base_url=gateway_base_url + ) as kubo_cas: + print("\n--- Reading Encrypted Zarr (Correct Key) ---") + hamt_read_ok = await HAMT.build( + cas=kubo_cas, root_node_id=root_cid, values_are_bytes=True, read_only=True + ) + ezhs_read_ok = SimpleEncryptedZarrHAMTStore( + hamt_read_ok, True, correct_key, header + ) + + ds_read_ok = xr.open_zarr(store=ezhs_read_ok) + print("Read successful. Verifying data...") + xr.testing.assert_identical(test_ds, ds_read_ok) + print("Data verified.") + + # --- Test: Read with Incorrect Key --- + print("\n--- Reading Encrypted Zarr (Incorrect Key) ---") + hamt_read_bad_key = await HAMT.build( + cas=kubo_cas, root_node_id=root_cid, values_are_bytes=True, read_only=True + ) + ezhs_read_bad_key = SimpleEncryptedZarrHAMTStore( + hamt_read_bad_key, True, wrong_key, header + ) + + with pytest.raises(ValueError, match="Decryption failed"): + xr.open_zarr(store=ezhs_read_bad_key) + print("Read failed as expected (ValueError).") + + # --- Test: Read without Decryption ("No Key") --- + print("\n--- Reading Encrypted Zarr (No Decryption) ---") + hamt_read_no_key = await HAMT.build( + cas=kubo_cas, root_node_id=root_cid, values_are_bytes=True, read_only=True + ) + # Use the *non-encrypted* store + zhs_read_no_key = ZarrHAMTStore(hamt_read_no_key, read_only=True) + + # Expect failure when trying to parse encrypted 'zarr.json' as JSON + with pytest.raises(Exception) as excinfo: + xr.open_zarr(store=zhs_read_no_key) + # Check if it's a JSON decode error or similar Zarr error. + # The exact error might vary, so checking for ValueError (from encryption) + # or JSONDecodeError or Zarr errors covers likely scenarios. + assert isinstance( + excinfo.value, + ( + ValueError, + json.JSONDecodeError, + ), + ) + print(f"Read failed as expected ({type(excinfo.value).__name__}).") + + # --- Basic Coverage Tests --- + assert await ezhs_read_ok.exists("zarr.json") + assert not await ezhs_read_ok.exists("non_existent_key") + assert ezhs_read_ok == ezhs_read_ok # Test __eq__ + assert ezhs_read_ok != ezhs_read_bad_key + assert not ezhs_read_ok.supports_writes + + keys_list = [k async for k in ezhs_read_ok.list()] + assert "zarr.json" in keys_list + assert "temp/c/0/0/0" in keys_list # Check for a known chunk key + + prefix_keys = [k async for k in ezhs_read_ok.list_prefix("temp/")] + assert all(k.startswith("temp/") for k in prefix_keys) + assert len(prefix_keys) > 0 + + dir_list = [k async for k in ezhs_read_ok.list_dir("")] + assert "zarr.json" in dir_list + assert "temp" in dir_list + + with pytest.raises(NotImplementedError): + await ezhs_read_ok.set_partial_values([]) + + with pytest.raises(NotImplementedError): + await ezhs_read_ok.get_partial_values( + zarr.core.buffer.default_buffer_prototype(), [] + ) + + with pytest.raises(Exception): + await ezhs_read_ok.set("new_key", np.array([b"a"], dtype=np.bytes_)) + + with pytest.raises(Exception): + await ezhs_read_ok.delete("zarr.json") diff --git a/uv.lock b/uv.lock index e14c0e7..9894562 100644 --- a/uv.lock +++ b/uv.lock @@ -1,19 +1,19 @@ version = 1 -revision = 1 +revision = 2 requires-python = ">=3.12" [[package]] name = "aiohappyeyeballs" version = "2.6.1" source = { registry = "https://pypi.org/simple" } -sdist = { url = "https://files.pythonhosted.org/packages/26/30/f84a107a9c4331c14b2b586036f40965c128aa4fee4dda5d3d51cb14ad54/aiohappyeyeballs-2.6.1.tar.gz", 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class SimpleEncryptedZarrHAMTStore(ZarrHAMTStore): """ Write and read Zarr v3s with a HAMT, encrypting *everything* for maximum privacy. @@ -141,10 +142,6 @@ async def get( byte_range: zarr.abc.store.ByteRequest | None = None, ) -> zarr.core.buffer.Buffer | None: """@private""" - if byte_range is not None: - raise NotImplementedError( - "Byte range requests are not supported by SimpleEncryptedZarrHAMTStore." - ) try: # Fetch raw (encrypted) value from HAMT raw_val = await self.hamt.get(key) # type: ignore @@ -162,4 +159,4 @@ async def set(self, key: str, value: zarr.core.buffer.Buffer) -> None: raw_bytes = value.to_bytes() # Encrypt it encrypted_bytes = self._encrypt(raw_bytes) - await self.hamt.set(key, encrypted_bytes) \ No newline at end of file + await self.hamt.set(key, encrypted_bytes) diff --git a/tests/test_zarr_ipfs_encrypted.py b/tests/test_zarr_ipfs_encrypted.py index a610e31..93878db 100644 --- a/tests/test_zarr_ipfs_encrypted.py +++ b/tests/test_zarr_ipfs_encrypted.py @@ -25,6 +25,51 @@ def random_zarr_dataset(): yield ds +async def test_invalid_encryption_key_length(): + """ + Tests that SimpleEncryptedZarrHAMTStore raises a ValueError + if the encryption key is not exactly 32 bytes long. + """ + async with KuboCAS() as kubo_cas: + hamt_write = await HAMT.build(cas=kubo_cas, values_are_bytes=True) + header = b"test-header" + # --- Test with a key that is too short (31 bytes) --- + short_key = get_random_bytes(31) + with pytest.raises( + ValueError, match="Encryption key must be exactly 32 bytes long." + ): + print("\nTesting with a 31-byte key...") + SimpleEncryptedZarrHAMTStore(hamt_write, False, short_key, header) + print("Failed as expected.") + + # --- Test with a key that is too long (33 bytes) --- + long_key = get_random_bytes(33) + with pytest.raises( + ValueError, match="Encryption key must be exactly 32 bytes long." + ): + print("Testing with a 33-byte key...") + SimpleEncryptedZarrHAMTStore(hamt_write, False, long_key, header) + print("Failed as expected.") + + # --- Test with an empty key --- + empty_key = b"" + with pytest.raises( + ValueError, match="Encryption key must be exactly 32 bytes long." + ): + print("Testing with an empty key...") + SimpleEncryptedZarrHAMTStore(hamt_write, False, empty_key, header) + print("Failed as expected.") + + # --- Test with a correct key (should NOT raise) --- + correct_key = get_random_bytes(32) + try: + print("Testing with a 32-byte key...") + SimpleEncryptedZarrHAMTStore(hamt_write, False, correct_key, header) + print("Initialized successfully (as expected).") + except ValueError as e: + pytest.fail(f"Should NOT raise ValueError for a 32-byte key, but got: {e}") + + # Assume create_ipfs fixture exists and provides (rpc_base_url, gateway_base_url) # You might need to add: @pytest.mark.asyncio(loop_scope="session") @pytest.mark.asyncio @@ -57,6 +102,10 @@ async def test_encrypted_write_read( hamt_write, False, correct_key, header ) + # __eq__ + assert ezhs_write == ezhs_write + assert ezhs_write != hamt_write + assert ezhs_write.supports_writes test_ds.to_zarr(store=ezhs_write, mode="w", zarr_format=3) # Use mode='w' From 6739d1c4149dd0fceb4d1b932d957dc4552c7653 Mon Sep 17 00:00:00 2001 From: Faolain Date: Thu, 29 May 2025 02:41:34 -0400 Subject: [PATCH 085/118] test: add typing to tests --- tests/performance_tests.py | 10 +++++----- tests/test_extract_bits.py | 2 +- tests/test_hamt.py | 25 ++++++++++++++----------- 3 files changed, 20 insertions(+), 17 deletions(-) diff --git a/tests/performance_tests.py b/tests/performance_tests.py index 41bfc61..3803e42 100644 --- a/tests/performance_tests.py +++ b/tests/performance_tests.py @@ -13,21 +13,21 @@ @pytest.mark.asyncio -async def test_large_kv_set(): +async def test_large_kv_set() -> None: """This test is meant for finding whether the HAMT performance scales linearly with increasing set size, an issue with HAMT v2. Feel free to tune and run the LARGE_KV_SET_SIZE variable as needed for gathering the different timepoints. """ - LARGE_KV_SET_SIZE = 1_000_000 + LARGE_KV_SET_SIZE: int = 1_000_000 cas = InMemoryCAS() hamt = await HAMT.build(cas=cas) - start = time.perf_counter() + start: float = time.perf_counter() await asyncio.gather( *[hamt.set(str(k_int), k_int) for k_int in range(LARGE_KV_SET_SIZE)] ) await hamt.make_read_only() - end = time.perf_counter() - elapsed = end - start + end: float = time.perf_counter() + elapsed: float = end - start print(f"Took {elapsed:.2f} seconds") assert ( len([key async for key in hamt.keys()]) diff --git a/tests/test_extract_bits.py b/tests/test_extract_bits.py index 1eb0d59..a5b9d0f 100644 --- a/tests/test_extract_bits.py +++ b/tests/test_extract_bits.py @@ -3,7 +3,7 @@ # Most of these tests were adapted over to python from rvagg's IAMap tests in JS -def test_extract_bits(): +def test_extract_bits() -> None: assert extract_bits(bytes([0b11111111]), 0, 5) == 0b11111 assert extract_bits(bytes([0b10101010]), 0, 5) == 0b10101 assert extract_bits(bytes([0b10000000]), 0, 5) == 0b10000 diff --git a/tests/test_hamt.py b/tests/test_hamt.py index 5ccd752..b666f1b 100644 --- a/tests/test_hamt.py +++ b/tests/test_hamt.py @@ -5,6 +5,7 @@ from multiformats import CID from hypothesis import given, settings from hypothesis import strategies as st +from typing import List, Tuple, Set, cast, Callable, Coroutine, Any import pytest from py_hamt.hamt import HAMT, Node @@ -18,7 +19,7 @@ @settings( deadline=1000 ) # increase for github CI which sometimes takes longer than the default 250 ms -async def test_fuzz(kvs: list[tuple[str, IPLDKind]]): +async def test_fuzz(kvs: list[tuple[str, IPLDKind]]) -> None: cas = InMemoryCAS() hamt = await HAMT.build(cas=cas) @@ -39,7 +40,7 @@ async def test_fuzz(kvs: list[tuple[str, IPLDKind]]): await hamt.make_read_only() # Verify completely concurrently - async def verify(k, v): + async def verify(k: str, v: IPLDKind): assert (await hamt.get(k)) == v await asyncio.gather(*[verify(k, v) for k, v in kvs]) @@ -57,7 +58,7 @@ async def verify(k, v): await hamt.enable_write() # HAMT should be throwing errors on keys that do not exist - ks = [k for k, _ in kvs] + ks: list[str] = [k for k, _ in kvs] key_that_cannot_exist = "".join(ks).join( "string to account for empty string key case" ) @@ -66,9 +67,9 @@ async def verify(k, v): with pytest.raises(KeyError): await hamt.delete(key_that_cannot_exist) - hamt_keys = [key async for key in hamt.keys()] - hamt_key_set = set(hamt_keys) - keys_set = set() + hamt_keys: list[str] = [key async for key in hamt.keys()] + hamt_key_set: set[str] = set(hamt_keys) + keys_set: set[str] = set() for key, _ in kvs: keys_set.add(key) @@ -76,7 +77,9 @@ async def verify(k, v): # Make sure all pointers actually exist in the store, this should not raise any exceptions for k, _ in kvs: - pointer: bytes = await hamt.get_pointer(k) # type: ignore we know that InMemoryCAS only returns bytes for its IDs + pointer: bytes = cast( + bytes, await hamt.get_pointer(k) + ) # we know that InMemoryCAS only returns bytes for its IDs await cas.load(pointer) await hamt.make_read_only() @@ -85,7 +88,7 @@ async def verify(k, v): with pytest.raises(Exception, match="Cannot call delete on a read only HAMT"): await hamt.delete("foo") - async def verify_kvs_and_len(h: HAMT): + async def verify_kvs_and_len(h: HAMT) -> None: for k, v in kvs: assert (await h.get(k)) == v assert len([key async for key in h.keys()]) == (await h.len()) == len(kvs) @@ -121,13 +124,13 @@ async def verify_kvs_and_len(h: HAMT): # Cache size management code branches coverage, do it all in async concurrency - small_cache_size_bytes = 1000 + small_cache_size_bytes: int = 1000 # Read cache read_hamt = await HAMT.build( cas=cas, root_node_id=hamt.root_node_id, read_only=True ) - async def get_and_vacate(k, v): + async def get_and_vacate(k: str, v: IPLDKind) -> None: assert (await read_hamt.get(k)) == v if (await read_hamt.cache_size()) > small_cache_size_bytes: await read_hamt.cache_vacate() @@ -139,7 +142,7 @@ async def get_and_vacate(k, v): # set small max bucket size to force more linking and more nodes small_memory_tree = await HAMT.build(cas=cas, max_bucket_size=1) - async def set_and_vacate(k, v): + async def set_and_vacate(k: str, v: IPLDKind) -> None: await small_memory_tree.set(k, v) assert (await small_memory_tree.get(k)) == v if (await small_memory_tree.cache_size()) > small_cache_size_bytes: From f44ed7f67bf927f1f5493ad2711c7f30aa19dfc4 Mon Sep 17 00:00:00 2001 From: Faolain Date: Thu, 29 May 2025 03:58:03 -0400 Subject: [PATCH 086/118] ci: integrate mypy into typing with some last additional types for tests --- .pre-commit-config.yaml | 4 ++++ py_hamt/hamt.py | 42 +++++++++++++++++--------------------- py_hamt/store.py | 27 ++++++++++++++++++------ py_hamt/zarr_hamt_store.py | 2 +- tests/test_hamt.py | 2 +- tests/test_kubo_cas.py | 20 ++++++++++++++---- tests/test_zarr_ipfs.py | 15 +++++++------- tests/testing_utils.py | 34 +++++++++++++++++------------- 8 files changed, 90 insertions(+), 56 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 75f6546..72c594e 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -26,3 +26,7 @@ repos: - id: slotscheck name: slotscheck entry: bash -c 'env PYTHONPATH=src slotscheck' + - repo: https://github.com/pre-commit/mirrors-mypy + rev: "v1.15.0" + hooks: + - id: mypy diff --git a/py_hamt/hamt.py b/py_hamt/hamt.py index 0371cb4..b238398 100644 --- a/py_hamt/hamt.py +++ b/py_hamt/hamt.py @@ -4,12 +4,8 @@ Iterator, AsyncIterator, Any, - Optional, - Union, cast, Dict, - List, - Tuple, ) import uuid import asyncio @@ -64,8 +60,8 @@ def blake3_hashfn(input_bytes: bytes) -> bytes: class Node: - def __init__(self): - self.data: List[IPLDKind] = [{} for _ in range(0, 256)] + def __init__(self) -> None: + self.data: list[IPLDKind] = [{} for _ in range(0, 256)] # empty dicts represent empty buckets # lists with one element are links, where list[0] is the real link @@ -82,14 +78,14 @@ def iter_link_indices(self) -> Iterator[int]: def iter_links(self) -> Iterator[IPLDKind]: for item in self.data: if isinstance(item, list): - yield cast(List[IPLDKind], item)[0] + yield cast(list[IPLDKind], item)[0] def get_link(self, index: int) -> IPLDKind: - link_wrapper: List[IPLDKind] = cast(List[IPLDKind], self.data[index]) + link_wrapper: list[IPLDKind] = cast(list[IPLDKind], self.data[index]) return link_wrapper[0] def set_link(self, index: int, link: IPLDKind): - wrapped: List[IPLDKind] = [link] + wrapped: list[IPLDKind] = [link] self.data[index] = wrapped # This assumes that there is only one unique link matching the old link, which is valid since we prune empty Nodes when reserializing and relinking @@ -100,7 +96,7 @@ def replace_link(self, old_link: IPLDKind, new_link: IPLDKind) -> None: self.set_link(link_index, new_link) return - def __deepcopy__(self, memo: Dict[int, Any]) -> "Node": + def __deepcopy__(self, memo: dict[int, Any]) -> "Node": new_node = Node() new_node.data = deepcopy(self.data) return new_node @@ -121,7 +117,7 @@ def deserialize(cls, data: bytes) -> "Node": # dag_cbor.decode() returns a union of many IPLD kinds. # We know a serialised Node is always a *list* of IPLDKinds, # so narrow the type for mypy. - decoded_data = cast(List[IPLDKind], dag_cbor.decode(data)) + decoded_data = cast(list[IPLDKind], dag_cbor.decode(data)) except: # noqa: E722 raise Exception( "Invalid dag-cbor encoded data from the store was attempted to be decoded" @@ -154,7 +150,7 @@ async def vacate(self): class ReadCacheStore(NodeStore): def __init__(self, hamt: "HAMT") -> None: self.hamt: HAMT = hamt - self.cache: Dict[IPLDKind, Node] = {} + self.cache: dict[IPLDKind, Node] = {} async def save(self, original_id: IPLDKind, node: Node) -> IPLDKind: raise Exception("Node was attempted to be written to the read cache") @@ -185,7 +181,7 @@ class InMemoryTreeStore(NodeStore): def __init__(self, hamt: "HAMT") -> None: self.hamt: HAMT = hamt # The integer key is a uuidv4 128-bit integer, for (almost perfectly) guaranteeing uniqueness - self.buffer: Dict[int, Node] = {} + self.buffer: dict[int, Node] = {} def is_buffer_id(self, id: IPLDKind) -> bool: return id in self.buffer @@ -218,7 +214,7 @@ def size(self) -> int: # This algorithm has an implicit assumption that the entire continuous line of branches up to an ancestor is in the memory buffer, which will happen because of the DFS style traversal in all HAMT operations async def vacate(self) -> None: # node stack is a list of tuples that look like (parent_id, self_id, node) - node_stack: List[Tuple[Optional[int], int, Node]] = [] + node_stack: list[tuple[int | None, int, Node]] = [] # The root node may not be in the buffer, e.g. this is HAMT initialized with a specific root node id if self.is_buffer_id(self.hamt.root_node_id): root_node: Node = self.buffer[cast(int, self.hamt.root_node_id)] @@ -226,7 +222,7 @@ async def vacate(self) -> None: while len(node_stack) > 0: parent_buffer_id, top_buffer_id, top_node = node_stack[-1] - new_nodes_on_stack: List[Tuple[int, int, Node]] = [] + new_nodes_on_stack: list[tuple[int, int, Node]] = [] for child_buffer_id in self.children_in_memory(top_node): child_node: Node = self.buffer[child_buffer_id] new_nodes_on_stack.append((top_buffer_id, child_buffer_id, child_node)) @@ -321,7 +317,7 @@ def __init__( self, cas: ContentAddressedStore, hash_fn: Callable[[bytes], bytes] = blake3_hashfn, - root_node_id: Optional[IPLDKind] = None, + root_node_id: IPLDKind | None = None, read_only: bool = False, max_bucket_size: int = 4, values_are_bytes: bool = False, @@ -450,7 +446,7 @@ async def cache_vacate(self) -> None: await self.node_store.vacate() async def _reserialize_and_link( - self, node_stack: List[Tuple[IPLDKind, Node]] + self, node_stack: list[tuple[IPLDKind, Node]] ) -> None: """ This function starts from the node at the end of the list and reserializes so that each node holds valid new IDs after insertion into the store @@ -508,13 +504,13 @@ async def set(self, key: str, val: IPLDKind) -> None: async def _set_pointer(self, key: str, val_ptr: IPLDKind) -> None: async with self.lock: - node_stack: List[Tuple[IPLDKind, Node]] = [] + node_stack: list[tuple[IPLDKind, Node]] = [] root_node: Node = await self.node_store.load(self.root_node_id) node_stack.append((self.root_node_id, root_node)) # FIFO queue to keep track of all the KVs we need to insert # This is needed if any buckets overflow and so we need to reinsert all those KVs - kvs_queue: List[Tuple[str, IPLDKind]] = [] + kvs_queue: list[tuple[str, IPLDKind]] = [] kvs_queue.append((key, val_ptr)) while len(kvs_queue) > 0: @@ -530,7 +526,7 @@ async def _set_pointer(self, key: str, val_ptr: IPLDKind) -> None: next_node: Node = await self.node_store.load(next_node_id) node_stack.append((next_node_id, next_node)) elif isinstance(item, dict): - bucket: Dict[str, IPLDKind] = item + bucket: dict[str, IPLDKind] = item # If this bucket already has this same key, or has space, just rewrite the value and then go work on the others in the queue if curr_key in bucket or len(bucket) < self.max_bucket_size: @@ -546,7 +542,7 @@ async def _set_pointer(self, key: str, val_ptr: IPLDKind) -> None: # Create a new link to a new node so that we can reflow these KVs into a new subtree new_node = Node() new_node_id: IPLDKind = await self.node_store.save(None, new_node) - link: List[IPLDKind] = [new_node_id] + link: list[IPLDKind] = [new_node_id] top_node.data[map_key] = link # Finally, reserialize and fix all links, deleting empty nodes as needed @@ -563,7 +559,7 @@ async def delete(self, key: str) -> None: async with self.lock: raw_hash: bytes = self.hash_fn(key.encode()) - node_stack: List[Tuple[IPLDKind, Node]] = [] + node_stack: list[tuple[IPLDKind, Node]] = [] root_node: Node = await self.node_store.load(self.root_node_id) node_stack.append((self.root_node_id, root_node)) @@ -658,7 +654,7 @@ async def _get_pointer(self, key: str) -> IPLDKind: # Callers MUST handle locking or not on their own async def _iter_nodes(self) -> AsyncIterator[tuple[IPLDKind, Node]]: - node_id_stack: List[IPLDKind] = [self.root_node_id] + node_id_stack: list[IPLDKind] = [self.root_node_id] while len(node_id_stack) > 0: top_id: IPLDKind = node_id_stack.pop() node: Node = await self.node_store.load(top_id) diff --git a/py_hamt/store.py b/py_hamt/store.py index cc8096a..aed57e9 100644 --- a/py_hamt/store.py +++ b/py_hamt/store.py @@ -1,6 +1,6 @@ import asyncio import aiohttp -from typing import Literal, Optional, Dict, cast, Any +from typing import Literal, cast, Any from abc import ABC, abstractmethod from dag_cbor.ipld import IPLDKind from multiformats import multihash @@ -37,7 +37,7 @@ async def load(self, id: IPLDKind) -> bytes: class InMemoryCAS(ContentAddressedStore): """Used mostly for faster testing, this is why this is not exported. It hashes all inputs and uses that as a key to an in-memory python dict, mimicking a content addressed storage system. The hash bytes are the ID that `save` returns and `load` takes in.""" - store: Dict[bytes, bytes] + store: dict[bytes, bytes] hash_alg: Multihash def __init__(self): @@ -49,11 +49,26 @@ async def save(self, data: bytes, codec: ContentAddressedStore.CodecInput) -> by self.store[hash] = data return hash - async def load(self, id: bytes) -> bytes: # type: ignore since bytes is a subset of the IPLDKind type - if id in self.store: - return self.store[id] + async def load(self, id: IPLDKind) -> bytes: + """ + `ContentAddressedStore` allows any IPLD scalar key. For the in-memory + backend we *require* a `bytes` hash; anything else is rejected at run + time. In OO type-checking, a subclass may widen (make more general) argument types, + but it must never narrow them; otherwise callers that expect the base-class contract can break. + Mypy enforces this contra-variance rule and emits the “violates Liskov substitution principle” error. + This is why we use `cast` here, to tell mypy that we know what we are doing. + h/t https://stackoverflow.com/questions/75209249/overriding-a-method-mypy-throws-an-incompatible-with-super-type-error-when-ch + """ + key = cast(bytes, id) + if not isinstance(key, (bytes, bytearray)): # defensive guard + raise TypeError( + f"InMemoryCAS only supports byte‐hash keys; got {type(id).__name__}" + ) - raise KeyError + try: + return self.store[key] + except KeyError as exc: + raise KeyError("Object not found in in-memory store") from exc class KuboCAS(ContentAddressedStore): diff --git a/py_hamt/zarr_hamt_store.py b/py_hamt/zarr_hamt_store.py index a1a3e1b..423dfbc 100644 --- a/py_hamt/zarr_hamt_store.py +++ b/py_hamt/zarr_hamt_store.py @@ -1,5 +1,5 @@ from collections.abc import AsyncIterator, Iterable -from typing import Optional, Dict, List, Tuple, cast +from typing import cast import zarr.abc.store import zarr.core.buffer from zarr.core.common import BytesLike diff --git a/tests/test_hamt.py b/tests/test_hamt.py index b666f1b..19f0fb3 100644 --- a/tests/test_hamt.py +++ b/tests/test_hamt.py @@ -5,7 +5,7 @@ from multiformats import CID from hypothesis import given, settings from hypothesis import strategies as st -from typing import List, Tuple, Set, cast, Callable, Coroutine, Any +from typing import cast import pytest from py_hamt.hamt import HAMT, Node diff --git a/tests/test_kubo_cas.py b/tests/test_kubo_cas.py index 956c404..2a08c34 100644 --- a/tests/test_kubo_cas.py +++ b/tests/test_kubo_cas.py @@ -1,6 +1,7 @@ import aiohttp import dag_cbor from dag_cbor import IPLDKind +from typing import Literal, cast from hypothesis import given, settings import pytest @@ -36,10 +37,16 @@ async def test_kubo_default_urls( async with KuboCAS(session=global_client_session) as kubo_cas_default: # print(f"Testing with default URLs: RPC={kubo_cas_default.rpc_base_url}, Gateway={kubo_cas_default.gateway_base_url}") encoded_data = dag_cbor.encode(data) + for codec in ["raw", "dag-cbor"]: + # The codec is a string, but we use Literal to ensure type safety + # where codec_raw = "raw" and codec_dag_cbor = "dag-cbor" + # necessary because when you iterate over a list of strings, + # even if they are literal strings, mypy widens the type to just str + codec_typed = cast(Literal["raw", "dag-cbor"], codec) # print(f"Saving with codec: {codec}, data: {data}") try: - cid = await kubo_cas_default.save(encoded_data, codec=codec) + cid = await kubo_cas_default.save(encoded_data, codec=codec_typed) # print(f"Saved. CID: {cid}") loaded_encoded_data = await kubo_cas_default.load(cid) # print(f"Loaded encoded data length: {len(loaded_encoded_data)}") @@ -64,8 +71,9 @@ async def test_kubo_default_urls( ) # Re-encode just in case, though it's the same data for codec in ["raw", "dag-cbor"]: # print(f"Saving with codec: {codec}, data: {data}") + codec_typed = cast(Literal["raw", "dag-cbor"], codec) try: - cid = await kubo_cas_none_urls.save(encoded_data, codec=codec) + cid = await kubo_cas_none_urls.save(encoded_data, codec=codec_typed) # print(f"Saved. CID: {cid}") loaded_encoded_data = await kubo_cas_none_urls.load(cid) # print(f"Loaded encoded data length: {len(loaded_encoded_data)}") @@ -114,7 +122,11 @@ async def test_kubo_cas(create_ipfs, data: IPLDKind): # noqa gateway_base_url=gateway_base_url, session=session, ) as kubo_cas: - for codec in ["raw", "dag-cbor"]: - cid = await kubo_cas.save(dag_cbor.encode(data), codec=codec) + # Use proper literal types for codec + codec_raw: Literal["raw"] = "raw" + codec_dag_cbor: Literal["dag-cbor"] = "dag-cbor" + for codec in [codec_raw, codec_dag_cbor]: + codec_typed = cast(Literal["raw", "dag-cbor"], codec) + cid = await kubo_cas.save(dag_cbor.encode(data), codec=codec_typed) result = dag_cbor.decode(await kubo_cas.load(cid)) assert data == result diff --git a/tests/test_zarr_ipfs.py b/tests/test_zarr_ipfs.py index 9b3bf35..11ffcb8 100644 --- a/tests/test_zarr_ipfs.py +++ b/tests/test_zarr_ipfs.py @@ -6,6 +6,7 @@ import pytest import zarr import zarr.core.buffer +from dag_cbor.ipld import IPLDKind from py_hamt import HAMT, KuboCAS @@ -58,7 +59,7 @@ def random_zarr_dataset(): # This test also collects miscellaneous statistics about performance, run with pytest -s to see these statistics being printed out @pytest.mark.asyncio(loop_scope="session") # ← match the loop of the fixture async def test_write_read( - create_ipfs, + create_ipfs: tuple[str, str], random_zarr_dataset: xr.Dataset, ): # noqa for fixture which is imported above but then "redefined" rpc_base_url, gateway_base_url = create_ipfs @@ -82,7 +83,7 @@ async def test_write_read( print(f"Total time in seconds: {elapsed:.2f}") print("=== Root CID") await hamt.make_read_only() - cid = hamt.root_node_id + cid: IPLDKind = hamt.root_node_id print(cid) print("=== Reading data back in and checking if identical") @@ -116,7 +117,7 @@ async def test_write_read( assert not zhs.supports_partial_writes assert not zhs.supports_deletes - hamt_keys = set() + hamt_keys: set[str] = set() async for k in zhs.hamt.keys(): hamt_keys.add(k) @@ -143,16 +144,16 @@ async def test_write_read( zarr.core.buffer.default_buffer_prototype(), [] ) - previous_zarr_json = await zhs.get( + previous_zarr_json: zarr.core.buffer.Buffer | None = await zhs.get( "zarr.json", zarr.core.buffer.default_buffer_prototype() ) assert previous_zarr_json is not None # Setting a metadata file that should always exist should not change anything await zhs.set_if_not_exists( "zarr.json", - np.array([b"a"], dtype=np.bytes_), # type: ignore - ) # type: ignore np.arrays, if dtype is bytes, is usable as a zarr buffer - zarr_json_now = await zhs.get( + np.array([b"a"], dtype=np.bytes_), # type: ignore[arg-type] + ) # np.arrays, if dtype is bytes, is usable as a zarr buffer + zarr_json_now: zarr.core.buffer.Buffer | None = await zhs.get( "zarr.json", zarr.core.buffer.default_buffer_prototype() ) assert zarr_json_now is not None diff --git a/tests/testing_utils.py b/tests/testing_utils.py index 5975a7b..7720299 100644 --- a/tests/testing_utils.py +++ b/tests/testing_utils.py @@ -6,6 +6,8 @@ import tempfile import time from pathlib import Path +from typing import Generator, Tuple, Any + import pytest from hypothesis import strategies as st @@ -59,10 +61,10 @@ def find_free_port() -> int: @pytest.fixture(scope="module") -def create_ipfs(): +def create_ipfs() -> Generator[Tuple[str, str], None, None]: # Create temporary directory, set it as the IPFS Path - temp_dir = Path(tempfile.mkdtemp()) - custom_env = os.environ.copy() + temp_dir: Path = Path(tempfile.mkdtemp()) + custom_env: dict[str, str] = os.environ.copy() custom_env["IPFS_PATH"] = str(temp_dir) # IPFS init @@ -71,21 +73,23 @@ def create_ipfs(): ) # Edit the config file so that it serves on randomly selected and available ports to not conflict with any currently running ipfs daemons - swarm_port = find_free_port() - rpc_port = find_free_port() - gateway_port = find_free_port() + swarm_port: int = find_free_port() + rpc_port: int = find_free_port() + gateway_port: int = find_free_port() - config_path = temp_dir / "config" - config: dict + config_path: Path = temp_dir / "config" + config: dict[str, Any] with open(config_path, "r") as f: config = json.load(f) swarm_addrs: list[str] = config["Addresses"]["Swarm"] - new_port_swarm_addrs = [s.replace("4001", str(swarm_port)) for s in swarm_addrs] + new_port_swarm_addrs: list[str] = [ + s.replace("4001", str(swarm_port)) for s in swarm_addrs + ] config["Addresses"]["Swarm"] = new_port_swarm_addrs - rpc_multiaddr = config["Addresses"]["API"] - gateway_multiaddr = config["Addresses"]["Gateway"] + rpc_multiaddr: str = config["Addresses"]["API"] + gateway_multiaddr: str = config["Addresses"]["Gateway"] config["Addresses"]["API"] = rpc_multiaddr.replace("5001", str(rpc_port)) config["Addresses"]["Gateway"] = gateway_multiaddr.replace( @@ -96,10 +100,12 @@ def create_ipfs(): json.dump(config, f, indent=2) # Start the daemon - rpc_uri_stem = f"http://127.0.0.1:{rpc_port}" - gateway_uri_stem = f"http://127.0.0.1:{gateway_port}" + rpc_uri_stem: str = f"http://127.0.0.1:{rpc_port}" + gateway_uri_stem: str = f"http://127.0.0.1:{gateway_port}" - ipfs_process = subprocess.Popen(["ipfs", "daemon"], env=custom_env) + ipfs_process: subprocess.Popen[bytes] = subprocess.Popen( + ["ipfs", "daemon"], env=custom_env + ) # Should be enough time for the ipfs daemon process to start up time.sleep(5) From 04a4a95d29a4e93a5728722c135deb7317f77840 Mon Sep 17 00:00:00 2001 From: Faolain Date: Thu, 29 May 2025 04:10:36 -0400 Subject: [PATCH 087/118] test: missing test after runtime bytes check inmemorycas --- tests/test_kubo_cas.py | 30 +++++++++++++++++++++++++++--- 1 file changed, 27 insertions(+), 3 deletions(-) diff --git a/tests/test_kubo_cas.py b/tests/test_kubo_cas.py index 2a08c34..61f1b15 100644 --- a/tests/test_kubo_cas.py +++ b/tests/test_kubo_cas.py @@ -19,6 +19,30 @@ async def test_memory_store_exception(): await s.load(bytes()) +@pytest.mark.asyncio +async def test_memory_store_invalid_key_type(): + """Test that InMemoryCAS.load raises TypeError for non-bytes keys""" + s = InMemoryCAS() + + # Test with various non-bytes types + invalid_keys = [ + "string_key", + 123, + 12.34, + ["list", "key"], + {"dict": "key"}, + None, + True, + ] + + for invalid_key in invalid_keys: + with pytest.raises( + TypeError, + match=f"InMemoryCAS only supports byte‐hash keys; got {type(invalid_key).__name__}", + ): + await s.load(invalid_key) + + @pytest.mark.asyncio(loop_scope="session") @given(data=ipld_strategy()) @settings( @@ -52,9 +76,9 @@ async def test_kubo_default_urls( # print(f"Loaded encoded data length: {len(loaded_encoded_data)}") result = dag_cbor.decode(loaded_encoded_data) # print(f"Decoded result: {result}") - assert data == result, ( - f"Data mismatch for codec {codec} with default URLs" - ) + assert ( + data == result + ), f"Data mismatch for codec {codec} with default URLs" except Exception as e: pytest.fail( f"Error during KuboCAS default URL test (codec: {codec}): {e}" From 381305a2b02ca7c8681d269df3989288d9512e2c Mon Sep 17 00:00:00 2001 From: Faolain Date: Thu, 29 May 2025 04:12:04 -0400 Subject: [PATCH 088/118] fix: ruff format --- tests/test_kubo_cas.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/tests/test_kubo_cas.py b/tests/test_kubo_cas.py index 61f1b15..b0cf12c 100644 --- a/tests/test_kubo_cas.py +++ b/tests/test_kubo_cas.py @@ -76,9 +76,9 @@ async def test_kubo_default_urls( # print(f"Loaded encoded data length: {len(loaded_encoded_data)}") result = dag_cbor.decode(loaded_encoded_data) # print(f"Decoded result: {result}") - assert ( - data == result - ), f"Data mismatch for codec {codec} with default URLs" + assert data == result, ( + f"Data mismatch for codec {codec} with default URLs" + ) except Exception as e: pytest.fail( f"Error during KuboCAS default URL test (codec: {codec}): {e}" From 7c4f7e65e9a09c3046f4c8cf8f49293f2b7af806 Mon Sep 17 00:00:00 2001 From: TheGreatAlgo <37487508+TheGreatAlgo@users.noreply.github.com> Date: Fri, 30 May 2025 09:11:27 -0400 Subject: [PATCH 089/118] fix: metadata read cache --- py_hamt/encryption_hamt_store.py | 23 +++++++++++++++++------ tests/test_zarr_ipfs_encrypted.py | 4 ++++ 2 files changed, 21 insertions(+), 6 deletions(-) diff --git a/py_hamt/encryption_hamt_store.py b/py_hamt/encryption_hamt_store.py index f8c0633..c517965 100644 --- a/py_hamt/encryption_hamt_store.py +++ b/py_hamt/encryption_hamt_store.py @@ -1,7 +1,5 @@ -from collections.abc import AsyncIterator, Iterable import zarr.abc.store import zarr.core.buffer -from zarr.core.common import BytesLike from py_hamt.hamt import HAMT from Crypto.Cipher import ChaCha20_Poly1305 from Crypto.Random import get_random_bytes @@ -17,6 +15,8 @@ class SimpleEncryptedZarrHAMTStore(ZarrHAMTStore): and data chunks. This provides strong privacy but means the Zarr store is completely opaque and unusable without the correct encryption key and header. + Note: For standard zarr encryption and decryption where metadata is available use the method in https://github.com/dClimate/jupyter-notebooks/blob/main/notebooks/202b%20-%20Encryption%20Example%20(Encryption%20with%20Zarr%20Codecs).ipynb + #### Encryption Details - Uses XChaCha20_Poly1305 (via pycryptodome's ChaCha20_Poly1305 with a 24-byte nonce). - Requires a 32-byte encryption key and a header. @@ -101,6 +101,7 @@ def __init__( raise ValueError("Encryption key must be exactly 32 bytes long.") self.encryption_key = encryption_key self.header = header + self.metadata_read_cache: dict[str, bytes] = dict() def _encrypt(self, val: bytes) -> bytes: """Encrypts data using ChaCha20-Poly1305.""" @@ -143,10 +144,18 @@ async def get( ) -> zarr.core.buffer.Buffer | None: """@private""" try: - # Fetch raw (encrypted) value from HAMT - raw_val = await self.hamt.get(key) # type: ignore - # Decrypt it - decrypted_val = self._decrypt(raw_val) + decrypted_val: bytes + is_metadata = ( + len(key) >= 9 and key[-9:] == "zarr.json" + ) # if path ends with zarr.json + + if is_metadata and key in self.metadata_read_cache: + decrypted_val = self.metadata_read_cache[key] + else: + raw_val = await self.hamt.get(key) # type: ignore + decrypted_val = self._decrypt(raw_val) + if is_metadata: + self.metadata_read_cache[key] = decrypted_val return prototype.buffer.from_bytes(decrypted_val) except KeyError: return None @@ -157,6 +166,8 @@ async def set(self, key: str, value: zarr.core.buffer.Buffer) -> None: raise Exception("Cannot write to a read-only store.") raw_bytes = value.to_bytes() + if key in self.metadata_read_cache: + self.metadata_read_cache[key] = raw_bytes # Encrypt it encrypted_bytes = self._encrypt(raw_bytes) await self.hamt.set(key, encrypted_bytes) diff --git a/tests/test_zarr_ipfs_encrypted.py b/tests/test_zarr_ipfs_encrypted.py index 93878db..736ab04 100644 --- a/tests/test_zarr_ipfs_encrypted.py +++ b/tests/test_zarr_ipfs_encrypted.py @@ -131,6 +131,10 @@ async def test_encrypted_write_read( xr.testing.assert_identical(test_ds, ds_read_ok) print("Data verified.") + # Open another zarr with the same store to ensure caching works + ds_check_again = xr.open_zarr(store=ezhs_read_ok) + xr.testing.assert_identical(test_ds, ds_check_again) + # --- Test: Read with Incorrect Key --- print("\n--- Reading Encrypted Zarr (Incorrect Key) ---") hamt_read_bad_key = await HAMT.build( From 5ff205ad9b715d6a9a62a7f5fa967d475fac8037 Mon Sep 17 00:00:00 2001 From: TheGreatAlgo <37487508+TheGreatAlgo@users.noreply.github.com> Date: Fri, 30 May 2025 10:39:19 -0400 Subject: [PATCH 090/118] fix: typing --- py_hamt/encryption_hamt_store.py | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/py_hamt/encryption_hamt_store.py b/py_hamt/encryption_hamt_store.py index c517965..6ca01e8 100644 --- a/py_hamt/encryption_hamt_store.py +++ b/py_hamt/encryption_hamt_store.py @@ -4,6 +4,7 @@ from Crypto.Cipher import ChaCha20_Poly1305 from Crypto.Random import get_random_bytes from py_hamt.zarr_hamt_store import ZarrHAMTStore +from typing import cast class SimpleEncryptedZarrHAMTStore(ZarrHAMTStore): @@ -101,7 +102,7 @@ def __init__( raise ValueError("Encryption key must be exactly 32 bytes long.") self.encryption_key = encryption_key self.header = header - self.metadata_read_cache: dict[str, bytes] = dict() + self.metadata_read_cache: dict[str, bytes] = {} def _encrypt(self, val: bytes) -> bytes: """Encrypts data using ChaCha20-Poly1305.""" @@ -145,14 +146,16 @@ async def get( """@private""" try: decrypted_val: bytes - is_metadata = ( + is_metadata: bool = ( len(key) >= 9 and key[-9:] == "zarr.json" ) # if path ends with zarr.json if is_metadata and key in self.metadata_read_cache: decrypted_val = self.metadata_read_cache[key] else: - raw_val = await self.hamt.get(key) # type: ignore + raw_val = cast( + bytes, await self.hamt.get(key) + ) # We know values received will always be bytes since we only store bytes in the HAMT decrypted_val = self._decrypt(raw_val) if is_metadata: self.metadata_read_cache[key] = decrypted_val From f9dd3b4f1671d53912478a3f0680776a938c6d27 Mon Sep 17 00:00:00 2001 From: TheGreatAlgo <37487508+TheGreatAlgo@users.noreply.github.com> Date: Fri, 30 May 2025 11:25:29 -0400 Subject: [PATCH 091/118] fix: update comments --- py_hamt/encryption_hamt_store.py | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/py_hamt/encryption_hamt_store.py b/py_hamt/encryption_hamt_store.py index 6ca01e8..39f3e80 100644 --- a/py_hamt/encryption_hamt_store.py +++ b/py_hamt/encryption_hamt_store.py @@ -32,7 +32,7 @@ class SimpleEncryptedZarrHAMTStore(ZarrHAMTStore): #### Sample Code ```python import xarray - from py_hamt import HAMT, IPFSStore # Assuming an IPFSStore or similar + from py_hamt import HAMT, KuboCAS # Assuming an KuboCAS or similar from Crypto.Random import get_random_bytes import numpy as np @@ -41,12 +41,12 @@ class SimpleEncryptedZarrHAMTStore(ZarrHAMTStore): {"data": (("y", "x"), np.arange(12).reshape(3, 4))}, coords={"y": [1, 2, 3], "x": [10, 20, 30, 40]} ) - cas = IPFSStore() # Example ContentAddressedStore + cas = KuboCAS() # Example ContentAddressedStore encryption_key = get_random_bytes(32) header = b"fully-encrypted-zarr" # --- Write --- - hamt_write = HAMT(cas=cas, values_are_bytes=True, read_only=False) + hamt_write = await HAMT.build(cas=kubo_cas, values_are_bytes=True) ezhs_write = SimpleEncryptedZarrHAMTStore( hamt_write, False, encryption_key, header ) @@ -57,7 +57,9 @@ class SimpleEncryptedZarrHAMTStore(ZarrHAMTStore): print(f"Wrote Zarr with root: {root_node_id}") # --- Read --- - hamt_read = HAMT(cas=cas, root_node_id=root_node_id, read_only=True, values_are_bytes=True) + hamt_read = await HAMT.build( + cas=kubo_cas, root_node_id=root_node_id, values_are_bytes=True, read_only=True + ) ezhs_read = SimpleEncryptedZarrHAMTStore( hamt_read, True, encryption_key, header ) From e8b4f429cfdf94b82ef6959cee6a2ba86a1595da Mon Sep 17 00:00:00 2001 From: Faolain Date: Sat, 31 May 2025 23:48:38 -0400 Subject: [PATCH 092/118] test: added deterministic anchor for full test coverage --- tests/test_branch_anchors.py | 17 +++++++++++++++++ 1 file changed, 17 insertions(+) create mode 100644 tests/test_branch_anchors.py diff --git a/tests/test_branch_anchors.py b/tests/test_branch_anchors.py new file mode 100644 index 0000000..289e0a0 --- /dev/null +++ b/tests/test_branch_anchors.py @@ -0,0 +1,17 @@ +# tests/test_branch_anchors.py +import pytest +from py_hamt import HAMT +from py_hamt.store import InMemoryCAS + + +@pytest.mark.asyncio +async def test_force_every_branch(): + cas = InMemoryCAS() + hamt = await HAMT.build(cas=cas, max_bucket_size=1) + for k in ("5", "15", "123"): + await hamt.set(k, b"x") + + await hamt.cache_size() + await hamt.cache_vacate() # writes -> vacate(write) + await hamt.make_read_only() # flush -> vacate(read) + await hamt.get("5") # _get_pointer follows link From b4a02900eb0bd8888655ad949c773c24278f60d0 Mon Sep 17 00:00:00 2001 From: Faolain Date: Sat, 31 May 2025 23:59:52 -0400 Subject: [PATCH 093/118] test: add deterministic anchor for cache vacate --- tests/test_branch_anchors.py | 25 +++++++++++++++++++++---- 1 file changed, 21 insertions(+), 4 deletions(-) diff --git a/tests/test_branch_anchors.py b/tests/test_branch_anchors.py index 289e0a0..bbf7217 100644 --- a/tests/test_branch_anchors.py +++ b/tests/test_branch_anchors.py @@ -7,11 +7,28 @@ @pytest.mark.asyncio async def test_force_every_branch(): cas = InMemoryCAS() + # 1 → guaranteed bucket overflow so we create links, etc. hamt = await HAMT.build(cas=cas, max_bucket_size=1) + + # Three colliding keys (covers children_in_memory / recurse) for k in ("5", "15", "123"): await hamt.set(k, b"x") - await hamt.cache_size() - await hamt.cache_vacate() # writes -> vacate(write) - await hamt.make_read_only() # flush -> vacate(read) - await hamt.get("5") # _get_pointer follows link + # ------------------------------------------------------------------ + # A. write-mode vacate + # ------------------------------------------------------------------ + await hamt.cache_vacate() # write-mode branch + + # ------------------------------------------------------------------ + # B. read-cache vacate + # ------------------------------------------------------------------ + await hamt.make_read_only() # flushes tree, swaps store + + # Build up the read-cache by touching one key + await hamt.get("5") + + # Now vacate the *read* cache + await hamt.cache_vacate() + + # quick sanity-check: cache really is empty + assert await hamt.cache_size() == 0 From 78752c8d2ae40ccdc41733eb848bc080436e2447 Mon Sep 17 00:00:00 2001 From: Faolain Date: Sun, 1 Jun 2025 00:17:18 -0400 Subject: [PATCH 094/118] test: another deterministic anchor attempt --- tests/test_branch_anchors.py | 46 ++++++++++++++++++++++++------------ 1 file changed, 31 insertions(+), 15 deletions(-) diff --git a/tests/test_branch_anchors.py b/tests/test_branch_anchors.py index bbf7217..5e328b4 100644 --- a/tests/test_branch_anchors.py +++ b/tests/test_branch_anchors.py @@ -1,34 +1,50 @@ # tests/test_branch_anchors.py import pytest -from py_hamt import HAMT +from py_hamt import HAMT, blake3_hashfn from py_hamt.store import InMemoryCAS +def find_colliding_keys(count: int = 3) -> list[str]: + """Find *count* decimal strings whose Blake3 hashes share byte[0].""" + chosen: list[str] = [] + wanted_byte: int | None = None + i: int = 0 + + while len(chosen) < count: + k = str(i) + b0 = blake3_hashfn(k.encode())[0] + if wanted_byte is None or b0 == wanted_byte: + wanted_byte = b0 + chosen.append(k) + i += 1 + return chosen + + @pytest.mark.asyncio async def test_force_every_branch(): cas = InMemoryCAS() - # 1 → guaranteed bucket overflow so we create links, etc. hamt = await HAMT.build(cas=cas, max_bucket_size=1) - # Three colliding keys (covers children_in_memory / recurse) - for k in ("5", "15", "123"): + # ------------------------------------------------------------------ + # 1. write some colliding keys → guarantees in-buffer links + # ------------------------------------------------------------------ + keys = find_colliding_keys() # save for later cache hit + for k in keys: await hamt.set(k, b"x") + # call cache_size() while still in WRITE mode + assert await hamt.cache_size() > 0 # executes lines 207-208 + # ------------------------------------------------------------------ - # A. write-mode vacate + # 2. write-mode cache_vacate() → covers HAMT.cache_vacate() write branch # ------------------------------------------------------------------ - await hamt.cache_vacate() # write-mode branch + await hamt.cache_vacate() # ------------------------------------------------------------------ - # B. read-cache vacate + # 3. switch to READ-ONLY, touch cache once, vacate again + # → covers ReadCacheStore.vacate() (line 177) # ------------------------------------------------------------------ - await hamt.make_read_only() # flushes tree, swaps store - - # Build up the read-cache by touching one key - await hamt.get("5") - - # Now vacate the *read* cache + await hamt.make_read_only() + await hamt.get(keys[0]) # populates read cache await hamt.cache_vacate() - - # quick sanity-check: cache really is empty assert await hamt.cache_size() == 0 From d7051a784eb0f1876d28573458bc62048a5ac17f Mon Sep 17 00:00:00 2001 From: Faolain Date: Sun, 1 Jun 2025 00:23:51 -0400 Subject: [PATCH 095/118] docs: update docstring for variable change typo --- py_hamt/encryption_hamt_store.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/py_hamt/encryption_hamt_store.py b/py_hamt/encryption_hamt_store.py index 39f3e80..6020d37 100644 --- a/py_hamt/encryption_hamt_store.py +++ b/py_hamt/encryption_hamt_store.py @@ -46,7 +46,7 @@ class SimpleEncryptedZarrHAMTStore(ZarrHAMTStore): header = b"fully-encrypted-zarr" # --- Write --- - hamt_write = await HAMT.build(cas=kubo_cas, values_are_bytes=True) + hamt_write = await HAMT.build(cas=cas, values_are_bytes=True) ezhs_write = SimpleEncryptedZarrHAMTStore( hamt_write, False, encryption_key, header ) @@ -58,7 +58,7 @@ class SimpleEncryptedZarrHAMTStore(ZarrHAMTStore): # --- Read --- hamt_read = await HAMT.build( - cas=kubo_cas, root_node_id=root_node_id, values_are_bytes=True, read_only=True + cas=cas, root_node_id=root_node_id, values_are_bytes=True, read_only=True ) ezhs_read = SimpleEncryptedZarrHAMTStore( hamt_read, True, encryption_key, header From e0832124f9fe46a4f2a2bde580c19f21ec9323d2 Mon Sep 17 00:00:00 2001 From: Faolain Date: Sun, 1 Jun 2025 01:50:03 -0400 Subject: [PATCH 096/118] fix: deduplicate key list in list_dir --- py_hamt/zarr_hamt_store.py | 9 +++++++-- tests/test_zarr_ipfs.py | 13 +++++++++++++ 2 files changed, 20 insertions(+), 2 deletions(-) diff --git a/py_hamt/zarr_hamt_store.py b/py_hamt/zarr_hamt_store.py index 423dfbc..7bbd140 100644 --- a/py_hamt/zarr_hamt_store.py +++ b/py_hamt/zarr_hamt_store.py @@ -181,12 +181,17 @@ async def list_dir(self, prefix: str) -> AsyncIterator[str]: """ @private """ + seen_names: set[str] = set() async for key in self.hamt.keys(): if key.startswith(prefix): suffix: str = key[len(prefix) :] first_slash: int = suffix.find("/") if first_slash == -1: - yield suffix + if suffix not in seen_names: + seen_names.add(suffix) + yield suffix else: name: str = suffix[0:first_slash] - yield name + if name not in seen_names: + seen_names.add(name) + yield name diff --git a/tests/test_zarr_ipfs.py b/tests/test_zarr_ipfs.py index 11ffcb8..4db3727 100644 --- a/tests/test_zarr_ipfs.py +++ b/tests/test_zarr_ipfs.py @@ -11,6 +11,7 @@ from py_hamt import HAMT, KuboCAS from py_hamt.zarr_hamt_store import ZarrHAMTStore +from py_hamt.store import InMemoryCAS @pytest.fixture(scope="module") @@ -177,3 +178,15 @@ async def test_write_read( ) assert zarr_json_now is not None assert previous_zarr_json.to_bytes() == zarr_json_now.to_bytes() + + +@pytest.mark.asyncio +async def test_list_dir_dedup(): + cas = InMemoryCAS() + hamt = await HAMT.build(cas=cas, values_are_bytes=True) + zhs = ZarrHAMTStore(hamt) + + await hamt.set("foo/bar/0", b"") + await hamt.set("foo/bar/1", b"") + results = [n async for n in zhs.list_dir("foo/")] + assert results == ["bar"] # no duplicates From 2b673610bafe58b5208e3857960ae2cec7ae390a Mon Sep 17 00:00:00 2001 From: Faolain Date: Sun, 1 Jun 2025 01:57:13 -0400 Subject: [PATCH 097/118] docs: added docstring for list_dirs function --- py_hamt/zarr_hamt_store.py | 39 ++++++++++++++++++++++++++++++++++++++ 1 file changed, 39 insertions(+) diff --git a/py_hamt/zarr_hamt_store.py b/py_hamt/zarr_hamt_store.py index 7bbd140..354f5e9 100644 --- a/py_hamt/zarr_hamt_store.py +++ b/py_hamt/zarr_hamt_store.py @@ -180,6 +180,45 @@ async def list_prefix(self, prefix: str) -> AsyncIterator[str]: async def list_dir(self, prefix: str) -> AsyncIterator[str]: """ @private + List *immediate* children that live directly under **prefix**. + + This is similar to :py:meth:`list_prefix` but collapses everything + below the first ``"/"`` after *prefix*. Each child name is yielded + **exactly once** in the order of first appearance while scanning the + HAMT keys. + + Parameters + ---------- + prefix : str + Logical directory path. *Must* end with ``"/"`` for the result to + make sense (e.g. ``"a/b/"``). + + Yields + ------ + str + The name of each direct child (file or sub-directory) of *prefix*. + + Examples + -------- + With keys :: + + a/b/c/d + a/b/c/e + a/b/f + a/b/g/h/i + + ``await list_dir("a/b/")`` produces :: + + c + f + g + + Notes + ----- + • Internally uses a :class:`set` to deduplicate names; memory grows + with the number of *unique* children, not the total number of keys. + • Order is **not** sorted; it reflects the first encounter while + iterating over :py:meth:`HAMT.keys`. """ seen_names: set[str] = set() async for key in self.hamt.keys(): From 29842a505b9ef786ee99a94128ad8804c2bf7a1c Mon Sep 17 00:00:00 2001 From: Faolain Date: Sun, 1 Jun 2025 02:04:35 -0400 Subject: [PATCH 098/118] docs: update py_hamt/encryption_hamt_store.py Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com> --- py_hamt/encryption_hamt_store.py | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/py_hamt/encryption_hamt_store.py b/py_hamt/encryption_hamt_store.py index 6020d37..e09c70e 100644 --- a/py_hamt/encryption_hamt_store.py +++ b/py_hamt/encryption_hamt_store.py @@ -72,9 +72,12 @@ class SimpleEncryptedZarrHAMTStore(ZarrHAMTStore): # --- Read with wrong key (demonstrates failure) --- wrong_key = get_random_bytes(32) - hamt_bad = HAMT(cas=cas, root_node_id=root_node_id, read_only=True, values_are_bytes=True) + hamt_bad = await HAMT.build( + cas=cas, root_node_id=root_node_id, read_only=True, values_are_bytes=True + ) ezhs_bad = SimpleEncryptedZarrHAMTStore( hamt_bad, True, wrong_key, header + hamt_bad, True, wrong_key, header ) print("\nAttempting to read with wrong key...") try: From 85e1f2ee60b32663d8dbacb2e0369aeb6cefb895 Mon Sep 17 00:00:00 2001 From: Faolain Date: Sun, 1 Jun 2025 02:53:48 -0400 Subject: [PATCH 099/118] docs: clarify docstrings --- py_hamt/encryption_hamt_store.py | 1 - py_hamt/zarr_hamt_store.py | 35 +++++++++++++++++++++++--------- 2 files changed, 25 insertions(+), 11 deletions(-) diff --git a/py_hamt/encryption_hamt_store.py b/py_hamt/encryption_hamt_store.py index e09c70e..67eaae0 100644 --- a/py_hamt/encryption_hamt_store.py +++ b/py_hamt/encryption_hamt_store.py @@ -77,7 +77,6 @@ class SimpleEncryptedZarrHAMTStore(ZarrHAMTStore): ) ezhs_bad = SimpleEncryptedZarrHAMTStore( hamt_bad, True, wrong_key, header - hamt_bad, True, wrong_key, header ) print("\nAttempting to read with wrong key...") try: diff --git a/py_hamt/zarr_hamt_store.py b/py_hamt/zarr_hamt_store.py index 423dfbc..eab9af8 100644 --- a/py_hamt/zarr_hamt_store.py +++ b/py_hamt/zarr_hamt_store.py @@ -11,27 +11,42 @@ class ZarrHAMTStore(zarr.abc.store.Store): """ Write and read Zarr v3s with a HAMT. + Read **or** write a Zarr-v3 store whose key/value pairs live inside a + py-hamt mapping. + + Keys are stored verbatim (``"temp/c/0/0/0"`` → same string in HAMT) and + the value is the raw byte payload produced by Zarr. No additional + framing, compression, or encryption is applied by this class. For a zarr encryption example + see where metadata is available use the method in https://github.com/dClimate/jupyter-notebooks/blob/main/notebooks/202b%20-%20Encryption%20Example%20(Encryption%20with%20Zarr%20Codecs).ipynb + For a fully encrypted zarr store, where metadata is not available, please see + :class:`SimpleEncryptedZarrHAMTStore` but we do not recommend using it. + #### A note about using the same `ZarrHAMTStore` for writing and then reading again If you write a Zarr to a HAMT, and then change it to read only mode, it's best to reinitialize a new ZarrHAMTStore with the proper read only setting. This is because this class, to err on the safe side, will not touch its super class's settings. #### Sample Code ```python - # Write + # --- Write --- ds: xarray.Dataset = # ... cas: ContentAddressedStore = # ... hamt: HAMT = # ... make sure values_are_bytes is True and read_only is False to enable writes - zhs = ZarrHAMTStore(hamt, False) - xarray.to_zarr(store=zhs) - await hamt.make_read_only() + hamt = await HAMT.build(cas, values_are_bytes=True) # write-enabled + zhs = ZarrHAMTStore(hamt, read_only=False) + ds.to_zarr(store=zhs, mode="w", zarr_format=3) + await hamt.make_read_only() # flush + freeze root_node_id = hamt.root_node_id print(root_node_id) - # Read - hamt_read = HAMT(cas=cas, root_node_id=root_node_id, read_only=True, values_are_bytes=True) - zhs_read = ZarrHAMTStore(hamt, True) - ds_read = xarray.open_zarr(store=zhs_read) - print(ds_read) - xarray.testing.assert_identical(ds, ds_read) + # --- read --- + hamt_ro = await HAMT.build( + cas, root_node_id=root_cid, read_only=True, values_are_bytes=True + ) + zhs_ro = ZarrHAMTStore(hamt_ro, read_only=True) + ds_ro = xarray.open_zarr(store=zhs_ro) + + + print(ds_ro) + xarray.testing.assert_identical(ds, ds_ro) ``` """ From 2a85afceddbec509ccd49edcd5950bba4a2b08e4 Mon Sep 17 00:00:00 2001 From: Faolain Date: Sun, 1 Jun 2025 03:01:03 -0400 Subject: [PATCH 100/118] chore: add sort to ruff to standardize import order --- pyproject.toml | 3 +++ 1 file changed, 3 insertions(+) diff --git a/pyproject.toml b/pyproject.toml index b8b36b5..3996236 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -34,3 +34,6 @@ dev = [ "mypy>=1.15.0", "pandas-stubs>=2.2.3.250527", ] + +[tool.ruff] +lint.extend-select = ["I"] From 345b702ba24c11e23d84a67bb0cd11f1c762ef2e Mon Sep 17 00:00:00 2001 From: Faolain Date: Mon, 2 Jun 2025 01:29:00 -0400 Subject: [PATCH 101/118] refactor: add concurrency as configurable option for semaphore --- py_hamt/store.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/py_hamt/store.py b/py_hamt/store.py index aed57e9..cacc3d5 100644 --- a/py_hamt/store.py +++ b/py_hamt/store.py @@ -91,6 +91,7 @@ def __init__( session: aiohttp.ClientSession | None = None, rpc_base_url: str | None = KUBO_DEFAULT_LOCAL_RPC_BASE_URL, gateway_base_url: str | None = KUBO_DEFAULT_LOCAL_GATEWAY_BASE_URL, + concurrency: int = 32, ): """ If None is passed into the rpc or gateway base url, then the default for kubo local daemons will be used. 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py_hamt/store.py | 78 ++++++++++++++++++++++++++++++++++++-- tests/test_kubocas_auth.py | 30 +++++++++++++++ 2 files changed, 104 insertions(+), 4 deletions(-) create mode 100644 tests/test_kubocas_auth.py diff --git a/py_hamt/store.py b/py_hamt/store.py index aed57e9..bbd0f46 100644 --- a/py_hamt/store.py +++ b/py_hamt/store.py @@ -73,9 +73,55 @@ async def load(self, id: IPLDKind) -> bytes: class KuboCAS(ContentAddressedStore): """ - Talks to a kubo daemon. The IDs in save and load are IPLD CIDs. + Connects to an **IPFS Kubo** daemon. + + The IDs in save and load are IPLD CIDs. + + * **save()** → RPC (`/api/v0/add`) + * **load()** → HTTP gateway (`/ipfs/{cid}`) `save` uses the RPC API and `load` uses the HTTP Gateway. This means that read-only HAMTs will only access the HTTP Gateway, so no RPC endpoint is required for use. + + ### Authentication / custom headers + You have two options: + + 1. **Bring your own `aiohttp.ClientSession`** + Pass it via `session=...` — any default headers or `BasicAuth` + configured on that session are reused for **every** request. + 2. **Let `KuboCAS` build the session** but pass + `headers=` *and*/or `auth=` kwargs; they are forwarded to the + internally–created `ClientSession`. + + ```python + import aiohttp + from py_hamt import KuboCAS + + # Option 1: user-supplied session + sess = aiohttp.ClientSession( + headers={"Authorization": "Bearer "}, + auth=aiohttp.BasicAuth("user", "pass"), + ) + cas = KuboCAS(session=sess) + + # Option 2: let KuboCAS create the session + cas = KuboCAS( + headers={"X-My-Header": "yes"}, + auth=aiohttp.BasicAuth("user", "pass"), + ) + ``` + + ### Parameters + - **hasher** (str): multihash name (defaults to *blake3*). + - **session** (`aiohttp.ClientSession | None`): reuse an existing + session; if *None* KuboCAS will create one lazily. + - **headers** (dict[str, str] | None): default headers for the + internally-created session. + - **auth** (`aiohttp.BasicAuth | None`): authentication object for + the internally-created session. + - **rpc_base_url / gateway_base_url** (str | None): override daemon + endpoints (defaults match the local daemon ports). + + ... """ KUBO_DEFAULT_LOCAL_GATEWAY_BASE_URL: str = "http://127.0.0.1:8080" @@ -91,15 +137,33 @@ def __init__( session: aiohttp.ClientSession | None = None, rpc_base_url: str | None = KUBO_DEFAULT_LOCAL_RPC_BASE_URL, gateway_base_url: str | None = KUBO_DEFAULT_LOCAL_GATEWAY_BASE_URL, + *, + headers: dict[str, str] | None = None, + auth: aiohttp.BasicAuth | None = None, ): """ If None is passed into the rpc or gateway base url, then the default for kubo local daemons will be used. The default local values will also be used if nothing is passed in at all. - ### `requests.Session` Management - If `requests_session` is not provided, it will be automatically initialized. It is the responsibility of the user to close this at an appropriate time, as a class instance cannot know when it will no longer be in use. + ### `aiohttp.ClientSession` Management + If `session` is not provided, it will be automatically initialized. It is the responsibility of the user to close this at an appropriate time, as a class instance cannot know when it will no longer be in use. + Usually the best way to do this is to use the `async with` syntax, which will automatically close the session when the block is exited. + ```python + async with aiohttp.ClientSession() as session, KuboCAS( + rpc_base_url=rpc_base_url, + gateway_base_url=gateway_base_url, + session=session, + ) as kubo_cas: + hamt = await HAMT.build(cas=kubo_cas, values_are_bytes=True) + zhs = ZarrHAMTStore(hamt) + # Use the KuboCAS instance as needed + # ... + ``` + If you do not use the `async with` syntax, you should call `await cas.aclose()` when you are done using the instance to ensure that all resources are cleaned up. ### Authenticated RPC/Gateway Access - Users can set whatever headers and auth credentials they need if they are connecting to an authenticated kubo instance by setting them in their own `requests.Session` and then passing that in. + Users can set whatever headers and auth credentials they need if they are connecting to an authenticated kubo instance by setting them in their own `aiohttp.ClientSession` and then passing that in. + Alternatively, they can pass in `headers` and `auth` parameters to the constructor, which will be used to create a new `aiohttp.ClientSession` if one is not provided. + If you do not need authentication, you can leave these parameters as `None`. ### RPC and HTTP Gateway Base URLs These are the first part of the url, defaults that refer to the default that kubo launches with on a local machine are provided. @@ -129,6 +193,10 @@ def __init__( else: self._owns_session = True # we’ll create sessions lazily + # store for later use by _loop_session() + self._default_headers = headers + self._default_auth = auth + self._sem: asyncio.Semaphore = asyncio.Semaphore(64) # --------------------------------------------------------------------- # @@ -142,6 +210,8 @@ def _loop_session(self) -> aiohttp.ClientSession: sess = aiohttp.ClientSession( timeout=aiohttp.ClientTimeout(total=60), connector=aiohttp.TCPConnector(limit=64, limit_per_host=32), + headers=self._default_headers, + auth=self._default_auth, ) self._session_per_loop[loop] = sess return sess diff --git a/tests/test_kubocas_auth.py b/tests/test_kubocas_auth.py new file mode 100644 index 0000000..244990a --- /dev/null +++ b/tests/test_kubocas_auth.py @@ -0,0 +1,30 @@ +# tests/test_kubocas_auth.py +import aiohttp +import pytest +import inspect +from py_hamt.store import KuboCAS + + +async def _maybe_await(x): + return await x if inspect.isawaitable(x) else x + + +@pytest.mark.asyncio +async def test_user_supplied_session_headers(): + sess = aiohttp.ClientSession(headers={"Authorization": "Bearer x"}) + cas = KuboCAS(session=sess) + assert (await _maybe_await(cas._loop_session())).headers[ + "Authorization" + ] == "Bearer x" + await cas.aclose() # must NOT close external session + assert not sess.closed + await sess.close() + + +@pytest.mark.asyncio +async def test_internal_session_headers() -> None: + cas = KuboCAS(headers={"X-Custom": "yes"}) + sess: aiohttp.ClientSession = await _maybe_await(cas._loop_session()) + assert sess.headers["X-Custom"] == "yes" + await cas.aclose() + assert sess.closed From 6d3178c834ea1fcc1a533eb30c82a885fdfc582e Mon Sep 17 00:00:00 2001 From: Faolain Date: Mon, 2 Jun 2025 14:27:16 -0400 Subject: [PATCH 104/118] docs: improve docstring clarity for using session w/ kubocas --- py_hamt/store.py | 14 +++++++++++--- 1 file changed, 11 insertions(+), 3 deletions(-) diff --git a/py_hamt/store.py b/py_hamt/store.py index bbd0f46..35b18bf 100644 --- a/py_hamt/store.py +++ b/py_hamt/store.py @@ -145,8 +145,10 @@ def __init__( If None is passed into the rpc or gateway base url, then the default for kubo local daemons will be used. The default local values will also be used if nothing is passed in at all. ### `aiohttp.ClientSession` Management - If `session` is not provided, it will be automatically initialized. It is the responsibility of the user to close this at an appropriate time, as a class instance cannot know when it will no longer be in use. - Usually the best way to do this is to use the `async with` syntax, which will automatically close the session when the block is exited. + If `session` is not provided, it will be automatically initialized. It is the responsibility of the user to close this at an appropriate time, using `await cas.aclose()` + as a class instance cannot know when it will no longer be in use, unless explicitly told to do so. + + If you are using the `KuboCAS` instance in an `async with` block, it will automatically close the session when the block is exited which is what we suggest below: ```python async with aiohttp.ClientSession() as session, KuboCAS( rpc_base_url=rpc_base_url, @@ -158,7 +160,13 @@ def __init__( # Use the KuboCAS instance as needed # ... ``` - If you do not use the `async with` syntax, you should call `await cas.aclose()` when you are done using the instance to ensure that all resources are cleaned up. + As mentioned, if you do not use the `async with` syntax, you should call `await cas.aclose()` when you are done using the instance to ensure that all resources are cleaned up. + ``` python + cas = KuboCAS(rpc_base_url=rpc_base_url, gateway_base_url=gateway_base_url) + # Use the KuboCAS instance as needed + # ... + await cas.aclose() # Ensure resources are cleaned up + ``` ### Authenticated RPC/Gateway Access Users can set whatever headers and auth credentials they need if they are connecting to an authenticated kubo instance by setting them in their own `aiohttp.ClientSession` and then passing that in. From c11324f3eb999445076231b689584051965335d9 Mon Sep 17 00:00:00 2001 From: Faolain Date: Mon, 2 Jun 2025 16:18:03 -0400 Subject: [PATCH 105/118] test: add missing auth test --- tests/test_kubocas_auth.py | 43 ++++++++++++++++++++++++++++++++++++++ 1 file changed, 43 insertions(+) diff --git a/tests/test_kubocas_auth.py b/tests/test_kubocas_auth.py index 244990a..ee28452 100644 --- a/tests/test_kubocas_auth.py +++ b/tests/test_kubocas_auth.py @@ -28,3 +28,46 @@ async def test_internal_session_headers() -> None: assert sess.headers["X-Custom"] == "yes" await cas.aclose() assert sess.closed + + +@pytest.mark.asyncio +async def test_user_supplied_session_auth() -> None: + """ + If the user *provides* an aiohttp.ClientSession that already carries + authentication, KuboCAS must reuse that session unchanged and must + **not** close it when `aclose()` is called. + """ + basic = aiohttp.BasicAuth("alice", "secret") + external_session = aiohttp.ClientSession(auth=basic) + + cas = KuboCAS(session=external_session) + sess = await _maybe_await(cas._loop_session()) + + # The session KuboCAS returns is *exactly* the one we passed in, + # and therefore must keep the same BasicAuth object. + assert sess is external_session + assert sess.auth == basic + + # Calling aclose() must leave the externally-owned session open + await cas.aclose() + assert not external_session.closed + await external_session.close() + + +@pytest.mark.asyncio +async def test_internal_session_auth() -> None: + """ + When the caller passes `auth=` to the constructor (but no session), + KuboCAS must create a ClientSession that carries that auth object, + and should close it on `aclose()`. + """ + basic = aiohttp.BasicAuth("bob", "pa55w0rd") + cas = KuboCAS(auth=basic) + + sess = await _maybe_await(cas._loop_session()) + assert isinstance(sess, aiohttp.ClientSession) + assert sess.auth == basic + + # aclose() should shut down the internally-owned session + await cas.aclose() + assert sess.closed From fdfcca6d8d12669a89a2cecaed2012d161c20882 Mon Sep 17 00:00:00 2001 From: Faolain Date: Mon, 2 Jun 2025 17:05:07 -0400 Subject: [PATCH 106/118] deps: add pre-commit to dev dependencies so ai can run pre-commit --- README.md | 4 ++- pyproject.toml | 1 + uv.lock | 77 ++++++++++++++++++++++++++++++++++++++++++++++++++ 3 files changed, 81 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index e443d7a..da4e00d 100644 --- a/README.md +++ b/README.md @@ -30,8 +30,10 @@ You can also see this library used in either our [data ETLs](https://github.com/ Once uv is installed, run ```sh uv sync +source .venv/bin/activate +pre-commit install ``` -to create the project virtual environment at `.venv`. Don't worry about activating this virtual environment to run tests or formatting and linting, uv will automatically take care of that. +to create the project virtual environment at `.venv`. ## Run tests, formatting, linting First, make sure you have the ipfs kubo daemon installed and running with the default endpoints open. Then run the script diff --git a/pyproject.toml b/pyproject.toml index ba86e99..f1310de 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -32,4 +32,5 @@ dev = [ "xarray[complete]>=2025.3.0", "mypy>=1.15.0", "pandas-stubs>=2.2.3.250527", + "pre-commit>=4.2.0", ] diff --git a/uv.lock b/uv.lock index a874e85..623ec9c 100644 --- a/uv.lock +++ b/uv.lock @@ -226,6 +226,15 @@ wheels = [ { url = "https://files.pythonhosted.org/packages/4a/7e/3db2bd1b1f9e95f7cddca6d6e75e2f2bd9f51b1246e546d88addca0106bd/certifi-2025.4.26-py3-none-any.whl", hash = "sha256:30350364dfe371162649852c63336a15c70c6510c2ad5015b21c2345311805f3", size = 159618 }, ] +[[package]] +name = "cfgv" +version = "3.4.0" +source = { registry = "https://pypi.org/simple" } +sdist = { url = "https://files.pythonhosted.org/packages/11/74/539e56497d9bd1d484fd863dd69cbbfa653cd2aa27abfe35653494d85e94/cfgv-3.4.0.tar.gz", hash = "sha256:e52591d4c5f5dead8e0f673fb16db7949d2cfb3f7da4582893288f0ded8fe560", size = 7114 } +wheels = [ + { url = 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}, +] + [[package]] name = "propcache" version = "0.3.1" @@ -1611,6 +1672,7 @@ dev = [ { name = "pandas" }, { name = "pandas-stubs" }, { name = "pdoc" }, + { name = "pre-commit" }, { name = "pytest" }, { name = "pytest-asyncio" }, { name = "pytest-cov" }, @@ -1638,6 +1700,7 @@ dev = [ { name = "pandas", specifier = ">=2.2.3" }, { name = "pandas-stubs", specifier = ">=2.2.3.250527" }, { name = "pdoc", specifier = ">=15.0.0" }, + { name = "pre-commit", specifier = ">=4.2.0" }, { name = "pytest", specifier = ">=8.3.3" }, { name = "pytest-asyncio", specifier = ">=0.25.3" }, { name = "pytest-cov", specifier = ">=6.0.0" }, @@ -2177,6 +2240,20 @@ wheels = [ { url = "https://files.pythonhosted.org/packages/6b/11/cc635220681e93a0183390e26485430ca2c7b5f9d33b15c74c2861cb8091/urllib3-2.4.0-py3-none-any.whl", hash = "sha256:4e16665048960a0900c702d4a66415956a584919c03361cac9f1df5c5dd7e813", size = 128680 }, ] +[[package]] +name = "virtualenv" +version = "20.31.2" +source = { registry = "https://pypi.org/simple" } +dependencies = [ + { name = "distlib" }, + { name = "filelock" }, + { name = "platformdirs" }, +] +sdist = { url = "https://files.pythonhosted.org/packages/56/2c/444f465fb2c65f40c3a104fd0c495184c4f2336d65baf398e3c75d72ea94/virtualenv-20.31.2.tar.gz", hash = "sha256:e10c0a9d02835e592521be48b332b6caee6887f332c111aa79a09b9e79efc2af", size = 6076316 } +wheels = [ + { url = "https://files.pythonhosted.org/packages/f3/40/b1c265d4b2b62b58576588510fc4d1fe60a86319c8de99fd8e9fec617d2c/virtualenv-20.31.2-py3-none-any.whl", hash = "sha256:36efd0d9650ee985f0cad72065001e66d49a6f24eb44d98980f630686243cf11", size = 6057982 }, +] + [[package]] name = "xarray" version = "2025.4.0" From 46399b5fc22d04f3be5e9daea6f91796b24cf53e Mon Sep 17 00:00:00 2001 From: Faolain Date: Mon, 2 Jun 2025 17:19:17 -0400 Subject: [PATCH 107/118] refactor: update run-checks to run pre-commit instead --- README.md | 7 ++++++- run-checks.sh | 7 ++----- 2 files changed, 8 insertions(+), 6 deletions(-) diff --git a/README.md b/README.md index da4e00d..85861c0 100644 --- a/README.md +++ b/README.md @@ -35,12 +35,17 @@ pre-commit install ``` to create the project virtual environment at `.venv`. +Then you can run `pre-commit` across the whole codebase with +```sh +pre-commit run --all-files +``` + ## Run tests, formatting, linting First, make sure you have the ipfs kubo daemon installed and running with the default endpoints open. Then run the script ```sh bash run-checks.sh ``` -This will run tests with code coverage, and check formatting and linting. +This will run tests with code coverage, and check formatting and linting. Under the hood it will be using the `pre-commit` command to run through all the checks within .pre-commit-config.yaml. We use `pytest` with 100% code coverage, and with test inputs that are both handwritten as well as generated by `hypothesis`. This allows us to try out millions of randomized inputs to create a more robust library. diff --git a/run-checks.sh b/run-checks.sh index b9c4eca..97e2eb5 100644 --- a/run-checks.sh +++ b/run-checks.sh @@ -6,8 +6,5 @@ uv run pytest --cov=py_hamt tests/ # Check coverage uv run coverage report --fail-under=100 --show-missing -# Check linting with ruff -uv run ruff check - -# Auto format with ruff -uv run ruff format +# Check for linting, formatting, and type checking using the pre-commit hooks found in .pre-commit-config.yaml +uv run pre-commit From 52464ea250b5954db589bf11ddbbf0468e6a1165 Mon Sep 17 00:00:00 2001 From: Faolain Date: Mon, 2 Jun 2025 18:30:21 -0400 Subject: [PATCH 108/118] test: use local daemon then fallback to docker if present otherwise skip integration tests --- pyproject.toml | 2 + tests/conftest.py | 26 +++++++ tests/test_kubo_cas.py | 1 + tests/testing_utils.py | 173 ++++++++++++++++++++++++++--------------- uv.lock | 56 +++++++++++++ 5 files changed, 197 insertions(+), 61 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index ba86e99..8873e18 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -32,4 +32,6 @@ dev = [ "xarray[complete]>=2025.3.0", "mypy>=1.15.0", "pandas-stubs>=2.2.3.250527", + "docker>=7.1.0", + "types-docker>=7.1.0.20250523", ] diff --git a/tests/conftest.py b/tests/conftest.py index 0951b74..bfabdc5 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -11,3 +11,29 @@ async def global_client_session(): async with aiohttp.ClientSession() as session: yield session # aiohttp’s async context manager awaits session.close() for us + + +import shutil, os, subprocess, json, tempfile, time, socket, textwrap +from pathlib import Path + + +def pytest_addoption(parser): + parser.addoption( + "--ipfs", + action="store_true", + default=False, + help="run tests that require a Kubo daemon", + ) + + +def pytest_configure(config): + config.addinivalue_line("markers", "ipfs: tests that need a live IPFS node") + + +def pytest_collection_modifyitems(config, items): + if config.getoption("--ipfs"): + return # user explicitly asked → run them + skip = pytest.mark.skip(reason="needs --ipfs to run") + for item in items: + if "ipfs" in item.keywords: + item.add_marker(skip) diff --git a/tests/test_kubo_cas.py b/tests/test_kubo_cas.py index b0cf12c..c6282ce 100644 --- a/tests/test_kubo_cas.py +++ b/tests/test_kubo_cas.py @@ -43,6 +43,7 @@ async def test_memory_store_invalid_key_type(): await s.load(invalid_key) +@pytest.mark.ipfs @pytest.mark.asyncio(loop_scope="session") @given(data=ipld_strategy()) @settings( diff --git a/tests/testing_utils.py b/tests/testing_utils.py index 7720299..aa32af9 100644 --- a/tests/testing_utils.py +++ b/tests/testing_utils.py @@ -1,13 +1,9 @@ -import json +from urllib.parse import urlparse import os -import shutil import socket -import subprocess -import tempfile import time -from pathlib import Path -from typing import Generator, Tuple, Any +import http.client import pytest from hypothesis import strategies as st @@ -53,66 +49,121 @@ def ipld_strategy() -> SearchStrategy: ], # ensure unique keys, otherwise we can't do the length and size checks when using these KVs for the HAMT ) +# ---------- helpers --------------------------------------------------------- -def find_free_port() -> int: - with socket.socket() as s: - s.bind(("", 0)) # Bind to a free port provided by the host. - return int(s.getsockname()[1]) # Return the port number assigned. - - -@pytest.fixture(scope="module") -def create_ipfs() -> Generator[Tuple[str, str], None, None]: - # Create temporary directory, set it as the IPFS Path - temp_dir: Path = Path(tempfile.mkdtemp()) - custom_env: dict[str, str] = os.environ.copy() - custom_env["IPFS_PATH"] = str(temp_dir) - - # IPFS init - subprocess.run( - ["ipfs", "init", "--profile", "pebbleds"], check=True, env=custom_env - ) - - # Edit the config file so that it serves on randomly selected and available ports to not conflict with any currently running ipfs daemons - swarm_port: int = find_free_port() - rpc_port: int = find_free_port() - gateway_port: int = find_free_port() - config_path: Path = temp_dir / "config" - config: dict[str, Any] - with open(config_path, "r") as f: - config = json.load(f) +def _rpc_is_up(url: str) -> bool: + """POST /api/v0/version on the *RPC* port (5001 by default).""" + p = urlparse(url) + try: + conn = http.client.HTTPConnection(p.hostname, p.port, timeout=1) + conn.request("POST", "/api/v0/version") + return conn.getresponse().status == 200 + except Exception: + return False - swarm_addrs: list[str] = config["Addresses"]["Swarm"] - new_port_swarm_addrs: list[str] = [ - s.replace("4001", str(swarm_port)) for s in swarm_addrs - ] - config["Addresses"]["Swarm"] = new_port_swarm_addrs - rpc_multiaddr: str = config["Addresses"]["API"] - gateway_multiaddr: str = config["Addresses"]["Gateway"] +def _gw_is_up(url: str) -> bool: + """HEAD / on the *gateway* port (8080 by default).""" + p = urlparse(url) + try: + conn = http.client.HTTPConnection(p.hostname, p.port, timeout=1) + conn.request("HEAD", "/") + return conn.getresponse().status in (200, 404) # 404 = empty root + except Exception: + return False - config["Addresses"]["API"] = rpc_multiaddr.replace("5001", str(rpc_port)) - config["Addresses"]["Gateway"] = gateway_multiaddr.replace( - "8080", str(gateway_port) - ) - - with open(config_path, "w") as f: - json.dump(config, f, indent=2) - - # Start the daemon - rpc_uri_stem: str = f"http://127.0.0.1:{rpc_port}" - gateway_uri_stem: str = f"http://127.0.0.1:{gateway_port}" - ipfs_process: subprocess.Popen[bytes] = subprocess.Popen( - ["ipfs", "daemon"], env=custom_env +def _free_port() -> int: + with socket.socket() as s: + s.bind(("", 0)) + return s.getsockname()[1] + + +try: + import docker +except ImportError: + docker = None + + +def _docker_client_or_none(): + # 1. first try env / default socket + try: + c = docker.from_env() + c.ping() + return c + except docker.errors.DockerException: + pass + + # 2. fall back to the *current* Docker context (Desktop, Colima, etc.) + try: + ctx_name = subprocess.check_output( + ["docker", "context", "show"], text=True + ).strip() + host = subprocess.check_output( + [ + "docker", + "context", + "inspect", + "--format", + '{{ index .Endpoints "docker" "Host" }}', + ctx_name, + ], + text=True, + ).strip() + if host: + os.environ["DOCKER_HOST"] = host # make visible to children + c = docker.DockerClient(base_url=host) + c.ping() + return c + except Exception: + pass + + return None # fixture will pytest.skip() + + +# ---------- fixture --------------------------------------------------------- + + +@pytest.fixture(scope="session") +def create_ipfs(): + """Yield `(rpc_url, gateway_url)`. + + Order of preference: + 1. reuse an already-running daemon (checked via RPC probe) + 2. launch Docker container (if docker is installed & running) + 3. skip the IPFS-marked tests + """ + rpc = os.getenv("IPFS_RPC_URL") or "http://127.0.0.1:5001" + gw = os.getenv("IPFS_GATEWAY_URL") or "http://127.0.0.1:8080" + + # 1. reuse existing node ------------------------------------------------- + if _rpc_is_up(rpc) and _gw_is_up(gw): + yield rpc, gw + return + + # 2. fall back to Docker ------------------------------------------------- + # if docker is None: + # pytest.skip("Docker not available and no IPFS node listening") + client = _docker_client_or_none() + if client is None: + pytest.skip("Neither IPFS daemon nor Docker available – skipping IPFS tests") + + client = docker.from_env() + image = "ipfs/kubo:v0.35.0" + rpc_p = _free_port() + gw_p = _free_port() + + container = client.containers.run( + image, + "daemon --init --offline", + ports={"5001/tcp": rpc_p, "8080/tcp": gw_p}, + detach=True, + auto_remove=True, ) - # Should be enough time for the ipfs daemon process to start up - time.sleep(5) - - yield rpc_uri_stem, gateway_uri_stem - - # Close the daemon - ipfs_process.kill() - # Delete the temporary directory - shutil.rmtree(temp_dir) + try: + time.sleep(6) # crude readiness wait + yield f"http://127.0.0.1:{rpc_p}", f"http://127.0.0.1:{gw_p}" + finally: + container.stop(timeout=3) diff --git a/uv.lock b/uv.lock index a874e85..dd96a94 100644 --- a/uv.lock +++ b/uv.lock @@ -516,6 +516,20 @@ wheels = [ { url = "https://files.pythonhosted.org/packages/25/65/89601dcc7383f0e5109e59eab90677daa9abb260d821570cd6089c8894bf/distributed-2025.5.1-py3-none-any.whl", hash = "sha256:74782b965ddb24ce59c6441fa777e944b5962d82325cc41f228537b59bb7fbbe", size = 1014789 }, ] +[[package]] +name = "docker" +version = "7.1.0" +source = { registry = "https://pypi.org/simple" } +dependencies = [ + { name = "pywin32", marker = "sys_platform == 'win32'" }, + { name = "requests" }, + { name = "urllib3" }, +] +sdist = { url = "https://files.pythonhosted.org/packages/91/9b/4a2ea29aeba62471211598dac5d96825bb49348fa07e906ea930394a83ce/docker-7.1.0.tar.gz", hash = "sha256:ad8c70e6e3f8926cb8a92619b832b4ea5299e2831c14284663184e200546fa6c", size = 117834 } +wheels = [ + { url = "https://files.pythonhosted.org/packages/e3/26/57c6fb270950d476074c087527a558ccb6f4436657314bfb6cdf484114c4/docker-7.1.0-py3-none-any.whl", hash = "sha256:c96b93b7f0a746f9e77d325bcfb87422a3d8bd4f03136ae8a85b37f1898d5fc0", size = 147774 }, +] + [[package]] name = "donfig" version = "0.8.1.post1" @@ -1604,6 +1618,7 @@ dependencies = [ [package.dev-dependencies] dev = [ + { name = "docker" }, { name = "hypothesis" }, { name = "memray" }, { name = "mypy" }, @@ -1616,6 +1631,7 @@ dev = [ { name = "pytest-cov" }, { name = "ruff" }, { name = "snakeviz" }, + { name = "types-docker" }, { name = "xarray", extra = ["complete"] }, ] @@ -1631,6 +1647,7 @@ requires-dist = [ [package.metadata.requires-dev] dev = [ + { name = "docker", specifier = ">=7.1.0" }, { name = "hypothesis", specifier = ">=6.115.5" }, { name = "memray", specifier = ">=1.14.0" }, { name = "mypy", specifier = 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"https://files.pythonhosted.org/packages/48/b0/5321e6eeba5d59e4347fcf9bf06a5052f085c3aa0f4876230566d6a4dc97/types_requests-2.32.0.20250602.tar.gz", hash = "sha256:ee603aeefec42051195ae62ca7667cd909a2f8128fdf8aad9e8a5219ecfab3bf", size = 23042 } +wheels = [ + { url = "https://files.pythonhosted.org/packages/da/18/9b782980e575c6581d5c0c1c99f4c6f89a1d7173dad072ee96b2756c02e6/types_requests-2.32.0.20250602-py3-none-any.whl", hash = "sha256:f4f335f87779b47ce10b8b8597b409130299f6971ead27fead4fe7ba6ea3e726", size = 20638 }, +] + [[package]] name = "typing-extensions" version = "4.13.2" From e1d933471e81a03313b9adf738e8387ed1d780d7 Mon Sep 17 00:00:00 2001 From: Faolain Date: Mon, 2 Jun 2025 18:35:07 -0400 Subject: [PATCH 109/118] lint(ruff): fix import order --- py_hamt/__init__.py | 2 +- py_hamt/encryption_hamt_store.py | 6 ++++-- py_hamt/hamt.py | 12 ++++++------ py_hamt/store.py | 8 ++++---- py_hamt/zarr_hamt_store.py | 1 + tests/conftest.py | 2 +- tests/performance_tests.py | 5 +++-- tests/test_branch_anchors.py | 1 + tests/test_extract_bits.py | 3 ++- tests/test_hamt.py | 9 ++++----- tests/test_kubo_cas.py | 8 ++++---- tests/test_kubocas_auth.py | 4 +++- tests/test_kubocas_session.py | 2 +- tests/test_zarr_ipfs.py | 5 ++--- tests/test_zarr_ipfs_encrypted.py | 4 +++- tests/testing_utils.py | 3 +-- 16 files changed, 41 insertions(+), 34 deletions(-) diff --git a/py_hamt/__init__.py b/py_hamt/__init__.py index 6098400..9be7257 100644 --- a/py_hamt/__init__.py +++ b/py_hamt/__init__.py @@ -1,7 +1,7 @@ +from .encryption_hamt_store import SimpleEncryptedZarrHAMTStore from .hamt import HAMT, blake3_hashfn from .store import ContentAddressedStore, KuboCAS from .zarr_hamt_store import ZarrHAMTStore -from .encryption_hamt_store import SimpleEncryptedZarrHAMTStore __all__ = [ "blake3_hashfn", diff --git a/py_hamt/encryption_hamt_store.py b/py_hamt/encryption_hamt_store.py index 67eaae0..f13e7c0 100644 --- a/py_hamt/encryption_hamt_store.py +++ b/py_hamt/encryption_hamt_store.py @@ -1,10 +1,12 @@ +from typing import cast + import zarr.abc.store import zarr.core.buffer -from py_hamt.hamt import HAMT from Crypto.Cipher import ChaCha20_Poly1305 from Crypto.Random import get_random_bytes + +from py_hamt.hamt import HAMT from py_hamt.zarr_hamt_store import ZarrHAMTStore -from typing import cast class SimpleEncryptedZarrHAMTStore(ZarrHAMTStore): diff --git a/py_hamt/hamt.py b/py_hamt/hamt.py index b238398..3bc9075 100644 --- a/py_hamt/hamt.py +++ b/py_hamt/hamt.py @@ -1,15 +1,15 @@ +import asyncio +import uuid from abc import ABC, abstractmethod +from copy import deepcopy from typing import ( + Any, + AsyncIterator, Callable, + Dict, Iterator, - AsyncIterator, - Any, cast, - Dict, ) -import uuid -import asyncio -from copy import deepcopy import dag_cbor from dag_cbor.ipld import IPLDKind diff --git a/py_hamt/store.py b/py_hamt/store.py index ca181de..dc7a67b 100644 --- a/py_hamt/store.py +++ b/py_hamt/store.py @@ -1,10 +1,10 @@ import asyncio -import aiohttp -from typing import Literal, cast, Any from abc import ABC, abstractmethod +from typing import Any, Literal, cast + +import aiohttp from dag_cbor.ipld import IPLDKind -from multiformats import multihash -from multiformats import CID +from multiformats import CID, multihash from multiformats.multihash import Multihash diff --git a/py_hamt/zarr_hamt_store.py b/py_hamt/zarr_hamt_store.py index b652cb4..8072c07 100644 --- a/py_hamt/zarr_hamt_store.py +++ b/py_hamt/zarr_hamt_store.py @@ -1,5 +1,6 @@ from collections.abc import AsyncIterator, Iterable from typing import cast + import zarr.abc.store import zarr.core.buffer from zarr.core.common import BytesLike diff --git a/tests/conftest.py b/tests/conftest.py index 0951b74..845bf38 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -2,7 +2,7 @@ import pytest # re-export helpers so existing imports keep working (optional) -from testing_utils import ipld_strategy, create_ipfs # noqa: F401 +from testing_utils import create_ipfs, ipld_strategy # noqa: F401 @pytest.fixture(scope="session") diff --git a/tests/performance_tests.py b/tests/performance_tests.py index 3803e42..d59b505 100644 --- a/tests/performance_tests.py +++ b/tests/performance_tests.py @@ -4,9 +4,10 @@ This test suite contains various performance tests, which are meant to be run individually. """ -import pytest -import time import asyncio +import time + +import pytest from py_hamt import HAMT from py_hamt.store import InMemoryCAS diff --git a/tests/test_branch_anchors.py b/tests/test_branch_anchors.py index 5e328b4..6b3792b 100644 --- a/tests/test_branch_anchors.py +++ b/tests/test_branch_anchors.py @@ -1,5 +1,6 @@ # tests/test_branch_anchors.py import pytest + from py_hamt import HAMT, blake3_hashfn from py_hamt.store import InMemoryCAS diff --git a/tests/test_extract_bits.py b/tests/test_extract_bits.py index a5b9d0f..7e7371d 100644 --- a/tests/test_extract_bits.py +++ b/tests/test_extract_bits.py @@ -1,6 +1,7 @@ -from py_hamt.hamt import extract_bits import pytest +from py_hamt.hamt import extract_bits + # Most of these tests were adapted over to python from rvagg's IAMap tests in JS def test_extract_bits() -> None: diff --git a/tests/test_hamt.py b/tests/test_hamt.py index 19f0fb3..d9fc7fd 100644 --- a/tests/test_hamt.py +++ b/tests/test_hamt.py @@ -1,18 +1,17 @@ import asyncio import random +from typing import cast +import pytest from dag_cbor import IPLDKind -from multiformats import CID from hypothesis import given, settings from hypothesis import strategies as st -from typing import cast -import pytest +from multiformats import CID +from testing_utils import key_value_list from py_hamt.hamt import HAMT, Node from py_hamt.store import InMemoryCAS -from testing_utils import key_value_list - @pytest.mark.asyncio @given(key_value_list) diff --git a/tests/test_kubo_cas.py b/tests/test_kubo_cas.py index b0cf12c..6f60db3 100644 --- a/tests/test_kubo_cas.py +++ b/tests/test_kubo_cas.py @@ -1,14 +1,14 @@ +from typing import Literal, cast + import aiohttp import dag_cbor +import pytest from dag_cbor import IPLDKind -from typing import Literal, cast from hypothesis import given, settings -import pytest +from testing_utils import create_ipfs, ipld_strategy # noqa from py_hamt import KuboCAS - from py_hamt.store import InMemoryCAS -from testing_utils import ipld_strategy, create_ipfs # noqa # Just to cover this one case that isn't covered within test_hamt diff --git a/tests/test_kubocas_auth.py b/tests/test_kubocas_auth.py index ee28452..9709cbf 100644 --- a/tests/test_kubocas_auth.py +++ b/tests/test_kubocas_auth.py @@ -1,7 +1,9 @@ # tests/test_kubocas_auth.py +import inspect + import aiohttp import pytest -import inspect + from py_hamt.store import KuboCAS diff --git a/tests/test_kubocas_session.py b/tests/test_kubocas_session.py index b9d1054..50b7006 100644 --- a/tests/test_kubocas_session.py +++ b/tests/test_kubocas_session.py @@ -1,6 +1,6 @@ import asyncio import inspect -from threading import Thread, Event +from threading import Event, Thread import pytest diff --git a/tests/test_zarr_ipfs.py b/tests/test_zarr_ipfs.py index 4db3727..b500d90 100644 --- a/tests/test_zarr_ipfs.py +++ b/tests/test_zarr_ipfs.py @@ -2,16 +2,15 @@ import numpy as np import pandas as pd -import xarray as xr import pytest +import xarray as xr import zarr import zarr.core.buffer from dag_cbor.ipld import IPLDKind from py_hamt import HAMT, KuboCAS - -from py_hamt.zarr_hamt_store import ZarrHAMTStore from py_hamt.store import InMemoryCAS +from py_hamt.zarr_hamt_store import ZarrHAMTStore @pytest.fixture(scope="module") diff --git a/tests/test_zarr_ipfs_encrypted.py b/tests/test_zarr_ipfs_encrypted.py index 736ab04..8d65d1c 100644 --- a/tests/test_zarr_ipfs_encrypted.py +++ b/tests/test_zarr_ipfs_encrypted.py @@ -1,11 +1,13 @@ import json + import numpy as np import pandas as pd -import xarray as xr import pytest +import xarray as xr import zarr import zarr.core.buffer from Crypto.Random import get_random_bytes + from py_hamt import HAMT, KuboCAS, SimpleEncryptedZarrHAMTStore from py_hamt.zarr_hamt_store import ZarrHAMTStore diff --git a/tests/testing_utils.py b/tests/testing_utils.py index 7720299..7ad3fb9 100644 --- a/tests/testing_utils.py +++ b/tests/testing_utils.py @@ -6,8 +6,7 @@ import tempfile import time from pathlib import Path -from typing import Generator, Tuple, Any - +from typing import Any, Generator, Tuple import pytest from hypothesis import strategies as st From 17c1ba0442fec22088723795dda87ed14b024f04 Mon Sep 17 00:00:00 2001 From: Faolain Date: Tue, 3 Jun 2025 01:55:45 -0400 Subject: [PATCH 110/118] fix: ensure that all tests can run depending on environment present dynamically --- .github/workflows/run-checks.yaml | 2 +- README.md | 29 ++++- run-checks.sh | 2 +- tests/conftest.py | 6 +- tests/test_kubo_cas.py | 196 +++++++++++++++++++++--------- tests/testing_utils.py | 90 +++++++++----- 6 files changed, 227 insertions(+), 98 deletions(-) diff --git a/.github/workflows/run-checks.yaml b/.github/workflows/run-checks.yaml index 112fd93..439dd5f 100644 --- a/.github/workflows/run-checks.yaml +++ b/.github/workflows/run-checks.yaml @@ -43,7 +43,7 @@ jobs: run_daemon: true - name: Run pytest with coverage - run: uv run pytest --cov=py_hamt tests/ --cov-report=xml + run: uv run pytest --ipfs --cov=py_hamt tests/ --cov-report=xml - name: Upload coverage reports to Codecov uses: codecov/codecov-action@18283e04ce6e62d37312384ff67231eb8fd56d24 # v5 diff --git a/README.md b/README.md index e443d7a..bc160b8 100644 --- a/README.md +++ b/README.md @@ -38,7 +38,7 @@ First, make sure you have the ipfs kubo daemon installed and running with the de ```sh bash run-checks.sh ``` -This will run tests with code coverage, and check formatting and linting. +This will run tests with code coverage, and check formatting and linting. If a local ipfs daemon is not running it will not run all tests, but it will spawn a docker ipfs container if docker is installed and run as many integration tests as possible. We use `pytest` with 100% code coverage, and with test inputs that are both handwritten as well as generated by `hypothesis`. This allows us to try out millions of randomized inputs to create a more robust library. @@ -48,6 +48,33 @@ We use `pytest` with 100% code coverage, and with test inputs that are both hand > [!NOTE] > Due to the restricted performance on GitHub actions runners, you may also sometimes see hypothesis tests running with errors because they exceeded test deadlines. Rerun the action if this happens. +### Tests + +Due to the dependency on [IPFS](https://github.com/ipfs/kubo) in order to be able to run all integration tests which use IPFS a local ipfs daemon is required. The Github Actions found in `.github/workflows/run-checks.yaml` uses the `setup-ipfs` step which ensures that a local ipfs daemon is available. Locally if you wish to run the full integration tests you must ensure a local ipfs daemon is running (by running `ipfs daemon` once installed). If not, pytest will spawn a local docker image to run the ipfs tests. If [Docker](https://www.docker.com/) is not installed then tests will simply run the unit tests. + +**To summarize:** + +*In GitHub Actions:* +```bash IPFS daemon is running on default ports +uv run pytest --ipfs # All tests run, including test_kubo_default_urls +``` + +*Locally with Docker (no local daemon):* +```bash +pytest --ipfs # test_kubo_default_urls auto-skips, other tests use Docker +``` + +*Locally with IPFS daemon:* +```bash +pytest --ipfs # All tests run +``` + +*Quick local testing (no IPFS):* +```bash +pytest # All IPFS tests skip +``` + + ## CPU and Memory Profiling We use python's native `cProfile` for running CPU profiles and snakeviz for visualizing the profile. We use `memray` for the memory profiling. We will walk through using the profiling tools on the test suite. diff --git a/run-checks.sh b/run-checks.sh index b9c4eca..b8232fd 100644 --- a/run-checks.sh +++ b/run-checks.sh @@ -1,7 +1,7 @@ #!/bin/bash # Run pytest with coverage -uv run pytest --cov=py_hamt tests/ +uv run pytest --ipfs --cov=py_hamt tests/ # Check coverage uv run coverage report --fail-under=100 --show-missing diff --git a/tests/conftest.py b/tests/conftest.py index bfabdc5..fa48698 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -10,11 +10,7 @@ async def global_client_session(): """One aiohttp.ClientSession shared by the whole test run.""" async with aiohttp.ClientSession() as session: yield session - # aiohttp’s async context manager awaits session.close() for us - - -import shutil, os, subprocess, json, tempfile, time, socket, textwrap -from pathlib import Path + # aiohttp's async context manager awaits session.close() for us def pytest_addoption(parser): diff --git a/tests/test_kubo_cas.py b/tests/test_kubo_cas.py index c6282ce..a1a808e 100644 --- a/tests/test_kubo_cas.py +++ b/tests/test_kubo_cas.py @@ -8,7 +8,7 @@ from py_hamt import KuboCAS from py_hamt.store import InMemoryCAS -from testing_utils import ipld_strategy, create_ipfs # noqa +from testing_utils import ipld_strategy # noqa # Just to cover this one case that isn't covered within test_hamt @@ -43,95 +43,173 @@ async def test_memory_store_invalid_key_type(): await s.load(invalid_key) +# @pytest.mark.ipfs +# @pytest.mark.asyncio(loop_scope="session") +# @given(data=ipld_strategy()) +# @settings( +# deadline=1000, print_blob=True +# ) # Increased deadline, print_blob for debugging +# async def test_kubo_default_urls( +# global_client_session, data: IPLDKind +# ): # Inject the session fixture +# """ +# Tests KuboCAS using its default URLs and when None is passed for URLs, +# leveraging a globally managed aiohttp.ClientSession. +# """ +# # Test Case 1: KuboCAS instantiated without explicit URLs (should use its defaults) +# # We pass the managed global_client_session to it. +# # KuboCAS itself is responsible for having default URLs if none are provided. +# async with KuboCAS(session=global_client_session) as kubo_cas_default: +# # print(f"Testing with default URLs: RPC={kubo_cas_default.rpc_base_url}, Gateway={kubo_cas_default.gateway_base_url}") +# encoded_data = dag_cbor.encode(data) + +# for codec in ["raw", "dag-cbor"]: +# # The codec is a string, but we use Literal to ensure type safety +# # where codec_raw = "raw" and codec_dag_cbor = "dag-cbor" +# # necessary because when you iterate over a list of strings, +# # even if they are literal strings, mypy widens the type to just str +# codec_typed = cast(Literal["raw", "dag-cbor"], codec) +# # print(f"Saving with codec: {codec}, data: {data}") +# try: +# cid = await kubo_cas_default.save(encoded_data, codec=codec_typed) +# # print(f"Saved. CID: {cid}") +# loaded_encoded_data = await kubo_cas_default.load(cid) +# # print(f"Loaded encoded data length: {len(loaded_encoded_data)}") +# result = dag_cbor.decode(loaded_encoded_data) +# # print(f"Decoded result: {result}") +# assert ( +# data == result +# ), f"Data mismatch for codec {codec} with default URLs" +# except Exception as e: +# pytest.fail( +# f"Error during KuboCAS default URL test (codec: {codec}): {e}" +# ) + +# # Test Case 2: KuboCAS instantiated with None for URLs (should also use its defaults) +# # We pass the managed global_client_session to it. +# async with KuboCAS( +# rpc_base_url=None, gateway_base_url=None, session=global_client_session +# ) as kubo_cas_none_urls: +# # print(f"Testing with None URLs: RPC={kubo_cas_none_urls.rpc_base_url}, Gateway={kubo_cas_none_urls.gateway_base_url}") +# encoded_data = dag_cbor.encode( +# data +# ) # Re-encode just in case, though it's the same data +# for codec in ["raw", "dag-cbor"]: +# # print(f"Saving with codec: {codec}, data: {data}") +# codec_typed = cast(Literal["raw", "dag-cbor"], codec) +# try: +# cid = await kubo_cas_none_urls.save(encoded_data, codec=codec_typed) +# # print(f"Saved. CID: {cid}") +# loaded_encoded_data = await kubo_cas_none_urls.load(cid) +# # print(f"Loaded encoded data length: {len(loaded_encoded_data)}") +# result = dag_cbor.decode(loaded_encoded_data) +# # print(f"Decoded result: {result}") +# assert data == result, f"Data mismatch for codec {codec} with None URLs" +# except Exception as e: +# pytest.fail(f"Error during KuboCAS None URL test (codec: {codec}): {e}") + + +# @given(data=ipld_strategy()) +# @settings(deadline=1000) +# @pytest.mark.asyncio +# async def test_kubo_default_urls(data: IPLDKind): +# try: +# async with KuboCAS() as kubo_cas: +# for codec in ("raw", "dag-cbor"): +# cid = await kubo_cas.save(dag_cbor.encode(data), codec=codec) +# result = dag_cbor.decode(await kubo_cas.load(cid)) +# assert data == result + +# async with KuboCAS(gateway_base_url=None, rpc_base_url=None) as kubo_cas: +# for codec in ("raw", "dag-cbor"): +# cid = await kubo_cas.save(dag_cbor.encode(data), codec=codec) +# result = dag_cbor.decode(await kubo_cas.load(cid)) +# assert data == result +# finally: +# # if Hypothesis cancels early, make sure every open CAS is closed +# for obj in list(globals().values()): +# if isinstance(obj, KuboCAS): +# await obj.aclose() + + +# Test that always works with Docker or local daemon @pytest.mark.ipfs @pytest.mark.asyncio(loop_scope="session") @given(data=ipld_strategy()) -@settings( - deadline=1000, print_blob=True -) # Increased deadline, print_blob for debugging -async def test_kubo_default_urls( - global_client_session, data: IPLDKind -): # Inject the session fixture +@settings(deadline=1000, print_blob=True) +async def test_kubo_urls_explicit(create_ipfs, global_client_session, data: IPLDKind): """ - Tests KuboCAS using its default URLs and when None is passed for URLs, - leveraging a globally managed aiohttp.ClientSession. + Tests KuboCAS functionality with explicitly provided URLs. + Works with both Docker containers and local IPFS daemons. """ - # Test Case 1: KuboCAS instantiated without explicit URLs (should use its defaults) - # We pass the managed global_client_session to it. - # KuboCAS itself is responsible for having default URLs if none are provided. - async with KuboCAS(session=global_client_session) as kubo_cas_default: - # print(f"Testing with default URLs: RPC={kubo_cas_default.rpc_base_url}, Gateway={kubo_cas_default.gateway_base_url}") + rpc_url, gateway_url = create_ipfs + + # Test the same functionality but with explicit URLs + async with KuboCAS( + rpc_base_url=rpc_url, + gateway_base_url=gateway_url, + session=global_client_session, + ) as kubo_cas: encoded_data = dag_cbor.encode(data) + for codec in ["raw", "dag-cbor"]: + codec_typed = cast(Literal["raw", "dag-cbor"], codec) + cid = await kubo_cas.save(encoded_data, codec=codec_typed) + loaded_encoded_data = await kubo_cas.load(cid) + result = dag_cbor.decode(loaded_encoded_data) + assert data == result + +@pytest.mark.ipfs +@pytest.mark.asyncio(loop_scope="session") +@given(data=ipld_strategy()) +@settings(deadline=1000, print_blob=True) +async def test_kubo_default_urls(global_client_session, data: IPLDKind): + """ + Tests KuboCAS using its default URLs and when None is passed for URLs. + Requires a local IPFS daemon on default ports. + """ + # Check if local IPFS daemon is available on default ports + import http.client + + try: + conn = http.client.HTTPConnection("127.0.0.1", 5001, timeout=1) + conn.request("POST", "/api/v0/version") + response = conn.getresponse() + if response.status != 200: + pytest.skip("No IPFS daemon running on default ports (127.0.0.1:5001)") + except Exception: + pytest.skip("No IPFS daemon running on default ports (127.0.0.1:5001)") + + # Your original test code continues here + async with KuboCAS(session=global_client_session) as kubo_cas_default: + encoded_data = dag_cbor.encode(data) for codec in ["raw", "dag-cbor"]: - # The codec is a string, but we use Literal to ensure type safety - # where codec_raw = "raw" and codec_dag_cbor = "dag-cbor" - # necessary because when you iterate over a list of strings, - # even if they are literal strings, mypy widens the type to just str codec_typed = cast(Literal["raw", "dag-cbor"], codec) - # print(f"Saving with codec: {codec}, data: {data}") try: cid = await kubo_cas_default.save(encoded_data, codec=codec_typed) - # print(f"Saved. CID: {cid}") loaded_encoded_data = await kubo_cas_default.load(cid) - # print(f"Loaded encoded data length: {len(loaded_encoded_data)}") result = dag_cbor.decode(loaded_encoded_data) - # print(f"Decoded result: {result}") - assert data == result, ( - f"Data mismatch for codec {codec} with default URLs" - ) + assert data == result except Exception as e: pytest.fail( f"Error during KuboCAS default URL test (codec: {codec}): {e}" ) - # Test Case 2: KuboCAS instantiated with None for URLs (should also use its defaults) - # We pass the managed global_client_session to it. async with KuboCAS( rpc_base_url=None, gateway_base_url=None, session=global_client_session ) as kubo_cas_none_urls: - # print(f"Testing with None URLs: RPC={kubo_cas_none_urls.rpc_base_url}, Gateway={kubo_cas_none_urls.gateway_base_url}") - encoded_data = dag_cbor.encode( - data - ) # Re-encode just in case, though it's the same data + encoded_data = dag_cbor.encode(data) for codec in ["raw", "dag-cbor"]: - # print(f"Saving with codec: {codec}, data: {data}") codec_typed = cast(Literal["raw", "dag-cbor"], codec) try: cid = await kubo_cas_none_urls.save(encoded_data, codec=codec_typed) - # print(f"Saved. CID: {cid}") loaded_encoded_data = await kubo_cas_none_urls.load(cid) - # print(f"Loaded encoded data length: {len(loaded_encoded_data)}") result = dag_cbor.decode(loaded_encoded_data) - # print(f"Decoded result: {result}") - assert data == result, f"Data mismatch for codec {codec} with None URLs" + assert data == result except Exception as e: pytest.fail(f"Error during KuboCAS None URL test (codec: {codec}): {e}") -# @given(data=ipld_strategy()) -# @settings(deadline=1000) -# @pytest.mark.asyncio -# async def test_kubo_default_urls(data: IPLDKind): -# try: -# async with KuboCAS() as kubo_cas: -# for codec in ("raw", "dag-cbor"): -# cid = await kubo_cas.save(dag_cbor.encode(data), codec=codec) -# result = dag_cbor.decode(await kubo_cas.load(cid)) -# assert data == result - -# async with KuboCAS(gateway_base_url=None, rpc_base_url=None) as kubo_cas: -# for codec in ("raw", "dag-cbor"): -# cid = await kubo_cas.save(dag_cbor.encode(data), codec=codec) -# result = dag_cbor.decode(await kubo_cas.load(cid)) -# assert data == result -# finally: -# # if Hypothesis cancels early, make sure every open CAS is closed -# for obj in list(globals().values()): -# if isinstance(obj, KuboCAS): -# await obj.aclose() - - @pytest.mark.asyncio @given(data=ipld_strategy()) @settings( diff --git a/tests/testing_utils.py b/tests/testing_utils.py index aa32af9..30326eb 100644 --- a/tests/testing_utils.py +++ b/tests/testing_utils.py @@ -2,7 +2,6 @@ import os import socket import time - import http.client import pytest @@ -55,6 +54,8 @@ def ipld_strategy() -> SearchStrategy: def _rpc_is_up(url: str) -> bool: """POST /api/v0/version on the *RPC* port (5001 by default).""" p = urlparse(url) + if not p.hostname: + return False try: conn = http.client.HTTPConnection(p.hostname, p.port, timeout=1) conn.request("POST", "/api/v0/version") @@ -66,6 +67,8 @@ def _rpc_is_up(url: str) -> bool: def _gw_is_up(url: str) -> bool: """HEAD / on the *gateway* port (8080 by default).""" p = urlparse(url) + if not p.hostname: + return False try: conn = http.client.HTTPConnection(p.hostname, p.port, timeout=1) conn.request("HEAD", "/") @@ -87,39 +90,58 @@ def _free_port() -> int: def _docker_client_or_none(): - # 1. first try env / default socket + """Try to get a working Docker client, with macOS Docker Desktop support.""" + + if docker is None: + return None + + # Common Docker socket locations (in order of preference) + socket_locations = [ + # Docker Desktop on macOS + f"unix://{os.path.expanduser('~')}/.docker/run/docker.sock", + # Docker Desktop alternative location + f"unix://{os.path.expanduser('~')}/.docker/desktop/docker.sock", + # Standard Linux locations + "unix:///var/run/docker.sock", + "unix:///run/docker.sock", + ] + + # First, try with DOCKER_HOST if it's already set + existing_host = os.environ.get("DOCKER_HOST") + if existing_host: + try: + c = docker.DockerClient(base_url=existing_host) + c.ping() + return c + except Exception: + pass + + # Try each known socket location + for socket_path in socket_locations: + try: + # Check if the socket file exists (for unix sockets) + if socket_path.startswith("unix://"): + socket_file = socket_path.replace("unix://", "") + if not os.path.exists(socket_file): + continue + + c = docker.DockerClient(base_url=socket_path) + c.ping() + # If successful, set DOCKER_HOST for any child processes + os.environ["DOCKER_HOST"] = socket_path + return c + except Exception: + continue + + # Last resort: try docker.from_env() which might work with some setups try: c = docker.from_env() c.ping() return c - except docker.errors.DockerException: - pass - - # 2. fall back to the *current* Docker context (Desktop, Colima, etc.) - try: - ctx_name = subprocess.check_output( - ["docker", "context", "show"], text=True - ).strip() - host = subprocess.check_output( - [ - "docker", - "context", - "inspect", - "--format", - '{{ index .Endpoints "docker" "Host" }}', - ctx_name, - ], - text=True, - ).strip() - if host: - os.environ["DOCKER_HOST"] = host # make visible to children - c = docker.DockerClient(base_url=host) - c.ping() - return c except Exception: pass - return None # fixture will pytest.skip() + return None # ---------- fixture --------------------------------------------------------- @@ -143,13 +165,10 @@ def create_ipfs(): return # 2. fall back to Docker ------------------------------------------------- - # if docker is None: - # pytest.skip("Docker not available and no IPFS node listening") client = _docker_client_or_none() if client is None: pytest.skip("Neither IPFS daemon nor Docker available – skipping IPFS tests") - client = docker.from_env() image = "ipfs/kubo:v0.35.0" rpc_p = _free_port() gw_p = _free_port() @@ -163,7 +182,16 @@ def create_ipfs(): ) try: - time.sleep(6) # crude readiness wait + # Wait for container to be ready + for _ in range(30): # 30 attempts, 0.5s each = 15s max + if _rpc_is_up(f"http://127.0.0.1:{rpc_p}") and _gw_is_up( + f"http://127.0.0.1:{gw_p}" + ): + break + time.sleep(0.5) + else: + raise RuntimeError("IPFS container failed to start within timeout") + yield f"http://127.0.0.1:{rpc_p}", f"http://127.0.0.1:{gw_p}" finally: container.stop(timeout=3) From 14385eefb7a7a9bbed4d4209c14bea2c2ab2b359 Mon Sep 17 00:00:00 2001 From: TheGreatAlgo <37487508+TheGreatAlgo@users.noreply.github.com> Date: Tue, 3 Jun 2025 14:23:07 -0400 Subject: [PATCH 111/118] fix: remove duplicated --- py_hamt/store.py | 5 ----- 1 file changed, 5 deletions(-) diff --git a/py_hamt/store.py b/py_hamt/store.py index dc7a67b..2a2e3e8 100644 --- a/py_hamt/store.py +++ b/py_hamt/store.py @@ -181,11 +181,6 @@ def __init__( self.hasher: str = hasher """The hash function to send to IPFS when storing bytes. Cannot be changed after initialization. The default blake3 follows the default hashing algorithm used by HAMT.""" - if rpc_base_url is None: - rpc_base_url = KuboCAS.KUBO_DEFAULT_LOCAL_RPC_BASE_URL - if gateway_base_url is None: - gateway_base_url = KuboCAS.KUBO_DEFAULT_LOCAL_GATEWAY_BASE_URL - self.rpc_url: str = f"{rpc_base_url}/api/v0/add?hash={self.hasher}&pin=false" """@private""" self.gateway_base_url: str = f"{gateway_base_url}/ipfs/" From 7b95f1cec1d48f8fb0b37d5026179dc93729ef0e Mon Sep 17 00:00:00 2001 From: Faolain Date: Wed, 4 Jun 2025 00:11:16 -0400 Subject: [PATCH 112/118] fix: readd parameter guard --- py_hamt/store.py | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/py_hamt/store.py b/py_hamt/store.py index 2a2e3e8..dc7a67b 100644 --- a/py_hamt/store.py +++ b/py_hamt/store.py @@ -181,6 +181,11 @@ def __init__( self.hasher: str = hasher """The hash function to send to IPFS when storing bytes. Cannot be changed after initialization. The default blake3 follows the default hashing algorithm used by HAMT.""" + if rpc_base_url is None: + rpc_base_url = KuboCAS.KUBO_DEFAULT_LOCAL_RPC_BASE_URL + if gateway_base_url is None: + gateway_base_url = KuboCAS.KUBO_DEFAULT_LOCAL_GATEWAY_BASE_URL + self.rpc_url: str = f"{rpc_base_url}/api/v0/add?hash={self.hasher}&pin=false" """@private""" self.gateway_base_url: str = f"{gateway_base_url}/ipfs/" From 87e3451e5087c055763a721e2ce67054c57747c7 Mon Sep 17 00:00:00 2001 From: Faolain Date: Wed, 4 Jun 2025 00:20:15 -0400 Subject: [PATCH 113/118] refactor: switch from old type alias to newer type syntax --- py_hamt/store.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/py_hamt/store.py b/py_hamt/store.py index dc7a67b..a35efb5 100644 --- a/py_hamt/store.py +++ b/py_hamt/store.py @@ -20,7 +20,7 @@ class ContentAddressedStore(ABC): 2. No `None` values since this is used in HAMT's `__init__` to indicate that an empty HAMT needs to be initialized. """ - type CodecInput = Literal["raw", "dag-cbor"] + CodecInput = Literal["raw", "dag-cbor"] @abstractmethod async def save(self, data: bytes, codec: CodecInput) -> IPLDKind: From 1632dca793541d028179349cfd96e8754e50c554 Mon Sep 17 00:00:00 2001 From: Faolain Date: Wed, 4 Jun 2025 00:30:50 -0400 Subject: [PATCH 114/118] refactor: ensure run-checks will check all files not just those that are staged --- run-checks.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/run-checks.sh b/run-checks.sh index c2fd395..bfbd222 100644 --- a/run-checks.sh +++ b/run-checks.sh @@ -7,4 +7,4 @@ uv run pytest --ipfs --cov=py_hamt tests/ uv run coverage report --fail-under=100 --show-missing # Check for linting, formatting, and type checking using the pre-commit hooks found in .pre-commit-config.yaml -uv run pre-commit +uv run pre-commit run --all-files --show-diff-on-failure From 7498c287b114ca39cd6443f0cc24ae32376c6205 Mon Sep 17 00:00:00 2001 From: Faolain Date: Wed, 4 Jun 2025 00:45:13 -0400 Subject: [PATCH 115/118] chore: remove commented out test code --- tests/test_kubo_cas.py | 89 ------------------------------------------ 1 file changed, 89 deletions(-) diff --git a/tests/test_kubo_cas.py b/tests/test_kubo_cas.py index 1d08136..54825b7 100644 --- a/tests/test_kubo_cas.py +++ b/tests/test_kubo_cas.py @@ -43,95 +43,6 @@ async def test_memory_store_invalid_key_type(): await s.load(invalid_key) -# @pytest.mark.ipfs -# @pytest.mark.asyncio(loop_scope="session") -# @given(data=ipld_strategy()) -# @settings( -# deadline=1000, print_blob=True -# ) # Increased deadline, print_blob for debugging -# async def test_kubo_default_urls( -# global_client_session, data: IPLDKind -# ): # Inject the session fixture -# """ -# Tests KuboCAS using its default URLs and when None is passed for URLs, -# leveraging a globally managed aiohttp.ClientSession. -# """ -# # Test Case 1: KuboCAS instantiated without explicit URLs (should use its defaults) -# # We pass the managed global_client_session to it. -# # KuboCAS itself is responsible for having default URLs if none are provided. -# async with KuboCAS(session=global_client_session) as kubo_cas_default: -# # print(f"Testing with default URLs: RPC={kubo_cas_default.rpc_base_url}, Gateway={kubo_cas_default.gateway_base_url}") -# encoded_data = dag_cbor.encode(data) - -# for codec in ["raw", "dag-cbor"]: -# # The codec is a string, but we use Literal to ensure type safety -# # where codec_raw = "raw" and codec_dag_cbor = "dag-cbor" -# # necessary because when you iterate over a list of strings, -# # even if they are literal strings, mypy widens the type to just str -# codec_typed = cast(Literal["raw", "dag-cbor"], codec) -# # print(f"Saving with codec: {codec}, data: {data}") -# try: -# cid = await kubo_cas_default.save(encoded_data, codec=codec_typed) -# # print(f"Saved. CID: {cid}") -# loaded_encoded_data = await kubo_cas_default.load(cid) -# # print(f"Loaded encoded data length: {len(loaded_encoded_data)}") -# result = dag_cbor.decode(loaded_encoded_data) -# # print(f"Decoded result: {result}") -# assert ( -# data == result -# ), f"Data mismatch for codec {codec} with default URLs" -# except Exception as e: -# pytest.fail( -# f"Error during KuboCAS default URL test (codec: {codec}): {e}" -# ) - -# # Test Case 2: KuboCAS instantiated with None for URLs (should also use its defaults) -# # We pass the managed global_client_session to it. -# async with KuboCAS( -# rpc_base_url=None, gateway_base_url=None, session=global_client_session -# ) as kubo_cas_none_urls: -# # print(f"Testing with None URLs: RPC={kubo_cas_none_urls.rpc_base_url}, Gateway={kubo_cas_none_urls.gateway_base_url}") -# encoded_data = dag_cbor.encode( -# data -# ) # Re-encode just in case, though it's the same data -# for codec in ["raw", "dag-cbor"]: -# # print(f"Saving with codec: {codec}, data: {data}") -# codec_typed = cast(Literal["raw", "dag-cbor"], codec) -# try: -# cid = await kubo_cas_none_urls.save(encoded_data, codec=codec_typed) -# # print(f"Saved. CID: {cid}") -# loaded_encoded_data = await kubo_cas_none_urls.load(cid) -# # print(f"Loaded encoded data length: {len(loaded_encoded_data)}") -# result = dag_cbor.decode(loaded_encoded_data) -# # print(f"Decoded result: {result}") -# assert data == result, f"Data mismatch for codec {codec} with None URLs" -# except Exception as e: -# pytest.fail(f"Error during KuboCAS None URL test (codec: {codec}): {e}") - - -# @given(data=ipld_strategy()) -# @settings(deadline=1000) -# @pytest.mark.asyncio -# async def test_kubo_default_urls(data: IPLDKind): -# try: -# async with KuboCAS() as kubo_cas: -# for codec in ("raw", "dag-cbor"): -# cid = await kubo_cas.save(dag_cbor.encode(data), codec=codec) -# result = dag_cbor.decode(await kubo_cas.load(cid)) -# assert data == result - -# async with KuboCAS(gateway_base_url=None, rpc_base_url=None) as kubo_cas: -# for codec in ("raw", "dag-cbor"): -# cid = await kubo_cas.save(dag_cbor.encode(data), codec=codec) -# result = dag_cbor.decode(await kubo_cas.load(cid)) -# assert data == result -# finally: -# # if Hypothesis cancels early, make sure every open CAS is closed -# for obj in list(globals().values()): -# if isinstance(obj, KuboCAS): -# await obj.aclose() - - # Test that always works with Docker or local daemon @pytest.mark.ipfs @pytest.mark.asyncio(loop_scope="session") From a300c247745fc3e93ecb2b506a3305c424ee5817 Mon Sep 17 00:00:00 2001 From: Faolain Date: Wed, 4 Jun 2025 01:45:07 -0400 Subject: [PATCH 116/118] docs: add AGENTS.md file --- AGENTS.md | 108 ++++++++++++++++++++++++++++++++++++++++++++++++++++++ README.md | 6 +++ 2 files changed, 114 insertions(+) create mode 100644 AGENTS.md diff --git a/AGENTS.md b/AGENTS.md new file mode 100644 index 0000000..c969e60 --- /dev/null +++ b/AGENTS.md @@ -0,0 +1,108 @@ +# Project Agents.md Guide for py-hamt + +This AGENTS.md file provides comprehensive guidance for OpenAI Codex and other AI agents working with this codebase. + +## Project Description + +This library is a python implementation of a HAMT, inspired by [rvagg's IAMap project written in JavaScript](https://github.com/rvagg/iamap). + +py-hamt provides efficient storage and retrieval of large sets of key-value mappings in a content-addressed storage system. The main target is IPFS, and the data model used is IPLD. + +dClimate primarily created this for storing large [zarrs](https://zarr.dev/) on IPFS. To see this in action, see our [data ETLs](https://github.com/dClimate/etl-scripts). + +## Project Architecture + +A user instantiates a ContentAddressedStore such as KuboCAS which is then used to instantiate a HAMT. This HAMT can then be passed to a ZarrHAMTStore to read/write zarr files. An IPFS daemon running locally can be used or a remote one can be accessed via gateway(reads) & rpc endpoints(writes) on their IPFS defaults. For tests, a local docker container is spun up if docker is available. + +## Project Structure for OpenAI Codex Navigation + +- `/py_hamt`: Source code of the py-hamt library + - `encryption_hamt_store.py` - Example using total encryption + - `hamt.py`- where the HAMT data structure is constructed and accesed + - `store.py`- Where various stores live that writes the data. Primarily used KuboCAS + - `zarr_hamt_store.py` - ZarrHAMTStore class used to directly write or read zarrs leveraging the HAMT data structure onto a Store usually a Content Addressed store like KuboCAS located in store.py. +- `/tests`: Test files that should be maintained and extended where possible. + +## Coding Conventions + +### General Conventions for AGENTS.md Implementation + +- Use the latest version of Python (3.12) for all new code generated by OpenAI Codex +- The AI Agent should follow the existing code style in each file +- Agents.md requires meaningful variable and function names +- The AI Agent should add comments for complex logic as guided by Agents.md + +### Python Guidelines +- Use functional easy to understand functions wherever possible. +- All functions need to be fully typed with mypy. +- All functions require tests to be written and coverage must be full. +- Example usage can be found in the `/tests` folder + +### Development Setup + +`py-hamt` uses uv for package management. If uv is not already present which can be checked with `uv` then it can be installed via + +`curl -LsSf https://astral.sh/uv/install.sh | sh` + +otherwise if uv is already present you can run + +`uv sync` to install all dependencies + +and then + +`source .venv/bin/activate` to activate the venv created by uv. + +Docker is also used for integration tests to test ipfs. Try to have docker installed to be able to run all tests with` pytest --ipfs` + +## Testing Requirements for the Agent + +All tests should be created within the `/tests` directory. + +The agent should run tests with the following commands: + +```bash +# Run all tests +pytest --ipfs + +# Run specific test file +pytest test tests/ + +# Run tests with coverage +pytest --ipfs --cov + +# If IPFS is not present use +pytest --cov +``` + +Tests should be kept as closed to 100% as possible. + +## Pull Request Guidelines for the Agent + +When the Agent helps create a PR, please ensure it: + +1. Includes a clear description of the changes as guided by AGENTS.md +2. References any related issues that the Agent is addressing +3. Ensures all tests pass for code generated by the Agent +4. Keeps PRs focused on a single concern as specified in AGENTS.md + +## Programmatic Checks for the Agent + +Before submitting changes generated by the Agent, run: + +```bash +bash run-checks.sh +``` + +**Note:** This assumes ipfs is running as `run-checks.sh` runs with the ``--ipfs` flag. If kubo ipfs is not running in a local daemon or docker was unable to instantiate simply run + +``` +pytest --cov +``` + +and + +``` +uv run pre-commit run --all-files --show-diff-on-failure +``` + +instead. All checks must pass before the Agent generated code can be merged. AGENTS.md helps ensure the Agent follows these requirements. diff --git a/README.md b/README.md index 522d991..6b17dd1 100644 --- a/README.md +++ b/README.md @@ -40,6 +40,8 @@ Then you can run `pre-commit` across the whole codebase with pre-commit run --all-files ``` +the below command `run-checks.sh` in the next section will also run this command inside its bash script. + ## Run tests, formatting, linting First, make sure you have the ipfs kubo daemon installed and running with the default endpoints open. Then run the script ```sh @@ -105,5 +107,9 @@ uv run memray flamegraph # e.g. = memray-pytest. uv run pdoc py_hamt ``` +## LLMs + +If you are an LLM reading this repo, refer to the `AGENTS.md` file. + ## Managing dependencies Use `uv add` and `uv remove`, e.g. `uv add numpy` or `uv add pytest --group dev`. For more information please see the [uv documentation](https://docs.astral.sh/uv/guides/projects/). From c4ba8eab9a59f89a33b690985a6988486ee7dfd5 Mon Sep 17 00:00:00 2001 From: Faolain Date: Wed, 4 Jun 2025 01:47:02 -0400 Subject: [PATCH 117/118] docs: add AGENTS.md file --- AGENTS.md | 13 ++++++++++++- 1 file changed, 12 insertions(+), 1 deletion(-) diff --git a/AGENTS.md b/AGENTS.md index c969e60..0d31d10 100644 --- a/AGENTS.md +++ b/AGENTS.md @@ -105,4 +105,15 @@ and uv run pre-commit run --all-files --show-diff-on-failure ``` -instead. All checks must pass before the Agent generated code can be merged. AGENTS.md helps ensure the Agent follows these requirements. +instead. + + +If there is an error with formatting for ruff and it can be autofixed you can normally run + +``` +uv run ruff check --fix +``` + +to fix it. + +All checks must pass before the Agent generated code can be merged. AGENTS.md helps ensure the Agent follows these requirements. From 48800e17da92f67e4651be7fea2323bf3f0cf7cc Mon Sep 17 00:00:00 2001 From: Faolain Date: Wed, 4 Jun 2025 02:11:31 -0400 Subject: [PATCH 118/118] docs: add more setup information to agents.md --- AGENTS.md | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/AGENTS.md b/AGENTS.md index 0d31d10..b1a2f04 100644 --- a/AGENTS.md +++ b/AGENTS.md @@ -52,6 +52,14 @@ and then `source .venv/bin/activate` to activate the venv created by uv. +Lastly while still setting up you can run + +``` +pre-commit install +``` + +to ensure pre-commit installed. + Docker is also used for integration tests to test ipfs. Try to have docker installed to be able to run all tests with` pytest --ipfs` ## Testing Requirements for the Agent