Bump numpy from 2.0.1 to 2.1.0

[dependabot]

Bumps numpy from 2.0.1 to 2.1.0.

Release notes

Sourced from numpy's releases.

2.1.0 (Aug 18, 2024)

NumPy 2.1.0 Release Notes

NumPy 2.1.0 provides support for the upcoming Python 3.13 release and drops support for Python 3.9. In addition to the usual bug fixes and updated Python support, it helps get us back into our usual release cycle after the extended development of 2.0. The highlights for this release are:

• Support for the array-api 2023.12 standard.
• Support for Python 3.13.
• Preliminary support for free threaded Python 3.13.

Python versions 3.10-3.13 are supported in this release.

New functions

New function numpy.unstack

A new function np.unstack(array, axis=...) was added, which splits an array into a tuple of arrays along an axis. It serves as the inverse of [numpy.stack]{.title-ref}.

(gh-26579)

Deprecations

• The fix_imports keyword argument in numpy.save is deprecated. Since NumPy 1.17, numpy.save uses a pickle protocol that no longer supports Python 2, and ignored fix_imports keyword. This keyword is kept only for backward compatibility. It is now deprecated.

  (gh-26452)

• Passing non-integer inputs as the first argument of [bincount]{.title-ref} is now deprecated, because such inputs are silently cast to integers with no warning about loss of precision.

  (gh-27076)

Expired deprecations

• Scalars and 0D arrays are disallowed for numpy.nonzero and numpy.ndarray.nonzero.

  (gh-26268)

• set_string_function internal function was removed and PyArray_SetStringFunction was stubbed out.

... (truncated)

Commits

• 2f7fe64 Merge pull request #27236 from charris/prepare-2.1.0
• b6f434f REL: Prepare for the NumPy 2.1.0 release [wheel build]
• 3cf9394 Merge pull request #27234 from charris/backport-25984
• 7443dcc Merge pull request #27233 from charris/backport-27223
• 85b1cab BUG: Allow fitting of degree zero polynomials with Polynomial.fit
• 395a81d DOC: reword discussion about shared arrays to hopefully be clearer
• 5af2e96 Move NUMUSERTYPES thread safety discussion to legacy DType API docs
• d902c24 DOC: add docs on thread safety in NumPy
• c080180 Merge pull request #27229 from charris/backport-27226
• 44ce7e8 BUG: Fix PyArray_ZeroContiguousBuffer (resize) with struct dtypes
• Additional commits viewable in compare view

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[jan-janssen]

@dependabot rebase

[dependabot]

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If you're happy for Dependabot to recreate it from scratch, overwriting any edits, you can request @dependabot recreate.

[jan-janssen]

@dependabot recreate

[jan-janssen]

======================================================================
FAIL: test_from_hdf_readonly (generic.test_datacontainer.TestDataContainer.test_from_hdf_readonly)
Reading from HDF should restore the read-only property.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Users/runner/work/pyiron_base/pyiron_base/tests/unit/generic/test_datacontainer.py", line 582, in test_from_hdf_readonly
    self.assertEqual(
AssertionError: 2 != 0 : from_hdf on read_only DataContainer should not call _read_only_error.

======================================================================
FAIL: test_rewrite_hdf5 (storage.test_fileHDFio.TestFileHDFio.test_rewrite_hdf5) [warning handling - log and catch job_name warning]
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Users/runner/work/pyiron_base/pyiron_base/tests/unit/storage/test_fileHDFio.py", line 414, in test_rewrite_hdf5
    self.assertEqual(len(w), 1)
AssertionError: 2 != 1

======================================================================
FAIL: test_rewrite_hdf5 (storage.test_fileHDFio.TestFileHDFio.test_rewrite_hdf5) [warning handling - deprecate exclude_groups]
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Users/runner/work/pyiron_base/pyiron_base/tests/unit/storage/test_fileHDFio.py", line 431, in test_rewrite_hdf5
    self.assertEqual(len(w), 1)
AssertionError: 2 != 1

======================================================================
FAIL: test_rewrite_hdf5 (storage.test_fileHDFio.TestFileHDFio.test_rewrite_hdf5) [warning handling - deprecate exclude_nodes]
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Users/runner/work/pyiron_base/pyiron_base/tests/unit/storage/test_fileHDFio.py", line 441, in test_rewrite_hdf5
    self.assertEqual(len(w), 1)
AssertionError: 2 != 1

----------------------------------------------------------------------
Ran 523 tests in 61.069s

[jan-janssen]

/home/runner/miniconda3/envs/my-env/lib/python3.12/site-packages/h5io/_h5io.py:582: DeprecationWarning: __array__ implementation doesn't accept a copy keyword, so passing copy=False failed. __array__ must implement 'dtype' and 'copy' keyword arguments.
  data = cast(np.array(node)[0])
/home/runner/miniconda3/envs/my-env/lib/python3.12/site-packages/h5io/_h5io.py:601: DeprecationWarning: __array__ implementation doesn't accept a copy keyword, so passing copy=False failed. __array__ must implement 'dtype' and 'copy' keyword arguments.
  node_unicode = str(np.array(node).tobytes().decode("utf-8"))
./home/runner/miniconda3/envs/my-env/lib/python3.12/site-packages/h5io/_h5io.py:599: DeprecationWarning: __array__ implementation doesn't accept a copy keyword, so passing copy=False failed. __array__ must implement 'dtype' and 'copy' keyword arguments.
  data = str(np.array(node).tobytes().decode(decoder))