search

cytomining / pycytominer

Python package for processing image-based profiling data
https://pycytominer.readthedocs.io
BSD 3-Clause "New" or "Revised" License
80 stars 36 forks source link

build(deps): bump the python-packages group with 15 updates #466

Closed dependabot[bot] closed 3 weeks ago

dependabot[bot] commented 3 weeks ago

Bumps the python-packages group with 15 updates:

Package From To
scipy 1.9.3 1.13.1
pandas 2.0.3 2.2.3
scikit-learn 1.5.0 1.5.2
boto3 1.34.51 1.35.36
fire 0.6.0 0.7.0
cytominer-database 0.3.4 0.3.5
pytest 8.1.1 8.3.3
commitizen 3.20.0 3.30.0
ruff 0.3.4 0.7.1
mypy 1.11.2 1.13.0
mkdocs 1.5.3 1.6.1
sphinx-autoapi 3.0.0 3.3.3
ipython 8.12.3 8.18.0
nbsphinx 0.9.3 0.9.5
dunamai 1.19.2 1.22.0

Updates scipy from 1.9.3 to 1.13.1

Release notes

Sourced from scipy's releases.

SciPy 1.13.1 Release Notes

SciPy 1.13.1 is a bug-fix release with no new features compared to 1.13.0. The version of OpenBLAS shipped with the PyPI binaries has been increased to 0.3.27.

Authors

  • Name (commits)
  • h-vetinari (1)
  • Jake Bowhay (2)
  • Evgeni Burovski (6)
  • Sean Cheah (2)
  • Lucas Colley (2)
  • DWesl (2)
  • Ralf Gommers (7)
  • Ben Greiner (1) +
  • Matt Haberland (2)
  • Gregory R. Lee (1)
  • Philip Loche (1) +
  • Sijo Valayakkad Manikandan (1) +
  • Matti Picus (1)
  • Tyler Reddy (62)
  • Atsushi Sakai (1)
  • Daniel Schmitz (2)
  • Dan Schult (3)
  • Scott Shambaugh (2)
  • Edgar Andrés Margffoy Tuay (1)

A total of 19 people contributed to this release. People with a "+" by their names contributed a patch for the first time. This list of names is automatically generated, and may not be fully complete.

SciPy 1.13.0 Release Notes

SciPy 1.13.0 is the culmination of 3 months of hard work. This out-of-band release aims to support NumPy 2.0.0, and is backwards compatible to NumPy 1.22.4. The version of OpenBLAS used to build the PyPI wheels has been increased to 0.3.26.dev.

This release requires Python 3.9+ and NumPy 1.22.4 or greater.

For running on PyPy, PyPy3 6.0+ is required.

Highlights of this release

... (truncated)

Commits
  • 44e4eba REL: SciPy 1.13.1 release commit [wheel build]
  • 2eb8e1b Merge pull request #20632 from tylerjereddy/treddy_prep_1_13_1_backports
  • 1a00d48 DOC: PR 20632 updates
  • 11e99ba BUG: stats: Fix zipf.pmf and zipfian.pmf for int32 k (#20702) [wheel bu...
  • 506cbeb MAINT: stats.wilcoxon: fix bug with Ndim>1, shape[axis]>50, NaN, 'auto' (#20592)
  • c9d8613 CI, MAINT: PR 20632 revisions
  • 95c50a4 MAINT: PR 20632 revisions [wheel build]
  • e7abaf1 MAINT: PR 20632 revisions [wheel build]
  • aa32933 CI: PR 20632 revisions [wheel build]
  • 023b0fb CI: MR 20632 revisions
  • Additional commits viewable in compare view


Updates pandas from 2.0.3 to 2.2.3

Release notes

Sourced from pandas's releases.

Pandas 2.2.3

We are pleased to announce the release of pandas 2.2.3. This release includes some new features, bug fixes, and performance improvements. We recommend that all users upgrade to this version.

See the full whatsnew for a list of all the changes. Pandas 2.2.3 supports Python 3.9 and higher.

The release will be available on the defaults and conda-forge channels:

conda install pandas

Or via PyPI:

python3 -m pip install --upgrade pandas

Please report any issues with the release on the pandas issue tracker.

Thanks to all the contributors who made this release possible.

Pandas 2.2.2

We are pleased to announce the release of pandas 2.2.2. This release includes some new features, bug fixes, and performance improvements. We recommend that all users upgrade to this version.

See the full whatsnew for a list of all the changes. Pandas 2.2.2 supports Python 3.9 and higher.

The release will be available on the defaults and conda-forge channels:

conda install pandas

Or via PyPI:

python3 -m pip install --upgrade pandas

Please report any issues with the release on the pandas issue tracker.

Thanks to all the contributors who made this release possible.

Pandas 2.2.1

We are pleased to announce the release of pandas 2.2.1. This release includes some new features, bug fixes, and performance improvements. We recommend that all users upgrade to this version.

See the full whatsnew for a list of all the changes. Pandas 2.2.1 supports Python 3.9 and higher.

The release will be available on the defaults and conda-forge channels:

conda install pandas

Or via PyPI:

... (truncated)

Commits


Updates scikit-learn from 1.5.0 to 1.5.2

Release notes

Sourced from scikit-learn's releases.

Scikit-learn 1.5.2

We're happy to announce the 1.5.2 release.

This release contains fixes for a few regressions introduced in 1.5.

You can see the changelog here: https://scikit-learn.org/stable/whats_new/v1.5.html#version-1-5-2

You can upgrade with pip as usual:

pip install -U scikit-learn

The conda-forge builds can be installed using:

conda install -c conda-forge scikit-learn

Thanks to everyone who contributed to this release !

Scikit-learn 1.5.1

We're happy to announce the 1.5.1 release.

This release contains fixes for a few regressions introduced in 1.5.

You can see the changelog here: https://scikit-learn.org/stable/whats_new/v1.5.html#version-1-5-1

You can upgrade with pip as usual:

pip install -U scikit-learn

The conda-forge builds can be installed using:

conda install -c conda-forge scikit-learn

Thanks to everyone who contributed to this release !

Commits
  • 156ef14 [cd build] trigger ci/cd
  • 40c7416 DOC update the list of contributors for 1.5.2 (#29819)
  • c119c7e DOC add orphan option to developers/index.rst
  • 4d838dc TST fix tolerance as in #29400
  • 2e79f52 DOC fix entry in changelog for backport happening in 1.5.2 (#29815)
  • c735641 MAINT install setuptools for debian-32bits
  • c993dd2 DOC update repr for NumPy 2.0
  • 8ade4f5 MAINT bump from 1.5.1 to 1.5.2
  • 04b71d2 FIX solve conflict git
  • b5b5017 MAINT update lock file
  • Additional commits viewable in compare view


Updates boto3 from 1.34.51 to 1.35.36

Commits
  • 75c521c Merge branch 'release-1.35.36'
  • 7a7570c Bumping version to 1.35.36
  • 321f031 Add changelog entries from botocore
  • cca432d Add support for Python 3.13 (#4296)
  • c6ad812 Merge branch 'release-1.35.35'
  • 0f3a8d0 Merge branch 'release-1.35.35' into develop
  • da4a59b Bumping version to 1.35.35
  • da83883 Add changelog entries from botocore
  • eb01c97 Merge branch 'release-1.35.34' into develop
  • 8e68079 Merge branch 'release-1.35.34'
  • Additional commits viewable in compare view


Updates fire from 0.6.0 to 0.7.0

Release notes

Sourced from fire's releases.

Python Fire v0.7.0

Notable in this release:

  • This release is the first to drop Python 2 support. For Python 2 users, use <= 0.6.0.
  • CI improvements from @​Borda including dependabot and an expanded build matrix

What's Changed

New Contributors

Full Changelog: https://github.com/google/python-fire/compare/v0.6.0...v0.7.0

Commits
  • 90b7f82 Replace Python 2 type hints with real type annotations (#559)
  • a0cb1ca Expand build matrix to include mac (#490)
  • efcf60f Lint improvements and type safety (#558)
  • 1c43c36 Bump version number in init to setup.py
  • 8227364 Update required Python 3.7 in setup.py (#555)
  • 36a56c0 Continue upgrade of codebase to Python 3 (#556)
  • d320437 Include Python 3.13 in github actions (#554)
  • 5b2dadd Move asyncio imports and update docs (#553)
  • 93b0e32 Remove six from console, eliminates six entirely (#552)
  • 4efd44d Remove .format in favor of f-strings (#551)
  • Additional commits viewable in compare view


Updates cytominer-database from 0.3.4 to 0.3.5

Release notes

Sourced from cytominer-database's releases.

v0.3.5

Compatibility release for newer Python versions which may not be compatible with backports.tempfile.

Please note: This package is deprecated and will no longer be supported. Please use at your own risk!

What's Changed

Full Changelog: https://github.com/cytomining/cytominer-database/compare/v0.3.4...v0.3.5

Commits
  • 596f9fc Reconcile v0.3.5 with changes in branch 0.3.4 (#135)
  • a138e95 Remove backports.tempfile for Python compatibility and bump version (#134)
  • 62f13b3 Update README.rst
  • 5aa00f5 Merge pull request #133 from cytomining/issues/132
  • 42c99c8 Create CITATION.cff
  • 9cf4340 Merge pull request #122 from diskontinuum/colab_updates
  • 91c871c Update cytominer_database/ingest.py
  • 1b2976c Addressed incomplete doctring in ingest.seed()
  • 799997f Added Hubis to copyright list and ran black again.
  • 6cfd9d1 Update cytominer_database/commands/command_ingest_variable_engine.py
  • Additional commits viewable in compare view


Updates pytest from 8.1.1 to 8.3.3

Release notes

Sourced from pytest's releases.

8.3.3

pytest 8.3.3 (2024-09-09)

Bug fixes

  • #12446: Avoid calling @property (and other instance descriptors) during fixture discovery -- by asottile{.interpreted-text role="user"}

  • #12659: Fixed the issue of not displaying assertion failure differences when using the parameter --import-mode=importlib in pytest>=8.1.

  • #12667: Fixed a regression where type change in [ExceptionInfo.errisinstance]{.title-ref} caused [mypy]{.title-ref} to fail.

  • #12744: Fixed typing compatibility with Python 3.9 or less -- replaced [typing.Self]{.title-ref} with [typing_extensions.Self]{.title-ref} -- by Avasam{.interpreted-text role="user"}

  • #12745: Fixed an issue with backslashes being incorrectly converted in nodeid paths on Windows, ensuring consistent path handling across environments.

  • #6682: Fixed bug where the verbosity levels where not being respected when printing the "msg" part of failed assertion (as in assert condition, msg).

  • #9422: Fix bug where disabling the terminal plugin via -p no:terminal would cause crashes related to missing the verbose option.

    -- by GTowers1{.interpreted-text role="user"}

Improved documentation

  • #12663: Clarify that the [pytest_deselected]{.title-ref} hook should be called from [pytest_collection_modifyitems]{.title-ref} hook implementations when items are deselected.
  • #12678: Remove erroneous quotes from [tmp_path_retention_policy]{.title-ref} example in docs.

Miscellaneous internal changes

  • #12769: Fix typos discovered by codespell and add codespell to pre-commit hooks.

8.3.2

pytest 8.3.2 (2024-07-24)

Bug fixes

  • #12652: Resolve regression [conda]{.title-ref} environments where no longer being automatically detected.

    -- by RonnyPfannschmidt{.interpreted-text role="user"}

8.3.1

pytest 8.3.1 (2024-07-20)

The 8.3.0 release failed to include the change notes and docs for the release. This patch release remedies this. There are no other changes.

... (truncated)

Commits


Updates commitizen from 3.20.0 to 3.30.0

Release notes

Sourced from commitizen's releases.

v3.30.0 (2024-10-23)

Feat

  • commands/commit: add force-edit functionality after answering questions

Refactor

  • remove redundant return None

[master bfe422fa] bump: version 3.29.1 → 3.30.0 4 files changed, 14 insertions(+), 4 deletions(-)

v3.29.1 (2024-09-26)

Fix

  • changelog: Factorized TAG_FORMAT_REGEXES
  • changelog: Handle tag format without version pattern
  • changelog: handle custom tag_format in changelog generation

Refactor

  • Use format strings

[master a3498aba] bump: version 3.29.0 → 3.29.1 4 files changed, 16 insertions(+), 4 deletions(-)

v3.29.0 (2024-08-11)

Feat

  • bump: add functionality to write the next version to stdout

[master d7e01aa9] bump: version 3.28.0 → 3.29.0 4 files changed, 10 insertions(+), 4 deletions(-)

v3.28.0 (2024-07-17)

Feat

  • add argument to limit length of commit message in checks

[master 545f1434] bump: version 3.27.0 → 3.28.0 4 files changed, 10 insertions(+), 4 deletions(-)

v3.27.0 (2024-05-22)

Feat

... (truncated)

Changelog

Sourced from commitizen's changelog.

v3.30.0 (2024-10-23)

Feat

  • commands/commit: add force-edit functionality after answering questions

Refactor

  • remove redundant return None

v3.29.1 (2024-09-26)

Fix

  • changelog: Factorized TAG_FORMAT_REGEXES
  • changelog: Handle tag format without version pattern
  • changelog: handle custom tag_format in changelog generation

Refactor

  • Use format strings

v3.29.0 (2024-08-11)

Feat

  • bump: add functionality to write the next version to stdout

v3.28.0 (2024-07-17)

Feat

  • add argument to limit length of commit message in checks

v3.27.0 (2024-05-22)

Feat

  • config_files: add support for "cz.toml" config file

v3.26.2 (2024-05-22)

Fix

  • base.py: add encoding when open changlelog_file

v3.26.1 (2024-05-22)

Fix

... (truncated)

Commits
  • bfe422f bump: version 3.29.1 → 3.30.0
  • 08a259d feat(commands/commit): add force-edit functionality after answering questions
  • 2f6b7cc docs(customization): Unify capitalization
  • 78dc765 docs(commit): add multiline option questions content table
  • e5aaec4 build(deps-dev): bump mypy from 1.12.1 to 1.13.0
  • af3553b build(deps-dev): bump rich from 13.9.2 to 13.9.3
  • 29d6e64 build(deps-dev): bump mkdocs-material from 9.5.41 to 9.5.42
  • 4968868 build(deps-dev): bump mypy from 1.12.0 to 1.12.1
  • 36cfcab build(deps-dev): bump ruff from 0.6.9 to 0.7.0
  • 1d5f295 docs(third-party-commitizen): uniformize the third party page
  • Additional commits viewable in compare view


Updates ruff from 0.3.4 to 0.7.1

Release notes

Sourced from ruff's releases.

0.7.1

Release Notes

Preview features

  • Fix E221 and E222 to flag missing or extra whitespace around == operator (#13890)
  • Formatter: Alternate quotes for strings inside f-strings in preview (#13860)
  • Formatter: Join implicit concatenated strings when they fit on a line (#13663)
  • [pylint] Restrict iteration-over-set to only work on sets of literals (PLC0208) (#13731)

Rule changes

  • [flake8-type-checking] Support auto-quoting when annotations contain quotes (#11811)

Server

  • Avoid indexing the workspace for single-file mode (#13770)

Bug fixes

  • Make ARG002 compatible with EM101 when raising NotImplementedError (#13714)

Other changes

  • Introduce more Docker tags for Ruff (similar to uv) (#13274)

Contributors

Install ruff 0.7.1

Install prebuilt binaries via shell script

... (truncated)

Changelog

Sourced from ruff's changelog.

0.7.1

Preview features

  • Fix E221 and E222 to flag missing or extra whitespace around == operator (#13890)
  • Formatter: Alternate quotes for strings inside f-strings in preview (#13860)
  • Formatter: Join implicit concatenated strings when they fit on a line (#13663)
  • [pylint] Restrict iteration-over-set to only work on sets of literals (PLC0208) (#13731)

Rule changes

  • [flake8-type-checking] Support auto-quoting when annotations contain quotes (#11811)

Server

  • Avoid indexing the workspace for single-file mode (#13770)

Bug fixes

  • Make ARG002 compatible with EM101 when raising NotImplementedError (#13714)

Other changes

  • Introduce more Docker tags for Ruff (similar to uv) (#13274)

0.7.0

Check out the blog post for a migration guide and overview of the changes!

Breaking changes

  • The pytest rules PT001 and PT023 now default to omitting the decorator parentheses when there are no arguments (#12838, #13292). This was a change that we attempted to make in Ruff v0.6.0, but only partially made due to an error on our part. See the blog post for more details.
  • The useless-try-except rule (in our tryceratops category) has been recoded from TRY302 to TRY203 (#13502). This ensures Ruff's code is consistent with the same rule in the tryceratops linter.
  • The lint.allow-unused-imports setting has been removed (#13677). Use lint.pyflakes.allow-unused-imports instead.

Formatter preview style

  • Normalize implicit concatenated f-string quotes per part (#13539)

Preview linter features

  • [refurb] implement hardcoded-string-charset (FURB156) (#13530)
  • [refurb] Count codepoints not bytes for slice-to-remove-prefix-or-suffix (FURB188) (#13631)

... (truncated)

Commits
  • 337af83 Bump version to 0.7.1 (#13913)
  • 113ce84 Fix normalize arguments when fstring_formatting is disabled (#13910)
  • 7272f83 Fix preview style name in can_omit_parentheses to is_f_string_formatting_en...
  • 3eb4546 [red-knot] Format mdtest Python snippets more concisely (#13905)
  • 77ae0cc [red-knot] Infer subscript expression types for bytes literals (#13901)
  • 73ee72b Join implicit concatenated strings when they fit on a line (#13663)
  • e402e27 Use referencial equality in traversal helper methods (#13895)
  • de4181d Remove "default" remark from ruff check (#13900)
  • 2c57c2d [red-knot] Type narrowing for isinstance checks (#13894)
  • 72c18c8 Fix E221 and E222 to flag missing or extra whitespace around == operator (#...
  • Additional commits viewable in compare view


Updates mypy from 1.11.2 to 1.13.0

Changelog

Sourced from mypy's changelog.

Mypy Release Notes

Next release

Change to enum membership semantics

As per the updated typing specification for enums, enum members must be left unannotated.

class Pet(Enum):
    CAT = 1  # Member attribute
    DOG = 2  # Member attribute
    WOLF: int = 3  # New error: Enum members must be left unannotated

species: str  # Considered a non-member attribute

In particular, the specification change can result in issues in type stubs (.pyi files), since historically it was common to leave the value absent:

# In a type stub (.pyi file)

class Pet(Enum):

# Change in semantics: previously considered members, now non-member attributes

CAT: int

DOG: int


# Mypy will now issue a warning if it detects this situation in type stubs:
# &gt; Detected enum &quot;Pet&quot; in a type stub with zero members.
# &gt; There is a chance this is due to a recent change in the semantics of enum membership.
# &gt; If so, use `member = value` to mark an enum member, instead of `member: type`



class Pet(Enum):

# As per the specification, you should now do one of the following:

DOG = 1  # Member attribute with value 1 and known type

WOLF = cast(int, ...)  # Member attribute with unknown value but known type

LION = ...  # Member attribute with unknown value and unknown type

Contributed by Terence Honles in PR 17207 and Shantanu Jain in PR 18068.

Mypy 1.13

We’ve just uploaded mypy 1.13 to the Python Package Index (PyPI). Mypy is a static type checker for Python. You can install it as follows:

python3 -m pip install -U mypy

... (truncated)

Commits


Updates mkdocs from 1.5.3 to 1.6.1

Release notes

Sourced from mkdocs's releases.

1.6.1

Version 1.6.1 (Friday 30th August, 2024)

Fixed

  • Fix build error when environment variable SOURCE_DATE_EPOCH=0 is set. #3795
  • Fix build error when mkdocs_theme.yml config is empty. #3700
  • Support python -W and PYTHONWARNINGS instead of overriding the configuration. #3809
  • Support running with Docker under strict mode, by removing 0.0.0.0 dev server warning. #3784
  • Drop unnecessary changefreq from sitemap.xml. #3629
  • Fix JavaScript console error when closing menu dropdown. #3774
  • Fix JavaScript console error that occur on repeated clicks. #3730
  • Fix JavaScript console error that can occur on dropdown selections. #3694

Added

  • Added translations for Dutch. #3804
  • Added and updated translations for Chinese (Simplified). #3684

1.6.0

Local preview

  • mkdocs serve no longer locks up the browser when more than 5 tabs are open. This is achieved by closing the polling connection whenever a tab becomes inactive. Background tabs will no longer auto-reload either - that will instead happen as soon the tab is opened again. Context: #3391

  • New flag serve --open to open the site in a browser.
    After the first build is finished, this flag will cause the default OS Web browser to be opened at the home page of the local site.
    Context: #3500

Drafts

[!warning] Changed from version 1.5:

The exclude_docs config was split up into two separate concepts.

The exclude_docs config no longer has any special behavior for mkdocs serve - it now always completely excludes the listed documents from the site.

If you wish to use the "drafts" functionality like the exclude_docs key used to do in MkDocs 1.5, please switch to the new config key draft_docs.

See documentation.

Other changes:

  • Reduce warning levels when a "draft" page has a link to a non-existent file. Context: #3449

Update to deduction of page titles

MkDocs 1.5 had a change in behavior in deducing the page titles from the first heading. Unfortunately this could cause unescaped HTML tags or entities to appear in edge cases.

Now tags are always fully sanitized from the title. Though it still remains the case that Page.title is expected to contain HTML entities and is passed directly to the themes.

... (truncated)

Commits
dependabot[bot] commented 3 weeks ago

Superseded by #472.