From d75d932a7bef422d4623b714b335cdaf4f612468 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 2 Feb 2026 04:35:41 +0000 Subject: [PATCH] Bump the py-updates group across 1 directory with 85 updates Bumps the py-updates group with 85 updates in the / directory: | Package | From | To | | --- | --- | --- | | [awscli](https://github.com/aws/aws-cli) | `1.40.17` | `1.44.29` | | [polars](https://github.com/pola-rs/polars) | `1.28.1` | `1.37.1` | | [requests](https://github.com/psf/requests) | `2.32.3` | `2.32.5` | | [biopython](https://github.com/biopython/biopython) | `1.85` | `1.86` | | [boto3](https://github.com/boto/boto3) | `1.38.18` | `1.42.39` | | [botocore](https://github.com/boto/botocore) | `1.38.18` | `1.42.39` | | [certifi](https://github.com/certifi/python-certifi) | `2025.4.26` | `2026.1.4` | | [charset-normalizer](https://github.com/jawah/charset_normalizer) | `3.4.2` | `3.4.4` | | [cloudpathlib](https://github.com/drivendataorg/cloudpathlib) | `0.21.1` | `0.23.0` | | [docutils](https://github.com/rtfd/recommonmark) | `0.19` | `0.22.4` | | [idna](https://github.com/kjd/idna) | `3.10` | `3.11` | | [jellyfish](https://jellyfish.jpt.sh/) | `1.2.0` | `1.2.1` | | [jmespath](https://github.com/jmespath/jmespath.py) | `1.0.1` | `1.1.0` | | [markdown-it-py](https://github.com/executablebooks/markdown-it-py) | `3.0.0` | `4.0.0` | | [numpy](https://github.com/numpy/numpy) | `2.2.5` | `2.4.2` | | [pandas](https://github.com/pandas-dev/pandas) | `2.2.3` | `3.0.0` | | [pyarrow](https://github.com/apache/arrow) | `20.0.0` | `23.0.0` | | [pyasn1](https://github.com/pyasn1/pyasn1) | `0.6.1` | `0.6.2` | | [pygments](https://github.com/pygments/pygments) | `2.19.1` | `2.19.2` | | [pyyaml](https://github.com/yaml/pyyaml) | `6.0.2` | `6.0.3` | | [rich](https://github.com/Textualize/rich) | `14.0.0` | `14.3.2` | | [rsa](https://github.com/sybrenstuvel/python-rsa) | `4.7.2` | `4.9.1` | | [s3transfer](https://github.com/boto/s3transfer) | `0.12.0` | `0.16.0` | | [structlog](https://github.com/hynek/structlog) | `25.3.0` | `25.5.0` | | [tqdm](https://github.com/tqdm/tqdm) | `4.67.1` | `4.67.2` | | [tzdata](https://github.com/python/tzdata) | `2025.2` | `2025.3` | | [urllib3](https://github.com/urllib3/urllib3) | `2.4.0` | `2.6.3` | | [zstandard](https://github.com/indygreg/python-zstandard) | `0.23.0` | `0.25.0` | | [boto3-stubs](https://github.com/youtype/mypy_boto3_builder) | `1.38.18` | `1.42.39` | | [botocore-stubs](https://github.com/youtype/botocore-stubs) | `1.38.18` | `1.42.39` | | [cffi](https://github.com/python-cffi/cffi) | `1.17.1` | `2.0.0` | | [coverage](https://github.com/coveragepy/coveragepy) | `7.8.0` | `7.13.2` | | [cryptography](https://github.com/pyca/cryptography) | `44.0.3` | `46.0.4` | | [freezegun](https://github.com/spulec/freezegun) | `1.5.1` | `1.5.5` | | [iniconfig](https://github.com/pytest-dev/iniconfig) | `2.1.0` | `2.3.0` | | [markupsafe](https://github.com/pallets/markupsafe) | `3.0.2` | `3.0.3` | | [moto](https://github.com/getmoto/moto) | `5.1.4` | `5.1.20` | | [mypy](https://github.com/python/mypy) | `1.15.0` | `1.19.1` | | [mypy-boto3-s3](https://github.com/youtype/mypy_boto3_builder) | `1.38.0` | `1.42.37` | | [packaging](https://github.com/pypa/packaging) | `25.0` | `26.0` | | [pycparser](https://github.com/eliben/pycparser) | `2.22` | `3.0` | | [pytest](https://github.com/pytest-dev/pytest) | `8.3.5` | `9.0.2` | | [pytest-mock](https://github.com/pytest-dev/pytest-mock) | `3.14.0` | `3.15.1` | | [responses](https://github.com/getsentry/responses) | `0.25.7` | `0.25.8` | | [ruff](https://github.com/astral-sh/ruff) | `0.11.10` | `0.14.14` | | [types-awscrt](https://github.com/youtype/types-awscrt) | `0.27.2` | `0.31.1` | | [types-requests](https://github.com/typeshed-internal/stub_uploader) | `2.32.0.20250515` | `2.32.4.20260107` | | [types-s3transfer](https://github.com/youtype/types-s3transfer) | `0.12.0` | `0.16.0` | | [typing-extensions](https://github.com/python/typing_extensions) | `4.13.2` | `4.15.0` | | [werkzeug](https://github.com/pallets/werkzeug) | `3.1.3` | `3.1.5` | | [xmltodict](https://github.com/martinblech/xmltodict) | `0.14.2` | `1.0.2` | | [alabaster](https://github.com/sphinx-doc/alabaster) | `0.7.16` | `1.0.0` | | [anyio](https://github.com/agronholm/anyio) | `4.9.0` | `4.12.1` | | [babel](https://github.com/python-babel/babel) | `2.17.0` | `2.18.0` | | [beautifulsoup4](https://www.crummy.com/software/BeautifulSoup/bs4/) | `4.13.4` | `4.14.3` | | [cachecontrol](https://github.com/psf/cachecontrol) | `0.14.3` | `0.14.4` | | [click](https://github.com/pallets/click) | `8.2.0` | `8.3.1` | | [contourpy](https://github.com/contourpy/contourpy) | `1.3.2` | `1.3.3` | | [filelock](https://github.com/tox-dev/py-filelock) | `3.18.0` | `3.20.3` | | [fonttools](https://github.com/fonttools/fonttools) | `4.58.0` | `4.61.1` | | [furo](https://github.com/pradyunsg/furo) | `2024.8.6` | `2025.12.19` | | [kiwisolver](https://github.com/nucleic/kiwi) | `1.4.8` | `1.4.9` | | [matplotlib](https://github.com/matplotlib/matplotlib) | `3.10.3` | `3.10.8` | | [mdit-py-plugins](https://github.com/executablebooks/mdit-py-plugins) | `0.4.2` | `0.5.0` | | [more-itertools](https://github.com/more-itertools/more-itertools) | `10.7.0` | `10.8.0` | | [msgpack](https://github.com/msgpack/msgpack-python) | `1.1.0` | `1.1.2` | | [myst-parser](https://github.com/executablebooks/MyST-Parser) | `4.0.1` | `5.0.0` | | [pillow](https://github.com/python-pillow/Pillow) | `11.2.1` | `12.1.0` | | [platformdirs](https://github.com/tox-dev/platformdirs) | `4.3.8` | `4.5.1` | | [pyparsing](https://github.com/pyparsing/pyparsing) | `3.2.3` | `3.3.2` | | ruamel-yaml | `0.18.10` | `0.19.1` | | ruamel-yaml-clib | `0.2.12` | `0.2.15` | | [soupsieve](https://github.com/facelessuser/soupsieve) | `2.7` | `2.8.3` | | [sphinx](https://github.com/sphinx-doc/sphinx) | `7.3.7` | `9.0.4` | | [sphinx-autobuild](https://github.com/sphinx-doc/sphinx-autobuild) | `2024.10.3` | `2025.8.25` | | [sphinx-autodoc-typehints](https://github.com/tox-dev/sphinx-autodoc-typehints) | `2.3.0` | `3.6.1` | | [sphinx-jinja2-compat](https://github.com/sphinx-toolbox/sphinx-jinja2-compat) | `0.3.0` | `0.4.1` | | [sphinx-prompt](https://github.com/sbrunner/sphinx-prompt) | `1.8.0` | `1.10.2` | | [sphinx-tabs](https://github.com/executablebooks/sphinx-tabs) | `3.4.5` | `3.4.7` | | [sphinx-toolbox](https://github.com/sphinx-toolbox/sphinx-toolbox) | `4.0.0` | `4.1.2` | | [sphinxext-opengraph](https://github.com/sphinx-doc/sphinxext-opengraph) | `0.10.0` | `0.13.0` | | [starlette](https://github.com/Kludex/starlette) | `0.46.2` | `0.52.1` | | [uvicorn](https://github.com/Kludex/uvicorn) | `0.34.2` | `0.40.0` | | [watchfiles](https://github.com/samuelcolvin/watchfiles) | `1.0.5` | `1.1.1` | | [websockets](https://github.com/python-websockets/websockets) | `15.0.1` | `16.0` | Updates `awscli` from 1.40.17 to 1.44.29 - [Release notes](https://github.com/aws/aws-cli/releases) - [Commits](https://github.com/aws/aws-cli/compare/1.40.17...1.44.29) Updates `polars` from 1.28.1 to 1.37.1 - [Release notes](https://github.com/pola-rs/polars/releases) - [Commits](https://github.com/pola-rs/polars/compare/py-1.28.1...py-1.37.1) Updates `requests` from 2.32.3 to 2.32.5 - [Release notes](https://github.com/psf/requests/releases) - [Changelog](https://github.com/psf/requests/blob/main/HISTORY.md) - [Commits](https://github.com/psf/requests/compare/v2.32.3...v2.32.5) Updates `biopython` from 1.85 to 1.86 - [Changelog](https://github.com/biopython/biopython/blob/master/NEWS.rst) - [Commits](https://github.com/biopython/biopython/commits) Updates `boto3` from 1.38.18 to 1.42.39 - [Release notes](https://github.com/boto/boto3/releases) - [Commits](https://github.com/boto/boto3/compare/1.38.18...1.42.39) Updates `botocore` from 1.38.18 to 1.42.39 - [Commits](https://github.com/boto/botocore/compare/1.38.18...1.42.39) Updates `certifi` from 2025.4.26 to 2026.1.4 - [Commits](https://github.com/certifi/python-certifi/compare/2025.04.26...2026.01.04) Updates `charset-normalizer` from 3.4.2 to 3.4.4 - [Release notes](https://github.com/jawah/charset_normalizer/releases) - [Changelog](https://github.com/jawah/charset_normalizer/blob/master/CHANGELOG.md) - [Commits](https://github.com/jawah/charset_normalizer/compare/3.4.2...3.4.4) Updates `cloudpathlib` from 0.21.1 to 0.23.0 - [Release notes](https://github.com/drivendataorg/cloudpathlib/releases) - [Changelog](https://github.com/drivendataorg/cloudpathlib/blob/master/HISTORY.md) - [Commits](https://github.com/drivendataorg/cloudpathlib/compare/v0.21.1...v0.23.0) Updates `docutils` from 0.19 to 0.22.4 - [Changelog](https://github.com/readthedocs/recommonmark/blob/master/CHANGELOG.md) - [Commits](https://github.com/rtfd/recommonmark/commits) Updates `idna` from 3.10 to 3.11 - [Release notes](https://github.com/kjd/idna/releases) - [Changelog](https://github.com/kjd/idna/blob/master/HISTORY.rst) - [Commits](https://github.com/kjd/idna/compare/v3.10...v3.11) Updates `jellyfish` from 1.2.0 to 1.2.1 Updates `jmespath` from 1.0.1 to 1.1.0 - [Changelog](https://github.com/jmespath/jmespath.py/blob/develop/CHANGELOG.rst) - [Commits](https://github.com/jmespath/jmespath.py/compare/1.0.1...1.1.0) Updates `markdown-it-py` from 3.0.0 to 4.0.0 - [Release notes](https://github.com/executablebooks/markdown-it-py/releases) - [Changelog](https://github.com/executablebooks/markdown-it-py/blob/master/CHANGELOG.md) - [Commits](https://github.com/executablebooks/markdown-it-py/compare/v3.0.0...v4.0.0) Updates `numpy` from 2.2.5 to 2.4.2 - [Release notes](https://github.com/numpy/numpy/releases) - [Changelog](https://github.com/numpy/numpy/blob/main/doc/RELEASE_WALKTHROUGH.rst) - [Commits](https://github.com/numpy/numpy/compare/v2.2.5...v2.4.2) Updates `pandas` from 2.2.3 to 3.0.0 - [Release notes](https://github.com/pandas-dev/pandas/releases) - [Commits](https://github.com/pandas-dev/pandas/compare/v2.2.3...v3.0.0) Updates `pyarrow` from 20.0.0 to 23.0.0 - [Release notes](https://github.com/apache/arrow/releases) - [Commits](https://github.com/apache/arrow/compare/apache-arrow-20.0.0...apache-arrow-23.0.0) Updates `pyasn1` from 0.6.1 to 0.6.2 - [Release notes](https://github.com/pyasn1/pyasn1/releases) - [Changelog](https://github.com/pyasn1/pyasn1/blob/main/CHANGES.rst) - [Commits](https://github.com/pyasn1/pyasn1/compare/v0.6.1...v0.6.2) Updates `pygments` from 2.19.1 to 2.19.2 - [Release notes](https://github.com/pygments/pygments/releases) - [Changelog](https://github.com/pygments/pygments/blob/master/CHANGES) - [Commits](https://github.com/pygments/pygments/compare/2.19.1...2.19.2) Updates `pyyaml` from 6.0.2 to 6.0.3 - [Release notes](https://github.com/yaml/pyyaml/releases) - [Changelog](https://github.com/yaml/pyyaml/blob/6.0.3/CHANGES) - [Commits](https://github.com/yaml/pyyaml/compare/6.0.2...6.0.3) Updates `rich` from 14.0.0 to 14.3.2 - [Release notes](https://github.com/Textualize/rich/releases) - [Changelog](https://github.com/Textualize/rich/blob/master/CHANGELOG.md) - [Commits](https://github.com/Textualize/rich/compare/v14.0.0...v14.3.2) Updates `rsa` from 4.7.2 to 4.9.1 - [Changelog](https://github.com/sybrenstuvel/python-rsa/blob/main/CHANGELOG.md) - [Commits](https://github.com/sybrenstuvel/python-rsa/commits) Updates `s3transfer` from 0.12.0 to 0.16.0 - [Changelog](https://github.com/boto/s3transfer/blob/develop/CHANGELOG.rst) - [Commits](https://github.com/boto/s3transfer/compare/0.12.0...0.16.0) Updates `structlog` from 25.3.0 to 25.5.0 - [Release notes](https://github.com/hynek/structlog/releases) - [Changelog](https://github.com/hynek/structlog/blob/main/CHANGELOG.md) - [Commits](https://github.com/hynek/structlog/compare/25.3.0...25.5.0) Updates `tqdm` from 4.67.1 to 4.67.2 - [Release notes](https://github.com/tqdm/tqdm/releases) - [Commits](https://github.com/tqdm/tqdm/compare/v4.67.1...v4.67.2) Updates `tzdata` from 2025.2 to 2025.3 - [Release notes](https://github.com/python/tzdata/releases) - [Changelog](https://github.com/python/tzdata/blob/master/NEWS.md) - [Commits](https://github.com/python/tzdata/compare/2025.2...2025.3) Updates `urllib3` from 2.4.0 to 2.6.3 - [Release notes](https://github.com/urllib3/urllib3/releases) - [Changelog](https://github.com/urllib3/urllib3/blob/main/CHANGES.rst) - [Commits](https://github.com/urllib3/urllib3/compare/2.4.0...2.6.3) Updates `zstandard` from 0.23.0 to 0.25.0 - [Release notes](https://github.com/indygreg/python-zstandard/releases) - [Changelog](https://github.com/indygreg/python-zstandard/blob/main/docs/news.rst) - [Commits](https://github.com/indygreg/python-zstandard/compare/0.23.0...0.25.0) Updates `boto3-stubs` from 1.38.18 to 1.42.39 - [Release notes](https://github.com/youtype/mypy_boto3_builder/releases) - [Commits](https://github.com/youtype/mypy_boto3_builder/commits) Updates `botocore-stubs` from 1.38.18 to 1.42.39 - [Release notes](https://github.com/youtype/botocore-stubs/releases) - [Commits](https://github.com/youtype/botocore-stubs/commits) Updates `cffi` from 1.17.1 to 2.0.0 - [Release notes](https://github.com/python-cffi/cffi/releases) - [Commits](https://github.com/python-cffi/cffi/compare/v1.17.1...v2.0.0) Updates `coverage` from 7.8.0 to 7.13.2 - [Release notes](https://github.com/coveragepy/coveragepy/releases) - [Changelog](https://github.com/coveragepy/coveragepy/blob/main/CHANGES.rst) - [Commits](https://github.com/coveragepy/coveragepy/compare/7.8.0...7.13.2) Updates `cryptography` from 44.0.3 to 46.0.4 - [Changelog](https://github.com/pyca/cryptography/blob/main/CHANGELOG.rst) - [Commits](https://github.com/pyca/cryptography/compare/44.0.3...46.0.4) Updates `freezegun` from 1.5.1 to 1.5.5 - [Release notes](https://github.com/spulec/freezegun/releases) - [Changelog](https://github.com/spulec/freezegun/blob/master/CHANGELOG) - [Commits](https://github.com/spulec/freezegun/compare/1.5.1...1.5.5) Updates `iniconfig` from 2.1.0 to 2.3.0 - [Release notes](https://github.com/pytest-dev/iniconfig/releases) - [Changelog](https://github.com/pytest-dev/iniconfig/blob/main/CHANGELOG) - [Commits](https://github.com/pytest-dev/iniconfig/compare/v2.1.0...v2.3.0) Updates `markupsafe` from 3.0.2 to 3.0.3 - [Release notes](https://github.com/pallets/markupsafe/releases) - [Changelog](https://github.com/pallets/markupsafe/blob/main/CHANGES.rst) - [Commits](https://github.com/pallets/markupsafe/compare/3.0.2...3.0.3) Updates `moto` from 5.1.4 to 5.1.20 - [Release notes](https://github.com/getmoto/moto/releases) - [Changelog](https://github.com/getmoto/moto/blob/master/CHANGELOG.md) - [Commits](https://github.com/getmoto/moto/compare/5.1.4...5.1.20) Updates `mypy` from 1.15.0 to 1.19.1 - [Changelog](https://github.com/python/mypy/blob/master/CHANGELOG.md) - [Commits](https://github.com/python/mypy/compare/v1.15.0...v1.19.1) Updates `mypy-boto3-s3` from 1.38.0 to 1.42.37 - [Release notes](https://github.com/youtype/mypy_boto3_builder/releases) - [Commits](https://github.com/youtype/mypy_boto3_builder/commits) Updates `packaging` from 25.0 to 26.0 - [Release notes](https://github.com/pypa/packaging/releases) - [Changelog](https://github.com/pypa/packaging/blob/main/CHANGELOG.rst) - [Commits](https://github.com/pypa/packaging/compare/25.0...26.0) Updates `pycparser` from 2.22 to 3.0 - [Release notes](https://github.com/eliben/pycparser/releases) - [Commits](https://github.com/eliben/pycparser/compare/release_v2.22...release_v3.00) Updates `pytest` from 8.3.5 to 9.0.2 - [Release notes](https://github.com/pytest-dev/pytest/releases) - [Changelog](https://github.com/pytest-dev/pytest/blob/main/CHANGELOG.rst) - [Commits](https://github.com/pytest-dev/pytest/compare/8.3.5...9.0.2) Updates `pytest-mock` from 3.14.0 to 3.15.1 - [Release notes](https://github.com/pytest-dev/pytest-mock/releases) - [Changelog](https://github.com/pytest-dev/pytest-mock/blob/main/CHANGELOG.rst) - [Commits](https://github.com/pytest-dev/pytest-mock/compare/v3.14.0...v3.15.1) Updates `responses` from 0.25.7 to 0.25.8 - [Release notes](https://github.com/getsentry/responses/releases) - [Changelog](https://github.com/getsentry/responses/blob/master/CHANGES) - [Commits](https://github.com/getsentry/responses/compare/0.25.7...0.25.8) Updates `ruff` from 0.11.10 to 0.14.14 - [Release notes](https://github.com/astral-sh/ruff/releases) - [Changelog](https://github.com/astral-sh/ruff/blob/main/CHANGELOG.md) - [Commits](https://github.com/astral-sh/ruff/compare/0.11.10...0.14.14) Updates `types-awscrt` from 0.27.2 to 0.31.1 - [Release notes](https://github.com/youtype/types-awscrt/releases) - [Commits](https://github.com/youtype/types-awscrt/commits) Updates `types-requests` from 2.32.0.20250515 to 2.32.4.20260107 - [Commits](https://github.com/typeshed-internal/stub_uploader/commits) Updates `types-s3transfer` from 0.12.0 to 0.16.0 - [Release notes](https://github.com/youtype/types-s3transfer/releases) - [Commits](https://github.com/youtype/types-s3transfer/commits) Updates `typing-extensions` from 4.13.2 to 4.15.0 - [Release notes](https://github.com/python/typing_extensions/releases) - [Changelog](https://github.com/python/typing_extensions/blob/main/CHANGELOG.md) - [Commits](https://github.com/python/typing_extensions/compare/4.13.2...4.15.0) Updates `werkzeug` from 3.1.3 to 3.1.5 - [Release notes](https://github.com/pallets/werkzeug/releases) - [Changelog](https://github.com/pallets/werkzeug/blob/main/CHANGES.rst) - [Commits](https://github.com/pallets/werkzeug/compare/3.1.3...3.1.5) Updates `xmltodict` from 0.14.2 to 1.0.2 - [Release notes](https://github.com/martinblech/xmltodict/releases) - [Changelog](https://github.com/martinblech/xmltodict/blob/master/CHANGELOG.md) - [Commits](https://github.com/martinblech/xmltodict/compare/v0.14.2...v1.0.2) Updates `alabaster` from 0.7.16 to 1.0.0 - [Release notes](https://github.com/sphinx-doc/alabaster/releases) - [Changelog](https://github.com/sphinx-doc/alabaster/blob/master/docs/changelog.rst) - [Commits](https://github.com/sphinx-doc/alabaster/compare/0.7.16...1.0.0) Updates `anyio` from 4.9.0 to 4.12.1 - [Release notes](https://github.com/agronholm/anyio/releases) - [Commits](https://github.com/agronholm/anyio/compare/4.9.0...4.12.1) Updates `babel` from 2.17.0 to 2.18.0 - [Release notes](https://github.com/python-babel/babel/releases) - [Changelog](https://github.com/python-babel/babel/blob/master/CHANGES.rst) - [Commits](https://github.com/python-babel/babel/compare/v2.17.0...v2.18.0) Updates `beautifulsoup4` from 4.13.4 to 4.14.3 Updates `cachecontrol` from 0.14.3 to 0.14.4 - [Release notes](https://github.com/psf/cachecontrol/releases) - [Changelog](https://github.com/psf/cachecontrol/blob/master/docs/release_notes.rst) - [Commits](https://github.com/psf/cachecontrol/compare/v0.14.3...v0.14.4) Updates `click` from 8.2.0 to 8.3.1 - [Release notes](https://github.com/pallets/click/releases) - [Changelog](https://github.com/pallets/click/blob/main/CHANGES.rst) - [Commits](https://github.com/pallets/click/compare/8.2.0...8.3.1) Updates `contourpy` from 1.3.2 to 1.3.3 - [Release notes](https://github.com/contourpy/contourpy/releases) - [Changelog](https://github.com/contourpy/contourpy/blob/main/docs/changelog.rst) - [Commits](https://github.com/contourpy/contourpy/compare/v1.3.2...v1.3.3) Updates `filelock` from 3.18.0 to 3.20.3 - [Release notes](https://github.com/tox-dev/py-filelock/releases) - [Changelog](https://github.com/tox-dev/filelock/blob/main/docs/changelog.rst) - [Commits](https://github.com/tox-dev/py-filelock/compare/3.18.0...3.20.3) Updates `fonttools` from 4.58.0 to 4.61.1 - [Release notes](https://github.com/fonttools/fonttools/releases) - [Changelog](https://github.com/fonttools/fonttools/blob/main/NEWS.rst) - [Commits](https://github.com/fonttools/fonttools/compare/4.58.0...4.61.1) Updates `furo` from 2024.8.6 to 2025.12.19 - [Release notes](https://github.com/pradyunsg/furo/releases) - [Changelog](https://github.com/pradyunsg/furo/blob/main/docs/changelog.md) - [Commits](https://github.com/pradyunsg/furo/compare/2024.08.06...2025.12.19) Updates `kiwisolver` from 1.4.8 to 1.4.9 - [Release notes](https://github.com/nucleic/kiwi/releases) - [Changelog](https://github.com/nucleic/kiwi/blob/main/releasenotes.rst) - [Commits](https://github.com/nucleic/kiwi/compare/1.4.8...1.4.9) Updates `matplotlib` from 3.10.3 to 3.10.8 - [Release notes](https://github.com/matplotlib/matplotlib/releases) - [Commits](https://github.com/matplotlib/matplotlib/compare/v3.10.3...v3.10.8) Updates `mdit-py-plugins` from 0.4.2 to 0.5.0 - [Release notes](https://github.com/executablebooks/mdit-py-plugins/releases) - [Changelog](https://github.com/executablebooks/mdit-py-plugins/blob/master/CHANGELOG.md) - [Commits](https://github.com/executablebooks/mdit-py-plugins/compare/v0.4.2...v0.5.0) Updates `more-itertools` from 10.7.0 to 10.8.0 - [Release notes](https://github.com/more-itertools/more-itertools/releases) - [Commits](https://github.com/more-itertools/more-itertools/compare/v10.7.0...v10.8.0) Updates `msgpack` from 1.1.0 to 1.1.2 - [Release notes](https://github.com/msgpack/msgpack-python/releases) - [Changelog](https://github.com/msgpack/msgpack-python/blob/main/ChangeLog.rst) - [Commits](https://github.com/msgpack/msgpack-python/compare/v1.1.0...v1.1.2) Updates `myst-parser` from 4.0.1 to 5.0.0 - [Release notes](https://github.com/executablebooks/MyST-Parser/releases) - [Changelog](https://github.com/executablebooks/MyST-Parser/blob/master/CHANGELOG.md) - [Commits](https://github.com/executablebooks/MyST-Parser/compare/v4.0.1...v5.0.0) Updates `pillow` from 11.2.1 to 12.1.0 - [Release notes](https://github.com/python-pillow/Pillow/releases) - [Changelog](https://github.com/python-pillow/Pillow/blob/main/CHANGES.rst) - [Commits](https://github.com/python-pillow/Pillow/compare/11.2.1...12.1.0) Updates `platformdirs` from 4.3.8 to 4.5.1 - [Release notes](https://github.com/tox-dev/platformdirs/releases) - [Changelog](https://github.com/tox-dev/platformdirs/blob/main/CHANGES.rst) - [Commits](https://github.com/tox-dev/platformdirs/compare/4.3.8...4.5.1) Updates `pyparsing` from 3.2.3 to 3.3.2 - [Release notes](https://github.com/pyparsing/pyparsing/releases) - [Changelog](https://github.com/pyparsing/pyparsing/blob/master/CHANGES) - [Commits](https://github.com/pyparsing/pyparsing/compare/3.2.3...3.3.2) Updates `ruamel-yaml` from 0.18.10 to 0.19.1 Updates `ruamel-yaml-clib` from 0.2.12 to 0.2.15 Updates `soupsieve` from 2.7 to 2.8.3 - [Release notes](https://github.com/facelessuser/soupsieve/releases) - [Commits](https://github.com/facelessuser/soupsieve/compare/2.7...2.8.3) Updates `sphinx` from 7.3.7 to 9.0.4 - [Release notes](https://github.com/sphinx-doc/sphinx/releases) - [Changelog](https://github.com/sphinx-doc/sphinx/blob/v9.0.4/CHANGES.rst) - [Commits](https://github.com/sphinx-doc/sphinx/compare/v7.3.7...v9.0.4) Updates `sphinx-autobuild` from 2024.10.3 to 2025.8.25 - [Release notes](https://github.com/sphinx-doc/sphinx-autobuild/releases) - [Changelog](https://github.com/sphinx-doc/sphinx-autobuild/blob/main/NEWS.rst) - [Commits](https://github.com/sphinx-doc/sphinx-autobuild/compare/2024.10.03...2025.08.25) Updates `sphinx-autodoc-typehints` from 2.3.0 to 3.6.1 - [Release notes](https://github.com/tox-dev/sphinx-autodoc-typehints/releases) - [Commits](https://github.com/tox-dev/sphinx-autodoc-typehints/compare/2.3.0...3.6.1) Updates `sphinx-jinja2-compat` from 0.3.0 to 0.4.1 - [Release notes](https://github.com/sphinx-toolbox/sphinx-jinja2-compat/releases) - [Commits](https://github.com/sphinx-toolbox/sphinx-jinja2-compat/compare/v0.3.0...v0.4.1) Updates `sphinx-prompt` from 1.8.0 to 1.10.2 - [Release notes](https://github.com/sbrunner/sphinx-prompt/releases) - [Commits](https://github.com/sbrunner/sphinx-prompt/compare/1.8.0...1.10.2) Updates `sphinx-tabs` from 3.4.5 to 3.4.7 - [Release notes](https://github.com/executablebooks/sphinx-tabs/releases) - [Changelog](https://github.com/executablebooks/sphinx-tabs/blob/master/CHANGELOG.md) - [Commits](https://github.com/executablebooks/sphinx-tabs/compare/v3.4.5...v3.4.7) Updates `sphinx-toolbox` from 4.0.0 to 4.1.2 - [Release notes](https://github.com/sphinx-toolbox/sphinx-toolbox/releases) - [Changelog](https://github.com/sphinx-toolbox/sphinx-toolbox/blob/master/doc-source/changelog.rst) - [Commits](https://github.com/sphinx-toolbox/sphinx-toolbox/compare/v4.0.0...v4.1.2) Updates `sphinxext-opengraph` from 0.10.0 to 0.13.0 - [Release notes](https://github.com/sphinx-doc/sphinxext-opengraph/releases) - [Commits](https://github.com/sphinx-doc/sphinxext-opengraph/compare/v0.10.0...v0.13.0) Updates `starlette` from 0.46.2 to 0.52.1 - [Release notes](https://github.com/Kludex/starlette/releases) - [Changelog](https://github.com/Kludex/starlette/blob/main/docs/release-notes.md) - [Commits](https://github.com/Kludex/starlette/compare/0.46.2...0.52.1) Updates `uvicorn` from 0.34.2 to 0.40.0 - [Release notes](https://github.com/Kludex/uvicorn/releases) - [Changelog](https://github.com/Kludex/uvicorn/blob/main/docs/release-notes.md) - [Commits](https://github.com/Kludex/uvicorn/compare/0.34.2...0.40.0) Updates `watchfiles` from 1.0.5 to 1.1.1 - [Release notes](https://github.com/samuelcolvin/watchfiles/releases) - [Commits](https://github.com/samuelcolvin/watchfiles/compare/v1.0.5...v1.1.1) Updates `websockets` from 15.0.1 to 16.0 - [Release notes](https://github.com/python-websockets/websockets/releases) - [Commits](https://github.com/python-websockets/websockets/compare/15.0.1...16.0) --- updated-dependencies: - dependency-name: awscli dependency-version: 1.44.29 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: py-updates - dependency-name: polars dependency-version: 1.37.1 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: py-updates - dependency-name: requests dependency-version: 2.32.5 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: py-updates - dependency-name: biopython dependency-version: '1.86' dependency-type: direct:production update-type: version-update:semver-minor dependency-group: py-updates - dependency-name: boto3 dependency-version: 1.42.39 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: py-updates - dependency-name: botocore dependency-version: 1.42.39 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: py-updates - dependency-name: certifi dependency-version: 2026.1.4 dependency-type: direct:production update-type: version-update:semver-major dependency-group: py-updates - dependency-name: charset-normalizer dependency-version: 3.4.4 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: py-updates - dependency-name: cloudpathlib dependency-version: 0.23.0 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: py-updates - dependency-name: docutils dependency-version: 0.22.4 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: py-updates - dependency-name: idna dependency-version: '3.11' dependency-type: direct:production update-type: version-update:semver-minor dependency-group: py-updates - dependency-name: jellyfish dependency-version: 1.2.1 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: py-updates - dependency-name: jmespath dependency-version: 1.1.0 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: py-updates - dependency-name: markdown-it-py dependency-version: 4.0.0 dependency-type: direct:production update-type: version-update:semver-major dependency-group: py-updates - dependency-name: numpy dependency-version: 2.4.2 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: py-updates - dependency-name: pandas dependency-version: 3.0.0 dependency-type: direct:production update-type: version-update:semver-major dependency-group: py-updates - dependency-name: pyarrow dependency-version: 23.0.0 dependency-type: direct:production update-type: version-update:semver-major dependency-group: py-updates - dependency-name: pyasn1 dependency-version: 0.6.2 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: py-updates - dependency-name: pygments dependency-version: 2.19.2 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: py-updates - dependency-name: pyyaml dependency-version: 6.0.3 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: py-updates - dependency-name: rich dependency-version: 14.3.2 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: py-updates - dependency-name: rsa dependency-version: 4.9.1 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: py-updates - dependency-name: s3transfer dependency-version: 0.16.0 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: py-updates - dependency-name: structlog dependency-version: 25.5.0 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: py-updates - dependency-name: tqdm dependency-version: 4.67.2 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: py-updates - dependency-name: tzdata dependency-version: '2025.3' dependency-type: direct:production update-type: version-update:semver-minor dependency-group: py-updates - dependency-name: urllib3 dependency-version: 2.6.3 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: py-updates - dependency-name: zstandard dependency-version: 0.25.0 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: py-updates - dependency-name: boto3-stubs dependency-version: 1.42.39 dependency-type: direct:development update-type: version-update:semver-minor dependency-group: py-updates - dependency-name: botocore-stubs dependency-version: 1.42.39 dependency-type: direct:development update-type: version-update:semver-minor dependency-group: py-updates - dependency-name: cffi dependency-version: 2.0.0 dependency-type: direct:development update-type: version-update:semver-major dependency-group: py-updates - dependency-name: coverage dependency-version: 7.13.2 dependency-type: direct:development update-type: version-update:semver-minor dependency-group: py-updates - dependency-name: cryptography dependency-version: 46.0.4 dependency-type: direct:development update-type: version-update:semver-major dependency-group: py-updates - dependency-name: freezegun dependency-version: 1.5.5 dependency-type: direct:development update-type: version-update:semver-patch dependency-group: py-updates - dependency-name: iniconfig dependency-version: 2.3.0 dependency-type: direct:development update-type: version-update:semver-minor dependency-group: py-updates - dependency-name: markupsafe dependency-version: 3.0.3 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: py-updates - dependency-name: moto dependency-version: 5.1.20 dependency-type: direct:development update-type: version-update:semver-patch dependency-group: py-updates - dependency-name: mypy dependency-version: 1.19.1 dependency-type: direct:development update-type: version-update:semver-minor dependency-group: py-updates - dependency-name: mypy-boto3-s3 dependency-version: 1.42.37 dependency-type: direct:development update-type: version-update:semver-minor dependency-group: py-updates - dependency-name: packaging dependency-version: '26.0' dependency-type: direct:production update-type: version-update:semver-major dependency-group: py-updates - dependency-name: pycparser dependency-version: '3.0' dependency-type: direct:development update-type: version-update:semver-major dependency-group: py-updates - dependency-name: pytest dependency-version: 9.0.2 dependency-type: direct:development update-type: version-update:semver-major dependency-group: py-updates - dependency-name: pytest-mock dependency-version: 3.15.1 dependency-type: direct:development update-type: version-update:semver-minor dependency-group: py-updates - dependency-name: responses dependency-version: 0.25.8 dependency-type: direct:development update-type: version-update:semver-patch dependency-group: py-updates - dependency-name: ruff dependency-version: 0.14.14 dependency-type: direct:development update-type: version-update:semver-minor dependency-group: py-updates - dependency-name: types-awscrt dependency-version: 0.31.1 dependency-type: direct:development update-type: version-update:semver-minor dependency-group: py-updates - dependency-name: types-requests dependency-version: 2.32.4.20260107 dependency-type: direct:development update-type: version-update:semver-patch dependency-group: py-updates - dependency-name: types-s3transfer dependency-version: 0.16.0 dependency-type: direct:development update-type: version-update:semver-minor dependency-group: py-updates - dependency-name: typing-extensions dependency-version: 4.15.0 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: py-updates - dependency-name: werkzeug dependency-version: 3.1.5 dependency-type: direct:development update-type: version-update:semver-patch dependency-group: py-updates - dependency-name: xmltodict dependency-version: 1.0.2 dependency-type: direct:development update-type: version-update:semver-major dependency-group: py-updates - dependency-name: alabaster dependency-version: 1.0.0 dependency-type: direct:production update-type: version-update:semver-major dependency-group: py-updates - dependency-name: anyio dependency-version: 4.12.1 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: py-updates - dependency-name: babel dependency-version: 2.18.0 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: py-updates - dependency-name: beautifulsoup4 dependency-version: 4.14.3 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: py-updates - dependency-name: cachecontrol dependency-version: 0.14.4 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: py-updates - dependency-name: click dependency-version: 8.3.1 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: py-updates - dependency-name: contourpy dependency-version: 1.3.3 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: py-updates - dependency-name: filelock dependency-version: 3.20.3 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: py-updates - dependency-name: fonttools dependency-version: 4.61.1 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: py-updates - dependency-name: furo dependency-version: 2025.12.19 dependency-type: direct:production update-type: version-update:semver-major dependency-group: py-updates - dependency-name: kiwisolver dependency-version: 1.4.9 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: py-updates - dependency-name: matplotlib dependency-version: 3.10.8 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: py-updates - dependency-name: mdit-py-plugins dependency-version: 0.5.0 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: py-updates - dependency-name: more-itertools dependency-version: 10.8.0 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: py-updates - dependency-name: msgpack dependency-version: 1.1.2 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: py-updates - dependency-name: myst-parser dependency-version: 5.0.0 dependency-type: direct:production update-type: version-update:semver-major dependency-group: py-updates - dependency-name: pillow dependency-version: 12.1.0 dependency-type: direct:production update-type: version-update:semver-major dependency-group: py-updates - dependency-name: platformdirs dependency-version: 4.5.1 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: py-updates - dependency-name: pyparsing dependency-version: 3.3.2 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: py-updates - dependency-name: ruamel-yaml dependency-version: 0.19.1 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: py-updates - dependency-name: ruamel-yaml-clib dependency-version: 0.2.15 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: py-updates - dependency-name: soupsieve dependency-version: 2.8.3 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: py-updates - dependency-name: sphinx dependency-version: 9.0.4 dependency-type: direct:production update-type: version-update:semver-major dependency-group: py-updates - dependency-name: sphinx-autobuild dependency-version: 2025.8.25 dependency-type: direct:production update-type: version-update:semver-major dependency-group: py-updates - dependency-name: sphinx-autodoc-typehints dependency-version: 3.6.1 dependency-type: direct:production update-type: version-update:semver-major dependency-group: py-updates - dependency-name: sphinx-jinja2-compat dependency-version: 0.4.1 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: py-updates - dependency-name: sphinx-prompt dependency-version: 1.10.2 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: py-updates - dependency-name: sphinx-tabs dependency-version: 3.4.7 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: py-updates - dependency-name: sphinx-toolbox dependency-version: 4.1.2 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: py-updates - dependency-name: sphinxext-opengraph dependency-version: 0.13.0 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: py-updates - dependency-name: starlette dependency-version: 0.52.1 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: py-updates - dependency-name: uvicorn dependency-version: 0.40.0 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: py-updates - dependency-name: watchfiles dependency-version: 1.1.1 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: py-updates - dependency-name: websockets dependency-version: '16.0' dependency-type: direct:production update-type: version-update:semver-major dependency-group: py-updates ... Signed-off-by: dependabot[bot] --- pyproject.toml | 2 +- requirements/requirements-dev.txt | 102 +++++++++++----------- requirements/requirements-docs.txt | 130 ++++++++++++++--------------- requirements/requirements.txt | 56 ++++++------- 4 files changed, 145 insertions(+), 145 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index ef3ad17..72685b7 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -37,7 +37,7 @@ dependencies = [ "cloudpathlib", "docker", "pandas", - "polars>=1.17.1,<1.29.0", + "polars>=1.17.1,<1.38.0", "pyarrow", "requests>=2.32.0", "rich", diff --git a/requirements/requirements-dev.txt b/requirements/requirements-dev.txt index f4c5f9a..b0adfa2 100644 --- a/requirements/requirements-dev.txt +++ b/requirements/requirements-dev.txt @@ -1,102 +1,102 @@ # This file was autogenerated by uv via the following command: # uv pip compile pyproject.toml --extra dev -o requirements/requirements-dev.txt -awscli==1.40.17 +awscli==1.44.29 # via cladetime (pyproject.toml) biobear==0.23.7 # via cladetime (pyproject.toml) -biopython==1.85 +biopython==1.86 # via cladetime (pyproject.toml) -boto3==1.38.18 +boto3==1.42.39 # via # cladetime (pyproject.toml) # moto -boto3-stubs==1.38.18 +boto3-stubs==1.42.39 # via cladetime (pyproject.toml) -botocore==1.38.18 +botocore==1.42.39 # via # awscli # boto3 # moto # s3transfer -botocore-stubs==1.38.18 +botocore-stubs==1.42.39 # via boto3-stubs -certifi==2025.4.26 +certifi==2026.1.4 # via requests -cffi==1.17.1 +cffi==2.0.0 # via cryptography -charset-normalizer==3.4.2 +charset-normalizer==3.4.4 # via requests -cloudpathlib==0.21.1 +cloudpathlib==0.23.0 # via cladetime (pyproject.toml) colorama==0.4.6 # via awscli -coverage==7.8.0 +coverage==7.13.2 # via cladetime (pyproject.toml) -cryptography==44.0.3 +cryptography==46.0.4 # via moto docker==7.1.0 # via cladetime (pyproject.toml) -docutils==0.19 +docutils==0.22.4 # via awscli -freezegun==1.5.1 +freezegun==1.5.5 # via cladetime (pyproject.toml) -idna==3.10 +idna==3.11 # via requests -iniconfig==2.1.0 +iniconfig==2.3.0 # via pytest -jellyfish==1.2.0 +jellyfish==1.2.1 # via us jinja2==3.1.6 # via # cladetime (pyproject.toml) # moto -jmespath==1.0.1 +jmespath==1.1.0 # via # boto3 # botocore -markdown-it-py==3.0.0 +markdown-it-py==4.0.0 # via rich -markupsafe==3.0.2 +markupsafe==3.0.3 # via # jinja2 # werkzeug mdurl==0.1.2 # via markdown-it-py -moto==5.1.4 +moto==5.1.20 # via cladetime (pyproject.toml) -mypy==1.15.0 +mypy==1.19.1 # via cladetime (pyproject.toml) -mypy-boto3-s3==1.38.0 +mypy-boto3-s3==1.42.37 # via boto3-stubs mypy-extensions==1.1.0 # via mypy -numpy==2.2.5 +numpy==2.4.2 # via # biopython # pandas -packaging==25.0 +packaging==26.0 # via pytest -pandas==2.2.3 +pandas==3.0.0 # via cladetime (pyproject.toml) pluggy==1.6.0 # via pytest -polars==1.28.1 +polars==1.37.1 # via cladetime (pyproject.toml) -pyarrow==20.0.0 +pyarrow==23.0.0 # via # cladetime (pyproject.toml) # biobear -pyasn1==0.6.1 +pyasn1==0.6.2 # via rsa -pycparser==2.22 +pycparser==3.0 # via cffi -pygments==2.19.1 +pygments==2.19.2 # via rich -pytest==8.3.5 +pytest==9.0.2 # via # cladetime (pyproject.toml) # pytest-mock -pytest-mock==3.14.0 +pytest-mock==3.15.1 # via cladetime (pyproject.toml) python-dateutil==2.9.0.post0 # via @@ -106,50 +106,50 @@ python-dateutil==2.9.0.post0 # pandas pytz==2025.2 # via pandas -pyyaml==6.0.2 +pyyaml==6.0.3 # via # awscli # responses -requests==2.32.3 +requests==2.32.5 # via # cladetime (pyproject.toml) # docker # moto # responses -responses==0.25.7 +responses==0.25.8 # via moto -rich==14.0.0 +rich==14.3.2 # via cladetime (pyproject.toml) -rsa==4.7.2 +rsa==4.9.1 # via awscli -ruff==0.11.10 +ruff==0.14.14 # via cladetime (pyproject.toml) -s3transfer==0.12.0 +s3transfer==0.16.0 # via # awscli # boto3 six==1.17.0 # via python-dateutil -structlog==25.3.0 +structlog==25.5.0 # via cladetime (pyproject.toml) -tqdm==4.67.1 +tqdm==4.67.2 # via cladetime (pyproject.toml) -types-awscrt==0.27.2 +types-awscrt==0.31.1 # via botocore-stubs types-python-dateutil==2.9.0.20250516 # via cladetime (pyproject.toml) -types-requests==2.32.0.20250515 +types-requests==2.32.4.20260107 # via cladetime (pyproject.toml) -types-s3transfer==0.12.0 +types-s3transfer==0.16.0 # via boto3-stubs -typing-extensions==4.13.2 +typing-extensions==4.15.0 # via # boto3-stubs # mypy # mypy-boto3-s3 -tzdata==2025.2 +tzdata==2025.3 # via pandas -urllib3==2.4.0 +urllib3==2.6.3 # via # cladetime (pyproject.toml) # botocore @@ -159,9 +159,9 @@ urllib3==2.4.0 # types-requests us==3.2.0 # via cladetime (pyproject.toml) -werkzeug==3.1.3 +werkzeug==3.1.5 # via moto -xmltodict==0.14.2 +xmltodict==1.0.2 # via moto -zstandard==0.23.0 +zstandard==0.25.0 # via cladetime (pyproject.toml) diff --git a/requirements/requirements-docs.txt b/requirements/requirements-docs.txt index cdca688..4d4f6ab 100644 --- a/requirements/requirements-docs.txt +++ b/requirements/requirements-docs.txt @@ -1,8 +1,8 @@ # This file was autogenerated by uv via the following command: # uv pip compile pyproject.toml --extra docs -o requirements/requirements-docs.txt -alabaster==0.7.16 +alabaster==1.0.0 # via sphinx -anyio==4.9.0 +anyio==4.12.1 # via # starlette # watchfiles @@ -12,40 +12,40 @@ apeye-core==1.1.5 # via apeye autodocsumm==0.2.14 # via sphinx-toolbox -awscli==1.40.17 +awscli==1.44.29 # via cladetime (pyproject.toml) -babel==2.17.0 +babel==2.18.0 # via sphinx -beautifulsoup4==4.13.4 +beautifulsoup4==4.14.3 # via # furo # sphinx-toolbox biobear==0.23.7 # via cladetime (pyproject.toml) -biopython==1.85 +biopython==1.86 # via cladetime (pyproject.toml) -boto3==1.38.18 +boto3==1.42.39 # via cladetime (pyproject.toml) -botocore==1.38.18 +botocore==1.42.39 # via # awscli # boto3 # s3transfer -cachecontrol==0.14.3 +cachecontrol==0.14.4 # via sphinx-toolbox -certifi==2025.4.26 +certifi==2026.1.4 # via requests -charset-normalizer==3.4.2 +charset-normalizer==3.4.4 # via requests -click==8.2.0 +click==8.3.1 # via uvicorn -cloudpathlib==0.21.1 +cloudpathlib==0.23.0 # via cladetime (pyproject.toml) colorama==0.4.6 # via # awscli # sphinx-autobuild -contourpy==1.3.2 +contourpy==1.3.3 # via matplotlib cssutils==2.11.1 # via dict2css @@ -55,7 +55,7 @@ dict2css==0.3.0.post1 # via sphinx-toolbox docker==7.1.0 # via cladetime (pyproject.toml) -docutils==0.19 +docutils==0.22.4 # via # awscli # myst-parser @@ -69,26 +69,26 @@ domdf-python-tools==3.10.0 # apeye-core # dict2css # sphinx-toolbox -filelock==3.18.0 +filelock==3.20.3 # via # cachecontrol # sphinx-toolbox -fonttools==4.58.0 +fonttools==4.61.1 # via matplotlib -furo==2024.8.6 +furo==2025.12.19 # via cladetime (pyproject.toml) h11==0.16.0 # via uvicorn html5lib==1.1 # via sphinx-toolbox -idna==3.10 +idna==3.11 # via # anyio # apeye-core # requests imagesize==1.4.1 # via sphinx -jellyfish==1.2.0 +jellyfish==1.2.1 # via us jinja2==3.1.6 # via @@ -96,67 +96,67 @@ jinja2==3.1.6 # myst-parser # sphinx # sphinx-jinja2-compat -jmespath==1.0.1 +jmespath==1.1.0 # via # boto3 # botocore -kiwisolver==1.4.8 +kiwisolver==1.4.9 # via matplotlib -markdown-it-py==3.0.0 +markdown-it-py==4.0.0 # via # mdit-py-plugins # myst-parser # rich -markupsafe==3.0.2 +markupsafe==3.0.3 # via # jinja2 # sphinx-jinja2-compat -matplotlib==3.10.3 +matplotlib==3.10.8 # via cladetime (pyproject.toml) -mdit-py-plugins==0.4.2 +mdit-py-plugins==0.5.0 # via myst-parser mdurl==0.1.2 # via markdown-it-py -more-itertools==10.7.0 +more-itertools==10.8.0 # via cssutils -msgpack==1.1.0 +msgpack==1.1.2 # via cachecontrol -myst-parser==4.0.1 +myst-parser==5.0.0 # via cladetime (pyproject.toml) natsort==8.4.0 # via domdf-python-tools -numpy==2.2.5 +numpy==2.4.2 # via # biopython # contourpy # matplotlib # pandas -packaging==25.0 +packaging==26.0 # via # matplotlib # sphinx -pandas==2.2.3 +pandas==3.0.0 # via cladetime (pyproject.toml) -pillow==11.2.1 +pillow==12.1.0 # via matplotlib -platformdirs==4.3.8 +platformdirs==4.5.1 # via apeye -polars==1.28.1 +polars==1.37.1 # via cladetime (pyproject.toml) -pyarrow==20.0.0 +pyarrow==23.0.0 # via # cladetime (pyproject.toml) # biobear -pyasn1==0.6.1 +pyasn1==0.6.2 # via rsa -pygments==2.19.1 +pygments==2.19.2 # via # furo # rich # sphinx # sphinx-prompt # sphinx-tabs -pyparsing==3.2.3 +pyparsing==3.3.2 # via matplotlib python-dateutil==2.9.0.post0 # via @@ -165,26 +165,26 @@ python-dateutil==2.9.0.post0 # pandas pytz==2025.2 # via pandas -pyyaml==6.0.2 +pyyaml==6.0.3 # via # awscli # myst-parser -requests==2.32.3 +requests==2.32.5 # via # cladetime (pyproject.toml) # apeye # cachecontrol # docker # sphinx -rich==14.0.0 +rich==14.3.2 # via cladetime (pyproject.toml) -rsa==4.7.2 +rsa==4.9.1 # via awscli -ruamel-yaml==0.18.10 +ruamel-yaml==0.19.1 # via sphinx-toolbox -ruamel-yaml-clib==0.2.12 +ruamel-yaml-clib==0.2.15 # via ruamel-yaml -s3transfer==0.12.0 +s3transfer==0.16.0 # via # awscli # boto3 @@ -196,9 +196,9 @@ sniffio==1.3.1 # via anyio snowballstemmer==3.0.1 # via sphinx -soupsieve==2.7 +soupsieve==2.8.3 # via beautifulsoup4 -sphinx==7.3.7 +sphinx==9.0.4 # via # cladetime (pyproject.toml) # autodocsumm @@ -213,9 +213,9 @@ sphinx==7.3.7 # sphinx-tabs # sphinx-toolbox # sphinxext-opengraph -sphinx-autobuild==2024.10.3 +sphinx-autobuild==2025.8.25 # via cladetime (pyproject.toml) -sphinx-autodoc-typehints==2.3.0 +sphinx-autodoc-typehints==3.6.1 # via sphinx-toolbox sphinx-basic-ng==1.0.0b2 # via furo @@ -223,13 +223,13 @@ sphinx-copybutton==0.5.2 # via cladetime (pyproject.toml) sphinx-github-style==1.2.2 # via cladetime (pyproject.toml) -sphinx-jinja2-compat==0.3.0 +sphinx-jinja2-compat==0.4.1 # via sphinx-toolbox -sphinx-prompt==1.8.0 +sphinx-prompt==1.10.2 # via sphinx-toolbox -sphinx-tabs==3.4.5 +sphinx-tabs==3.4.7 # via sphinx-toolbox -sphinx-toolbox==4.0.0 +sphinx-toolbox==4.1.2 # via cladetime (pyproject.toml) sphinxcontrib-applehelp==2.0.0 # via sphinx @@ -243,25 +243,25 @@ sphinxcontrib-qthelp==2.0.0 # via sphinx sphinxcontrib-serializinghtml==2.0.0 # via sphinx -sphinxext-opengraph==0.10.0 +sphinxext-opengraph==0.13.0 # via cladetime (pyproject.toml) -starlette==0.46.2 +starlette==0.52.1 # via sphinx-autobuild -structlog==25.3.0 +structlog==25.5.0 # via cladetime (pyproject.toml) tabulate==0.9.0 # via sphinx-toolbox -tqdm==4.67.1 +tqdm==4.67.2 # via cladetime (pyproject.toml) -typing-extensions==4.13.2 +typing-extensions==4.15.0 # via # anyio # beautifulsoup4 # domdf-python-tools # sphinx-toolbox -tzdata==2025.2 +tzdata==2025.3 # via pandas -urllib3==2.4.0 +urllib3==2.6.3 # via # cladetime (pyproject.toml) # botocore @@ -269,13 +269,13 @@ urllib3==2.4.0 # requests us==3.2.0 # via cladetime (pyproject.toml) -uvicorn==0.34.2 +uvicorn==0.40.0 # via sphinx-autobuild -watchfiles==1.0.5 +watchfiles==1.1.1 # via sphinx-autobuild webencodings==0.5.1 # via html5lib -websockets==15.0.1 +websockets==16.0 # via sphinx-autobuild -zstandard==0.23.0 +zstandard==0.25.0 # via cladetime (pyproject.toml) diff --git a/requirements/requirements.txt b/requirements/requirements.txt index 30399c6..eb1abc5 100644 --- a/requirements/requirements.txt +++ b/requirements/requirements.txt @@ -1,57 +1,57 @@ # This file was autogenerated by uv via the following command: # uv pip compile pyproject.toml -o requirements/requirements.txt -awscli==1.40.17 +awscli==1.44.29 # via cladetime (pyproject.toml) biobear==0.23.7 # via cladetime (pyproject.toml) -biopython==1.85 +biopython==1.86 # via cladetime (pyproject.toml) -boto3==1.38.18 +boto3==1.42.39 # via cladetime (pyproject.toml) -botocore==1.38.18 +botocore==1.42.39 # via # awscli # boto3 # s3transfer -certifi==2025.4.26 +certifi==2026.1.4 # via requests -charset-normalizer==3.4.2 +charset-normalizer==3.4.4 # via requests -cloudpathlib==0.21.1 +cloudpathlib==0.23.0 # via cladetime (pyproject.toml) colorama==0.4.6 # via awscli docker==7.1.0 # via cladetime (pyproject.toml) -docutils==0.19 +docutils==0.22.4 # via awscli -idna==3.10 +idna==3.11 # via requests -jellyfish==1.2.0 +jellyfish==1.2.1 # via us -jmespath==1.0.1 +jmespath==1.1.0 # via # boto3 # botocore -markdown-it-py==3.0.0 +markdown-it-py==4.0.0 # via rich mdurl==0.1.2 # via markdown-it-py -numpy==2.2.5 +numpy==2.4.2 # via # biopython # pandas -pandas==2.2.3 +pandas==3.0.0 # via cladetime (pyproject.toml) -polars==1.28.1 +polars==1.37.1 # via cladetime (pyproject.toml) -pyarrow==20.0.0 +pyarrow==23.0.0 # via # cladetime (pyproject.toml) # biobear -pyasn1==0.6.1 +pyasn1==0.6.2 # via rsa -pygments==2.19.1 +pygments==2.19.2 # via rich python-dateutil==2.9.0.post0 # via @@ -59,29 +59,29 @@ python-dateutil==2.9.0.post0 # pandas pytz==2025.2 # via pandas -pyyaml==6.0.2 +pyyaml==6.0.3 # via awscli -requests==2.32.3 +requests==2.32.5 # via # cladetime (pyproject.toml) # docker -rich==14.0.0 +rich==14.3.2 # via cladetime (pyproject.toml) -rsa==4.7.2 +rsa==4.9.1 # via awscli -s3transfer==0.12.0 +s3transfer==0.16.0 # via # awscli # boto3 six==1.17.0 # via python-dateutil -structlog==25.3.0 +structlog==25.5.0 # via cladetime (pyproject.toml) -tqdm==4.67.1 +tqdm==4.67.2 # via cladetime (pyproject.toml) -tzdata==2025.2 +tzdata==2025.3 # via pandas -urllib3==2.4.0 +urllib3==2.6.3 # via # cladetime (pyproject.toml) # botocore @@ -89,5 +89,5 @@ urllib3==2.4.0 # requests us==3.2.0 # via cladetime (pyproject.toml) -zstandard==0.23.0 +zstandard==0.25.0 # via cladetime (pyproject.toml)