From 797e6656c750535ea27defc46e3cfcc704a12b4b Mon Sep 17 00:00:00 2001 From: Casey Clements Date: Wed, 15 Oct 2025 15:52:14 -0400 Subject: [PATCH 01/14] Initial addition of numpy ndarrays to BinaryVector. New tests --- bson/binary.py | 126 ++++++++++++++++++++---- pyproject.toml | 1 + requirements/numpy.txt | 1 + test/test_bson.py | 62 ++++++++++++ uv.lock | 215 ++++++++++++++++++++++++++++++++++++++++- 5 files changed, 384 insertions(+), 21 deletions(-) create mode 100644 requirements/numpy.txt diff --git a/bson/binary.py b/bson/binary.py index 48eb12b0ac..cc0027b3e1 100644 --- a/bson/binary.py +++ b/bson/binary.py @@ -66,6 +66,15 @@ from mmap import mmap as _mmap +_NUMPY_AVAILABLE = False +try: + import numpy as np + + _NUMPY_AVAILABLE = True +except ImportError: + np = None # type: ignore + + class UuidRepresentation: UNSPECIFIED = 0 """An unspecified UUID representation. @@ -234,13 +243,22 @@ class BinaryVector: __slots__ = ("data", "dtype", "padding") - def __init__(self, data: Sequence[float | int], dtype: BinaryVectorDtype, padding: int = 0): + def __init__( + self, + data: Union[Sequence[float | int], np.ndarray], + dtype: BinaryVectorDtype, + padding: int = 0, + ): """ :param data: Sequence of numbers representing the mathematical vector. :param dtype: The data type stored in binary :param padding: The number of bits in the final byte that are to be ignored when a vector element's size is less than a byte and the length of the vector is not a multiple of 8. + (This is equivalent to a negative value of `count` in`numpy.unpackbits`_) + + .. _numpy.unpackbits: https://numpy.org/doc/stable/reference/generated/numpy.unpackbits.html + """ self.data = data self.dtype = dtype @@ -425,9 +443,19 @@ def from_vector( ... @classmethod + @overload def from_vector( cls: Type[Binary], - vector: Union[BinaryVector, list[int], list[float]], + vector: np.ndarray, + dtype: BinaryVectorDtype, + padding: int = 0, + ) -> Binary: + ... + + @classmethod + def from_vector( + cls: Type[Binary], + vector: Union[BinaryVector, list[int], list[float], np.ndarray], dtype: Optional[BinaryVectorDtype] = None, padding: Optional[int] = None, ) -> Binary: @@ -459,25 +487,29 @@ def from_vector( vector = vector.data # type: ignore padding = 0 if padding is None else padding - if dtype == BinaryVectorDtype.INT8: # pack ints in [-128, 127] as signed int8 - format_str = "b" - if padding: - raise ValueError(f"padding does not apply to {dtype=}") - elif dtype == BinaryVectorDtype.PACKED_BIT: # pack ints in [0, 255] as unsigned uint8 - format_str = "B" - if 0 <= padding > 7: - raise ValueError(f"{padding=}. It must be in [0,1, ..7].") - if padding and not vector: - raise ValueError("Empty vector with non-zero padding.") - elif dtype == BinaryVectorDtype.FLOAT32: # pack floats as float32 - format_str = "f" - if padding: - raise ValueError(f"padding does not apply to {dtype=}") + metadata = struct.pack(" 7: + raise ValueError(f"{padding=}. It must be in [0,1, ..7].") + if padding and not vector: + raise ValueError("Empty vector with non-zero padding.") + elif dtype == BinaryVectorDtype.FLOAT32: # pack floats as float32 + format_str = "f" + if padding: + raise ValueError(f"padding does not apply to {dtype=}") + else: + raise NotImplementedError("%s not yet supported" % dtype) + data = struct.pack(f"<{len(vector)}{format_str}", *vector) # type: ignore - metadata = struct.pack(" int: """Subtype of this binary data.""" return self.__subtype + def as_numpy_vector(self) -> BinaryVector: + """From the Binary, create a BinaryVector where data is a 1-dim numpy array. + dtype still follows our typing (BinaryVectorDtype), + and padding is as we define it, notably equivalent to a negative value of count + in `numpy.unpackbits `_. + + :return: BinaryVector + + .. versionadded:: 4.16 + """ + if self.subtype != VECTOR_SUBTYPE: + raise ValueError(f"Cannot decode subtype {self.subtype} as a vector") + if not _NUMPY_AVAILABLE: + raise ImportError("Converting binary to numpy.ndarray requires numpy to be installed.") + dtype, padding = struct.unpack_from(" Tuple[bytes, int]: # type: ignore[override] # Work around http://bugs.python.org/issue7382 data = super().__getnewargs__()[0] @@ -575,3 +634,32 @@ def __repr__(self) -> str: return f"" else: return f"Binary({bytes.__repr__(self)}, {self.__subtype})" + + +def _numpy_vector_to_bytes( + vector: np.ndarray, + dtype: BinaryVectorDtype, +) -> bytes: + if not _NUMPY_AVAILABLE: + raise ImportError("Converting numpy.ndarray to binary requires numpy to be installed.") + + assert isinstance(vector, np.ndarray) + assert ( + vector.ndim == 1 + ), "from_numpy_vector only supports 1D arrays as it creates a single vector." + + if dtype == BinaryVectorDtype.FLOAT32: + vector = vector.astype(np.dtype("float32"), copy=False) + elif dtype == BinaryVectorDtype.INT8: + if vector.min() >= -128 and vector.max() <= 127: + vector = vector.astype(np.dtype("int8"), copy=False) + else: + raise ValueError("Values found outside INT8 range.") + elif dtype == BinaryVectorDtype.PACKED_BIT: + if vector.min() >= 0 and vector.max() <= 127: + vector = vector.astype(np.dtype("uint8"), copy=False) + else: + raise ValueError("Values found outside UINT8 range.") + else: + raise NotImplementedError("%s not yet supported" % dtype) + return vector.tobytes() diff --git a/pyproject.toml b/pyproject.toml index 623eb6c164..c3df1440ed 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -87,6 +87,7 @@ ocsp = ["requirements/ocsp.txt"] snappy = ["requirements/snappy.txt"] test = ["requirements/test.txt"] zstd = ["requirements/zstd.txt"] +numpy = ["requirements/numpy.txt"] [tool.pytest.ini_options] minversion = "7" diff --git a/requirements/numpy.txt b/requirements/numpy.txt new file mode 100644 index 0000000000..e0485aa7fe --- /dev/null +++ b/requirements/numpy.txt @@ -0,0 +1 @@ +numpy>=1.21 diff --git a/test/test_bson.py b/test/test_bson.py index f792db1e89..5b5378f170 100644 --- a/test/test_bson.py +++ b/test/test_bson.py @@ -71,6 +71,14 @@ from bson.timestamp import Timestamp from bson.tz_util import FixedOffset, utc +_NUMPY_AVAILABLE = False +try: + import numpy as np + + _NUMPY_AVAILABLE = True +except ImportError: + np = None # type: ignore + class NotADict(abc.MutableMapping): """Non-dict type that implements the mapping protocol.""" @@ -735,6 +743,60 @@ def test_uuid_legacy(self): transformed = bin.as_uuid(UuidRepresentation.PYTHON_LEGACY) self.assertEqual(id, transformed) + @unittest.skipIf(not _NUMPY_AVAILABLE, "numpy optional-dependency not installed.") + def test_vector_from_numpy(self): + """Follows test_vector except for input type numpy.ndarray""" + # Simple data values could be treated as any of our BinaryVectorDtypes + arr = np.array([2, 3]) + # INT8 + binary_vector_int8 = Binary.from_vector(arr, BinaryVectorDtype.INT8) + # as_vector + vector = binary_vector_int8.as_vector() + assert isinstance(vector, BinaryVector) + assert vector.data == arr.tolist() + # as_numpy_vector + vector_np = binary_vector_int8.as_numpy_vector() + assert isinstance(vector_np, BinaryVector) + assert np.all(vector.data == arr) + # PACKED_BIT + binary_vector_uint8 = Binary.from_vector(arr, BinaryVectorDtype.PACKED_BIT) + # as_vector + vector = binary_vector_uint8.as_vector() + assert isinstance(vector, BinaryVector) + assert vector.data == arr.tolist() + # as_numpy_vector + vector_np = binary_vector_uint8.as_numpy_vector() + assert isinstance(vector_np, BinaryVector) + assert np.all(vector_np.data == arr) + # FLOAT32 + binary_vector_float32 = Binary.from_vector(arr, BinaryVectorDtype.FLOAT32) + # as_vector + vector = binary_vector_float32.as_vector() + assert isinstance(vector, BinaryVector) + assert vector.data == arr.tolist() + # as_numpy_vector + vector_np = binary_vector_float32.as_numpy_vector() + assert isinstance(vector_np, BinaryVector) + assert np.all(vector_np.data == arr) + + # Invalid cases + with self.assertRaises(ValueError): + Binary.from_vector(np.array([-1]), BinaryVectorDtype.PACKED_BIT) + with self.assertRaises(ValueError): + Binary.from_vector(np.array([128]), BinaryVectorDtype.PACKED_BIT) + with self.assertRaises(ValueError): + Binary.from_vector(np.array([-198]), BinaryVectorDtype.INT8) + + # Unexpected cases + # Creating a vector of INT8 from a list of doubles will be caught by struct.pack + # Numpy's default behavior is to cast to the type requested. + list_floats = [-1.1, 1.1] + cast_bin = Binary.from_vector(np.array(list_floats), BinaryVectorDtype.INT8) + vector = cast_bin.as_vector() + vector_np = cast_bin.as_numpy_vector() + assert vector.data != list_floats + assert vector.data == vector_np.data.tolist() == [-1, 1] + def test_vector(self): """Tests of subtype 9""" # We start with valid cases, across the 3 dtypes implemented. diff --git a/uv.lock b/uv.lock index f9a389c896..9a97206db4 100644 --- a/uv.lock +++ b/uv.lock @@ -1,5 +1,5 @@ version = 1 -revision = 3 +revision = 2 requires-python = 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version = "2.2.6", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version == '3.10.*'" }, + { name = "numpy", version = "2.3.4", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version >= '3.11'" }, +] ocsp = [ { name = "certifi", marker = "os_name == 'nt' or sys_platform == 'darwin'" }, { name = "cryptography" }, @@ -1166,6 +1376,7 @@ requires-dist = [ { name = "dnspython", specifier = ">=2.6.1,<3.0.0" }, { name = "furo", marker = "extra == 'docs'", specifier = "==2025.9.25" }, { name = "importlib-metadata", marker = "python_full_version < '3.13' and extra == 'test'", specifier = ">=7.0" }, + { name = "numpy", marker = "extra == 'numpy'", specifier = ">=1.21" }, { name = "pykerberos", marker = "os_name != 'nt' and extra == 'gssapi'" }, { name = "pymongo-auth-aws", marker = "extra == 'aws'", specifier = ">=1.1.0,<2.0.0" }, { name = "pymongo-auth-aws", marker = "extra == 'encryption'", specifier = ">=1.1.0,<2.0.0" }, @@ -1184,7 +1395,7 @@ requires-dist = [ { name = "winkerberos", marker = "os_name == 'nt' and extra == 'gssapi'", specifier = ">=0.5.0" }, { name = "zstandard", marker = "extra == 'zstd'" }, ] -provides-extras = ["aws", "docs", "encryption", "gssapi", "ocsp", "snappy", "test", "zstd"] +provides-extras = ["aws", "docs", "encryption", "gssapi", "numpy", "ocsp", "snappy", "test", "zstd"] [package.metadata.requires-dev] coverage = [ From 47fc92cb52cfd2e50c3e36014bd9fb4a7d3dd515 Mon Sep 17 00:00:00 2001 From: Casey Clements Date: Wed, 15 Oct 2025 16:10:49 -0400 Subject: [PATCH 02/14] Updates changelog --- doc/changelog.rst | 1 + 1 file changed, 1 insertion(+) diff --git a/doc/changelog.rst b/doc/changelog.rst index f3eb4f6f23..e7a642aeed 100644 --- a/doc/changelog.rst +++ b/doc/changelog.rst @@ -16,6 +16,7 @@ PyMongo 4.16 brings a number of changes including: Python 3.10+. The minimum version is ``2.6.1`` to account for `CVE-2023-29483 `_. - Removed support for Eventlet. Eventlet is actively being sunset by its maintainers and has compatibility issues with PyMongo's dnspython dependency. +- Added support for NumPy 1D-arrays in BSON Binary Vectors. Changes in Version 4.15.3 (2025/10/07) -------------------------------------- From 7882f75e129cebdb3d09815d44b27f81ce5ebdcd Mon Sep 17 00:00:00 2001 From: Casey Clements Date: Wed, 15 Oct 2025 16:37:15 -0400 Subject: [PATCH 03/14] Typing --- bson/binary.py | 1 + 1 file changed, 1 insertion(+) diff --git a/bson/binary.py b/bson/binary.py index cc0027b3e1..3f9236f0eb 100644 --- a/bson/binary.py +++ b/bson/binary.py @@ -487,6 +487,7 @@ def from_vector( vector = vector.data # type: ignore padding = 0 if padding is None else padding + assert isinstance(dtype, BinaryVectorDtype) metadata = struct.pack(" Date: Wed, 15 Oct 2025 16:43:34 -0400 Subject: [PATCH 04/14] Added numpy extra to typing_run --- justfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/justfile b/justfile index 17b95e87b7..999985e57e 100644 --- a/justfile +++ b/justfile @@ -2,7 +2,7 @@ set shell := ["bash", "-c"] # Commonly used command segments. -typing_run := "uv run --group typing --extra aws --extra encryption --extra ocsp --extra snappy --extra test --extra zstd" +typing_run := "uv run --group typing --extra aws --extra encryption --extra numpy --extra ocsp --extra snappy --extra test --extra zstd" docs_run := "uv run --extra docs" doc_build := "./doc/_build" mypy_args := "--install-types --non-interactive" From 5753e3ba5bf3d6027c5897d2a9dd581ec74ae0d1 Mon Sep 17 00:00:00 2001 From: Casey Clements Date: Wed, 15 Oct 2025 17:10:18 -0400 Subject: [PATCH 05/14] Adds numpy.typing.NDArray --- bson/binary.py | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/bson/binary.py b/bson/binary.py index 3f9236f0eb..7efa6b4ea8 100644 --- a/bson/binary.py +++ b/bson/binary.py @@ -69,6 +69,7 @@ _NUMPY_AVAILABLE = False try: import numpy as np + import numpy.typing as npt _NUMPY_AVAILABLE = True except ImportError: @@ -446,7 +447,7 @@ def from_vector( @overload def from_vector( cls: Type[Binary], - vector: np.ndarray, + vector: npt.NDArray[np.number], dtype: BinaryVectorDtype, padding: int = 0, ) -> Binary: @@ -455,7 +456,7 @@ def from_vector( @classmethod def from_vector( cls: Type[Binary], - vector: Union[BinaryVector, list[int], list[float], np.ndarray], + vector: Union[BinaryVector, list[int], list[float], npt.NDArray[np.number]], dtype: Optional[BinaryVectorDtype] = None, padding: Optional[int] = None, ) -> Binary: @@ -638,7 +639,7 @@ def __repr__(self) -> str: def _numpy_vector_to_bytes( - vector: np.ndarray, + vector: npt.NDArray[np.number], dtype: BinaryVectorDtype, ) -> bytes: if not _NUMPY_AVAILABLE: From d3407d7928e7bd3348c6640553c8abcfb9529c99 Mon Sep 17 00:00:00 2001 From: Casey Clements Date: Wed, 15 Oct 2025 17:13:09 -0400 Subject: [PATCH 06/14] Adds numpy.typing.NDArray --- bson/binary.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bson/binary.py b/bson/binary.py index 7efa6b4ea8..be6f71cacd 100644 --- a/bson/binary.py +++ b/bson/binary.py @@ -246,7 +246,7 @@ class BinaryVector: def __init__( self, - data: Union[Sequence[float | int], np.ndarray], + data: Union[Sequence[float | int], npt.NDArray[np.number]], dtype: BinaryVectorDtype, padding: int = 0, ): From 9ae90e8f2759ee07272cd939a6ebeac2e2da9dee Mon Sep 17 00:00:00 2001 From: Casey Clements Date: Wed, 15 Oct 2025 17:24:08 -0400 Subject: [PATCH 07/14] Removed match/case that will have to wait. --- bson/binary.py | 18 +++++++++--------- 1 file changed, 9 insertions(+), 9 deletions(-) diff --git a/bson/binary.py b/bson/binary.py index be6f71cacd..a53ff36ff2 100644 --- a/bson/binary.py +++ b/bson/binary.py @@ -599,15 +599,15 @@ def as_numpy_vector(self) -> BinaryVector: raise ImportError("Converting binary to numpy.ndarray requires numpy to be installed.") dtype, padding = struct.unpack_from(" Tuple[bytes, int]: # type: ignore[override] From aae159f8c3cebafd6eb5b03d5b42e85f27b0e512 Mon Sep 17 00:00:00 2001 From: Casey Clements Date: Thu, 16 Oct 2025 09:42:28 -0400 Subject: [PATCH 08/14] Put guard around check involving numpy --- bson/binary.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bson/binary.py b/bson/binary.py index a53ff36ff2..a800b71b6a 100644 --- a/bson/binary.py +++ b/bson/binary.py @@ -491,7 +491,7 @@ def from_vector( assert isinstance(dtype, BinaryVectorDtype) metadata = struct.pack(" Date: Thu, 16 Oct 2025 09:43:25 -0400 Subject: [PATCH 09/14] Moved test_vector_from_numpy to end of vector tests --- test/test_bson.py | 108 +++++++++++++++++++++++----------------------- 1 file changed, 54 insertions(+), 54 deletions(-) diff --git a/test/test_bson.py b/test/test_bson.py index 5b5378f170..b45d32a38f 100644 --- a/test/test_bson.py +++ b/test/test_bson.py @@ -743,60 +743,6 @@ def test_uuid_legacy(self): transformed = bin.as_uuid(UuidRepresentation.PYTHON_LEGACY) self.assertEqual(id, transformed) - @unittest.skipIf(not _NUMPY_AVAILABLE, "numpy optional-dependency not installed.") - def test_vector_from_numpy(self): - """Follows test_vector except for input type numpy.ndarray""" - # Simple data values could be treated as any of our BinaryVectorDtypes - arr = np.array([2, 3]) - # INT8 - binary_vector_int8 = Binary.from_vector(arr, BinaryVectorDtype.INT8) - # as_vector - vector = binary_vector_int8.as_vector() - assert isinstance(vector, BinaryVector) - assert vector.data == arr.tolist() - # as_numpy_vector - vector_np = binary_vector_int8.as_numpy_vector() - assert isinstance(vector_np, BinaryVector) - assert np.all(vector.data == arr) - # PACKED_BIT - binary_vector_uint8 = Binary.from_vector(arr, BinaryVectorDtype.PACKED_BIT) - # as_vector - vector = binary_vector_uint8.as_vector() - assert isinstance(vector, BinaryVector) - assert vector.data == arr.tolist() - # as_numpy_vector - vector_np = binary_vector_uint8.as_numpy_vector() - assert isinstance(vector_np, BinaryVector) - assert np.all(vector_np.data == arr) - # FLOAT32 - binary_vector_float32 = Binary.from_vector(arr, BinaryVectorDtype.FLOAT32) - # as_vector - vector = binary_vector_float32.as_vector() - assert isinstance(vector, BinaryVector) - assert vector.data == arr.tolist() - # as_numpy_vector - vector_np = binary_vector_float32.as_numpy_vector() - assert isinstance(vector_np, BinaryVector) - assert np.all(vector_np.data == arr) - - # Invalid cases - with self.assertRaises(ValueError): - Binary.from_vector(np.array([-1]), BinaryVectorDtype.PACKED_BIT) - with self.assertRaises(ValueError): - Binary.from_vector(np.array([128]), BinaryVectorDtype.PACKED_BIT) - with self.assertRaises(ValueError): - Binary.from_vector(np.array([-198]), BinaryVectorDtype.INT8) - - # Unexpected cases - # Creating a vector of INT8 from a list of doubles will be caught by struct.pack - # Numpy's default behavior is to cast to the type requested. - list_floats = [-1.1, 1.1] - cast_bin = Binary.from_vector(np.array(list_floats), BinaryVectorDtype.INT8) - vector = cast_bin.as_vector() - vector_np = cast_bin.as_numpy_vector() - assert vector.data != list_floats - assert vector.data == vector_np.data.tolist() == [-1, 1] - def test_vector(self): """Tests of subtype 9""" # We start with valid cases, across the 3 dtypes implemented. @@ -933,6 +879,60 @@ def test_binaryvector_equality(self): BinaryVector([1], BinaryVectorDtype.INT8), BinaryVector([2], BinaryVectorDtype.INT8) ) + @unittest.skipIf(not _NUMPY_AVAILABLE, "numpy optional-dependency not installed.") + def test_vector_from_numpy(self): + """Follows test_vector except for input type numpy.ndarray""" + # Simple data values could be treated as any of our BinaryVectorDtypes + arr = np.array([2, 3]) + # INT8 + binary_vector_int8 = Binary.from_vector(arr, BinaryVectorDtype.INT8) + # as_vector + vector = binary_vector_int8.as_vector() + assert isinstance(vector, BinaryVector) + assert vector.data == arr.tolist() + # as_numpy_vector + vector_np = binary_vector_int8.as_numpy_vector() + assert isinstance(vector_np, BinaryVector) + assert np.all(vector.data == arr) + # PACKED_BIT + binary_vector_uint8 = Binary.from_vector(arr, BinaryVectorDtype.PACKED_BIT) + # as_vector + vector = binary_vector_uint8.as_vector() + assert isinstance(vector, BinaryVector) + assert vector.data == arr.tolist() + # as_numpy_vector + vector_np = binary_vector_uint8.as_numpy_vector() + assert isinstance(vector_np, BinaryVector) + assert np.all(vector_np.data == arr) + # FLOAT32 + binary_vector_float32 = Binary.from_vector(arr, BinaryVectorDtype.FLOAT32) + # as_vector + vector = binary_vector_float32.as_vector() + assert isinstance(vector, BinaryVector) + assert vector.data == arr.tolist() + # as_numpy_vector + vector_np = binary_vector_float32.as_numpy_vector() + assert isinstance(vector_np, BinaryVector) + assert np.all(vector_np.data == arr) + + # Invalid cases + with self.assertRaises(ValueError): + Binary.from_vector(np.array([-1]), BinaryVectorDtype.PACKED_BIT) + with self.assertRaises(ValueError): + Binary.from_vector(np.array([128]), BinaryVectorDtype.PACKED_BIT) + with self.assertRaises(ValueError): + Binary.from_vector(np.array([-198]), BinaryVectorDtype.INT8) + + # Unexpected cases + # Creating a vector of INT8 from a list of doubles will be caught by struct.pack + # Numpy's default behavior is to cast to the type requested. + list_floats = [-1.1, 1.1] + cast_bin = Binary.from_vector(np.array(list_floats), BinaryVectorDtype.INT8) + vector = cast_bin.as_vector() + vector_np = cast_bin.as_numpy_vector() + assert vector.data != list_floats + assert vector.data == vector_np.data.tolist() == [-1, 1] + def test_unicode_regex(self): """Tests we do not get a segfault for C extension on unicode RegExs. This had been happening. From 40120e7d6dded164d36ff05ef8e756c9de40e75b Mon Sep 17 00:00:00 2001 From: Casey Clements Date: Thu, 16 Oct 2025 10:26:30 -0400 Subject: [PATCH 10/14] Fixed link in BinaryVector docstring --- bson/binary.py | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/bson/binary.py b/bson/binary.py index a800b71b6a..64a52fd7f4 100644 --- a/bson/binary.py +++ b/bson/binary.py @@ -256,10 +256,8 @@ def __init__( :param padding: The number of bits in the final byte that are to be ignored when a vector element's size is less than a byte and the length of the vector is not a multiple of 8. - (This is equivalent to a negative value of `count` in`numpy.unpackbits`_) - - .. _numpy.unpackbits: https://numpy.org/doc/stable/reference/generated/numpy.unpackbits.html - + (This is equivalent to a negative value of `count` in + `numpy.unpackbits `_) """ self.data = data self.dtype = dtype From be06ce77c72068dfc3903ea6be46a943a0a11dd1 Mon Sep 17 00:00:00 2001 From: Casey Clements Date: Thu, 16 Oct 2025 10:29:52 -0400 Subject: [PATCH 11/14] Tiny adjustment of BinaryVector docstring --- bson/binary.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bson/binary.py b/bson/binary.py index 64a52fd7f4..83dd969cd1 100644 --- a/bson/binary.py +++ b/bson/binary.py @@ -256,7 +256,7 @@ def __init__( :param padding: The number of bits in the final byte that are to be ignored when a vector element's size is less than a byte and the length of the vector is not a multiple of 8. - (This is equivalent to a negative value of `count` in + (Padding is equivalent to a negative value of `count` in `numpy.unpackbits `_) """ self.data = data From f03b94303aa1fc41cd7bc12639d9902e6ad04050 Mon Sep 17 00:00:00 2001 From: Casey Clements Date: Fri, 17 Oct 2025 11:57:35 -0400 Subject: [PATCH 12/14] Convert Assertion to Value and Type Errors --- bson/binary.py | 13 ++++++++----- 1 file changed, 8 insertions(+), 5 deletions(-) diff --git a/bson/binary.py b/bson/binary.py index 83dd969cd1..470eaa7e52 100644 --- a/bson/binary.py +++ b/bson/binary.py @@ -486,7 +486,10 @@ def from_vector( vector = vector.data # type: ignore padding = 0 if padding is None else padding - assert isinstance(dtype, BinaryVectorDtype) + if not isinstance(dtype, BinaryVectorDtype): + raise TypeError( + "dtype must be a bson.BinaryVectorDtype, such as BinaryVectorDtype.FLOAT32" + ) metadata = struct.pack(" Date: Fri, 17 Oct 2025 15:16:46 -0400 Subject: [PATCH 13/14] Numpy now lazily imported. For typing, removed numpy extra. justfile now uses with --- bson/binary.py | 80 ++++++++------- justfile | 20 ++-- pyproject.toml | 1 - requirements/numpy.txt | 1 - test/test_bson.py | 11 +-- uv.lock | 215 +---------------------------------------- 6 files changed, 57 insertions(+), 271 deletions(-) delete mode 100644 requirements/numpy.txt diff --git a/bson/binary.py b/bson/binary.py index 470eaa7e52..4588c62ae7 100644 --- a/bson/binary.py +++ b/bson/binary.py @@ -65,16 +65,9 @@ from array import array as _array from mmap import mmap as _mmap - -_NUMPY_AVAILABLE = False -try: import numpy as np import numpy.typing as npt - _NUMPY_AVAILABLE = True -except ImportError: - np = None # type: ignore - class UuidRepresentation: UNSPECIFIED = 0 @@ -492,9 +485,7 @@ def from_vector( ) metadata = struct.pack("= -128 and vector.max() <= 127: + vector = vector.astype(np.dtype("int8"), copy=False) + else: + raise ValueError("Values found outside INT8 range.") + elif dtype == BinaryVectorDtype.PACKED_BIT: + if vector.min() >= 0 and vector.max() <= 127: + vector = vector.astype(np.dtype("uint8"), copy=False) + else: + raise ValueError("Values found outside UINT8 range.") + else: + raise NotImplementedError("%s not yet supported" % dtype) + data = vector.tobytes() if padding and len(vector) and not (data[-1] & ((1 << padding) - 1)) == 0: raise ValueError( @@ -596,8 +616,13 @@ def as_numpy_vector(self) -> BinaryVector: """ if self.subtype != VECTOR_SUBTYPE: raise ValueError(f"Cannot decode subtype {self.subtype} as a vector") - if not _NUMPY_AVAILABLE: - raise ImportError("Converting binary to numpy.ndarray requires numpy to be installed.") + try: + import numpy as np + except ImportError as exc: + raise ImportError( + "Converting binary to numpy.ndarray requires numpy to be installed." + ) from exc + dtype, padding = struct.unpack_from(" str: return f"" else: return f"Binary({bytes.__repr__(self)}, {self.__subtype})" - - -def _numpy_vector_to_bytes( - vector: npt.NDArray[np.number], - dtype: BinaryVectorDtype, -) -> bytes: - if not _NUMPY_AVAILABLE: - raise ImportError("Converting numpy.ndarray to binary requires numpy to be installed.") - - if not isinstance(vector, np.ndarray): - raise TypeError("Vector must be a numpy array.") - if vector.ndim != 1: - raise ValueError("from_numpy_vector only supports 1D arrays as it creates a single vector.") - - if dtype == BinaryVectorDtype.FLOAT32: - vector = vector.astype(np.dtype("float32"), copy=False) - elif dtype == BinaryVectorDtype.INT8: - if vector.min() >= -128 and vector.max() <= 127: - vector = vector.astype(np.dtype("int8"), copy=False) - else: - raise ValueError("Values found outside INT8 range.") - elif dtype == BinaryVectorDtype.PACKED_BIT: - if vector.min() >= 0 and vector.max() <= 127: - vector = vector.astype(np.dtype("uint8"), copy=False) - else: - raise ValueError("Values found outside UINT8 range.") - else: - raise NotImplementedError("%s not yet supported" % dtype) - return vector.tobytes() diff --git a/justfile b/justfile index 999985e57e..50957149e8 100644 --- a/justfile +++ b/justfile @@ -2,7 +2,7 @@ set shell := ["bash", "-c"] # Commonly used command segments. -typing_run := "uv run --group typing --extra aws --extra encryption --extra numpy --extra ocsp --extra snappy --extra test --extra zstd" +typing_run := "uv run --group typing --extra aws --extra encryption --with numpy --extra ocsp --extra snappy --extra test --extra zstd" docs_run := "uv run --extra docs" doc_build := "./doc/_build" mypy_args := "--install-types --non-interactive" @@ -39,14 +39,14 @@ typing: && resync [group('typing')] typing-mypy: && resync - {{typing_run}} mypy {{mypy_args}} bson gridfs tools pymongo - {{typing_run}} mypy {{mypy_args}} --config-file mypy_test.ini test - {{typing_run}} mypy {{mypy_args}} test/test_typing.py test/test_typing_strict.py + {{typing_run}} python -m mypy {{mypy_args}} bson gridfs tools pymongo + {{typing_run}} python -m mypy {{mypy_args}} --config-file mypy_test.ini test + {{typing_run}} python -m mypy {{mypy_args}} test/test_typing.py test/test_typing_strict.py [group('typing')] typing-pyright: && resync - {{typing_run}} pyright test/test_typing.py test/test_typing_strict.py - {{typing_run}} pyright -p strict_pyrightconfig.json test/test_typing_strict.py + {{typing_run}} python -m pyright test/test_typing.py test/test_typing_strict.py + {{typing_run}} python -m pyright -p strict_pyrightconfig.json test/test_typing_strict.py [group('lint')] lint *args="": && resync @@ -58,7 +58,13 @@ lint-manual *args="": && resync [group('test')] test *args="-v --durations=5 --maxfail=10": && resync - uv run --extra test pytest {{args}} + uv run --extra test python -m pytest {{args}} + +[group('test')] +test-bson *args="-v --durations=5 --maxfail=10": && resync + uv run --extra test --with numpy python -m pytest test/test_bson.py + + [group('test')] run-tests *args: && resync diff --git a/pyproject.toml b/pyproject.toml index c3df1440ed..623eb6c164 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -87,7 +87,6 @@ ocsp = ["requirements/ocsp.txt"] snappy = ["requirements/snappy.txt"] test = ["requirements/test.txt"] zstd = ["requirements/zstd.txt"] -numpy = ["requirements/numpy.txt"] [tool.pytest.ini_options] minversion = "7" diff --git a/requirements/numpy.txt b/requirements/numpy.txt deleted file mode 100644 index e0485aa7fe..0000000000 --- a/requirements/numpy.txt +++ /dev/null @@ -1 +0,0 @@ -numpy>=1.21 diff --git a/test/test_bson.py b/test/test_bson.py index b45d32a38f..cc670bc228 100644 --- a/test/test_bson.py +++ b/test/test_bson.py @@ -19,6 +19,7 @@ import array import collections import datetime +import importlib.util import mmap import os import pickle @@ -71,13 +72,7 @@ from bson.timestamp import Timestamp from bson.tz_util import FixedOffset, utc -_NUMPY_AVAILABLE = False -try: - 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Padding ({padding}) must be between 0 and 7.") data = np.frombuffer(self[2:], dtype="uint8") + if padding and np.unpackbits(data[-1])[-padding:].sum() > 0: + warnings.warn( + "Vector has a padding P, but bits in the final byte lower than P are non-zero. For pymongo>=5.0, they must be zero.", + DeprecationWarning, + stacklevel=2, + ) else: raise ValueError(f"Unsupported dtype code: {dtype!r}") return BinaryVector(data, dtype, padding)