Bump the apptainer group across 1 directory with 3 updates

[dependabot]

Bumps the apptainer group with 3 updates in the /apptainer/python directory: numpy, setuptools and psutil.

Updates numpy from 2.1.1 to 2.1.2

Release notes

Sourced from numpy's releases.

2.1.2 (Oct 5, 2024)

NumPy 2.1.2 Release Notes

NumPy 2.1.2 is a maintenance release that fixes bugs and regressions discovered after the 2.1.1 release.

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

Contributors

A total of 11 people contributed to this release. People with a "+" by their names contributed a patch for the first time.

• Charles Harris
• Chris Sidebottom
• Ishan Koradia +
• João Eiras +
• Katie Rust +
• Marten van Kerkwijk
• Matti Picus
• Nathan Goldbaum
• Peter Hawkins
• Pieter Eendebak
• Slava Gorloff +

Pull requests merged

A total of 14 pull requests were merged for this release.

• #27333: MAINT: prepare 2.1.x for further development
• #27400: BUG: apply critical sections around populating the dispatch cache
• #27406: BUG: Stub out get_build_msvc_version if distutils.msvccompiler...
• #27416: BUILD: fix missing include for std::ptrdiff_t for C++23 language...
• #27433: BLD: pin setuptools to avoid breaking numpy.distutils
• #27437: BUG: Allow unsigned shift argument for np.roll
• #27439: BUG: Disable SVE VQSort
• #27471: BUG: rfftn axis bug
• #27479: BUG: Fix extra decref of PyArray_UInt8DType.
• #27480: CI: use PyPI not scientific-python-nightly-wheels for CI doc...
• #27481: MAINT: Check for SVE support on demand
• #27484: BUG: initialize the promotion state to be weak
• #27501: MAINT: Bump pypa/cibuildwheel from 2.20.0 to 2.21.2
• #27506: BUG: avoid segfault on bad arguments in ndarray.__array_function__

Checksums

MD5

4aae28b7919b126485c1aaccee37a6ba  numpy-2.1.2-cp310-cp310-macosx_10_9_x86_64.whl
172614423a82ef73d8752ad8a59cbafc  numpy-2.1.2-cp310-cp310-macosx_11_0_arm64.whl

... (truncated)

Commits

• f5afe3d Merge pull request #27507 from charris/prepare-2.1.2
• 6b9ef48 REL: Prepare for the NumPy 2.1.2 release [wheel build]
• 6d85a24 MAINT: Pin setuptools for Python < 3.12 [wheel build]
• 7f327d8 Merge pull request #27506 from charris/backport-27503
• 09e9cd9 BUG: avoid segfault on bad arguments in ndarray.array_function
• 06b4793 Merge pull request #27501 from charris/backport-27495
• 364efb5 MAINT: Bump pypa/cibuildwheel from 2.21.1 to 2.21.2
• df0e261 Merge pull request #27484 from ngoldbaum/use-weak-default
• fa61bc6 Merge pull request #27481 from charris/backport-27472
• d6d06ae Merge pull request #27480 from charris/backport-27475
• Additional commits viewable in compare view

Updates setuptools from 75.1.0 to 75.2.0

Changelog

Sourced from setuptools's changelog.

v75.2.0

Features

• Made errors when parsing Distribution data more explicit about the expected type (tuple[str, ...] | list[str]) -- by :user:Avasam (#4578)

Bugfixes

• Fix a TypeError when a Distribution's old included attribute was a tuple -- by :user:Avasam (#4578)
• Add workaround for bdist_wheel --dist-info-dir errors when customisation does not inherit from setuptools. (#4684)

v75.1.1

Bugfixes

• Re-use pre-existing .dist-info dir when creating wheels via the build backend APIs (PEP 517) and the metadata_directory argument is passed -- by :user:pelson. (#1825)
• Changed egg_info command to avoid adding an empty .egg-info directory while iterating over entry-points. This avoids triggering integration problems with importlib.metadata/importlib_metadata (reference: pypa/pyproject-hooks#206). (#4680)

Commits

• 61a5a03 Bump version: 75.1.1 → 75.2.0
• 8ad3ea7 Workaround for bdist_wheel.dist_info_dir problems (#4684)
• 9af0877 Type sequence checks in setuptools/dist.py (#4578)
• 0534fde Add news fragment
• 50b732a Check for more specific error message
• a663287 Add pragma for edge-case code path
• 96be735 Workaround for bdist_wheel.dist_info_dir problems
• 000a413 Deprecate public access to setuptools.dist.sequence
• 00995c1 Use variable msg instead of tmpl in setuptools/dist
• d457d0e Type sequence checks in setuptools/dist.py
• Additional commits viewable in compare view

Updates psutil from 6.0.0 to 6.1.0

Changelog

Sourced from psutil's changelog.

6.1.0

2024-10-17

Enhancements

• 2366_, [Windows]: drastically speedup process_iter(). We now determine process unique identity by using process "fast" create time method. This will considerably speedup those apps which use process_iter() only once, e.g. to look for a process with a certain name.
• 2446_: use pytest instead of unittest.
• 2448_: add make install-sysdeps target to install the necessary system dependencies (python-dev, gcc, etc.) on all supported UNIX flavors.
• 2449_: add make install-pydeps-test and make install-pydeps-dev targets. They can be used to install dependencies meant for running tests and for local development. They can also be installed via pip install .[test] and pip install .[dev].
• 2456_: allow to run tests via python3 -m psutil.tests even if pytest module is not installed. This is useful for production environments that don't have pytest installed, but still want to be able to test psutil installation.

Bug fixes

• 2427_: psutil (segfault) on import in the free-threaded (no GIL) version of Python 3.13. (patch by Sam Gross)
• 2455_, [Linux]: IndexError may occur when reading /proc/pid/stat and field 40 (blkio_ticks) is missing.
• 2457_, [AIX]: significantly improve the speed of Process.open_files()_ for some edge cases.
• 2460_, [OpenBSD]: Process.num_fds()_ and Process.open_files()_ may fail with NoSuchProcess_ for PID 0. Instead, we now return "null" values (0 and [] respectively).

Commits

• fb68f9f pre release
• 567438c [Windows] speed up process_iter() (#2444)
• b1a7593 Use pytest.skip instead of unittest.SkipTest (#2461)
• b19d5bd AIX: improve open_files() regexp speed (#2457)
• 223938f Use @pytest.mark.skipif decorator instead of @unittest.skipIf (#2459)
• f65fe44 [OpenBSD] Process num_fds() and open_files() may raise NSP for PID 0 (#2460)
• 0a71d0e enable ruff cache (faster)
• 4649a88 Run tests without pytests (#2456)
• 80af879 revert change which broke python 2 tests
• 4e85bee change call_until() signature so that it can be used with lambda
• Additional commits viewable in compare view

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[github-actions]

Dependency Review

✅ No vulnerabilities or license issues or OpenSSF Scorecard issues found.

OpenSSF Scorecard

Package	Version	Score	Details
pip/numpy	2.1.2	🟢 7.9	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 15 out of 15 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 16 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 🟢 9 detected GitHub workflow tokens with excessive permissions Vulnerabilities 🟢 10 0 existing vulnerabilities detected
pip/psutil	6.1.0	🟢 5.8	Details Check Score Reason Code-Review ⚠️ 2 Found 6/30 approved changesets -- score normalized to 2 Maintained 🟢 10 23 commit(s) and 12 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 Signed-Releases ⚠️ -1 no releases found License 🟢 10 license file detected Security-Policy 🟢 10 security policy file detected Packaging ⚠️ -1 packaging workflow not detected Dangerous-Workflow 🟢 10 no dangerous workflow patterns detected Branch-Protection ⚠️ 0 branch protection not enabled on development/release branches Binary-Artifacts 🟢 10 no binaries found in the repo Token-Permissions ⚠️ 0 detected GitHub workflow tokens with excessive permissions Pinned-Dependencies ⚠️ 0 dependency not pinned by hash detected -- score normalized to 0 Fuzzing 🟢 10 project is fuzzed Vulnerabilities 🟢 10 0 existing vulnerabilities detected SAST ⚠️ 0 SAST tool is not run on all commits -- score normalized to 0
pip/setuptools	75.2.0	🟢 5.2	Details Check Score Reason Maintained 🟢 10 30 commit(s) and 5 issue activity found in the last 90 days -- score normalized to 10 Code-Review 🟢 3 Found 4/11 approved changesets -- score normalized to 3 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 Security-Policy 🟢 10 security policy file detected Dangerous-Workflow 🟢 10 no dangerous workflow patterns detected Token-Permissions ⚠️ 0 detected GitHub workflow tokens with excessive permissions Branch-Protection ⚠️ 0 branch protection not enabled on development/release branches Packaging ⚠️ -1 packaging workflow not detected Binary-Artifacts ⚠️ 2 binaries present in source code Pinned-Dependencies ⚠️ 0 dependency not pinned by hash detected -- score normalized to 0 Vulnerabilities 🟢 10 0 existing vulnerabilities detected 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

• numpy@2.1.2
• psutil@6.1.0
• setuptools@75.2.0
• numpy@2.1.1
• psutil@6.0.0
• setuptools@75.1.0

[dependabot]

Looks like these dependencies are updatable in another way, so this is no longer needed.