chore(deps): update indirect python dependencies #1023
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This PR contains the following updates:
==0.3.9->==0.4.0==1.51.0->==1.53.0==7.0.7.99.1.2a1->==7.0.7.99.1.2a2==4.58.5->==4.59.0==4.24.0->==4.24.1==2.2.6->==2.3.1==0.11->==0.12==3.10.18->==3.11.0==2.33.2->==2.35.2==1.0.0->==1.1.0==26.3.0->==26.4.0==0.12.3->==0.12.4==2.32.0->==2.33.0Release Notes
pypa/distlib (distlib)
v0.4.0Compare Source
DiamondLightSource/dodal (dls-dodal)
v1.53.0Compare Source
What's Changed
Full Changelog: DiamondLightSource/dodal@1.52.0...1.53.0
v1.52.0Compare Source
What's Changed
New Contributors
Full Changelog: DiamondLightSource/dodal@1.51.0...1.52.0
fonttools/fonttools (fonttools)
v4.59.0Compare Source
fspackage) fromfonttools[ufo]extra. This is replaced by thefontTools.misc.filesystempackage, a stdlib-only, drop-in replacement for the subset of the pyfilesystem2's API used byfontTools.ufoLib. The latter should continue to work with the upstreamfs(we even test with/without). However, clients who wish to continue usingfscan do so by depending on it directly instead of via thefonttools[ufo]extra (#3885, #3620)..addComponent()implementations, in particularbaseGlyphNamevsglyphName(#3880).python-jsonschema/jsonschema (jsonschema)
v4.24.1Compare Source
=======
ValidationError.json_path(#139).numpy/numpy (numpy)
v2.3.1: (Jun 21, 2025)Compare Source
NumPy 2.3.1 Release Notes
The NumPy 2.3.1 release is a patch release with several bug fixes,
annotation improvements, and better support for OpenBSD. Highlights are:
matmulfor non-contiguous out kwarg parameternp.vectorizecasting errorsThis release supports Python versions 3.11-3.13, Python 3.14 will be
supported when it is released.
Contributors
A total of 9 people contributed to this release. People with a "+" by
their names contributed a patch for the first time.
Pull requests merged
A total of 12 pull requests were merged for this release.
np.vectorizecasting to legacy behavior (#29196)Checksums
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v2.3.0: (June 7, 2025)Compare Source
NumPy 2.3.0 Release Notes
The NumPy 2.3.0 release continues the work to improve free threaded
Python support and annotations together with the usual set of bug fixes.
It is unusual in the number of expired deprecations, code
modernizations, and style cleanups. The latter may not be visible to
users, but is important for code maintenance over the long term. Note
that we have also upgraded from manylinux2014 to manylinux_2_28.
Users running on a Mac having an M4 cpu might see various warnings about
invalid values and such. The warnings are a known problem with
Accelerate. They are annoying, but otherwise harmless. Apple promises to
fix them.
This release supports Python versions 3.11-3.13, Python 3.14 will be
supported when it is released.
Highlights
New functions
New function
numpy.strings.sliceThe new function
numpy.strings.slicewas added, which implements fastnative slicing of string arrays. It supports the full slicing API
including negative slice offsets and steps.
(gh-27789)
Deprecations
The
numpy.typing.mypy_pluginhas been deprecated in favor ofplatform-agnostic static type inference. Please remove
numpy.typing.mypy_pluginfrom thepluginssection of your mypyconfiguration. If this change results in new errors being reported,
kindly open an issue.
(gh-28129)
The
numpy.typing.NBitBasetype has been deprecated and will beremoved in a future version.
This type was previously intended to be used as a generic upper
bound for type-parameters, for example:
But in NumPy 2.2.0,
float64andcomplex128were changed toconcrete subtypes, causing static type-checkers to reject
x: np.float64 = f(np.complex128(42j)).So instead, the better approach is to use
typing.overload:(gh-28884)
Expired deprecations
Remove deprecated macros like
NPY_OWNDATAfrom Cython interfacesin favor of
NPY_ARRAY_OWNDATA(deprecated since 1.7)(gh-28254)
Remove
numpy/npy_1_7_deprecated_api.hand C macros likeNPY_OWNDATAin favor ofNPY_ARRAY_OWNDATA(deprecated since 1.7)(gh-28254)
Remove alias
generate_divbyzero_errortonpy_set_floatstatus_divbyzeroandgenerate_overflow_errortonpy_set_floatstatus_overflow(deprecated since 1.10)(gh-28254)
Remove
np.tostring(deprecated since 1.19)(gh-28254)
Raise on
np.conjugateof non-numeric types (deprecated since 1.13)(gh-28254)
Raise when using
np.bincount(...minlength=None), use 0 instead(deprecated since 1.14)
(gh-28254)
Passing
shape=Noneto functions with a non-optional shape argumenterrors, use
()instead (deprecated since 1.20)(gh-28254)
Inexact matches for
modeandsearchsideraise (deprecated since1.20)
(gh-28254)
Setting
__array_finalize__ = Noneerrors (deprecated since 1.23)(gh-28254)
np.fromfileandnp.fromstringerror on bad data, previously theywould guess (deprecated since 1.18)
(gh-28254)
datetime64andtimedelta64construction with a tuple no longeraccepts an
eventvalue, either use a two-tuple of (unit, num) or a4-tuple of (unit, num, den, 1) (deprecated since 1.14)
(gh-28254)
When constructing a
dtypefrom a class with adtypeattribute,that attribute must be a dtype-instance rather than a thing that can
be parsed as a dtype instance (deprecated in 1.19). At some point
the whole construct of using a dtype attribute will be deprecated
(see #25306)
(gh-28254)
Passing booleans as partition index errors (deprecated since 1.23)
(gh-28254)
Out-of-bounds indexes error even on empty arrays (deprecated since
1.20)
(gh-28254)
np.tostringhas been removed, usetobytesinstead (deprecatedsince 1.19)
(gh-28254)
Disallow make a non-writeable array writeable for arrays with a base
that do not own their data (deprecated since 1.17)
(gh-28254)
concatenate()withaxis=Noneusessame-kindcasting bydefault, not
unsafe(deprecated since 1.20)(gh-28254)
Unpickling a scalar with object dtype errors (deprecated since 1.20)
(gh-28254)
The binary mode of
fromstringnow errors, usefrombufferinstead(deprecated since 1.14)
(gh-28254)
Converting
np.inexactornp.floatingto a dtype errors(deprecated since 1.19)
(gh-28254)
Converting
np.complex,np.integer,np.signedinteger,np.unsignedinteger,np.genericto a dtype errors (deprecatedsince 1.19)
(gh-28254)
The Python built-in
rounderrors for complex scalars. Usenp.roundorscalar.roundinstead (deprecated since 1.19)(gh-28254)
'np.bool' scalars can no longer be interpreted as an index
(deprecated since 1.19)
(gh-28254)
Parsing an integer via a float string is no longer supported.
(deprecated since 1.23) To avoid this error you can
converters=floatkeyword argument.np.loadtxt(...).astype(np.int64)(gh-28254)
The use of a length 1 tuple for the ufunc
signatureerrors. Usedtypeor fill the tuple withNone(deprecated since 1.19)(gh-28254)
Special handling of matrix is in np.outer is removed. Convert to a
ndarray via
matrix.A(deprecated since 1.20)(gh-28254)
Removed the
np.compatpackage source code (removed in 2.0)(gh-28961)
C API changes
NpyIter_GetTransferFlagsis now available to check if the iteratorneeds the Python API or if casts may cause floating point errors
(FPE). FPEs can for example be set when casting
float64(1e300)tofloat32(overflow to infinity) or a NaN to an integer (invalidvalue).
(gh-27883)
NpyIternow has no limit on the number of operands it supports.(gh-28080)
New
NpyIter_GetTransferFlagsandNpyIter_IterationNeedsAPIchangeNumPy now has the new
NpyIter_GetTransferFlagsfunction as a moreprecise way checking of iterator/buffering needs. I.e. whether the
Python API/GIL is required or floating point errors may occur. This
function is also faster if you already know your needs without
buffering.
The
NpyIter_IterationNeedsAPIfunction now performs all the checksthat were previously performed at setup time. While it was never
necessary to call it multiple times, doing so will now have a larger
cost.
(gh-27998)
New Features
The type parameter of
np.dtypenow defaults totyping.Any. Thisway, static type-checkers will infer
dtype: np.dtypeasdtype: np.dtype[Any], without reporting an error.(gh-28669)
Static type-checkers now interpret:
_: np.ndarrayas_: npt.NDArray[typing.Any]._: np.flatiteras_: np.flatiter[np.ndarray].This is because their type parameters now have default values.
(gh-28940)
NumPy now registers its pkg-config paths with the pkgconf PyPI package
The pkgconf PyPI
package provides an interface for projects like NumPy to register their
own paths to be added to the pkg-config search path. This means that
when using pkgconf
from PyPI, NumPy will be discoverable without needing for any custom
environment configuration.
(gh-28214)
Allow
out=...in ufuncs to ensure array resultNumPy has the sometimes difficult behavior that it currently usually
returns scalars rather than 0-D arrays (even if the inputs were 0-D
arrays). This is especially problematic for non-numerical dtypes (e.g.
object).For ufuncs (i.e. most simple math functions) it is now possible to use
out=...(literally `...`, e.g.out=Ellipsis) which is identicalin behavior to
outnot being passed, but will ensure a non-scalarreturn. This spelling is borrowed from
arr1d[0, ...]where the...also ensures a non-scalar return.
Other functions with an
out=kwarg should gain support eventually.Downstream libraries that interoperate via
__array_ufunc__or__array_function__may need to adapt to support this.(gh-28576)
Building NumPy with OpenMP Parallelization
NumPy now supports OpenMP parallel processing capabilities when built
with the
-Denable_openmp=trueMeson build flag. This feature isdisabled by default. When enabled,
np.sortandnp.argsortfunctionscan utilize OpenMP for parallel thread execution, improving performance
for these operations.
(gh-28619)
Interactive examples in the NumPy documentation
The NumPy documentation includes a number of examples that can now be
run interactively in your browser using WebAssembly and Pyodide.
Please note that the examples are currently experimental in nature and
may not work as expected for all methods in the public API.
(gh-26745)
Improvements
Scalar comparisons between non-comparable dtypes such as
np.array(1) == np.array('s')now return a NumPy bool instead of aPython bool.
(gh-27288)
np.nditernow has no limit on the number of supported operands(C-integer).
(gh-28080)
No-copy pickling is now supported for any array that can be
transposed to a C-contiguous array.
(gh-28105)
The
__repr__for user-defined dtypes now prefers the__name__ofthe custom dtype over a more generic name constructed from its
kindanditemsize.(gh-28250)
np.dotnow reports floating point exceptions.(gh-28442)
np.dtypes.StringDTypeis now a generictype which
accepts a type argument for
na_objectthat defaults totyping.Never. For example,StringDType(na_object=None)returns aStringDType[None], andStringDType()returns aStringDType[typing.Never].(gh-28856)
Added warnings to
np.iscloseAdded warning messages if at least one of atol or rtol are either
np.nanornp.infwithinnp.isclose.np.seterrsettings(gh-28205)
Performance improvements and changes
Performance improvements to
np.uniquenp.uniquenow tries to use a hash table to find unique values insteadof sorting values before finding unique values. This is limited to
certain dtypes for now, and the function is now faster for those dtypes.
The function now also exposes a
sortedparameter to allow returningunique values as they were found, instead of sorting them afterwards.
(gh-26018)
Performance improvements to
np.sortandnp.argsortnp.sortandnp.argsortfunctions now can leverage OpenMP forparallel thread execution, resulting in up to 3.5x speedups on x86
architectures with AVX2 or AVX-512 instructions. This opt-in feature
requires NumPy to be built with the -Denable_openmp Meson flag. Users
can control the number of threads used by setting the OMP_NUM_THREADS
environment variable.
(gh-28619)
Performance improvements for
np.float16castsEarlier, floating point casts to and from
np.float16types wereemulated in software on all platforms.
Now, on ARM devices that support Neon float16 intrinsics (such as recent
Apple Silicon), the native float16 path is used to achieve the best
performance.
(gh-28769)
Changes
The vector norm
ord=infand the matrix normsord={1, 2, inf, 'nuc'}now always returns zero for empty arrays.Empty arrays have at least one axis of size zero. This affects
np.linalg.norm,np.linalg.vector_norm, andnp.linalg.matrix_norm. Previously, NumPy would raises errors orreturn zero depending on the shape of the array.
(gh-28343)
A spelling error in the error message returned when converting a
string to a float with the method
np.format_float_positionalhasbeen fixed.
(gh-28569)
NumPy's
__array_api_version__was upgraded from2023.12to2024.12.numpy.count_nonzeroforaxis=None(default) now returns a NumPyscalar instead of a Python integer.
The parameter
axisinnumpy.take_along_axisfunction has now adefault value of
-1.(gh-28615)
Printing of
np.float16andnp.float32scalars and arrays havebeen improved by adjusting the transition to scientific notation
based on the floating point precision. A new legacy
np.printoptionsmode'2.2'has been added for backwardscompatibility.
(gh-28703)
Multiplication between a string and integer now raises OverflowError
instead of MemoryError if the result of the multiplication would
create a string that is too large to be represented. This follows
Python's behavior.
(gh-29060)
unique_valuesmay return unsorted dataThe relatively new function (added in NumPy 2.0)
unique_valuesmay nowreturn unsorted results. Just as
unique_countsandunique_allthesenever guaranteed a sorted result, however, the result was sorted until
now. In cases where these do return a sorted result, this may change in
future releases to improve performance.
(gh-26018)
Changes to the main iterator and potential numerical changes
The main iterator, used in math functions and via
np.nditerfromPython and
NpyIterin C, now behaves differently for some bufferediterations. This means that:
sized allowed by the
buffersizeparameter.no operand requires buffering.
For
np.sum()such changes in buffersize may slightly change numericalresults of floating point operations. Users who use "growinner" for
custom reductions could notice changes in precision (for example, in
NumPy we removed it from
einsumto avoid most precision changes andimprove precision for some 64bit floating point inputs).
(gh-27883)
The minimum supported GCC version is now 9.3.0
The minimum supported version was updated from 8.4.0 to 9.3.0, primarily
in order to reduce the chance of platform-specific bugs in old GCC
versions from causing issues.
(gh-28102)
Changes to automatic bin selection in numpy.histogram
The automatic bin selection algorithm in
numpy.histogramhas beenmodified to avoid out-of-memory errors for samples with low variation.
For full control over the selected bins the user can use set the
binor
rangeparameters ofnumpy.histogram.(gh-28426)
Build manylinux_2_28 wheels
Wheels for linux systems will use the
manylinux_2_28tag (instead ofthe
manylinux2014tag), which means dropping support forredhat7/centos7, amazonlinux2, debian9, ubuntu18.04, and other
pre-glibc2.28 operating system versions, as per the PEP 600 support
table.
(gh-28436)
Remove use of -Wl,-ld_classic on macOS
Remove use of -Wl,-ld_classic on macOS. This hack is no longer needed by
Spack, and results in libraries that cannot link to other libraries
built with ld (new).
(gh-28713)
Re-enable overriding functions in the
numpy.stringsRe-enable overriding functions in the
numpy.stringsmodule.(gh-28741)
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bluesky/ophyd-async (ophyd-async)
v0.12Compare Source
Breaking changes
Flyscanning plan stubs have been deleted
In preparation for flyscanning development, the following have been deleted from
ophyd_async.plan_stubs:fly_and_collect. Plans should now usebps.collect_while_completingprepare_*plan stubs will eventually make their way back here, but only when we've defined a bunch of specific ones to make a generic plan stub out of*_fly_and_collect_*plan stubs that wrap together the preparing and the flying should be wrapped into a generic plan at a later dateWhat's Changed
New Contributors
Full Changelog: bluesky/ophyd-async@v0.11...v0.12
ijl/orjson (orjson)
v3.11.0Compare Source
Changed
buffer allocated on import.
pydantic/pydantic-core (pydantic_core)
v2.35.2: 2025-06-26Compare Source
What's Changed
speedate0.16 by @davidhewitt in [https://github.com/update tospeedate0.16 pydantic/pydantic-core#1740](https://redirect.github.com/pydantic/pydantic-coreConfiguration
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