Bump the apptainer group across 1 directory with 5 updates

[dependabot]

Bumps the apptainer group with 5 updates in the /apptainer/python directory:

Package	From	To
numpy	2.0.1	2.1.0
setuptools	72.1.0	72.2.0
mkl	2024.2.0	2024.2.1
mkl-include	2024.2.0	2024.2.1
intel-openmp	2024.2.0	2024.2.1

Updates 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

Updates setuptools from 72.1.0 to 72.2.0

Changelog

Sourced from setuptools's changelog.

v72.2.0

Features

• pypa/distutils#272pypa/distutils#237pypa/distuils#228#4538)

Commits

• 76942cf Bump version: 72.1.0 → 72.2.0
• 780a782 Correct reference in news fragment. Ref #4539
• 64f10c5 Merge pull request #4539 from pypa/feature/distutils-b7ee725f3
• d4ad24b Add news fragment.
• 0ab156c Merge https://github.com/pypa/distutils
• b7ee725 Apply isort. Ref pypa/distutils#240
• 32e5fea Rely on monkeysession to monkeypatch.
• 5f79f22 Merge pull request pypa/distutils#274 from msys2-contrib/ci-msvc-python-mingw...
• 6748224 Merge pull request pypa/distutils#273 from msys2-contrib/tests-fix-venv_insta...
• 1f999b9 Remove unused RangeMap
• Additional commits viewable in compare view

Updates mkl from 2024.2.0 to 2024.2.1

Commits

• See full diff in compare view

Updates mkl-include from 2024.2.0 to 2024.2.1

Updates intel-openmp from 2024.2.0 to 2024.2.1

Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting @dependabot rebase.

---

Dependabot commands and options

You can trigger Dependabot actions by commenting on this PR:

• @dependabot rebase will rebase this PR
• @dependabot recreate will recreate this PR, overwriting any edits that have been made to it
• @dependabot merge will merge this PR after your CI passes on it
• @dependabot squash and merge will squash and merge this PR after your CI passes on it
• @dependabot cancel merge will cancel a previously requested merge and block automerging
• @dependabot reopen will reopen this PR if it is closed
• @dependabot close will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually
• @dependabot show <dependency name> ignore conditions will show all of the ignore conditions of the specified dependency
• @dependabot ignore <dependency name> major version will close this group update PR and stop Dependabot creating any more for the specific dependency's major version (unless you unignore this specific dependency's major version or upgrade to it yourself)
• @dependabot ignore <dependency name> minor version will close this group update PR and stop Dependabot creating any more for the specific dependency's minor version (unless you unignore this specific dependency's minor version or upgrade to it yourself)
• @dependabot ignore <dependency name> will close this group update PR and stop Dependabot creating any more for the specific dependency (unless you unignore this specific dependency or upgrade to it yourself)
• @dependabot unignore <dependency name> will remove all of the ignore conditions of the specified dependency
• @dependabot unignore <dependency name> <ignore condition> will remove the ignore condition of the specified dependency and ignore conditions

[github-actions]

Dependency Review

The following issues were found:

• ✅ 0 vulnerable package(s)
• ✅ 0 package(s) with incompatible licenses
• ✅ 0 package(s) with invalid SPDX license definitions
• ⚠️ 3 package(s) with unknown licenses.

See the Details below.

License Issues

apptainer/python/requirements.txt

Package	Version	License	Issue Type
intel-openmp	2024.2.1	Null	Unknown License
mkl-include	2024.2.1	Null	Unknown License
mkl	2024.2.1	Null	Unknown License

OpenSSF Scorecard

Package	Version	Score	Details
pip/intel-openmp	2024.2.1	Unknown	Unknown
pip/mkl	2024.2.1	Unknown	Unknown
pip/mkl-include	2024.2.1	Unknown	Unknown
pip/numpy	2.1.0	🟢 8	Details Check Score Reason Binary-Artifacts 🟢 10 no binaries found in the repo Branch-Protection 🟢 3 branch protection is not maximal on development and all release branches CI-Tests 🟢 10 17 out of 17 merged PRs checked by a CI test -- score normalized to 10 CII-Best-Practices ⚠️ 0 no effort to earn an OpenSSF best practices badge detected Code-Review 🟢 10 all changesets reviewed Contributors 🟢 10 project has 93 contributing companies or organizations Dangerous-Workflow 🟢 10 no dangerous workflow patterns detected Dependency-Update-Tool 🟢 10 update tool detected Fuzzing 🟢 10 project is fuzzed License 🟢 9 license file detected Maintained 🟢 10 30 commit(s) and 19 issue activity found in the last 90 days -- score normalized to 10 Packaging ⚠️ -1 packaging workflow not detected Pinned-Dependencies 🟢 3 dependency not pinned by hash detected -- score normalized to 3 SAST 🟢 9 SAST tool detected but not run on all commits Security-Policy 🟢 9 security policy file detected Signed-Releases ⚠️ 0 Project has not signed or included provenance with any releases. Token-Permissions 🟢 10 GitHub workflow tokens follow principle of least privilege Vulnerabilities 🟢 10 0 existing vulnerabilities detected
pip/setuptools	72.2.0	🟢 6.3	Details Check Score Reason Code-Review 🟢 7 Found 11/14 approved changesets -- score normalized to 7 Maintained 🟢 10 30 commit(s) and 13 issue activity found in the last 90 days -- score normalized to 10 CII-Best-Practices ⚠️ 0 no effort to earn an OpenSSF best practices badge detected License 🟢 10 license file detected Signed-Releases ⚠️ -1 no releases found Packaging ⚠️ -1 packaging workflow not detected Security-Policy 🟢 10 security policy file detected Token-Permissions 🟢 10 GitHub workflow tokens follow principle of least privilege Branch-Protection ⚠️ 0 branch protection not enabled on development/release branches Dangerous-Workflow 🟢 10 no dangerous workflow patterns detected Binary-Artifacts ⚠️ 0 binaries present in source code Vulnerabilities 🟢 10 0 existing vulnerabilities detected Pinned-Dependencies ⚠️ 0 dependency not pinned by hash detected -- score normalized to 0 Fuzzing 🟢 10 project is fuzzed SAST ⚠️ 0 SAST tool is not run on all commits -- score normalized to 0

Scanned Manifest Files

apptainer/python/requirements.txt

• intel-openmp@2024.2.1
• mkl@2024.2.1
• mkl-include@2024.2.1
• numpy@2.1.0
• setuptools@72.2.0
• intel-openmp@2024.2.0
• mkl@2024.2.0
• mkl-include@2024.2.0
• numpy@2.0.1
• setuptools@72.1.0

[dependabot]

Superseded by #335.