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Bump the apptainer group in /apptainer/python with 3 updates #632

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Bumps the apptainer group in /apptainer/python with 3 updates: numpy, psutil and intel-openmp.

Updates numpy from 2.2.2 to 2.2.3

Release notes

Sourced from numpy's releases.

2.2.3 (Feb 13, 2025)

NumPy 2.2.3 Release Notes

NumPy 2.2.3 is a patch release that fixes bugs found after the 2.2.2 release. The majority of the changes are typing improvements and fixes for free threaded Python. Both of those areas are still under development, so if you discover new problems, please report them.

This release supports Python versions 3.10-3.13.

Contributors

A total of 9 people contributed to this release. People with a "+" by their names contributed a patch for the first time.

  • !amotzop
  • Charles Harris
  • Chris Sidebottom
  • Joren Hammudoglu
  • Matthew Brett
  • Nathan Goldbaum
  • Raghuveer Devulapalli
  • Sebastian Berg
  • Yakov Danishevsky +

Pull requests merged

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

  • #28185: MAINT: Prepare 2.2.x for further development
  • #28201: BUG: fix data race in a more minimal way on stable branch
  • #28208: BUG: Fix from_float_positional errors for huge pads
  • #28209: BUG: fix data race in np.repeat
  • #28212: MAINT: Use VQSORT_COMPILER_COMPATIBLE to determine if we should...
  • #28224: MAINT: update highway to latest
  • #28236: BUG: Add cpp atomic support (#28234)
  • #28237: BLD: Compile fix for clang-cl on WoA
  • #28243: TYP: Avoid upcasting float64 in the set-ops
  • #28249: BLD: better fix for clang / ARM compiles
  • #28266: TYP: Fix timedelta64.__divmod__ and timedelta64.__mod__...
  • #28274: TYP: Fixed missing typing information of set_printoptions
  • #28278: BUG: backport resource cleanup bugfix from gh-28273
  • #28282: BUG: fix incorrect bytes to stringdtype coercion
  • #28283: TYP: Fix scalar constructors
  • #28284: TYP: stub numpy.matlib
  • #28285: TYP: stub the missing numpy.testing modules
  • #28286: CI: Fix the github label for TYP: PR's and issues
  • #28305: TYP: Backport typing updates from main
  • #28321: BUG: fix race initializing legacy dtype casts
  • #28324: CI: update test_moderately_small_alpha

... (truncated)

Commits
  • a274561 Merge pull request #28322 from charris/prepare-2.2.3
  • 5ab0f71 REL: Prepare for the NumPy 2.2.3 release [wheel build]
  • 010ad9b Merge pull request #28324 from charris/update-test_dirichlet_moderately_small...
  • 6338746 CI: update test_moderately_small_alpha [wheel build]
  • 56f8d5b Merge pull request #28321 from charris/backport-28290
  • 48515a3 MAINT: Update some testing files from main
  • 96ca7e3 MAINT: respond to code review
  • c20ac88 MAINT: use a try/finally to make the deadlock protection more robust
  • d494647 MAINT: fix indentation and clarify comment
  • 3f8fbd6 MAINT: go back to try/except
  • Additional commits viewable in compare view

Updates psutil from 6.1.1 to 7.0.0

Changelog

Sourced from psutil's changelog.

7.0.0

2025-02-13

Enhancements

  • 669_, [Windows]: net_if_addrs()_ also returns the broadcast address instead of None.
  • 2480_: Python 2.7 is no longer supported. Latest version supporting Python 2.7 is psutil 6.1.X. Install it with: pip2 install psutil==6.1.*.
  • 2490_: removed long deprecated Process.memory_info_ex() method. It was deprecated in psutil 4.0.0, released 8 years ago. Substitute is Process.memory_full_info().

Bug fixes

  • 2496_, [Linux]: Avoid segfault (a cPython bug) on Process.memory_maps() for processes that use hundreds of GBs of memory.
  • 2502_, [macOS]: virtual_memory()_ now relies on host_statistics64 instead of host_statistics. This is the same approach used by vm_stat CLI tool, and should grant more accurate results.

Compatibility notes

  • 2480_: Python 2.7 is no longer supported.
  • 2490_: removed long deprecated Process.memory_info_ex() method.
Commits
  • ea5b556 pre-release
  • d6e28b7 try to fix tests
  • 104bb32 test cpu_times() for process children
  • 16c091b test cpu_times() for process children
  • eee09da [OSX] proc.c: Fix goo.gl link in comment for source reference (#2505)
  • 17e2780 ci: build aarch64 wheel on GHA aarch64 runner (#2503)
  • 1ba8667 pin black version to 24.X, because new 25.X breaks style
  • 9c114a5 [OSX] use host_statistics64 to get memory metrics (#2502)
  • 08d7d43 pin black version to 24.X, because new 25.X breaks style
  • a509e5a 669 windows broadcast addr (#2501)
  • Additional commits viewable in compare view

Updates intel-openmp from 2025.0.4 to 2025.0.5

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Bumps the apptainer group in /apptainer/python with 3 updates: [numpy](https://github.com/numpy/numpy), [psutil](https://github.com/giampaolo/psutil) and [intel-openmp](https://www.intel.com/content/www/us/en/developer/tools/oneapi/dpc-compiler.html).


Updates `numpy` from 2.2.2 to 2.2.3
- [Release notes](https://github.com/numpy/numpy/releases)
- [Changelog](https://github.com/numpy/numpy/blob/main/doc/RELEASE_WALKTHROUGH.rst)
- [Commits](numpy/numpy@v2.2.2...v2.2.3)

Updates `psutil` from 6.1.1 to 7.0.0
- [Changelog](https://github.com/giampaolo/psutil/blob/master/HISTORY.rst)
- [Commits](giampaolo/psutil@release-6.1.1...release-7.0.0)

Updates `intel-openmp` from 2025.0.4 to 2025.0.5

---
updated-dependencies:
- dependency-name: numpy
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: apptainer
- dependency-name: psutil
  dependency-type: direct:production
  update-type: version-update:semver-major
  dependency-group: apptainer
- dependency-name: intel-openmp
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: apptainer
...

Signed-off-by: dependabot[bot] <[email protected]>
@dependabot dependabot bot requested a review from sramakintel as a code owner February 17, 2025 14:56
@dependabot dependabot bot added dependencies Pull requests that update a dependency file python Pull requests that update Python code labels Feb 17, 2025
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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
  • ⚠️ 1 package(s) with unknown licenses.
See the Details below.

License Issues

apptainer/python/requirements.txt

PackageVersionLicenseIssue Type
intel-openmp2025.0.5NullUnknown License

OpenSSF Scorecard

PackageVersionScoreDetails
pip/intel-openmp 2025.0.5 UnknownUnknown
pip/numpy 2.2.3 🟢 7.8
Details
CheckScoreReason
Binary-Artifacts🟢 10no binaries found in the repo
Branch-Protection🟢 3branch protection is not maximal on development and all release branches
CI-Tests🟢 1018 out of 18 merged PRs checked by a CI test -- score normalized to 10
CII-Best-Practices⚠️ 0no effort to earn an OpenSSF best practices badge detected
Code-Review🟢 9Found 17/18 approved changesets -- score normalized to 9
Contributors🟢 10project has 95 contributing companies or organizations
Dangerous-Workflow🟢 10no dangerous workflow patterns detected
Dependency-Update-Tool🟢 10update tool detected
Fuzzing🟢 10project is fuzzed
License🟢 9license file detected
Maintained🟢 1030 commit(s) and 20 issue activity found in the last 90 days -- score normalized to 10
Packaging⚠️ -1packaging workflow not detected
Pinned-Dependencies🟢 3dependency not pinned by hash detected -- score normalized to 3
SAST🟢 9SAST tool detected but not run on all commits
Security-Policy🟢 9security policy file detected
Signed-Releases⚠️ 0Project has not signed or included provenance with any releases.
Token-Permissions🟢 9detected GitHub workflow tokens with excessive permissions
Vulnerabilities🟢 100 existing vulnerabilities detected
pip/psutil 7.0.0 🟢 5.7
Details
CheckScoreReason
Code-Review⚠️ 1Found 4/30 approved changesets -- score normalized to 1
Security-Policy🟢 10security policy file detected
Packaging⚠️ -1packaging workflow not detected
Dangerous-Workflow🟢 10no dangerous workflow patterns detected
Maintained🟢 1030 commit(s) and 16 issue activity found in the last 90 days -- score normalized to 10
Token-Permissions⚠️ 0detected GitHub workflow tokens with excessive permissions
Binary-Artifacts🟢 10no binaries found in the repo
CII-Best-Practices⚠️ 0no effort to earn an OpenSSF best practices badge detected
Pinned-Dependencies⚠️ 0dependency not pinned by hash detected -- score normalized to 0
License🟢 10license file detected
Fuzzing🟢 10project is fuzzed
Signed-Releases⚠️ -1no releases found
Vulnerabilities🟢 100 existing vulnerabilities detected
Branch-Protection⚠️ 0branch protection not enabled on development/release branches
SAST⚠️ 0SAST tool is not run on all commits -- score normalized to 0

Scanned Files

  • apptainer/python/requirements.txt

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