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build(deps): bump the python-packages group across 1 directory with 13 updates; retain cytominer-database 0.3.4 #473

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merged 2 commits into from
Nov 4, 2024
Merged

build(deps): bump the python-packages group across 1 directory with 13 updates; retain cytominer-database 0.3.4 #473

merged 2 commits into from
Nov 4, 2024

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Bumps the python-packages group with 13 updates in the / directory:

Package From To
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 0.7.2
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 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: google/python-fire@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: cytomining/cytominer-database@v0.3.4...v0.3.5

Commits

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 0.7.2

Release notes

Sourced from ruff's releases.

0.7.2

Release Notes

Preview features

  • Fix formatting of single with-item with trailing comment (#14005)
  • [pyupgrade] Add PEP 646 Unpack conversion to * with fix (UP044) (#13988)

Rule changes

  • Regenerate known_stdlibs.rs with stdlibs 2024.10.25 (#13963)
  • [flake8-no-pep420] Skip namespace package enforcement for PEP 723 scripts (INP001) (#13974)

Server

  • Fix server panic when undoing an edit (#14010)

Bug fixes

  • Fix issues in discovering ruff in pip build environments (#13881)
  • [flake8-type-checking] Fix false positive for singledispatchmethod (TCH003) (#13941)
  • [flake8-type-checking] Treat return type of singledispatch as runtime-required (TCH003) (#13957)

Documentation

  • [flake8-simplify] Include caveats of enabling if-else-block-instead-of-if-exp (SIM108) (#14019)

Install ruff 0.7.2

Install prebuilt binaries via shell script

curl --proto '=https' --tlsv1.2 -LsSf https://github.com/astral-sh/ruff/releases/download/0.7.2/ruff-installer.sh | sh

Install prebuilt binaries via powershell script

powershell -ExecutionPolicy ByPass -c "irm https://github.com/astral-sh/ruff/releases/download/0.7.2/ruff-installer.ps1 | iex"

Download ruff 0.7.2

File Platform Checksum
ruff-aarch64-apple-darwin.tar.gz Apple Silicon macOS checksum
ruff-x86_64-apple-darwin.tar.gz Intel macOS checksum
ruff-aarch64-pc-windows-msvc.zip ARM64 Windows checksum
ruff-i686-pc-windows-msvc.zip x86 Windows checksum
ruff-x86_64-pc-windows-msvc.zip x64 Windows checksum

... (truncated)

Changelog

Sourced from ruff's changelog.

0.7.2

Preview features

  • Fix formatting of single with-item with trailing comment (#14005)
  • [pyupgrade] Add PEP 646 Unpack conversion to * with fix (UP044) (#13988)

Rule changes

  • Regenerate known_stdlibs.rs with stdlibs 2024.10.25 (#13963)
  • [flake8-no-pep420] Skip namespace package enforcement for PEP 723 scripts (INP001) (#13974)

Server

  • Fix server panic when undoing an edit (#14010)

Bug fixes

  • Fix issues in discovering ruff in pip build environments (#13881)
  • [flake8-type-checking] Fix false positive for singledispatchmethod (TCH003) (#13941)
  • [flake8-type-checking] Treat return type of singledispatch as runtime-required (TCH003) (#13957)

Documentation

  • [flake8-simplify] Include caveats of enabling if-else-block-instead-of-if-exp (SIM108) (#14019)

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)

... (truncated)

Commits

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

Updates sphinx-autoapi from 3.0.0 to 3.3.3

Release notes

Sourced from sphinx-autoapi's releases.

v3.3.3

Bugfixes

  • Document packages and modules under a single "submodules" heading (#450)
  • Fix crash when __init__ is assigned to (#488)
  • Fix documenting incorrect attributes from __init__ (#497)

Misc

v3.3.2

Bugfixes

  • Fix types missing from documentation generated by autodoc-style directives. (#473)

v3.3.1

Bugfixes

  • Fix all class members missing when documenting a module with the same name as a standard library module. Members inherited from the standard library can also have their skip value overridden by autoapi-skip-member. (#478)

Misc

  • Updated all github actions.

v3.3.0

Features

  • Do not document members inherited from standard library classes (#467)

Bugfixes

  • Fix instance attributes not being documented by inherited-members (#477)

Misc

  • #425
  • Fix the parser returning a dictionary instead of a list in the empty parse scenario
  • Rename testenvs to all follow similar naming style

v3.2.1

Bugfixes

  • Fix error or duplicates definitions when __init__ assigns to a property (#466)

v3.2.0

Features

  • functools.cached_property is considered a property (#436)

... (truncated)

Changelog

Sourced from sphinx-autoapi's changelog.

v3.3.3 (2024-10-25)

Bugfixes ^^^^^^^^

  • Document packages and modules under a single "submodules" heading (#450)
  • Fix crash when init is assigned to (#488)
  • Fix documenting incorrect attributes from init (#497)

Misc ^^^^

v3.3.2 (2024-09-25)

Bugfixes ^^^^^^^^

  • Fix types missing from documentation generated by autodoc-style directives. (#473)

v3.3.1 (2024-09-01)

Bugfixes ^^^^^^^^

  • Fix all class members missing when documenting a module with the same name as a standard library module

    Members inherited from the standard library can also have their skip value overridden by autoapi-skip-member. (#478)

Misc ^^^^

  • Updated all github actions.

v3.3.0 (2024-08-28)

Features ^^^^^^^^

... (truncated)

Commits
  • f5c7295 Version 3.3.3
  • eb2d7f2 Fix crash when init is assigned to
  • 0e9bb9b Document package and modules under a "submodules" heading
  • 53c2abc Attach release note to correct issue
  • 489abb1 Add missing release note
  • 9dd7851 Fix adding incorrect attributes from init
  • bedadd4 Add newline before a property's doc string
  • fac7695 Remove old workaround for towncrier
  • 2b31d39 Switch to flit
  • fb73609 PEP 621: Migrate from setup.cfg to pyproject.toml
  • Additional commits viewable in compare view

Updates ipython from 8.12.3 to 8.18.0

Commits

@dependabot
build(deps): bump the python-packages group across 1 directory with 1…
fee5773 
…3 updates

Bumps the python-packages group with 13 updates in the / directory:

| Package | From | To |
| --- | --- | --- |
| [scikit-learn](https://github.com/scikit-learn/scikit-learn) | `1.5.0` | `1.5.2` |
| [boto3](https://github.com/boto/boto3) | `1.34.51` | `1.35.36` |
| [fire](https://github.com/google/python-fire) | `0.6.0` | `0.7.0` |
| [cytominer-database](https://github.com/cytomining/cytominer-database) | `0.3.4` | `0.3.5` |
| [pytest](https://github.com/pytest-dev/pytest) | `8.1.1` | `8.3.3` |
| [commitizen](https://github.com/commitizen-tools/commitizen) | `3.20.0` | `3.30.0` |
| [ruff](https://github.com/astral-sh/ruff) | `0.3.4` | `0.7.2` |
| [mypy](https://github.com/python/mypy) | `1.11.2` | `1.13.0` |
| [mkdocs](https://github.com/mkdocs/mkdocs) | `1.5.3` | `1.6.1` |
| [sphinx-autoapi](https://github.com/readthedocs/sphinx-autoapi) | `3.0.0` | `3.3.3` |
| [ipython](https://github.com/ipython/ipython) | `8.12.3` | `8.18.0` |
| [nbsphinx](https://github.com/spatialaudio/nbsphinx) | `0.9.3` | `0.9.5` |
| [dunamai](https://github.com/mtkennerly/dunamai) | `1.19.2` | `1.22.0` |



Updates `scikit-learn` from 1.5.0 to 1.5.2
- [Release notes](https://github.com/scikit-learn/scikit-learn/releases)
- [Commits](scikit-learn/scikit-learn@1.5.0...1.5.2)

Updates `boto3` from 1.34.51 to 1.35.36
- [Release notes](https://github.com/boto/boto3/releases)
- [Commits](boto/boto3@1.34.51...1.35.36)

Updates `fire` from 0.6.0 to 0.7.0
- [Release notes](https://github.com/google/python-fire/releases)
- [Commits](google/python-fire@v0.6.0...v0.7.0)

Updates `cytominer-database` from 0.3.4 to 0.3.5
- [Release notes](https://github.com/cytomining/cytominer-database/releases)
- [Commits](cytomining/cytominer-database@v0.3.4...v0.3.5)

Updates `pytest` from 8.1.1 to 8.3.3
- [Release notes](https://github.com/pytest-dev/pytest/releases)
- [Changelog](https://github.com/pytest-dev/pytest/blob/main/CHANGELOG.rst)
- [Commits](pytest-dev/pytest@8.1.1...8.3.3)

Updates `commitizen` from 3.20.0 to 3.30.0
- [Release notes](https://github.com/commitizen-tools/commitizen/releases)
- [Changelog](https://github.com/commitizen-tools/commitizen/blob/master/CHANGELOG.md)
- [Commits](commitizen-tools/commitizen@v3.20.0...v3.30.0)

Updates `ruff` from 0.3.4 to 0.7.2
- [Release notes](https://github.com/astral-sh/ruff/releases)
- [Changelog](https://github.com/astral-sh/ruff/blob/main/CHANGELOG.md)
- [Commits](astral-sh/ruff@v0.3.4...0.7.2)

Updates `mypy` from 1.11.2 to 1.13.0
- [Changelog](https://github.com/python/mypy/blob/master/CHANGELOG.md)
- [Commits](python/mypy@v1.11.2...v1.13.0)

Updates `mkdocs` from 1.5.3 to 1.6.1
- [Release notes](https://github.com/mkdocs/mkdocs/releases)
- [Commits](mkdocs/mkdocs@1.5.3...1.6.1)

Updates `sphinx-autoapi` from 3.0.0 to 3.3.3
- [Release notes](https://github.com/readthedocs/sphinx-autoapi/releases)
- [Changelog](https://github.com/readthedocs/sphinx-autoapi/blob/main/CHANGELOG.rst)
- [Commits](readthedocs/sphinx-autoapi@v3.0.0...v3.3.3)

Updates `ipython` from 8.12.3 to 8.18.0
- [Release notes](https://github.com/ipython/ipython/releases)
- [Commits](ipython/ipython@8.12.3...8.18.0)

Updates `nbsphinx` from 0.9.3 to 0.9.5
- [Release notes](https://github.com/spatialaudio/nbsphinx/releases)
- [Changelog](https://github.com/spatialaudio/nbsphinx/blob/master/NEWS.rst)
- [Commits](spatialaudio/nbsphinx@0.9.3...0.9.5)

Updates `dunamai` from 1.19.2 to 1.22.0
- [Release notes](https://github.com/mtkennerly/dunamai/releases)
- [Changelog](https://github.com/mtkennerly/dunamai/blob/master/CHANGELOG.md)
- [Commits](mtkennerly/dunamai@v1.19.2...v1.22.0)

---
updated-dependencies:
- dependency-name: scikit-learn
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: python-packages
- dependency-name: boto3
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: python-packages
- dependency-name: fire
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: python-packages
- dependency-name: cytominer-database
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: python-packages
- dependency-name: pytest
  dependency-type: direct:development
  update-type: version-update:semver-minor
  dependency-group: python-packages
- dependency-name: commitizen
  dependency-type: direct:development
  update-type: version-update:semver-minor
  dependency-group: python-packages
- dependency-name: ruff
  dependency-type: direct:development
  update-type: version-update:semver-minor
  dependency-group: python-packages
- dependency-name: mypy
  dependency-type: direct:development
  update-type: version-update:semver-minor
  dependency-group: python-packages
- dependency-name: mkdocs
  dependency-type: direct:development
  update-type: version-update:semver-minor
  dependency-group: python-packages
- dependency-name: sphinx-autoapi
  dependency-type: direct:development
  update-type: version-update:semver-minor
  dependency-group: python-packages
- dependency-name: ipython
  dependency-type: direct:development
  update-type: version-update:semver-minor
  dependency-group: python-packages
- dependency-name: nbsphinx
  dependency-type: direct:development
  update-type: version-update:semver-patch
  dependency-group: python-packages
- dependency-name: dunamai
  dependency-type: direct:development
  update-type: version-update:semver-minor
  dependency-group: python-packages
...

Signed-off-by: dependabot[bot] <[email protected]>
@dependabot dependabot bot added dependencies Pull requests that update a dependency file python Pull requests that update Python code labels Nov 1, 2024
@d33bs d33bs changed the title build(deps): bump the python-packages group across 1 directory with 13 updates build(deps): bump the python-packages group across 1 directory with 13 updates; retain cytominer-database 0.3.4 Nov 2, 2024
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codecov-commenter commented Nov 2, 2024 •
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Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 94.73%. Comparing base (3f82cc4) to head (ec11724).

Additional details and impacted files 
@@           Coverage Diff           @@
##             main     #473   +/-   ##
=======================================
  Coverage   94.73%   94.73%           
=======================================
  Files          57       57           
  Lines        3155     3155           
=======================================
  Hits         2989     2989           
  Misses        166      166
Flag Coverage Δ
unittests 94.73% <ø> (ø)

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@d33bs d33bs mentioned this pull request Nov 3, 2024
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@d33bs d33bs requested review from gwaybio and kenibrewer November 4, 2024 13:33
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d33bs commented Nov 4, 2024

Hi @gwaybio and @kenibrewer - I made some additional changes here to help pass tests. When there's a chance could I ask for your review of the work (since I've added to what Dependabot changed)?

kenibrewer
kenibrewer approved these changes Nov 4, 2024
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LGTM!

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d33bs commented Nov 4, 2024

Thanks @kenibrewer ! Merging this in.

@d33bs d33bs merged commit 83956c1 into main Nov 4, 2024
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@d33bs d33bs deleted the dependabot/pip/python-packages-08d06714b7 branch November 4, 2024 18:49
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@kenibrewer kenibrewer kenibrewer approved these changes

@gwaybio gwaybio Awaiting requested review from gwaybio

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