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Bump the poetry-dependencies group with 20 updates #38

Merged
merged 1 commit into from
Feb 1, 2025
Merged

Bump the poetry-dependencies group with 20 updates #38

merged 1 commit into from
Feb 1, 2025

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@dependabot dependabot bot commented on behalf of github Feb 1, 2025

Bumps the poetry-dependencies group with 20 updates:

Package From To
numpy 2.2.1 2.2.2
scipy 1.14.1 1.15.1
biopython 1.84 1.85
pygments 2.18.0 2.19.1
black 24.10.0 25.1.0
pre-commit 4.0.1 4.1.0
ruff 0.8.4 0.9.4
sphinx-autodoc-typehints 2.5.0 3.0.1
anyio 4.7.0 4.8.0
certifi 2024.12.14 2025.1.31
executing 2.1.0 2.2.0
filelock 3.16.1 3.17.0
identify 2.6.4 2.6.6
ipython 8.31.0 8.32.0
prompt-toolkit 3.0.48 3.0.50
ruamel-yaml 0.18.7 0.18.10
starlette 0.45.1 0.45.3
virtualenv 20.28.0 20.29.1
watchfiles 1.0.3 1.0.4
websockets 14.1 14.2

Updates numpy from 2.2.1 to 2.2.2

Release notes

Sourced from numpy's releases.

2.2.2 (Jan 18, 2025)

NumPy 2.2.2 Release Notes

NumPy 2.2.2 is a patch release that fixes bugs found after the 2.2.1 release. The number of typing fixes/updates is notable. This release supports Python versions 3.10-3.13.

Contributors

A total of 8 people contributed to this release. People with a "+" by their names contributed a patch for the first time.

  • Alicia Boya García +
  • Charles Harris
  • Joren Hammudoglu
  • Kai Germaschewski +
  • Nathan Goldbaum
  • PTUsumit +
  • Rohit Goswami
  • Sebastian Berg

Pull requests merged

A total of 16 pull requests were merged for this release.

  • #28050: MAINT: Prepare 2.2.x for further development
  • #28055: TYP: fix void arrays not accepting str keys in __setitem__
  • #28066: TYP: fix unnecessarily broad integer binop return types (#28065)
  • #28112: TYP: Better ndarray binop return types for float64 &...
  • #28113: TYP: Return the correct bool from issubdtype
  • #28114: TYP: Always accept date[time] in the datetime64 constructor
  • #28120: BUG: Fix auxdata initialization in ufunc slow path
  • #28131: BUG: move reduction initialization to ufunc initialization
  • #28132: TYP: Fix interp to accept and return scalars
  • #28137: BUG: call PyType_Ready in f2py to avoid data races
  • #28145: BUG: remove unnecessary call to PyArray_UpdateFlags
  • #28160: BUG: Avoid data race in PyArray_CheckFromAny_int
  • #28175: BUG: Fix f2py directives and --lower casing
  • #28176: TYP: Fix overlapping overloads issue in 2->1 ufuncs
  • #28177: TYP: preserve shape-type in ndarray.astype()
  • #28178: TYP: Fix missing and spurious top-level exports

Checksums

MD5

749cb2adf8043551aae22bbf0ed3130a  numpy-2.2.2-cp310-cp310-macosx_10_9_x86_64.whl
bc79fa2e44316b7ce9bacb48a993ed91  numpy-2.2.2-cp310-cp310-macosx_11_0_arm64.whl
c6b2caa2bbb645b5950dccb77efb1dbb  numpy-2.2.2-cp310-cp310-macosx_14_0_arm64.whl
8c410efac169af880cacbbac8a731658  numpy-2.2.2-cp310-cp310-macosx_14_0_x86_64.whl

... (truncated)

Commits
  • fd8a68e Merge pull request #28184 from charris/prepare-2.2.2
  • 0d106a5 REL: Prepare for the NumPy 2.2.2 release [wheel build]
  • dfdd35a Merge pull request #28175 from charris/backport-28056
  • e4517a8 Merge pull request #28176 from charris/backport-28168
  • 2c0432b Merge pull request #28178 from charris/backport-28170
  • 2230a08 Merge pull request #28177 from charris/backport-28169
  • b04e32c TYP: Fix missing and spurious top-level exports
  • 6a5f537 TYP: preserve shape-type in ndarray.astype()
  • f782790 TYP: Fix overlapping overloads issue in 2->1 ufuncs
  • a19acf1 BUG: Fix casing for f2py directives
  • Additional commits viewable in compare view

Updates scipy from 1.14.1 to 1.15.1

Release notes

Sourced from scipy's releases.

SciPy 1.15.1 Release Notes

SciPy 1.15.1 is a bug-fix release with no new features compared to 1.15.0. Importantly, an issue with the import of scipy.optimize breaking other packages has been fixed.

Authors

  • Name (commits)
  • Ralf Gommers (3)
  • Rohit Goswami (1)
  • Matt Haberland (2)
  • Tyler Reddy (7)
  • Daniel Schmitz (1)

A total of 5 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 1.15.0 Release Notes

SciPy 1.15.0 is the culmination of 6 months of hard work. It contains many new features, numerous bug-fixes, improved test coverage and better documentation. There have been a number of deprecations and API changes in this release, which are documented below. All users are encouraged to upgrade to this release, as there are a large number of bug-fixes and optimizations. Before upgrading, we recommend that users check that their own code does not use deprecated SciPy functionality (to do so, run your code with python -Wd and check for DeprecationWarning s). Our development attention will now shift to bug-fix releases on the 1.15.x branch, and on adding new features on the main branch.

This release requires Python 3.10-3.13 and NumPy 1.23.5 or greater.

Highlights of this release

  • Sparse arrays are now fully functional for 1-D and 2-D arrays. We recommend that all new code use sparse arrays instead of sparse matrices and that developers start to migrate their existing code from sparse matrix to sparse array: migration_to_sparray. Both sparse.linalg and sparse.csgraph work with either sparse matrix or sparse array and work internally with sparse array.
  • Sparse arrays now provide basic support for n-D arrays in the COO format

... (truncated)

Commits
  • df134ea REL: 1.15.1 rel commit [wheel build]
  • f939c19 Merge pull request #22296 from tylerjereddy/treddy_1.15.1_backports
  • 609bb3c DOC: PR 22296 revisions
  • 5bfd6a2 TST: stats.Normal: bump tolerance on test of logcdf (#22276)
  • f9a549c DOC: update 1.15.1 relnotes
  • 6f011d8 MAINT: Update highs subproject commit
  • 0ff01de TST: fix thread safety issue in interpolate.bsplines memmap test
  • 21c65ab BLD: fix some issues with undeclared internal build dependencies
  • 826759e MAINT: fix url for array-api-extra git submodule
  • 9af1fcd Merge pull request #22235 from tylerjereddy/treddy_prep_1.15.1
  • Additional commits viewable in compare view

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 pygments from 2.18.0 to 2.19.1

Release notes

Sourced from pygments's releases.

2.19.1

  • Updated lexers:

    • Ini: Fix quoted string regression introduced in 2.19.0
    • Lua: Fix a regression introduced in 2.19.0

2.19.0

  • New lexers:

  • Updated lexers:

    • BQN: Various improvements (#2789)
    • C#: Fix number highlighting (#986, #2727), add file keyword (#2726, #2805, #2806), add various other keywords (#2745, #2770)
    • CSS: Add revert (#2766, #2775)
    • Debian control: Add Change-By field (#2757)
    • Elip: Improve punctuation handling (#2651)
    • Igor: Add int (#2801)
    • Ini: Fix quoted strings with embedded comment characters (#2767, #2720)
    • Java: Support functions returning types containing a question mark (#2737)
    • JavaScript: Support private identiiers (#2729, #2671)
    • LLVM: Add splat, improve floating-point number parsing (#2755)
    • Lua: Improve variable detection, add built-in functions (#2829)
    • Macaulay2: Update to 1.24.11 (#2800)
    • PostgreSQL: Add more EXPLAIN keywords (#2785), handle / (#2774)
    • S-Lexer: Fix keywords (#2082, #2750)
    • TransactSQL: Fix single-line comments (#2717)
    • Turtle: Fix triple quoted strings (#2744, #2758)
    • Typst: Various improvements (#2724)
    • Various: Add ^ as an operator to Matlab, Octave and Scilab (#2798)
    • Vyper: Add staticcall and extcall (#2719)
  • Mark file extensions for HTML/XML+Evoque as aliases (#2743)
  • Add a color for Operator.Word to the rrt style (#2709)
  • Fix broken link in the documentation (#2803, #2804)
  • Drop executable bit where not needed (#2781)
  • Reduce Mojo priority relative to Python in ``analyze_text´` (#2771, #2772)
  • Fix documentation builds (#2712)
  • Match example file names to the lexer's name (#2713, #2715)

... (truncated)

Changelog

Sourced from pygments's changelog.

Version 2.19.1

(released January 6th, 2025)

  • Updated lexers:

    • Ini: Fix quoted string regression introduced in 2.19.0
    • Lua: Fix a regression introduced in 2.19.0

Version 2.19.0

(released January 5th, 2025)

  • New lexers:

  • Updated lexers:

    • BQN: Various improvements (#2789)
    • C#: Fix number highlighting (#986, #2727), add file keyword (#2726, #2805, #2806), add various other keywords (#2745, #2770)
    • CSS: Add revert (#2766, #2775)
    • Debian control: Add Change-By field (#2757)
    • Elip: Improve punctuation handling (#2651)
    • Igor: Add int (#2801)
    • Ini: Fix quoted strings with embedded comment characters (#2767, #2720)
    • Java: Support functions returning types containing a question mark (#2737)
    • JavaScript: Support private identiiers (#2729, #2671)
    • LLVM: Add splat, improve floating-point number parsing (#2755)
    • Lua: Improve variable detection, add built-in functions (#2829)
    • Macaulay2: Update to 1.24.11 (#2800)
    • PostgreSQL: Add more EXPLAIN keywords (#2785), handle / (#2774)
    • S-Lexer: Fix keywords (#2082, #2750)
    • TransactSQL: Fix single-line comments (#2717)
    • Turtle: Fix triple quoted strings (#2744, #2758)
    • Typst: Various improvements (#2724)
    • Various: Add ^ as an operator to Matlab, Octave and Scilab (#2798)
    • Vyper: Add staticcall and extcall (#2719)
  • Mark file extensions for HTML/XML+Evoque as aliases (#2743)

... (truncated)

Commits

Updates black from 24.10.0 to 25.1.0

Release notes

Sourced from black's releases.

25.1.0

Highlights

This release introduces the new 2025 stable style (#4558), stabilizing the following changes:

  • Normalize casing of Unicode escape characters in strings to lowercase (#2916)
  • Fix inconsistencies in whether certain strings are detected as docstrings (#4095)
  • Consistently add trailing commas to typed function parameters (#4164)
  • Remove redundant parentheses in if guards for case blocks (#4214)
  • Add parentheses to if clauses in case blocks when the line is too long (#4269)
  • Whitespace before # fmt: skip comments is no longer normalized (#4146)
  • Fix line length computation for certain expressions that involve the power operator (#4154)
  • Check if there is a newline before the terminating quotes of a docstring (#4185)
  • Fix type annotation spacing between * and more complex type variable tuple (#4440)

The following changes were not in any previous release:

  • Remove parentheses around sole list items (#4312)
  • Generic function definitions are now formatted more elegantly: parameters are split over multiple lines first instead of type parameter definitions (#4553)

Stable style

  • Fix formatting cells in IPython notebooks with magic methods and starting or trailing empty lines (#4484)
  • Fix crash when formatting with statements containing tuple generators/unpacking (#4538)

Preview style

  • Fix/remove string merging changing f-string quotes on f-strings with internal quotes (#4498)
  • Collapse multiple empty lines after an import into one (#4489)
  • Prevent string_processing and wrap_long_dict_values_in_parens from removing parentheses around long dictionary values (#4377)
  • Move wrap_long_dict_values_in_parens from the unstable to preview style (#4561)

Packaging

  • Store license identifier inside the License-Expression metadata field, see PEP 639. (#4479)

Performance

  • Speed up the is_fstring_start function in Black's tokenizer (#4541)

Integrations

  • If using stdin with --stdin-filename set to a force excluded path, stdin won't be

... (truncated)

Changelog

Sourced from black's changelog.

25.1.0

Highlights

This release introduces the new 2025 stable style (#4558), stabilizing the following changes:

  • Normalize casing of Unicode escape characters in strings to lowercase (#2916)
  • Fix inconsistencies in whether certain strings are detected as docstrings (#4095)
  • Consistently add trailing commas to typed function parameters (#4164)
  • Remove redundant parentheses in if guards for case blocks (#4214)
  • Add parentheses to if clauses in case blocks when the line is too long (#4269)
  • Whitespace before # fmt: skip comments is no longer normalized (#4146)
  • Fix line length computation for certain expressions that involve the power operator (#4154)
  • Check if there is a newline before the terminating quotes of a docstring (#4185)
  • Fix type annotation spacing between * and more complex type variable tuple (#4440)

The following changes were not in any previous release:

  • Remove parentheses around sole list items (#4312)
  • Generic function definitions are now formatted more elegantly: parameters are split over multiple lines first instead of type parameter definitions (#4553)

Stable style

  • Fix formatting cells in IPython notebooks with magic methods and starting or trailing empty lines (#4484)
  • Fix crash when formatting with statements containing tuple generators/unpacking (#4538)

Preview style

  • Fix/remove string merging changing f-string quotes on f-strings with internal quotes (#4498)
  • Collapse multiple empty lines after an import into one (#4489)
  • Prevent string_processing and wrap_long_dict_values_in_parens from removing parentheses around long dictionary values (#4377)
  • Move wrap_long_dict_values_in_parens from the unstable to preview style (#4561)

Packaging

  • Store license identifier inside the License-Expression metadata field, see PEP 639. (#4479)

Performance

  • Speed up the is_fstring_start function in Black's tokenizer (#4541)

Integrations

... (truncated)

Commits

Updates pre-commit from 4.0.1 to 4.1.0

Release notes

Sourced from pre-commit's releases.

pre-commit v4.1.0

Features

Fixes

Changelog

Sourced from pre-commit's changelog.

4.1.0 - 2025-01-20

Features

Fixes

Commits
  • b152e92 v4.1.0
  • c3125a4 Merge pull request #3389 from lorenzwalthert/dev-always-unset-renv
  • c2c061c fix: ensure env patch is applied for vanilla emulation
  • cd429db Merge pull request #3382 from pre-commit/pre-commit-ci-update-config
  • 9b9f8e2 [pre-commit.ci] pre-commit autoupdate
  • 86300a4 Merge pull request #3376 from pre-commit/r-gone
  • 77edad8 install r on ubuntu runners
  • 18b3939 Merge pull request #3375 from pre-commit/dotnet-tests-ubuntu-latest
  • 31cb945 Merge pull request #3374 from pre-commit/docker-image-tests-ubuntu-22-not-pre...
  • 28c3d81 update .net tests to use .net 8
  • Additional commits viewable in compare view

Updates ruff from 0.8.4 to 0.9.4

Release notes

Sourced from ruff's releases.

0.9.4

Release Notes

Preview features

  • [airflow] Extend airflow context parameter check for BaseOperator.execute (AIR302) (#15713)
  • [airflow] Update AIR302 to check for deprecated context keys (#15144)
  • [flake8-bandit] Permit suspicious imports within stub files (S4) (#15822)
  • [pylint] Do not trigger PLR6201 on empty collections (#15732)
  • [refurb] Do not emit diagnostic when loop variables are used outside loop body (FURB122) (#15757)
  • [ruff] Add support for more re patterns (RUF055) (#15764)
  • [ruff] Check for shadowed map before suggesting fix (RUF058) (#15790)
  • [ruff] Do not emit diagnostic when all arguments to zip() are variadic (RUF058) (#15744)
  • [ruff] Parenthesize fix when argument spans multiple lines for unnecessary-round (RUF057) (#15703)

Rule changes

  • Preserve quote style in generated code (#15726, #15778, #15794)
  • [flake8-bugbear] Exempt NewType calls where the original type is immutable (B008) (#15765)
  • [pylint] Honor banned top-level imports by TID253 in PLC0415. (#15628)
  • [pyupgrade] Ignore is_typeddict and TypedDict for deprecated-import (UP035) (#15800)

CLI

  • Fix formatter warning message for flake8-quotes option (#15788)
  • Implement tab autocomplete for ruff config (#15603)

Bug fixes

  • [flake8-comprehensions] Do not emit unnecessary-map diagnostic when lambda has different arity (C417) (#15802)
  • [flake8-comprehensions] Parenthesize sorted when needed for unnecessary-call-around-sorted (C413) (#15825)
  • [pyupgrade] Handle end-of-line comments for quoted-annotation (UP037) (#15824)

Documentation

  • Add missing config docstrings (#15803)
  • Add references to trio.run_process and anyio.run_process (#15761)
  • Use uv init --lib in tutorial (#15718)

Contributors

... (truncated)

Changelog

Sourced from ruff's changelog.

0.9.4

Preview features

  • [airflow] Extend airflow context parameter check for BaseOperator.execute (AIR302) (#15713)
  • [airflow] Update AIR302 to check for deprecated context keys (#15144)
  • [flake8-bandit] Permit suspicious imports within stub files (S4) (#15822)
  • [pylint] Do not trigger PLR6201 on empty collections (#15732)
  • [refurb] Do not emit diagnostic when loop variables are used outside loop body (FURB122) (#15757)
  • [ruff] Add support for more re patterns (RUF055) (#15764)
  • [ruff] Check for shadowed map before suggesting fix (RUF058) (#15790)
  • [ruff] Do not emit diagnostic when all arguments to zip() are variadic (RUF058) (#15744)
  • [ruff] Parenthesize fix when argument spans multiple lines for unnecessary-round (RUF057) (#15703)

Rule changes

  • Preserve quote style in generated code (#15726, #15778, #15794)
  • [flake8-bugbear] Exempt NewType calls where the original type is immutable (B008) (#15765)
  • [pylint] Honor banned top-level imports by TID253 in PLC0415. (#15628)
  • [pyupgrade] Ignore is_typeddict and TypedDict for deprecated-import (UP035) (#15800)

CLI

  • Fix formatter warning message for flake8-quotes option (#15788)
  • Implement tab autocomplete for ruff config (#15603)

Bug fixes

  • [flake8-comprehensions] Do not emit unnecessary-map diagnostic when lambda has different arity (C417) (#15802)
  • [flake8-comprehensions] Parenthesize sorted when needed for unnecessary-call-around-sorted (C413) (#15825)
  • [pyupgrade] Handle end-of-line comments for quoted-annotation (UP037) (#15824)

Documentation

  • Add missing config docstrings (#15803)
  • Add references to trio.run_process and anyio.run_process (#15761)
  • Use uv init --lib in tutorial (#15718)

0.9.3

Preview features

  • [airflow] Argument fail_stop in DAG has been renamed as fail_fast (AIR302) (#15633)
  • [airflow] Extend AIR303 with more symbols (#15611)
  • [flake8-bandit] Report all references to suspicious functions (S3) (#15541)
  • [flake8-pytest-style] Do not emit diagnostics for empty for loops (PT012, PT031) (#15542)
  • [flake8-simplify] Avoid double negations (SIM103) (#15562)
  • [pyflakes] Fix infinite loop with unused local import in __init__.py (F401) (#15517)
  • [pylint] Do not report methods with only one EM101-compatible raise (PLR6301) (#15507)
  • [pylint] Implement redefined-slots-in-subclass (W0244) (#9640)

... (truncated)

Commits
  • 854ab03 Bump version to 0.9.4 (#15831)
  • b0b8b06 Remove semicolon after TypeScript interface definition (#15827)
  • 451f251 [red-knot] Clarify behavior when redeclaring base class attributes (#15826)
  • 13cf3e6 [flake8-comprehensions] Parenthesize sorted when needed for `unnecessary-...
  • 56f956a [pyupgrade] Handle end-of-line comments for quoted-annotation (UP037) (...
  • 7a10a40 [flake8-bandit] Permit suspicious imports within stub files (S4) (#15822)
  • 3125332 [red-knot] Format mdtest snippets with the latest version of black (#15819)
  • 15d886a [red-knot] Consider all definitions after terminal statements unreachable (#1...
  • e1c9d10 [flake8-comprehensions] Do not emit unnecessary-map diagnostic when lambd...
  • 23c9884 Preserve quotes in generated f-strings (#15794)
  • Additional commits viewable in compare view

Updates sphinx-autodoc-typehints from 2.5.0 to 3.0.1

Release notes

Sourced from sphinx-autodoc-typehints's releases.

3.0.1

What's Changed

Full Changelog: tox-dev/sphinx-autodoc-typehints@3.0.0...3.0.1

3.0.0

What's Changed

New Contributors

Full Changelog: tox-dev/sphinx-autodoc-typehints@2.5.0...3.0.0

Commits

Updates anyio from 4.7.0 to 4.8.0

Release notes

Sourced from anyio's releases.

4.8.0

  • Added experimental support for running functions in subinterpreters on Python 3.13 and later
  • Added support for the copy(), copy_into(), move() and move_into() methods in anyio.Path, available in Python 3.14
  • Changed TaskGroup on asyncio to always spawn tasks non-eagerly, even if using a task factory created via asyncio.create_eager_task_factory(), to preserve expected Trio-like task scheduling semantics (PR by @​agronholm and @​graingert)
  • Configure SO_RCVBUF, SO_SNDBUF and TCP_NODELAY on the selector thread waker socket pair (this should improve the performance of wait_readable() and wait_writable() when using the ProactorEventLoop) (#836; PR by @​graingert)
  • Fixed AssertionError when using nest-asyncio (#840)Description has been truncated

@dependabot
Bump the poetry-dependencies group with 20 updates
72c3446 
Bumps the poetry-dependencies group with 20 updates:

| Package | From | To |
| --- | --- | --- |
| [numpy](https://github.com/numpy/numpy) | `2.2.1` | `2.2.2` |
| [scipy](https://github.com/scipy/scipy) | `1.14.1` | `1.15.1` |
| [biopython](https://github.com/biopython/biopython) | `1.84` | `1.85` |
| [pygments](https://github.com/pygments/pygments) | `2.18.0` | `2.19.1` |
| [black](https://github.com/psf/black) | `24.10.0` | `25.1.0` |
| [pre-commit](https://github.com/pre-commit/pre-commit) | `4.0.1` | `4.1.0` |
| [ruff](https://github.com/astral-sh/ruff) | `0.8.4` | `0.9.4` |
| [sphinx-autodoc-typehints](https://github.com/tox-dev/sphinx-autodoc-typehints) | `2.5.0` | `3.0.1` |
| [anyio](https://github.com/agronholm/anyio) | `4.7.0` | `4.8.0` |
| [certifi](https://github.com/certifi/python-certifi) | `2024.12.14` | `2025.1.31` |
| [executing](https://github.com/alexmojaki/executing) | `2.1.0` | `2.2.0` |
| [filelock](https://github.com/tox-dev/py-filelock) | `3.16.1` | `3.17.0` |
| [identify](https://github.com/pre-commit/identify) | `2.6.4` | `2.6.6` |
| [ipython](https://github.com/ipython/ipython) | `8.31.0` | `8.32.0` |
| [prompt-toolkit](https://github.com/prompt-toolkit/python-prompt-toolkit) | `3.0.48` | `3.0.50` |
| ruamel-yaml | `0.18.7` | `0.18.10` |
| [starlette](https://github.com/encode/starlette) | `0.45.1` | `0.45.3` |
| [virtualenv](https://github.com/pypa/virtualenv) | `20.28.0` | `20.29.1` |
| [watchfiles](https://github.com/samuelcolvin/watchfiles) | `1.0.3` | `1.0.4` |
| [websockets](https://github.com/python-websockets/websockets) | `14.1` | `14.2` |


Updates `numpy` from 2.2.1 to 2.2.2
- [Release notes](https://github.com/numpy/numpy/releases)
- [Changelog](https://github.com/numpy/numpy/blob/main/doc/RELEASE_WALKTHROUGH.rst)
- [Commits](numpy/numpy@v2.2.1...v2.2.2)

Updates `scipy` from 1.14.1 to 1.15.1
- [Release notes](https://github.com/scipy/scipy/releases)
- [Commits](scipy/scipy@v1.14.1...v1.15.1)

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 `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 `black` from 24.10.0 to 25.1.0
- [Release notes](https://github.com/psf/black/releases)
- [Changelog](https://github.com/psf/black/blob/main/CHANGES.md)
- [Commits](psf/black@24.10.0...25.1.0)

Updates `pre-commit` from 4.0.1 to 4.1.0
- [Release notes](https://github.com/pre-commit/pre-commit/releases)
- [Changelog](https://github.com/pre-commit/pre-commit/blob/main/CHANGELOG.md)
- [Commits](pre-commit/pre-commit@v4.0.1...v4.1.0)

Updates `ruff` from 0.8.4 to 0.9.4
- [Release notes](https://github.com/astral-sh/ruff/releases)
- [Changelog](https://github.com/astral-sh/ruff/blob/main/CHANGELOG.md)
- [Commits](astral-sh/ruff@0.8.4...0.9.4)

Updates `sphinx-autodoc-typehints` from 2.5.0 to 3.0.1
- [Release notes](https://github.com/tox-dev/sphinx-autodoc-typehints/releases)
- [Commits](tox-dev/sphinx-autodoc-typehints@2.5.0...3.0.1)

Updates `anyio` from 4.7.0 to 4.8.0
- [Release notes](https://github.com/agronholm/anyio/releases)
- [Changelog](https://github.com/agronholm/anyio/blob/master/docs/versionhistory.rst)
- [Commits](agronholm/anyio@4.7.0...4.8.0)

Updates `certifi` from 2024.12.14 to 2025.1.31
- [Commits](certifi/python-certifi@2024.12.14...2025.01.31)

Updates `executing` from 2.1.0 to 2.2.0
- [Release notes](https://github.com/alexmojaki/executing/releases)
- [Commits](alexmojaki/executing@v2.1.0...v2.2.0)

Updates `filelock` from 3.16.1 to 3.17.0
- [Release notes](https://github.com/tox-dev/py-filelock/releases)
- [Changelog](https://github.com/tox-dev/filelock/blob/main/docs/changelog.rst)
- [Commits](tox-dev/filelock@3.16.1...3.17.0)

Updates `identify` from 2.6.4 to 2.6.6
- [Commits](pre-commit/identify@v2.6.4...v2.6.6)

Updates `ipython` from 8.31.0 to 8.32.0
- [Release notes](https://github.com/ipython/ipython/releases)
- [Commits](ipython/ipython@8.31.0...8.32.0)

Updates `prompt-toolkit` from 3.0.48 to 3.0.50
- [Release notes](https://github.com/prompt-toolkit/python-prompt-toolkit/releases)
- [Changelog](https://github.com/prompt-toolkit/python-prompt-toolkit/blob/master/CHANGELOG)
- [Commits](prompt-toolkit/python-prompt-toolkit@3.0.48...3.0.50)

Updates `ruamel-yaml` from 0.18.7 to 0.18.10

Updates `starlette` from 0.45.1 to 0.45.3
- [Release notes](https://github.com/encode/starlette/releases)
- [Changelog](https://github.com/encode/starlette/blob/master/docs/release-notes.md)
- [Commits](encode/starlette@0.45.1...0.45.3)

Updates `virtualenv` from 20.28.0 to 20.29.1
- [Release notes](https://github.com/pypa/virtualenv/releases)
- [Changelog](https://github.com/pypa/virtualenv/blob/main/docs/changelog.rst)
- [Commits](pypa/virtualenv@20.28.0...20.29.1)

Updates `watchfiles` from 1.0.3 to 1.0.4
- [Release notes](https://github.com/samuelcolvin/watchfiles/releases)
- [Commits](samuelcolvin/watchfiles@v1.0.3...v1.0.4)

Updates `websockets` from 14.1 to 14.2
- [Release notes](https://github.com/python-websockets/websockets/releases)
- [Commits](python-websockets/websockets@14.1...14.2)

---
updated-dependencies:
- dependency-name: numpy
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: poetry-dependencies
- dependency-name: scipy
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: poetry-dependencies
- dependency-name: biopython
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: poetry-dependencies
- dependency-name: pygments
  dependency-type: direct:development
  update-type: version-update:semver-minor
  dependency-group: poetry-dependencies
- dependency-name: black
  dependency-type: direct:development
  update-type: version-update:semver-major
  dependency-group: poetry-dependencies
- dependency-name: pre-commit
  dependency-type: direct:development
  update-type: version-update:semver-minor
  dependency-group: poetry-dependencies
- dependency-name: ruff
  dependency-type: direct:development
  update-type: version-update:semver-minor
  dependency-group: poetry-dependencies
- dependency-name: sphinx-autodoc-typehints
  dependency-type: direct:development
  update-type: version-update:semver-major
  dependency-group: poetry-dependencies
- dependency-name: anyio
  dependency-type: indirect
  update-type: version-update:semver-minor
  dependency-group: poetry-dependencies
- dependency-name: certifi
  dependency-type: indirect
  update-type: version-update:semver-major
  dependency-group: poetry-dependencies
- dependency-name: executing
  dependency-type: indirect
  update-type: version-update:semver-minor
  dependency-group: poetry-dependencies
- dependency-name: filelock
  dependency-type: indirect
  update-type: version-update:semver-minor
  dependency-group: poetry-dependencies
- dependency-name: identify
  dependency-type: indirect
  update-type: version-update:semver-patch
  dependency-group: poetry-dependencies
- dependency-name: ipython
  dependency-type: indirect
  update-type: version-update:semver-minor
  dependency-group: poetry-dependencies
- dependency-name: prompt-toolkit
  dependency-type: indirect
  update-type: version-update:semver-patch
  dependency-group: poetry-dependencies
- dependency-name: ruamel-yaml
  dependency-type: indirect
  update-type: version-update:semver-patch
  dependency-group: poetry-dependencies
- dependency-name: starlette
  dependency-type: indirect
  update-type: version-update:semver-patch
  dependency-group: poetry-dependencies
- dependency-name: virtualenv
  dependency-type: indirect
  update-type: version-update:semver-minor
  dependency-group: poetry-dependencies
- dependency-name: watchfiles
  dependency-type: indirect
  update-type: version-update:semver-patch
  dependency-group: poetry-dependencies
- dependency-name: websockets
  dependency-type: indirect
  update-type: version-update:semver-minor
  dependency-group: poetry-dependencies
...

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 Feb 1, 2025
@semenko semenko merged commit 563baec into main Feb 1, 2025
11 of 12 checks passed
@semenko semenko deleted the dependabot/pip/poetry-dependencies-165d16a09c branch February 1, 2025 12:14
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