Bump numpy from 1.26.4 to 2.0.1

[dependabot]

Bumps numpy from 1.26.4 to 2.0.1.

Release notes

Sourced from numpy's releases.

v2.0.1

NumPy 2.0.1 Release Notes

NumPy 2.0.1 is a maintenance release that fixes bugs and regressions discovered after the 2.0.0 release. NumPy 2.0.1 is the last planned release in the 2.0.x series, 2.1.0rc1 should be out shortly.

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

NOTE: Do not use the GitHub generated "Source code" files listed in the "Assets", they are garbage.

Improvements

np.quantile with method closest_observation chooses nearest even order statistic

This changes the definition of nearest for border cases from the nearest odd order statistic to nearest even order statistic. The numpy implementation now matches other reference implementations.

(gh-26656)

Contributors

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

• @​vahidmech +
• Alex Herbert +
• Charles Harris
• Giovanni Del Monte +
• Leo Singer
• Lysandros Nikolaou
• Matti Picus
• Nathan Goldbaum
• Patrick J. Roddy +
• Raghuveer Devulapalli
• Ralf Gommers
• Rostan Tabet +
• Sebastian Berg
• Tyler Reddy
• Yannik Wicke +

Pull requests merged

A total of 24 pull requests were merged for this release.

• #26711: MAINT: prepare 2.0.x for further development
• #26792: TYP: fix incorrect import in ma/extras.pyi stub
• #26793: DOC: Mention '1.25' legacy printing mode in set_printoptions
• #26794: DOC: Remove mention of NaN and NAN aliases from constants

... (truncated)

Commits

• 4c9f431 Merge pull request #27000 from charris/prepare-2.0.1
• 0e70e00 REL: Prepare for the NumPy 2.0.1 release [wheel build]
• 4d10ffc Merge pull request #26995 from charris/backport-26985
• 764b667 BUG: Add object cast to avoid warning with limited API
• 9be6ad6 Merge pull request #26971 from charris/backport-26935
• 6d950e9 BUG: fix f2py tests to work with v2 API
• 89630c0 Merge pull request #26962 from charris/backport-26919
• 88fa840 TST: Apply test suggestion by Nathan for rlstrip fixes
• a9da01e BUG,MAINT: Fix utf-8 character stripping memory access
• 6afbbf8 Merge pull request #26963 from charris/backport-26930
• Additional commits viewable in compare view

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[dependabot]

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[jan-janssen]

======================================================================
ERROR: test_get_frame (test_visualize.TestAtoms.test_get_frame)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/runner/work/structuretoolkit/structuretoolkit/tests/test_visualize.py", line 34, in test_get_frame
    self.assertEqual(dx.ptp(), 1, msg="Frames not drawn along the nearest edges")
                     ^^^^^^
AttributeError: `ptp` was removed from the ndarray class in NumPy 2.0. Use np.ptp(arr, ...) instead.

----------------------------------------------------------------------

[jan-janssen]

  The following packages are incompatible
  ├─ numpy 2.0.1**  is installable with the potential options
  │  ├─ numpy 2.0.1, which can be installed;
  │  ├─ numpy [1.26.4|2.0.1] would require
  │  │  └─ python_abi 3.10.* *_cp310, which can be installed;
  │  ├─ numpy [1.26.4|2.0.1] would require
  │  │  └─ python_abi 3.11.* *_cp311, which can be installed;
  │  └─ numpy [1.26.4|2.0.1] would require
  │     └─ python_abi 3.9.* *_cp39, which can be installed;
  ├─ pymatgen 2024.7.18**  is installable with the potential options
  │  ├─ pymatgen 2024.7.18 would require
  │  │  └─ numpy >=1.26.4,<2.0a0  with the potential options
  │  │     ├─ numpy 1.26.4 conflicts with any installable versions previously reported;
  │  │     ├─ numpy [1.26.4|2.0.1], which can be installed (as previously explained);
  │  │     ├─ numpy [1.26.4|2.0.1], which can be installed (as previously explained);
  │  │     ├─ numpy [1.26.4|2.0.1], which can be installed (as previously explained);
  │  │     └─ numpy 1.26.4 would require
  │  │        └─ python_abi 3.9 *_pypy39_pp73, which can be installed;
  │  ├─ pymatgen 2024.7.18 would require
  │  │  └─ python_abi 3.10.* *_cp310, which can be installed;
  │  ├─ pymatgen 2024.7.18 would require
  │  │  └─ python_abi 3.11.* *_cp311, which can be installed;
  │  └─ pymatgen 2024.7.18 would require
  │     └─ python_abi 3.9.* *_cp39, which can be installed;
  ├─ python 3.12**  is not installable because there are no viable options
  │  ├─ python [3.12.0|3.12.1|3.12.2|3.12.3|3.12.4] would require
  │  │  └─ python_abi 3.12.* *_cp312, which conflicts with any installable versions previously reported;
  │  ├─ python 3.12.0rc3 would require
  │  │  └─ _python_rc, which does not exist (perhaps a missing channel);
  │  └─ python [3.12.0|3.12.1|3.12.2|3.12.3|3.12.4] conflicts with any installable versions previously reported;
  └─ scipy 1.14.0**  is installable with the potential options
     ├─ scipy 1.14.0 would require
     │  └─ python_abi 3.10.* *_cp310, which can be installed;
     ├─ scipy 1.14.0 would require
     │  └─ python_abi 3.11.* *_cp311, which can be installed;
     └─ scipy 1.14.0 would require
        └─ python_abi 3.12.* *_cp312, which conflicts with any installable versions previously reported.

[dependabot]

A newer version of numpy exists, but since this PR has been edited by someone other than Dependabot I haven't updated it. You'll get a PR for the updated version as normal once this PR is merged.

[jan-janssen]

  └─ pyxtal 1.0.3**  is installable and it requires
     ├─ numpy >=1.26,<2  with the potential options
     │  ├─ numpy [1.26.0|1.26.2|1.26.3|1.26.4|2.1.1], which can be installed (as previously explained);
     │  ├─ numpy [1.26.0|1.26.2|1.26.3|1.26.4|2.1.1], which can be installed (as previously explained);
     │  ├─ numpy [1.26.0|1.26.2|1.26.3|1.26.4] conflicts with any installable versions previously reported;
     │  ├─ numpy 1.26.0 would require
     │  │  └─ pypy3.9 >=7.3.12 , which can be installed;
     │  ├─ numpy [1.26.0|1.26.2|1.26.3|1.26.4] would require
     │  │  └─ python_abi 3.9.* *_cp39, which can be installed;
     │  ├─ numpy [1.26.2|1.26.3] would require
     │  │  └─ pypy3.9 >=7.3.13 , which can be installed;
     │  ├─ numpy 1.26.4 would require
     │  │  └─ pypy3.9 >=7.3.15 , which can be installed;
     │  └─ numpy [2.0.0rc1|2.0.0rc2] would require
     │     └─ _numpy_rc, which does not exist (perhaps a missing channel);