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Bump the pip group across 1 directory with 28 updates #3682

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Bumps the pip group with 28 updates in the /src directory:

Package From To
coverage 7.6.2 7.6.12
pytest 8.3.3 8.3.4
pytest-cov 5.0.0 6.0.0
ruff 0.6.9 0.9.9
vcrpy 6.0.2 7.0.0
beautifulsoup4 4.12.3 4.13.3
biopython 1.84 1.85
bokeh 3.6.0 3.6.2
certifi 2024.8.30 2025.1.31
cryptography 43.0.1 44.0.1
decorator 5.1.1 5.2.1
markupsafe 3.0.1 3.0.2
networkx 3.4 3.4.2
numpy 2.1.2 2.2.3
pillow 10.4.0 11.1.0
pycurl 7.45.3 7.45.4
pygments 2.18.0 2.19.1
pyopenssl 24.2.1 25.0.0
python-daemon 3.0.1 3.1.2
scipy 1.14.1 1.15.2
setuptools 75.1.0 75.8.2
six 1.16.0 1.17.0
wordcloud 1.9.3 1.9.4
ipython 8.28.2 8.33.0
jinja2 3.1.4 3.1.5
pymongo 4.10.1 4.11.1
scikit-learn 1.5.2 1.6.1
tornado 6.4.1 6.4.2

Updates coverage from 7.6.2 to 7.6.12

Changelog

Sourced from coverage's changelog.

Version 7.6.12 — 2025-02-11

  • Fix: some aarch64 distributions were missing (issue 1927_). These are now building reliably.

.. _issue 1927: nedbat/coveragepy#1927

.. _changes_7-6-11:

Version 7.6.11 — 2025-02-08

  • Fix: a memory leak in CTracer has been fixed. The details are in issue 1924_ and pytest-dev 676_. This should reduce the memory footprint for everyone even if it hadn't caused a problem before.

  • We now ship a py3-none-any.whl wheel file. Thanks, Russell Keith-Magee <pull 1914_>_.

.. _pull 1914: nedbat/coveragepy#1914 .. _issue 1924: nedbat/coveragepy#1924 .. _pytest-dev 676: pytest-dev/pytest-cov#676

.. _changes_7-6-10:

Version 7.6.10 — 2024-12-26

  • Fix: some descriptions of missing branches in HTML and LCOV reports were incorrect when multi-line statements were involved (issue 1874_ and issue 1875_). These are now fixed.

  • Fix: Python 3.14 defers evaluation of annotations <pep649_>_ by moving them into separate code objects. That code is rarely executed, so coverage.py would mark them as missing, as reported in issue 1908_. Now they are ignored by coverage automatically.

  • Fixed an obscure and mysterious problem on PyPy 3.10 seemingly involving mocks, imports, and trace functions: issue 1902_. To be honest, I don't understand the problem or the solution, but git bisect helped find it, and now it's fixed.

  • Docs: re-wrote the :ref:subprocess page to put multiprocessing first and to highlight the correct use of :class:multiprocessing.Pool <python:multiprocessing.pool.Pool>.

.. _issue 1874: nedbat/coveragepy#1874 .. _issue 1875: nedbat/coveragepy#1875 .. _issue 1902: nedbat/coveragepy#1902

... (truncated)

Commits
  • 7e5373e docs: sample HTML for 7.6.12
  • a4ed38b docs: prep for 7.6.12
  • ce4efdc build: fix aarch64 kits #1927
  • a1f3192 build: don't publish if kit building failed
  • bb68f99 chore: bump the action-dependencies group with 2 updates (#1926)
  • f3d6b4a refactor: check for more kinds of constant tests
  • 67899ea refactor: we no longer care what kind of constant the compile-time constants are
  • c850f20 refactor: macOS is MACOS, not OSX
  • a1b2c1a build: there are always tweaks to howto.txt
  • 9c03039 build: bump version to 7.6.12
  • Additional commits viewable in compare view

Updates pytest from 8.3.3 to 8.3.4

Release notes

Sourced from pytest's releases.

8.3.4

pytest 8.3.4 (2024-12-01)

Bug fixes

  • #12592: Fixed KeyError{.interpreted-text role="class"} crash when using --import-mode=importlib in a directory layout where a directory contains a child directory with the same name.

  • #12818: Assertion rewriting now preserves the source ranges of the original instructions, making it play well with tools that deal with the AST, like executing.

  • #12849: ANSI escape codes for colored output now handled correctly in pytest.fail{.interpreted-text role="func"} with [pytrace=False]{.title-ref}.

  • #9353: pytest.approx{.interpreted-text role="func"} now uses strict equality when given booleans.

Improved documentation

  • #10558: Fix ambiguous docstring of pytest.Config.getoption{.interpreted-text role="func"}.

  • #10829: Improve documentation on the current handling of the --basetemp option and its lack of retention functionality (temporary directory location and retention{.interpreted-text role="ref"}).

  • #12866: Improved cross-references concerning the recwarn{.interpreted-text role="fixture"} fixture.

  • #12966: Clarify filterwarnings{.interpreted-text role="ref"} docs on filter precedence/order when using multiple @pytest.mark.filterwarnings <pytest.mark.filterwarnings ref>{.interpreted-text role="ref"} marks.

Contributor-facing changes

  • #12497: Fixed two failing pdb-related tests on Python 3.13.
Commits
  • 53f8b4e Update pypa/gh-action-pypi-publish to v1.12.2
  • 98dff36 Prepare release version 8.3.4
  • 1b474e2 approx: use exact comparison for bool (#13013)
  • b541721 docs: Fix wrong statement about sys.modules with importlib import mode (#1298...
  • 16cb87b pytest.fail: fix ANSI escape codes for colored output (#12959) (#12990)
  • be6bc81 Issue #12966 Clarify filterwarnings docs on precedence when using multiple ma...
  • 7aeb72b Improve docs on basetemp and retention (#12912) (#12928)
  • c875841 Merge pull request #12917 from pytest-dev/patchback/backports/8.3.x/ded1f44e5...
  • 6502816 Merge pull request #12913 from jakkdl/dontfailonbadpath
  • 52135b0 Merge pull request #12885 from The-Compiler/pdb-py311 (#12887)
  • Additional commits viewable in compare view

Updates pytest-cov from 5.0.0 to 6.0.0

Changelog

Sourced from pytest-cov's changelog.

6.0.0 (2024-10-29)

  • Updated various documentation inaccuracies, especially on subprocess handling.
  • Changed fail under checks to use the precision set in the coverage configuration. Now it will perform the check just like coverage report would.
  • Added a --cov-precision cli option that can override the value set in your coverage configuration.
  • Dropped support for now EOL Python 3.8.
Commits
  • 9540437 Bump version: 5.0.0 → 6.0.0
  • 9f81754 Further trim down envs and drop Python 3.8.
  • b12b5ec Update conf.
  • 23f4b27 Update changelog.
  • 291a04f Bump test deps and trim config.
  • 08f1101 Add --cov-precision option. Close #655.
  • 76fe2a7 Move the warnings/errors in a place that doesn't import anything.
  • a9ea7b7 Implement error/warning for the bad dynamic_context being set in config.
  • c299e01 Add explicit suffixing to make it easier to see the identify the sources/usag...
  • c87e546 Add reproducer for weird xdist dynamic_context interaction. Ref #604.
  • Additional commits viewable in compare view

Updates ruff from 0.6.9 to 0.9.9

Release notes

Sourced from ruff's releases.

0.9.9

Release Notes

Preview features

  • Fix caching of unsupported-syntax errors (#16425)

Bug fixes

  • Only show unsupported-syntax errors in editors when preview mode is enabled (#16429)

Contributors

Install ruff 0.9.9

Install prebuilt binaries via shell script

curl --proto '=https' --tlsv1.2 -LsSf https://github.com/astral-sh/ruff/releases/download/0.9.9/ruff-installer.sh | sh

Install prebuilt binaries via powershell script

powershell -ExecutionPolicy ByPass -c "irm https://github.com/astral-sh/ruff/releases/download/0.9.9/ruff-installer.ps1 | iex"

Download ruff 0.9.9

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
ruff-aarch64-unknown-linux-gnu.tar.gz ARM64 Linux checksum
ruff-i686-unknown-linux-gnu.tar.gz x86 Linux checksum
ruff-powerpc64-unknown-linux-gnu.tar.gz PPC64 Linux checksum
ruff-powerpc64le-unknown-linux-gnu.tar.gz PPC64LE Linux checksum
ruff-s390x-unknown-linux-gnu.tar.gz S390x Linux checksum
ruff-x86_64-unknown-linux-gnu.tar.gz x64 Linux checksum
ruff-armv7-unknown-linux-gnueabihf.tar.gz ARMv7 Linux checksum
ruff-aarch64-unknown-linux-musl.tar.gz ARM64 MUSL Linux checksum

... (truncated)

Changelog

Sourced from ruff's changelog.

0.9.9

Preview features

  • Fix caching of unsupported-syntax errors (#16425)

Bug fixes

  • Only show unsupported-syntax errors in editors when preview mode is enabled (#16429)

0.9.8

Preview features

  • Start detecting version-related syntax errors in the parser (#16090)

Rule changes

  • [pylint] Mark fix unsafe (PLW1507) (#16343)
  • [pylint] Catch case np.nan/case math.nan in match statements (PLW0177) (#16378)
  • [ruff] Add more Pydantic models variants to the list of default copy semantics (RUF012) (#16291)

Server

  • Avoid indexing the project if configurationPreference is editorOnly (#16381)
  • Avoid unnecessary info at non-trace server log level (#16389)
  • Expand ruff.configuration to allow inline config (#16296)
  • Notify users for invalid client settings (#16361)

Configuration

  • Add per-file-target-version option (#16257)

Bug fixes

  • [refurb] Do not consider docstring(s) (FURB156) (#16391)
  • [flake8-self] Ignore attribute accesses on instance-like variables (SLF001) (#16149)
  • [pylint] Fix false positives, add missing methods, and support positional-only parameters (PLE0302) (#16263)
  • [flake8-pyi] Mark PYI030 fix unsafe when comments are deleted (#16322)

Documentation

  • Fix example for S611 (#16316)
  • Normalize inconsistent markdown headings in docstrings (#16364)
  • Document MSRV policy (#16384)

0.9.7

Preview features

... (truncated)

Commits
  • 091d0af Bump version to Ruff 0.9.9 (#16434)
  • 3d72138 Check LinterSettings::preview for version-related syntax errors (#16429)
  • 4a23756 Avoid caching files with unsupported syntax errors (#16425)
  • af62f79 Prioritize "bug" label for changelog sections (#16433)
  • 0ced8d0 [flake8-copyright] Add links to applicable options (CPY001) (#16421)
  • a8e171f Fix string-length limit in documentation for PYI054 (#16432)
  • cf83584 Show version-related syntax errors in the playground (#16419)
  • 764aa0e Allow passing ParseOptions to inline tests (#16357)
  • 568cf88 Bump version to 0.9.8 (#16414)
  • 040071b [red-knot] Ignore surrounding whitespace when looking for `<!-- snapshot-diag...
  • Additional commits viewable in compare view

Updates vcrpy from 6.0.2 to 7.0.0

Release notes

Sourced from vcrpy's releases.

v7.0.0

What's Changed

- Drop support for python 3.8 (major version bump) - thanks @jairhenrique
- Various linting and test fixes - thanks @jairhenrique
- Bugfix for urllib2>=2.3.0 - missing version_string ([#888](https://github.com/kevin1024/vcrpy/issues/888))
- Bugfix for asyncio.run - thanks @alekeik1

New Contributors

Changelog

Sourced from vcrpy's changelog.

Changelog

For a full list of triaged issues, bugs and PRs and what release they are targeted for please see the following link.

ROADMAP MILESTONES <https://github.com/kevin1024/vcrpy/milestones>_

All help in providing PRs to close out bug issues is appreciated. Even if that is providing a repo that fully replicates issues. We have very generous contributors that have added these to bug issues which meant another contributor picked up the bug and closed it out.

  • 7.0.0

  • 6.0.2

  • 6.0.1

    • Bugfix with to Tornado cassette generator (thanks @​graingert)

  • 6.0.0

    • BREAKING: Fix issue with httpx support (thanks @​parkerhancock) in #784. NOTE: You may have to recreate some of your cassettes produced in previous releases due to the binary format being saved incorrectly in previous releases
    • BREAKING: Drop support for boto (vcrpy still supports boto3, but is dropping the deprecated boto support in this release. (thanks @​jairhenrique)
    • Fix compatibility issue with Python 3.12 (thanks @​hartwork)
    • Drop simplejson (fixes some compatibility issues) (thanks @​jairhenrique)
    • Run CI on Python 3.12 and PyPy 3.9-3.10 (thanks @​mgorny)
    • Various linting and docs improvements (thanks @​jairhenrique)
    • Tornado fixes (thanks @​graingert)

  • 5.1.0

  • 5.0.0

    • BREAKING CHANGE: Drop support for Python 3.7. 3.7 is EOL as of 6/27/23 Thanks @​jairhenrique
    • BREAKING CHANGE: Custom Cassette persisters no longer catch ValueError. If you have implemented a custom persister (has anyone implemented a custom persister? Let us know!) then you will need to throw a CassetteNotFoundError when unable to find a cassette. See #681 for discussion and reason for this change. Thanks @​amosjyng for the PR and the review from @​hartwork

  • 4.4.0

    • HUGE thanks to @​hartwork for all the work done on this release!
    • Bring vcr/unittest in to vcrpy as a full feature of vcr instead of a separate library. Big thanks to @​hartwork for doing this and to @​agriffis for originally creating the library
    • Make decompression robust towards already decompressed input (thanks @​hartwork)

... (truncated)

Commits
  • 3278619 Release v7.0.0
  • 3fb62e0 fix: correctly handle asyncio.run when loop exists
  • 8197865 build(deps): update sphinx requirement from <8 to <9
  • be651bd pre-commit: Autoupdate
  • a6698ed Fix aiohttp tests
  • 48d0a2e Fixed missing version_string attribute when used with urllib3>=2.3.0
  • 5b858b1 Fix lint
  • c8d99a9 Fix ruff configuration
  • ce27c63 Merge pull request #736 from kevin1024/drop-python38
  • ab8944d Drop python 3.8 support
  • Additional commits viewable in compare view

Updates beautifulsoup4 from 4.12.3 to 4.13.3

Updates biopython from 1.84 to 1.85

Changelog

Sourced from biopython's changelog.

15 January 2025: Biopython 1.85

This release of Biopython supports Python 3.9, 3.10, 3.11, 3.12 and 3.13. It has also been tested on PyPy3.9 v7.3.13. Python 3.9 is approaching end of life, our support for it is now deprecated.

Some optimisation work was done for Bio.SeqIO including avoiding nested iterators, and speeding up both FASTA and FASTQ parsing.

Bio.motifs now supports reading PFM from Cys2His2 Zinc Finger Proteins PWM Predictor and reading motifs in pfm-four-columns format will set motif name to "" instead of None, when no motif name was found.

Tests that use assertAlmostEqual calls now use places parameter with enough presision when comparing very small numbers in scientific notation.

Bio.motifs now supports reverse complementing RNA motifs and correctly generating degenerate consensus sequences for RNA motifs.

Bio.motifs.minimal now supports parsing RNA motifs and parsing motifs for which not all statistics are provided (e.g. missing E-values or nsites).

Bio.motifs.clusterbuster now supports parsing GAP and WEIGHT parameters and can optionally write Cluster Buster motif files with floats instead of integers, by specifying the precision=<int> parameter when writing: e.g. motifs.write(motifs, "clusterbuster", precision=2)

Additionally, a number of small bugs and typos have been fixed with additions to the test suite and type annotations.

Many thanks to the Biopython developers and community for making this release possible, especially the following contributors:

  • Alan Medlar
  • Carlos Peña
  • Gert Hulselmans
  • Peter Cock
  • Michiel de Hoon
Commits

Updates bokeh from 3.6.0 to 3.6.2

Changelog

Sourced from bokeh's changelog.

2024-12-03 3.6.2:

  • bugfixes:

    • #14082 [BUG] p.circle(..) can't be added as renderer to PointDrawTool since 3.6
    • #14153 [component: bokehjs] ScaleBar positioning doesn't work correctly
    • #14160 [component: docs] Search box on start page has no surrounding line
    • #14168 [component: bokehjs] [BUG] using add_tile to add multiple layers causes error on JScript side

  • tasks:

    • #14088 [component: docs] [BUG] Missing radius parameter in code example
    • #14086 Update links to sponsor page
    • #14155 Backports for 3.6.2

2024-11-06 3.6.1:

  • bugfixes:

    • #14082 [BUG] p.circle(..) can't be added as renderer to PointDrawTool since 3.6
    • #14090 [component: bokehjs] [BUG] Google Chrome 130 fails to draw figure, throws TypeError: Failed to execute 'fill' on 'CanvasRenderingContext2D'
    • #14107 [component: bokehjs] [BUG] Loss of mobile touch scrolling with update to Bokeh 3.6.0

  • tasks:

2024-09-26 3.6:

  • bugfixes:

    • #4951 ModelExtensions - all resources from a whole module are loaded
    • #7524 GroupFilter only accepts strings
    • #13827 [component: bokehjs] [BUG] Lack of range expansion when there remains unbounded directions, even when maintain_focus=False
    • #13886 [component: bokehjs] [BUG] NPM package has types (*.d.ts) in incorrect location
    • #13957 [component: bokehjs] Explicit selection glyph example broken
    • #13959 [BUG] Reset Tool Error in Bokeh Gridplot with Single Plot
    • #13964 [component: bokehjs] [BUG] page won't render if CustomJS args has a dict with key "constructor"
    • #13965 [component: bokehjs] [BUG] CategoricalSlider shows ‘undefined’ value and skip that value
    • #13972 BOKEH_MINIFIED not working
    • #13984 [component: tests] [BUG] Deprecation warning treated as error in pytest hook
    • #14014 [component: bokehjs] [BUG] StringFormatter nan_format seems broken
    • #14054 [component: bokehjs] [BUG] Custom hover tooltip on image plot shows all the image data.
    • #14058 [component: bokehjs] [BUG] Clearing selection with ESC only works on first selection tool
    • #14068 [component: bokehjs] [BUG] Unable to change figures displayed by altering children attribute of gridplot (or other layout classes) in JS callback
    • #14072 [component: bokehjs] [BUG] Spinner input not responding to wheel event
    • #13968 [component: docs] fix indentation in offset parameter for Title
    • #14038 [component: bokehjs] Allow is_equal(0, -0) to be true to match ===
    • #14055 [component: docs] fix some typos
    • #14065 [component: build] Generate correct *.d.ts files for CSS modules

  • features:

    • #601 [component: bokehjs] Add support for click events on categorical axes
    • #11104 [component: bokehjs] [FEATURE] Option for DataTable column sorting to place NaNs last
    • #13130 [component: bokehjs] Add CustomJSTicker

... (truncated)

Commits

Updates certifi from 2024.8.30 to 2025.1.31

Commits
  • 088f931 2025.01.31 (#336)
  • 1c17795 Bump pypa/gh-action-pypi-publish from 1.12.3 to 1.12.4 (#335)
  • a2e88f0 Bump actions/upload-artifact from 4.5.0 to 4.6.0 (#334)
  • 82284ed Bump peter-evans/create-pull-request from 7.0.5 to 7.0.6 (#333)
  • 10d3d1d Bump actions/upload-artifact from 4.4.3 to 4.5.0 (#332)
  • 4ba3900 2024.12.14 (#329)
  • 9164660 Bump pypa/gh-action-pypi-publish from 1.12.2 to 1.12.3 (#331)
  • 3dc3651 Bump pypa/gh-action-pypi-publish from 1.11.0 to 1.12.2 (#328)
  • c5bf18d Bump pypa/gh-action-pypi-publish from 1.10.3 to 1.11.0 (#327)
  • b908391 Bump actions/setup-python from 5.2.0 to 5.3.0 (#326)
  • Additional commits viewable in compare view

Updates cryptography from 43.0.1 to 44.0.1

Changelog

Sourced from cryptography's changelog.

44.0.1 - 2025-02-11


* Updated Windows, macOS, and Linux wheels to be compiled with OpenSSL 3.4.1.
* We now build ``armv7l`` ``manylinux`` wheels and publish them to PyPI.
* We now build ``manylinux_2_34`` wheels and publish them to PyPI.

.. _v44-0-0:


44.0.0 - 2024-11-27

  • BACKWARDS INCOMPATIBLE: Dropped support for LibreSSL < 3.9.
  • Deprecated Python 3.7 support. Python 3.7 is no longer supported by the Python core team. Support for Python 3.7 will be removed in a future cryptography release.
  • Updated Windows, macOS, and Linux wheels to be compiled with OpenSSL 3.4.0.
  • macOS wheels are now built against the macOS 10.13 SDK. Users on older versions of macOS should upgrade, or they will need to build cryptography themselves.
  • Enforce the :rfc:5280 requirement that extended key usage extensions must not be empty.
  • Added support for timestamp extraction to the :class:~cryptography.fernet.MultiFernet class.
  • Relax the Authority Key Identifier requirements on root CA certificates during X.509 verification to allow fields permitted by :rfc:5280 but forbidden by the CA/Browser BRs.
  • Added support for :class:~cryptography.hazmat.primitives.kdf.argon2.Argon2id when using OpenSSL 3.2.0+.
  • Added support for the :class:~cryptography.x509.Admissions certificate extension.
  • Added basic support for PKCS7 decryption (including S/MIME 3.2) via :func:~cryptography.hazmat.primitives.serialization.pkcs7.pkcs7_decrypt_der, :func:~cryptography.hazmat.primitives.serialization.pkcs7.pkcs7_decrypt_pem, and :func:~cryptography.hazmat.primitives.serialization.pkcs7.pkcs7_decrypt_smime.

.. _v43-0-3:

43.0.3 - 2024-10-18


* Fixed release metadata for ``cryptography-vectors``

.. _v43-0-2:


43.0.2 - 2024-10-18

  • Fixed compilation when using LibreSSL 4.0.0.

.. _v43-0-1:

Commits

Updates decorator from 5.1.1 to 5.2.1

Changelog

Sourced from decorator's changelog.

5.2.1 (2025-02-24)

Shiv Krishna Jaiswal suggested how to manage che case of functions without name. Michał Górny contributed a fix for the generation of the source package.

5.2.0 (2025-02-22)

Changed the build procedure to use pyproject.toml and moved the tests outside of the generated wheel/tarball.

Added official support for Python 3.11, 3.12, 3.13 (thanks to Hugo van Kemenade).

Dropped official support for Python < 3.8: the module is expected to work on older Python versions, but I cannot test such versions on GitHub actions, so I cannot claim that it is officially supported.

Dafu Wu provided support for decorating partial functions, i.e. functions wrapped by functools.partial.

Commits

Updates markupsafe from 3.0.1 to 3.0.2

Release notes

Sourced from markupsafe's releases.

3.0.2

This is the MarkupSafe 3.0.2 fix release, which fixes bugs but does not otherwise change behavior and should not result in breaking changes.

PyPI: https://pypi.org/project/MarkupSafe/3.0.2/ Changes: https://markupsafe.palletsprojects.com/en/stable/changes/#version-3-0-2 Milestone: https://github.com/pallets/markupsafe/milestone/14?closed=1

  • Fix compatibility when __str__ returns a str subclass. #472
  • Build requires setuptools >= 70.1. #475
Changelog

Sourced from markupsafe's changelog.

Version 3.0.2

Released 2024-10-18

  • Fix compatibility when __str__ returns a str subclass. :issue:472
  • Build requires setuptools >= 70.1. :issue:475
Commits

Updates networkx from 3.4 to 3.4.2

Release notes

Sourced from networkx's releases.

NetworkX 3.4.2

We're happy to announce the release of networkx 3.4.2!

Bug Fixes

  • Fix docstrings of dispatchable functions (#7679).
  • Fix draw_networkx_nodes return type (#7685).

Documentation

  • Add disclaimer about LLM driven PRs (#7683).

Maintenance

  • Fix doc warnings from recently added docs (#7682).

Contributors

6 authors added to this release (alphabetically):

4 reviewers added to this release (alphabetically):

These lists are automatically generated, and may not be complete or may contain duplicates.

NetworkX 3.4.1

networkx 3.4.1

We're happy to announce the release of networkx 3.4.1!

Maintenance

  • Remove old deprecation decorator (#7669).
  • MAINT: delay loading of backend_info to after imports (#7672).

Contributors

2 authors added to this release (alphabetically):

... (truncated)

Commits

@dependabot
Bump the pip group across 1 directory with 28 updates
cd36888 
Bumps the pip group with 28 updates in the /src directory:

| Package | From | To |
| --- | --- | --- |
| [coverage](https://github.com/nedbat/coveragepy) | `7.6.2` | `7.6.12` |
| [pytest](https://github.com/pytest-dev/pytest) | `8.3.3` | `8.3.4` |
| [pytest-cov](https://github.com/pytest-dev/pytest-cov) | `5.0.0` | `6.0.0` |
| [ruff](https://github.com/astral-sh/ruff) | `0.6.9` | `0.9.9` |
| [vcrpy](https://github.com/kevin1024/vcrpy) | `6.0.2` | `7.0.0` |
| [beautifulsoup4](https://www.crummy.com/software/BeautifulSoup/bs4/) | `4.12.3` | `4.13.3` |
| [biopython](https://github.com/biopython/biopython) | `1.84` | `1.85` |
| [bokeh](https://github.com/bokeh/bokeh) | `3.6.0` | `3.6.2` |
| [certifi](https://github.com/certifi/python-certifi) | `2024.8.30` | `2025.1.31` |
| [cryptography](https://github.com/pyca/cryptography) | `43.0.1` | `44.0.1` |
| [decorator](https://github.com/micheles/decorator) | `5.1.1` | `5.2.1` |
| [markupsafe](https://github.com/pallets/markupsafe) | `3.0.1` | `3.0.2` |
| [networkx](https://github.com/networkx/networkx) | `3.4` | `3.4.2` |
| [numpy](https://github.com/numpy/numpy) | `2.1.2` | `2.2.3` |
| [pillow](https://github.com/python-pillow/Pillow) | `10.4.0` | `11.1.0` |
| [pycurl](https://github.com/pycurl/pycurl) | `7.45.3` | `7.45.4` |
| [pygments](https://github.com/pygments/pygments) | `2.18.0` | `2.19.1` |
| [pyopenssl](https://github.com/pyca/pyopenssl) | `24.2.1` | `25.0.0` |
| python-daemon | `3.0.1` | `3.1.2` |
| [scipy](https://github.com/scipy/scipy) | `1.14.1` | `1.15.2` |
| [setuptools](https://github.com/pypa/setuptools) | `75.1.0` | `75.8.2` |
| [six](https://github.com/benjaminp/six) | `1.16.0` | `1.17.0` |
| [wordcloud](https://github.com/amueller/word_cloud) | `1.9.3` | `1.9.4` |
| [ipython](https://github.com/ipython/ipython) | `8.28.2` | `8.33.0` |
| [jinja2](https://github.com/pallets/jinja) | `3.1.4` | `3.1.5` |
| [pymongo](https://github.com/mongodb/mongo-python-driver) | `4.10.1` | `4.11.1` |
| [scikit-learn](https://github.com/scikit-learn/scikit-learn) | `1.5.2` | `1.6.1` |
| [tornado](https://github.com/tornadoweb/tornado) | `6.4.1` | `6.4.2` |



Updates `coverage` from 7.6.2 to 7.6.12
- [Release notes](https://github.com/nedbat/coveragepy/releases)
- [Changelog](https://github.com/nedbat/coveragepy/blob/master/CHANGES.rst)
- [Commits](nedbat/coveragepy@7.6.2...7.6.12)

Updates `pytest` from 8.3.3 to 8.3.4
- [Release notes](https://github.com/pytest-dev/pytest/releases)
- [Changelog](https://github.com/pytest-dev/pytest/blob/main/CHANGELOG.rst)
- [Commits](pytest-dev/pytest@8.3.3...8.3.4)

Updates `pytest-cov` from 5.0.0 to 6.0.0
- [Changelog](https://github.com/pytest-dev/pytest-cov/blob/master/CHANGELOG.rst)
- [Commits](pytest-dev/pytest-cov@v5.0.0...v6.0.0)

Updates `ruff` from 0.6.9 to 0.9.9
- [Release notes](https://github.com/astral-sh/ruff/releases)
- [Changelog](https://github.com/astral-sh/ruff/blob/main/CHANGELOG.md)
- [Commits](astral-sh/ruff@0.6.9...0.9.9)

Updates `vcrpy` from 6.0.2 to 7.0.0
- [Release notes](https://github.com/kevin1024/vcrpy/releases)
- [Changelog](https://github.com/kevin1024/vcrpy/blob/master/docs/changelog.rst)
- [Commits](kevin1024/vcrpy@v6.0.2...v7.0.0)

Updates `beautifulsoup4` from 4.12.3 to 4.13.3

Updates `biopython` from 1.84 to 1.85
- [Changelog](https://github.com/biopython/biopython/blob/master/NEWS.rst)
- [Commits](https://github.com/biopython/biopython/commits)

Updates `bokeh` from 3.6.0 to 3.6.2
- [Changelog](https://github.com/bokeh/bokeh/blob/3.6.2/docs/CHANGELOG)
- [Commits](bokeh/bokeh@3.6.0...3.6.2)

Updates `certifi` from 2024.8.30 to 2025.1.31
- [Commits](certifi/python-certifi@2024.08.30...2025.01.31)

Updates `cryptography` from 43.0.1 to 44.0.1
- [Changelog](https://github.com/pyca/cryptography/blob/main/CHANGELOG.rst)
- [Commits](pyca/cryptography@43.0.1...44.0.1)

Updates `decorator` from 5.1.1 to 5.2.1
- [Release notes](https://github.com/micheles/decorator/releases)
- [Changelog](https://github.com/micheles/decorator/blob/5.2.1/CHANGES.md)
- [Commits](micheles/decorator@5.1.1...5.2.1)

Updates `markupsafe` from 3.0.1 to 3.0.2
- [Release notes](https://github.com/pallets/markupsafe/releases)
- [Changelog](https://github.com/pallets/markupsafe/blob/main/CHANGES.rst)
- [Commits](pallets/markupsafe@3.0.1...3.0.2)

Updates `networkx` from 3.4 to 3.4.2
- [Release notes](https://github.com/networkx/networkx/releases)
- [Commits](networkx/networkx@networkx-3.4...networkx-3.4.2)

Updates `numpy` from 2.1.2 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@v2.1.2...v2.2.3)

Updates `pillow` from 10.4.0 to 11.1.0
- [Release notes](https://github.com/python-pillow/Pillow/releases)
- [Changelog](https://github.com/python-pillow/Pillow/blob/main/CHANGES.rst)
- [Commits](python-pillow/Pillow@10.4.0...11.1.0)

Updates `pycurl` from 7.45.3 to 7.45.4
- [Changelog](https://github.com/pycurl/pycurl/blob/master/ChangeLog)
- [Commits](https://github.com/pycurl/pycurl/commits)

Updates `pygments` from 2.18.0 to 2.19.1
- [Release notes](https://github.com/pygments/pygments/releases)
- [Changelog](https://github.com/pygments/pygments/blob/master/CHANGES)
- [Commits](pygments/pygments@2.18.0...2.19.1)

Updates `pyopenssl` from 24.2.1 to 25.0.0
- [Changelog](https://github.com/pyca/pyopenssl/blob/main/CHANGELOG.rst)
- [Commits](pyca/pyopenssl@24.2.1...25.0.0)

Updates `python-daemon` from 3.0.1 to 3.1.2

Updates `scipy` from 1.14.1 to 1.15.2
- [Release notes](https://github.com/scipy/scipy/releases)
- [Commits](scipy/scipy@v1.14.1...v1.15.2)

Updates `setuptools` from 75.1.0 to 75.8.2
- [Release notes](https://github.com/pypa/setuptools/releases)
- [Changelog](https://github.com/pypa/setuptools/blob/main/NEWS.rst)
- [Commits](pypa/setuptools@v75.1.0...v75.8.2)

Updates `six` from 1.16.0 to 1.17.0
- [Changelog](https://github.com/benjaminp/six/blob/main/CHANGES)
- [Commits](benjaminp/six@1.16.0...1.17.0)

Updates `wordcloud` from 1.9.3 to 1.9.4
- [Release notes](https://github.com/amueller/word_cloud/releases)
- [Changelog](https://github.com/amueller/word_cloud/blob/main/doc/changelog.rst)
- [Commits](amueller/word_cloud@1.9.3...1.9.4)

Updates `ipython` from 8.28.2 to 8.33.0
- [Release notes](https://github.com/ipython/ipython/releases)
- [Commits](https://github.com/ipython/ipython/commits/8.33.0)

Updates `jinja2` from 3.1.4 to 3.1.5
- [Release notes](https://github.com/pallets/jinja/releases)
- [Changelog](https://github.com/pallets/jinja/blob/main/CHANGES.rst)
- [Commits](pallets/jinja@3.1.4...3.1.5)

Updates `pymongo` from 4.10.1 to 4.11.1
- [Release notes](https://github.com/mongodb/mongo-python-driver/releases)
- [Changelog](https://github.com/mongodb/mongo-python-driver/blob/master/doc/changelog.rst)
- [Commits](mongodb/mongo-python-driver@4.10.1...4.11.1)

Updates `scikit-learn` from 1.5.2 to 1.6.1
- [Release notes](https://github.com/scikit-learn/scikit-learn/releases)
- [Commits](scikit-learn/scikit-learn@1.5.2...1.6.1)

Updates `tornado` from 6.4.1 to 6.4.2
- [Changelog](https://github.com/tornadoweb/tornado/blob/v6.4.2/docs/releases.rst)
- [Commits](tornadoweb/tornado@v6.4.1...v6.4.2)

---
updated-dependencies:
- dependency-name: coverage
  dependency-type: direct:development
  update-type: version-update:semver-patch
  dependency-group: pip
- dependency-name: pytest
  dependency-type: direct:development
  update-type: version-update:semver-patch
  dependency-group: pip
- dependency-name: pytest-cov
  dependency-type: direct:development
  update-type: version-update:semver-major
  dependency-group: pip
- dependency-name: ruff
  dependency-type: direct:development
  update-type: version-update:semver-minor
  dependency-group: pip
- dependency-name: vcrpy
  dependency-type: direct:development
  update-type: version-update:semver-major
  dependency-group: pip
- dependency-name: beautifulsoup4
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: pip
- dependency-name: biopython
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: pip
- dependency-name: bokeh
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: pip
- dependency-name: certifi
  dependency-type: direct:production
  update-type: version-update:semver-major
  dependency-group: pip
- dependency-name: cryptography
  dependency-type: direct:production
  update-type: version-update:semver-major
  dependency-group: pip
- dependency-name: decorator
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: pip
- dependency-name: markupsafe
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: pip
- dependency-name: networkx
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: pip
- dependency-name: numpy
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: pip
- dependency-name: pillow
  dependency-type: direct:production
  update-type: version-update:semver-major
  dependency-group: pip
- dependency-name: pycurl
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: pip
- dependency-name: pygments
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: pip
- dependency-name: pyopenssl
  dependency-type: direct:production
  update-type: version-update:semver-major
  dependency-group: pip
- dependency-name: python-daemon
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: pip
- dependency-name: scipy
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: pip
- dependency-name: setuptools
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: pip
- dependency-name: six
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: pip
- dependency-name: wordcloud
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: pip
- dependency-name: ipython
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: pip
- dependency-name: jinja2
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: pip
- dependency-name: pymongo
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: pip
- dependency-name: scikit-learn
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: pip
- dependency-name: tornado
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: pip
...

Signed-off-by: dependabot[bot] <support@github.com>
@dependabot dependabot bot added dependencies Pull requests that update a dependency file python Pull requests that update Python code labels Mar 1, 2025
@sonarqubecloud SonarQubeCloud
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sonarqubecloud bot commented Mar 1, 2025

Quality Gate Passed Quality Gate passed

Issues
0 New issues
0 Accepted issues

Measures
0 Security Hotspots
0.0% Coverage on New Code
0.0% Duplication on New Code

See analysis details on SonarQube Cloud

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dependabot bot commented on behalf of github Mar 17, 2025

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

@dependabot dependabot bot closed this Mar 17, 2025
@dependabot dependabot bot deleted the dependabot/pip/src/pip-8ce0f8af73 branch March 17, 2025 15:10
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