cfe-lab / MiCall

Pipeline for processing FASTQ data from an Illumina MiSeq to genotype human RNA viruses like HIV and hepatitis C
https://cfe-lab.github.io/MiCall
GNU Affero General Public License v3.0
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Bump numpy from 1.24.3 to 2.0.1 #1136

Closed dependabot[bot] closed 3 months ago

dependabot[bot] commented 4 months ago

Bumps numpy from 1.24.3 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[bot] commented 3 months ago

Superseded by #1146.