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Update dependency numpy to v2 #103

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@renovate renovate bot commented Jun 16, 2024

This PR contains the following updates:

Package Change Age Adoption Passing Confidence
numpy (changelog) ==1.24.3 -> ==2.2.1 age adoption passing confidence

Release Notes

numpy/numpy (numpy)

v2.2.1

Compare Source

v2.2.0: 2.2.0 (Dec 8, 2024)

Compare Source

NumPy 2.2.0 Release Notes

The NumPy 2.2.0 release is quick release that brings us back into sync
with the usual twice yearly release cycle. There have been an number of
small cleanups, as well as work bringing the new StringDType to
completion and improving support for free threaded Python. Highlights
are:

  • New functions matvec and vecmat, see below.
  • Many improved annotations.
  • Improved support for the new StringDType.
  • Improved support for free threaded Python
  • Fixes for f2py

This release supports Python versions 3.10-3.13.

Deprecations

  • _add_newdoc_ufunc is now deprecated. ufunc.__doc__ = newdoc
    should be used instead.

    (gh-27735)

Expired deprecations

  • bool(np.array([])) and other empty arrays will now raise an error.
    Use arr.size > 0 instead to check whether an array has no
    elements.

    (gh-27160)

Compatibility notes

  • numpy.cov now properly transposes single-row (2d
    array) design matrices when rowvar=False. Previously, single-row
    design matrices would return a scalar in this scenario, which is not
    correct, so this is a behavior change and an array of the
    appropriate shape will now be returned.

    (gh-27661)

New Features

  • New functions for matrix-vector and vector-matrix products

    Two new generalized ufuncs were defined:

    • numpy.matvec - matrix-vector product, treating the
      arguments as stacks of matrices and column vectors,
      respectively.
    • numpy.vecmat - vector-matrix product, treating the
      arguments as stacks of column vectors and matrices,
      respectively. For complex vectors, the conjugate is taken.

    These add to the existing numpy.matmul as well as to
    numpy.vecdot, which was added in numpy 2.0.

    Note that numpy.matmul never takes a complex
    conjugate, also not when its left input is a vector, while both
    numpy.vecdot and numpy.vecmat do take
    the conjugate for complex vectors on the left-hand side (which are
    taken to be the ones that are transposed, following the physics
    convention).

    (gh-25675)

  • np.complexfloating[T, T] can now also be written as
    np.complexfloating[T]

    (gh-27420)

  • UFuncs now support __dict__ attribute and allow overriding
    __doc__ (either directly or via ufunc.__dict__["__doc__"]).
    __dict__ can be used to also override other properties, such as
    __module__ or __qualname__.

    (gh-27735)

  • The "nbit" type parameter of np.number and its subtypes now
    defaults to typing.Any. This way, type-checkers will infer
    annotations such as x: np.floating as x: np.floating[Any], even
    in strict mode.

    (gh-27736)

Improvements

  • The datetime64 and timedelta64 hashes now correctly match the
    Pythons builtin datetime and timedelta ones. The hashes now
    evaluated equal even for equal values with different time units.

    (gh-14622)

  • Fixed a number of issues around promotion for string ufuncs with
    StringDType arguments. Mixing StringDType and the fixed-width DTypes
    using the string ufuncs should now generate much more uniform
    results.

    (gh-27636)

  • Improved support for empty memmap. Previously an empty
    memmap would fail unless a non-zero offset was set.
    Now a zero-size memmap is supported even if
    offset=0. To achieve this, if a memmap is mapped to
    an empty file that file is padded with a single byte.

    (gh-27723)

  • A regression has been fixed which allows F2PY users to expose variables
    to Python in modules with only assignments, and also fixes situations
    where multiple modules are present within a single source file.

    (gh-27695)

Performance improvements and changes

  • Improved multithreaded scaling on the free-threaded build when many
    threads simultaneously call the same ufunc operations.

    (gh-27896)

  • NumPy now uses fast-on-failure attribute lookups for protocols. This
    can greatly reduce overheads of function calls or array creation
    especially with custom Python objects. The largest improvements will
    be seen on Python 3.12 or newer.

    (gh-27119)

  • OpenBLAS on x86_64 and i686 is built with fewer kernels. Based on
    benchmarking, there are 5 clusters of performance around these
    kernels: PRESCOTT NEHALEM SANDYBRIDGE HASWELL SKYLAKEX.

  • OpenBLAS on windows is linked without quadmath, simplifying
    licensing

  • Due to a regression in OpenBLAS on windows, the performance
    improvements when using multiple threads for OpenBLAS 0.3.26 were
    reverted.

    (gh-27147)

  • NumPy now indicates hugepages also for large np.zeros allocations
    on linux. Thus should generally improve performance.

    (gh-27808)

Changes

  • numpy.fix now won't perform casting to a floating
    data-type for integer and boolean data-type input arrays.

    (gh-26766)

  • The type annotations of numpy.float64 and numpy.complex128 now
    reflect that they are also subtypes of the built-in float and
    complex types, respectively. This update prevents static
    type-checkers from reporting errors in cases such as:

    x: float = numpy.float64(6.28)  # valid
    z: complex = numpy.complex128(-1j)  # valid

    (gh-27334)

  • The repr of arrays large enough to be summarized (i.e., where
    elements are replaced with ...) now includes the shape of the
    array, similar to what already was the case for arrays with zero
    size and non-obvious shape. With this change, the shape is always
    given when it cannot be inferred from the values. Note that while
    written as shape=..., this argument cannot actually be passed in
    to the np.array constructor. If you encounter problems, e.g., due
    to failing doctests, you can use the print option legacy=2.1 to
    get the old behaviour.

    (gh-27482)

  • Calling __array_wrap__ directly on NumPy arrays or scalars now
    does the right thing when return_scalar is passed (Added in NumPy
    2). It is further safe now to call the scalar __array_wrap__ on a
    non-scalar result.

    (gh-27807)

  • Bump the musllinux CI image and wheels to 1_2 from 1_1. This is because
    1_1 is end of life.

    (gh-27088)

  • The NEP 50 promotion state settings are now removed. They were always
    meant as temporary means for testing. A warning will be given if the
    environment variable is set to anything but NPY_PROMOTION_STATE=weak
    while _set_promotion_state and _get_promotion_state are removed. In
    case code used _no_nep50_warning, a contextlib.nullcontext could be
    used to replace it when not available.

    (gh-27156)

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v2.1.3: 2.1.3 (Nov 2, 2024)

Compare Source

NumPy 2.1.3 Release Notes

NumPy 2.1.3 is a maintenance release that fixes bugs and regressions
discovered after the 2.1.2 release. This release also adds support
for free threaded Python 3.13 on Windows.

The Python versions supported by this release are 3.10-3.13.

Improvements

  • Fixed a number of issues around promotion for string ufuncs with
    StringDType arguments. Mixing StringDType and the fixed-width DTypes
    using the string ufuncs should now generate much more uniform
    results.

    (gh-27636)

Changes

  • numpy.fix now won't perform casting to a floating
    data-type for integer and boolean data-type input arrays.

    (gh-26766)

Contributors

A total of 15 people contributed to this release. People with a "+" by
their names contributed a patch for the first time.

  • Abhishek Kumar +
  • Austin +
  • Benjamin A. Beasley +
  • Charles Harris
  • Christian Lorentzen
  • Marcel Telka +
  • Matti Picus
  • Michael Davidsaver +
  • Nathan Goldbaum
  • Peter Hawkins
  • Raghuveer Devulapalli
  • Ralf Gommers
  • Sebastian Berg
  • dependabot[bot]
  • kp2pml30 +

Pull requests merged

A total of 21 pull requests were merged for this release.

  • #​27512: MAINT: prepare 2.1.x for further development
  • #​27537: MAINT: Bump actions/cache from 4.0.2 to 4.1.1
  • #​27538: MAINT: Bump pypa/cibuildwheel from 2.21.2 to 2.21.3
  • #​27539: MAINT: MSVC does not support #warning directive
  • #​27543: BUG: Fix user dtype can-cast with python scalar during promotion
  • #​27561: DEV: bump python to 3.12 in environment.yml
  • #​27562: BLD: update vendored Meson to 1.5.2
  • #​27563: BUG: weighted quantile for some zero weights (#​27549)
  • #​27565: MAINT: Use miniforge for macos conda test.
  • #​27566: BUILD: satisfy gcc-13 pendantic errors
  • #​27569: BUG: handle possible error for PyTraceMallocTrack
  • #​27570: BLD: start building Windows free-threaded wheels [wheel build]
  • #​27571: BUILD: vendor tempita from Cython
  • #​27574: BUG: Fix warning "differs in levels of indirection" in npy_atomic.h...
  • #​27592: MAINT: Update Highway to latest
  • #​27593: BUG: Adjust numpy.i for SWIG 4.3 compatibility
  • #​27616: BUG: Fix Linux QEMU CI workflow
  • #​27668: BLD: Do not set __STDC_VERSION__ to zero during build
  • #​27669: ENH: fix wasm32 runtime type error in numpy._core
  • #​27672: BUG: Fix a reference count leak in npy_find_descr_for_scalar.
  • #​27673: BUG: fixes for StringDType/unicode promoters

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aa08e04e08aaf974d4458def539dece0d28146d866a39da5639596f4921fd761  numpy-2.1.3.tar.gz

v2.1.2

Compare Source

v2.1.1: 2.1.1 (Sep 3, 2024)

Compare Source

NumPy 2.1.1 Release Notes

NumPy 2.1.1 is a maintenance release that fixes bugs and regressions
discovered after the 2.1.0 release.

The Python versions supported by this release are 3.10-3.13.

Contributors

A total of 7 people contributed to this release. People with a "+" by
their names contributed a patch for the first time.

  • Andrew Nelson
  • Charles Harris
  • Mateusz Sokół
  • Maximilian Weigand +
  • Nathan Goldbaum
  • Pieter Eendebak
  • Sebastian Berg
Pull requests merged

A total of 10 pull requests were merged for this release.

  • #​27236: REL: Prepare for the NumPy 2.1.0 release [wheel build]
  • #​27252: MAINT: prepare 2.1.x for further development
  • #​27259: BUG: revert unintended change in the return value of set_printoptions
  • #​27266: BUG: fix reference counting bug in __array_interface__ implementation...
  • #​27267: TST: Add regression test for missing descr in array-interface
  • #​27276: BUG: Fix #​27256 and #​27257
  • #​27278: BUG: Fix array_equal for numeric and non-numeric scalar types
  • #​27287: MAINT: Update maintenance/2.1.x after the 2.0.2 release
  • #​27303: BLD: cp311- macosx_arm64 wheels [wheel build]
  • #​27304: BUG: f2py: better handle filtering of public/private subroutines
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v2.1.0

Compare Source

v2.0.2: NumPy 2.0.2 release (Aug 26, 2024)

Compare Source

NumPy 2.0.2 Release Notes

NumPy 2.0.2 is a maintenance release that fixes bugs and regressions
discovered after the 2.0.1 release.

The Python versions supported by this release are 3.9-3.12.

Contributors

A total of 13 people contributed to this release. People with a "+" by
their names contributed a patch for the first time.

  • Bruno Oliveira +
  • Charles Harris
  • Chris Sidebottom
  • Christian Heimes +
  • Christopher Sidebottom
  • Mateusz Sokół
  • Matti Picus
  • Nathan Goldbaum
  • Pieter Eendebak
  • Raghuveer Devulapalli
  • Ralf Gommers
  • Sebastian Berg
  • Yair Chuchem +
Pull requests merged

A total of 19 pull requests were merged for this release.

  • #​27000: REL: Prepare for the NumPy 2.0.1 release [wheel build]
  • #​27001: MAINT: prepare 2.0.x for further development
  • #​27021: BUG: cfuncs.py: fix crash when sys.stderr is not available
  • #​27022: DOC: Fix migration note for alltrue and sometrue
  • #​27061: BUG: use proper input and output descriptor in array_assign_subscript...
  • #​27073: BUG: Mirror VQSORT_ENABLED logic in Quicksort
  • #​27074: BUG: Bump Highway to latest master
  • #​27077: BUG: Off by one in memory overlap check
  • #​27122: BUG: Use the new npyv_loadable_stride_ functions for ldexp and...
  • #​27126: BUG: Bump Highway to latest
  • #​27128: BUG: add missing error handling in public_dtype_api.c
  • #​27129: BUG: fix another cast setup in array_assign_subscript
  • #​27130: BUG: Fix building NumPy in FIPS mode
  • #​27131: BLD: update vendored Meson for cross-compilation patches
  • #​27146: MAINT: Scipy openblas 0.3.27.44.4
  • #​27151: BUG: Do not accidentally store dtype metadata in np.save
  • #​27195: REV: Revert undef I and document it
  • #​27213: BUG: Fix NPY_RAVEL_AXIS on backwards compatible NumPy 2 builds
  • #​27279: BUG: Fix array_equal for numeric and non-numeric scalar types
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@renovate renovate bot requested a review from 200km as a code owner June 16, 2024 16:12
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⚠️ Artifact update problem

Renovate failed to update an artifact related to this branch. You probably do not want to merge this PR as-is.

♻ Renovate will retry this branch, including artifacts, only when one of the following happens:

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The artifact failure details are included below:

File name: s2e-ff/scripts/Plot/Pipfile.lock
Command failed: pipenv lock
Creating a virtualenv for this project
Pipfile: /tmp/renovate/repos/github/ut-issl/s2e-ff/s2e-ff/scripts/Plot/Pipfile
Using /opt/containerbase/tools/python/3.8.20/bin/python3.83.8.20 to create 
virtualenv...
created virtual environment CPython3.8.20.final.0-64 in 878ms
  creator 
CPython3Posix(dest=/tmp/renovate/cache/others/virtualenvs/Plot--jOFPzuB, 
clear=False, no_vcs_ignore=False, global=False)
  seeder FromAppData(download=False, pip=bundle, setuptools=bundle, 
wheel=bundle, via=copy, 
app_data_dir=/tmp/containerbase/cache/.local/share/virtualenv)
    added seed packages: pip==24.3.1, setuptools==75.3.0, wheel==0.45.1
  activators 
BashActivator,CShellActivator,FishActivator,NushellActivator,PowerShellActivator
,PythonActivator

✔ Successfully created virtual environment!
Virtualenv location: /tmp/renovate/cache/others/virtualenvs/Plot--jOFPzuB
Locking [packages] dependencies...
False
<console width=80 None>
Traceback (most recent call last):
  File "/opt/containerbase/tools/pipenv/2024.4.0/3.8.20/bin/pipenv", line 8, in <module>
    sys.exit(cli())
  File "/opt/containerbase/tools/pipenv/2024.4.0/3.8.20/lib/python3.8/site-packages/pipenv/vendor/click/core.py", line 1157, in __call__
    return self.main(*args, **kwargs)
  File "/opt/containerbase/tools/pipenv/2024.4.0/3.8.20/lib/python3.8/site-packages/pipenv/cli/options.py", line 52, in main
    return super().main(*args, **kwargs, windows_expand_args=False)
  File "/opt/containerbase/tools/pipenv/2024.4.0/3.8.20/lib/python3.8/site-packages/pipenv/vendor/click/core.py", line 1078, in main
    rv = self.invoke(ctx)
  File "/opt/containerbase/tools/pipenv/2024.4.0/3.8.20/lib/python3.8/site-packages/pipenv/vendor/click/core.py", line 1688, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/opt/containerbase/tools/pipenv/2024.4.0/3.8.20/lib/python3.8/site-packages/pipenv/vendor/click/core.py", line 1434, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/opt/containerbase/tools/pipenv/2024.4.0/3.8.20/lib/python3.8/site-packages/pipenv/vendor/click/core.py", line 783, in invoke
    return __callback(*args, **kwargs)
  File "/opt/containerbase/tools/pipenv/2024.4.0/3.8.20/lib/python3.8/site-packages/pipenv/vendor/click/decorators.py", line 92, in new_func
    return ctx.invoke(f, obj, *args, **kwargs)
  File "/opt/containerbase/tools/pipenv/2024.4.0/3.8.20/lib/python3.8/site-packages/pipenv/vendor/click/core.py", line 783, in invoke
    return __callback(*args, **kwargs)
  File "/opt/containerbase/tools/pipenv/2024.4.0/3.8.20/lib/python3.8/site-packages/pipenv/vendor/click/decorators.py", line 33, in new_func
    return f(get_current_context(), *args, **kwargs)
  File "/opt/containerbase/tools/pipenv/2024.4.0/3.8.20/lib/python3.8/site-packages/pipenv/cli/command.py", line 342, in lock
    do_lock(
  File "/opt/containerbase/tools/pipenv/2024.4.0/3.8.20/lib/python3.8/site-packages/pipenv/routines/lock.py", line 67, in do_lock
    venv_resolve_deps(
  File "/opt/containerbase/tools/pipenv/2024.4.0/3.8.20/lib/python3.8/site-packages/pipenv/utils/resolver.py", line 907, in venv_resolve_deps
    c = resolve(cmd, st, project=project)
  File "/opt/containerbase/tools/pipenv/2024.4.0/3.8.20/lib/python3.8/site-packages/pipenv/utils/resolver.py", line 771, in resolve
    raise RuntimeError("Failed to lock Pipfile.lock!")
RuntimeError: Failed to lock Pipfile.lock!

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