Merge branch 'master' into single_thread

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 1.6.0
+current_version = 1.6.4
 files = setup.py strax/__init__.py docs/source/conf.py
 commit = True
 tag = True

.github/workflows/pytest.yml

@@ -36,6 +36,8 @@ jobs:
           python-version: ${{ matrix.python-version }}
           cache: 'pip'
           cache-dependency-path: 'extra_requirements/requirements-tests.txt'
+      - name: Install dependencies
+        run: sudo apt-get install -y graphviz
       - name: Install requirements
         run: pip install -r extra_requirements/requirements-tests.txt
       - name: Start MongoDB

.pre-commit-config.yaml

@@ -2,15 +2,15 @@
 # See https://pre-commit.com/hooks.html for more hooks
 repos:
 -   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.5.0
+    rev: v4.6.0
     hooks:
     -   id: trailing-whitespace
     -   id: end-of-file-fixer
     -   id: check-yaml
     -   id: check-added-large-files
 
 -   repo: https://github.com/psf/black
-    rev: 23.12.1
+    rev: 24.4.2
     hooks:
     -   id: black
         args: [--safe, --line-length=100, --preview]
@@ -24,7 +24,7 @@ repos:
     -   id: docformatter
 
 -   repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.8.0
+    rev: v1.10.0
     hooks:
     -   id: mypy
         additional_dependencies: [

HISTORY.md

@@ -1,3 +1,62 @@
+1.6.4 / 2024-05-27
+---------------------
+* Minor fix on `_is_superrun` variable  names by @dachengx in https://github.com/AxFoundation/strax/pull/837
+* Implement Hyperrun by @dachengx in https://github.com/AxFoundation/strax/pull/838
+* Add function to collect `data_type` and `data_kind` by @dachengx in https://github.com/AxFoundation/strax/pull/839
+* Check `include_tags` and `exclude_tags` by @dachengx in https://github.com/AxFoundation/strax/pull/841
+
+**Full Changelog**: https://github.com/AxFoundation/strax/compare/v1.6.3...v1.6.4
+
+
+1.6.3 / 2024-04-30
+---------------------
+* Install `graphviz` for the pytests by @dachengx in https://github.com/AxFoundation/strax/pull/817
+* Increase the timing precision of progress bar by @dachengx in https://github.com/AxFoundation/strax/pull/819
+* Initialize plugin because `depends_on` can be property by @dachengx in https://github.com/AxFoundation/strax/pull/820
+* Update context.py by @WenzDaniel in https://github.com/AxFoundation/strax/pull/821
+* Disable tqdm progress bar when `check_available` is empty by @dachengx in https://github.com/AxFoundation/strax/pull/822
+* Check the consistency of number of items in metadata and data in `dry_load_files` function by @dachengx in https://github.com/AxFoundation/strax/pull/824
+* Remove `strax.plugin` by @dachengx in https://github.com/AxFoundation/strax/pull/825
+* Pick out selection applying function by @dachengx in https://github.com/AxFoundation/strax/pull/826
+* Add `CutList` by @dachengx in https://github.com/AxFoundation/strax/pull/827
+* Update tags handling, added comment field. Allows to define superuns … by @WenzDaniel in https://github.com/AxFoundation/strax/pull/798
+* Prevent start being negative by @dachengx in https://github.com/AxFoundation/strax/pull/828
+* Tiny change on the trailing space by @dachengx in https://github.com/AxFoundation/strax/pull/830
+* Add `register_cut_list` by @dachengx in https://github.com/AxFoundation/strax/pull/831
+* Record all base classes when multiple inheritance by @dachengx in https://github.com/AxFoundation/strax/pull/832
+* Multiple output `DownChunkingPlugin` by @dachengx in https://github.com/AxFoundation/strax/pull/833
+* Add `ExhaustPlugin` that exhausts all chunks when fetching data by @dachengx in https://github.com/AxFoundation/strax/pull/835
+
+**Full Changelog**: https://github.com/AxFoundation/strax/compare/v1.6.2...v1.6.3
+
+
+1.6.2 / 2024-04-04
+---------------------
+* Use parentheses to separate the class name and attributes in the representation of StorageFrontend by @dachengx in https://github.com/AxFoundation/strax/pull/809
+* Specifically install `lxml_html_clean` by @dachengx in https://github.com/AxFoundation/strax/pull/812
+* Add a function to purge unused configs by @dachengx in https://github.com/AxFoundation/strax/pull/800
+* Warn if user checks is_stored for plugin not always saved by @cfuselli in https://github.com/AxFoundation/strax/pull/796
+* Bump urllib3 from 2.2.0 to 2.2.1 in /extra_requirements by @dependabot in https://github.com/AxFoundation/strax/pull/808
+* Do not call `get_components` in `is_stored` by @dachengx in https://github.com/AxFoundation/strax/pull/813
+
+New Contributors
+* @cfuselli made their first contribution in https://github.com/AxFoundation/strax/pull/796
+
+**Full Changelog**: https://github.com/AxFoundation/strax/compare/v1.6.1...v1.6.2
+
+
+1.6.1 / 2024-02-17
+---------------------
+* Remove a redundant function and fix some style by @dachengx in https://github.com/AxFoundation/strax/pull/795
+* Find the frontends which stored the targets by @dachengx in https://github.com/AxFoundation/strax/pull/802
+* Simpler chunk length check, avoid recursion limit crash by @JelleAalbers in https://github.com/AxFoundation/strax/pull/803
+* Deprecate the usage of `XENONnT/ax_env` by @dachengx in https://github.com/AxFoundation/strax/pull/804
+* Add a function to directly load file from strax folder by @dachengx in https://github.com/AxFoundation/strax/pull/801
+
+
+**Full Changelog**: https://github.com/AxFoundation/strax/compare/v1.6.0...v1.6.1
+
+
 1.6.0 / 2024-01-15
 ---------------------
 * `np.float` is deprecated by @dachengx in https://github.com/AxFoundation/strax/pull/789

docs/source/conf.py

@@ -66,9 +66,9 @@
 # built documents.
 #
 # The short X.Y version.
-version = "1.6.0"
+version = "1.6.4"
 # The full version, including alpha/beta/rc tags.
-release = "1.6.0"
+release = "1.6.4"
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

extra_requirements/requirements-docs.txt

@@ -6,4 +6,5 @@ recommonmark
 graphviz
 m2r
 mistune==0.8.4
-urllib3==2.1.0
+urllib3==2.2.1
+lxml_html_clean

extra_requirements/requirements-tests.txt

@@ -1,4 +1,2 @@
 # File for the requirements of strax with the automated tests
-git+https://github.com/XENONnT/ax_env
-deepdiff
-ipython==8.12.1
+git+https://github.com/XENONnT/base_environment

setup.py

@@ -20,7 +20,7 @@ def open_requirements(path):
 
 setuptools.setup(
     name="strax",
-    version="1.6.0",
+    version="1.6.4",
     description="Streaming analysis for xenon TPCs",
     author="strax developers",
     url="https://github.com/AxFoundation/strax",

strax/__init__.py

@@ -1,5 +1,5 @@
 # flake8: noqa
-__version__ = "1.6.0"
+__version__ = "1.6.4"
 
 # Glue the package together
 # See https://www.youtube.com/watch?v=0oTh1CXRaQ0 if this confuses you

strax/chunk.py

@@ -1,5 +1,4 @@
 import typing as ty
-from functools import wraps
 
 import numpy as np
 import numba
@@ -72,6 +71,8 @@ def __init__(
             raise ValueError(
                 f"Attempt to create chunk {self} with data of {dtype}, should be {expected_dtype}"
             )
+        if self.start < 0:
+            raise ValueError(f"Attempt to create chunk {self} with negative start time")
         if self.start > self.end:
             raise ValueError(f"Attempt to create chunk {self} with negative length")
 
@@ -107,8 +108,7 @@ def __repr__(self):
         return (
             f"[{self.run_id}.{self.data_type}: "
             f"{self._t_fmt(self.start)} - {self._t_fmt(self.end)}, "
-            f"{len(self)} items, "
-            + "{0:.1f} MB/s]".format(self._mbs())
+            f"{len(self)} items, " + "{0:.1f} MB/s]".format(self._mbs())
         )
 
     @property
@@ -245,7 +245,7 @@ def merge(cls, chunks, data_type="<UNKNOWN>"):
         )
 
     @classmethod
-    def concatenate(cls, chunks):
+    def concatenate(cls, chunks, allow_hyperrun=False):
         """Create chunk by concatenating chunks of same data type You can pass None's, they will be
         ignored."""
         chunks = [c for c in chunks if c is not None]
@@ -261,7 +261,7 @@ def concatenate(cls, chunks):
 
         run_ids = [c.run_id for c in chunks]
 
-        if len(set(run_ids)) != 1:
+        if len(set(run_ids)) != 1 and not allow_hyperrun:
             raise ValueError(
                 f"Cannot concatenate {data_type} chunks with different run ids: {run_ids}"
             )
@@ -422,29 +422,6 @@ def _update_subruns_in_chunk(chunks):
     return subruns
 
 
-@export
-def check_chunk_n(f):
-    @wraps(f)
-    def wrapper(self, *args, **kwargs):
-        # assume chunk_info is the second argument
-        if "chunk_info" not in kwargs:
-            raise ValueError(
-                "chunk_info not passed to function, check_chunk_n ",
-                "can only be used with functions that take chunk_info as an argument, ",
-                "usually it is the strax.StorageBackend._read_chunk method.",
-            )
-        chunk_info = kwargs["chunk_info"]
-        chunk = f(self, *args, **kwargs)
-        if len(chunk) != chunk_info["n"]:
-            raise strax.DataCorrupted(
-                f"Chunk {chunk_info['filename']} of {chunk_info['run_id']} has {len(chunk)} items, "
-                f"but chunk_info {chunk_info} says {chunk_info['n']}"
-            )
-        return chunk
-
-    return wrapper
-
-
 @export
 class Rechunker:
     """Helper class for rechunking.

strax/config.py

@@ -122,11 +122,13 @@ def __init__(
         #                   DeprecationWarning)
 
         if (
-            sum([
-                self.default is not OMITTED,
-                self.default_factory is not OMITTED,
-                self.default_by_run is not OMITTED,
-            ])
+            sum(
+                [
+                    self.default is not OMITTED,
+                    self.default_factory is not OMITTED,
+                    self.default_by_run is not OMITTED,
+                ]
+            )
             > 1
         ):
             raise RuntimeError(f"Tried to specify more than one default for option {self.name}.")