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chanzuckerberg / single-cell-curation

Code and documentation for the curation of cellxgene datasets
MIT License
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chore(deps): bump the non-major-updates group in /cellxgene_schema_cli with 8 updates #923

Closed dependabot[bot] closed 4 weeks ago

dependabot[bot] commented 4 weeks ago

Bumps the non-major-updates group in /cellxgene_schema_cli with 8 updates:

Package From To
anndata 0.8.0 0.10.7
click 8.1.3 8.1.7
numpy 1.23.2 1.26.4
pyyaml 6.0 6.0.1
wheel 0.40.0 0.43.0
semver 3.0.0 3.0.2
xxhash 3.3.0 3.4.1
matplotlib 3.7.3 3.9.0

Updates anndata from 0.8.0 to 0.10.7

Commits


Updates click from 8.1.3 to 8.1.7

Release notes

Sourced from click's releases.

8.1.7

This is a fix release for the 8.1.x feature branch.

8.1.6

This is a fix release for the 8.1.x feature branch. If you were having issues with type checking tools like pyright or mypy not accepting uses of Click's decorators, this should fix that.

8.1.5

This is a fix release for the 8.1.x feature branch. This fixes an issue with decorator type annotations that caused type checkers to fail for valid code. There are no runtime behavior changes.

8.1.4

This is a fix release for the 8.1.x feature branch.

Changelog

Sourced from click's changelog.

Version 8.1.7

Released 2023-08-17

  • Fix issue with regex flags in shell completion. :issue:2581
  • Bash version detection issues a warning instead of an error. :issue:2574
  • Fix issue with completion script for Fish shell. :issue:2567

Version 8.1.6

Released 2023-07-18

  • Fix an issue with type hints for @click.group(). :issue:2558

Version 8.1.5

Released 2023-07-13

  • Fix an issue with type hints for @click.command(), @click.option(), and other decorators. Introduce typing tests. :issue:2558

Version 8.1.4

Released 2023-07-06

  • Replace all typing.Dict occurrences to typing.MutableMapping for parameter hints. :issue:2255
  • Improve type hinting for decorators and give all generic types parameters. :issue:2398
  • Fix return value and type signature of shell_completion.add_completion_class function. :pr:2421
  • Bash version detection doesn't fail on Windows. :issue:2461
  • Completion works if there is a dot (.) in the program name. :issue:2166
  • Improve type annotations for pyright type checker. :issue:2268
  • Improve responsiveness of click.clear(). :issue:2284
  • Improve command name detection when using Shiv or PEX. :issue:2332
  • Avoid showing empty lines if command help text is empty. :issue:2368
  • ZSH completion script works when loaded from fpath. :issue:2344.
  • EOFError and KeyboardInterrupt tracebacks are not suppressed when standalone_mode is disabled. :issue:2380
  • @group.command does not fail if the group was created with a custom command_class. :issue:2416
  • multiple=True is allowed for flag options again and does not require

... (truncated)

Commits
  • 874ca2b release version 8.1.7
  • 6e1f6d3 completion(fish): add back ; as line endings in fish script (#2570)
  • a955c77 update fish enabling script
  • 3c1529e add back semicolons in fish script
  • a260ca6 Replace bash shell completion version error with warning (#2576)
  • d9db70c bash version support shows warning instead of error
  • 22b9b1c Fix incorrect passing of flags to re.sub (#2581)
  • d69d210 fix flake8 finding
  • af2da1e Fix incorrect passing of flags to re.sub
  • bb6a872 start version 8.1.7
  • Additional commits viewable in compare view


Updates numpy from 1.23.2 to 1.26.4

Release notes

Sourced from numpy's releases.

v1.26.4

NumPy 1.26.4 Release Notes

NumPy 1.26.4 is a maintenance release that fixes bugs and regressions discovered after the 1.26.3 release. The Python versions supported by this release are 3.9-3.12. This is the last planned release in the 1.26.x series.

Contributors

A total of 13 people contributed to this release. People with a "+" by their names contributed a patch for the first time.

  • Charles Harris
  • Elliott Sales de Andrade
  • Lucas Colley +
  • Mark Ryan +
  • Matti Picus
  • Nathan Goldbaum
  • Ola x Nilsson +
  • Pieter Eendebak
  • Ralf Gommers
  • Sayed Adel
  • Sebastian Berg
  • Stefan van der Walt
  • Stefano Rivera

Pull requests merged

A total of 19 pull requests were merged for this release.

  • #25323: BUG: Restore missing asstr import
  • #25523: MAINT: prepare 1.26.x for further development
  • #25539: BUG: numpy.array_api: fix linalg.cholesky upper decomp...
  • #25584: CI: Bump azure pipeline timeout to 120 minutes
  • #25585: MAINT, BLD: Fix unused inline functions warnings on clang
  • #25599: BLD: include fix for MinGW platform detection
  • #25618: TST: Fix test_numeric on riscv64
  • #25619: BLD: fix building for windows ARM64
  • #25620: MAINT: add newaxis to __all__ in numpy.array_api
  • #25630: BUG: Use large file fallocate on 32 bit linux platforms
  • #25643: TST: Fix test_warning_calls on Python 3.12
  • #25645: TST: Bump pytz to 2023.3.post1
  • #25658: BUG: Fix AVX512 build flags on Intel Classic Compiler
  • #25670: BLD: fix potential issue with escape sequences in __config__.py
  • #25718: CI: pin cygwin python to 3.9.16-1 and fix typing tests [skip...
  • #25720: MAINT: Bump cibuildwheel to v2.16.4
  • #25748: BLD: unvendor meson-python on 1.26.x and upgrade to meson-python...
  • #25755: MAINT: Include header defining backtrace
  • #25756: BUG: Fix np.quantile([Fraction(2,1)], 0.5) (#24711)

... (truncated)

Commits
  • 9815c16 Merge pull request #25770 from charris/prepare-1.26.4
  • 114ed25 REL: Prepare for the NumPy 1.26.4 release
  • 2fae4d3 Merge pull request #25323 from stefanor/import-asstr
  • ce89a0a Merge pull request #25756 from charris/backport-24711
  • f62dfc6 Merge pull request #25755 from charris/backport-25709
  • fee88ab BUG: Fix np.quantile([Fraction(2,1)], 0.5) (#24711)
  • 659be68 MAINT: Include header defining backtrace
  • 837cd38 Merge pull request #25748 from rgommers/unvendor-mesonpython
  • f984240 CI: upgrade cibuildwheel from 2.16.4 to 2.16.5 [wheel build]
  • 3548f9d BLD: unvendor meson-python [wheel build]
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Updates pyyaml from 6.0 to 6.0.1

Changelog

Sourced from pyyaml's changelog.

6.0.1 (2023-07-18)

Commits


Updates wheel from 0.40.0 to 0.43.0

Release notes

Sourced from wheel's releases.

0.43.0

  • Dropped support for Python 3.7
  • Updated vendored packaging to 24.0

0.42.0

  • Allowed removing build tag with wheel tags --build ""
  • Fixed wheel pack and wheel tags writing updated WHEEL fields after a blank line, causing other tools to ignore them
  • Fixed wheel pack and wheel tags writing WHEEL with CRLF line endings or a mix of CRLF and LF
  • Fixed wheel pack --build-number "" not removing build tag from WHEEL (above changes by Benjamin Gilbert)

0.41.3

  • Updated vendored packaging to 23.2
  • Fixed ABI tag generation for CPython 3.13a1 on Windows (PR by Sam Gross)
Changelog

Sourced from wheel's changelog.

Release Notes

UNRELEASED

  • Canonicalize requirements in METADATA file (PR by Wim Jeantine-Glenn)

0.43.0 (2024-03-11)

  • Dropped support for Python 3.7
  • Updated vendored packaging to 24.0

0.42.0 (2023-11-26)

  • Allowed removing build tag with wheel tags --build ""
  • Fixed wheel pack and wheel tags writing updated WHEEL fields after a blank line, causing other tools to ignore them
  • Fixed wheel pack and wheel tags writing WHEEL with CRLF line endings or a mix of CRLF and LF
  • Fixed wheel pack --build-number "" not removing build tag from WHEEL (above changes by Benjamin Gilbert)

0.41.3 (2023-10-30)

  • Updated vendored packaging to 23.2
  • Fixed ABI tag generation for CPython 3.13a1 on Windows (PR by Sam Gross)

0.41.2 (2023-08-22)

  • Fixed platform tag detection for GraalPy and 32-bit python running on an aarch64 kernel (PR by Matthieu Darbois)
  • Fixed wheel tags to not list directories in RECORD files (PR by Mike Taves)
  • Fixed ABI tag generation for GraalPy (PR by Michael Simacek)

0.41.1 (2023-08-05)

  • Fixed naming of the data_dir directory in the presence of local version segment given via egg_info.tag_build (PR by Anderson Bravalheri)
  • Fixed version specifiers in Requires-Dist being wrapped in parentheses

0.41.0 (2023-07-22)

  • Added full support of the build tag syntax to wheel tags (you can now set a build tag like 123mytag)
  • Fixed warning on Python 3.12 about onerror deprecation. (PR by Henry Schreiner)
  • Support testing on Python 3.12 betas (PR by Ewout ter Hoeven)

0.40.0 (2023-03-14)

... (truncated)

Commits
  • fa33dfd Created a new release
  • b2c8272 Removed PyPy + Windows from the test matrix for now
  • dedcc19 Worked around a bizarre PyPy+Windows issue with bdist_egg
  • fa480d6 Added Codecov.io token to the test workflow
  • 1280f03 Skip the test_platform_linux32 test on non-Linux platforms
  • 0b4b259 Removed failing test code
  • b91b377 Fixed erroneous attribute access on the capsys fixture
  • 819baa3 Updated more GitHub actions and improved test workflow
  • 92921a0 Updated vendored packaging to 24.0
  • a9119c8 Updated GitHub actions to their latest versions
  • Additional commits viewable in compare view


Updates semver from 3.0.0 to 3.0.2

Release notes

Sourced from semver's releases.

3.0.2

Documentation: https://python-semver.rtfd.io/en/3.0.2/ PyPI: https://pypi.org/project/semver/3.0.2/ Full Changelog: https://github.com/python-semver/python-semver/compare/3.0.1...3.0.2 Full Changelog between last 2 release and 3: https://github.com/python-semver/python-semver/compare/3.0.1...3.0.2

What's Changed

New Contributors

Full Changelog: https://github.com/python-semver/python-semver/compare/3.0.1...3.0.2

3.0.1

Related pr: #413

Documentation: https://python-semver.rtfd.io/en/3.0.1/ PyPI: https://pypi.org/project/semver/3.0.1/ Full Changelog: https://github.com/python-semver/python-semver/compare/3.0.0...3.0.1 Full Changelog between last 2 release and 3: https://github.com/python-semver/python-semver/compare/2.13.0...3.0.1

What's Changed

New Contributors

... (truncated)

Changelog

Sourced from semver's changelog.

Version 3.0.2

:Released: 2023-10-09 :Maintainer:

Bug Fixes

  • :pr:418: Replace :class:~collection.OrderedDict with :class:dict.

    The dict datatype is ordered since Python 3.7. As we do not support Python 3.6 anymore, it can be considered safe to avoid :class:~collection.OrderedDict. Related to :gh:419.

  • :pr:426: Fix :meth:~semver.version.Version.replace method to use the derived class of an instance instead of :class:~semver.version.Version class.

Improved Documentation

  • :pr:431: Clarify version policy for the different semver versions (v2, v3, >v3) and the supported Python versions.

  • :gh:432: Improve external doc links to Python and Pydantic.

Features

  • :pr:417: Amend GitHub Actions to check against MacOS.

Trivial/Internal Changes

  • :pr:420: Introduce :py:class:~typing.ClassVar for some :class:~semver.version.Version class variables, mainly :data:~semver.version.Version.NAMES and some private.

  • :pr:421: Insert mypy configuration into :file:pyproject.toml and remove config options from :file:tox.ini.

... (truncated)

Commits
  • ec9348a Add missing .readthedocs.yaml
  • f65feab Correct some smaller issues when building
  • 2154ce7 Merge pull request #433 from tomschr/release/3.0.2
  • fb02b3b Build 3.0.2 release of semver
  • c534e3f Merge pull request #432 from tomschr/improve-intersphinx
  • 23e0e73 Improve external docs with intersphinx extension
  • 9a98394 Merge pull request #431 from tomschr/version-policy
  • 083b592 Clarify version policy for semver
  • 9391f8a Rename a news fragment for Towncrier
  • bd313ed Merge pull request #430 from apiwat-chantawibul/fix-semver-pydantic-serializa...
  • Additional commits viewable in compare view


Updates xxhash from 3.3.0 to 3.4.1

Release notes

Sourced from xxhash's releases.

v3.4.1

  • Build wheels for Python 3.12
  • Remove setuptools_scm

Full list of changes: https://github.com/ifduyue/python-xxhash/compare/v3.3.0...v3.4.1

Changelog

Sourced from xxhash's changelog.

v3.4.1 2023-10-05


- Build wheels for Python 3.12
- Remove setuptools_scm

v3.4.0 2023-10-05

Yanked due to wheels building problem.

Commits


Updates matplotlib from 3.7.3 to 3.9.0

Release notes

Sourced from matplotlib's releases.

REL: 3.9.0

Highlights of this release include:

  • Plotting and Annotation improvements
    • Axes.inset_axes is no longer experimental
    • Legend support for Boxplot
    • Percent sign in pie labels auto-escaped with usetex=True
    • hatch parameter for stackplot
    • Add option to plot only one half of violin plot
    • axhline and axhspan on polar axes
    • Subplot titles can now be automatically aligned
    • axisartist can now be used together with standard Formatters
    • Toggle minorticks on Axis
    • StrMethodFormatter now respects axes.unicode_minus
  • Figure, Axes, and Legend Layout
    • Subfigures now have controllable zorders
    • Getters for xmargin, ymargin and zmargin
  • Mathtext improvements
    • mathtext documentation improvements
    • mathtext spacing corrections
  • Widget Improvements
    • Check and Radio Button widgets support clearing
  • 3D plotting improvements
    • Setting 3D axis limits now set the limits exactly
  • Other improvements
    • New BackendRegistry for plotting backends
    • Add widths, heights and angles setter to EllipseCollection
    • image.interpolation_stage rcParam
    • Arrow patch position is now modifiable
    • NonUniformImage now has mouseover support

REL: v3.9.0rc2

This is the second release candidate for the meso release 3.9.0.

REL: v3.8.4

This is the fourth micro release of the 3.8 series.

Highlights of the 3.8.4 release include:

  • Enable building against numpy 2.0; released wheels are built against numpy 2
  • macosx: Clean up single-shot timers correctly
  • Add a draw during show for macos backend
  • Fix color sequence data for Set2 and Set3
  • gtk: Ensure pending draws are done before GTK draw
  • Update "Created with" url in hand.svg
  • Avoid modifying user input to Axes.bar
  • fix quiver3d incorrect arrow colors

REL: v3.8.3

This is the third micro release of the 3.8 series.

... (truncated)

Commits
  • be56634 REL: v3.9.0
  • 846ce8a DOC: Finish documentation for 3.9.0
  • 8604f67 Merge pull request #28206 from meeseeksmachine/auto-backport-of-pr-28205-on-v...
  • 196c8db TST: Followup corrections to #28205
  • d8f3016 Backport PR #28205: TST: Fix tests with older versions of ipython
  • 4db5ac9 Merge pull request #28203 from QuLogic/auto-backport-of-pr-28164-on-v3.9.x
  • ef1a2db Merge pull request #28204 from meeseeksmachine/auto-backport-of-pr-28195-on-v...
  • e4384b8 Merge pull request #28191 from QuLogic/no-dev-theme
  • 3b65546 Backport PR #28195: TST: Prepare for pytest 9
  • 1b526c3 Backport PR #28164: CI: Ensure code coverage is always uploaded
  • Additional commits viewable in compare view


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dependabot[bot] commented 4 weeks ago

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