Replace poetry with uv

for lightning-fast Python dependency updates.

To update all dependencies (as done by the GitHub action):

$ make update-dependencies

To update only one package:

./lib/galaxy/dependencies/update.sh -p <PKG>

.github/workflows/dependencies.yaml

@@ -17,9 +17,7 @@ jobs:
         with:
           python-version: ${{ matrix.python-version }}
       - name: Update dependencies
-        run: | 
-          python -m venv .venv
-          make update-dependencies
+        run: make update-dependencies
       - name: Create pull request
         uses: peter-evans/create-pull-request@v6
         with:

lib/galaxy/dependencies/dev-requirements.txt

@@ -1,188 +1,188 @@
---extra-index-url https://wheels.galaxyproject.org/simple
-
-aiohappyeyeballs==2.4.3 ; python_version >= "3.8" and python_version < "3.13"
-aiohttp==3.10.10 ; python_version >= "3.8" and python_version < "3.13"
-aiosignal==1.3.1 ; python_version >= "3.8" and python_version < "3.13"
-alabaster==0.7.13 ; python_version >= "3.8" and python_version < "3.13"
-anyio==4.5.2 ; python_version >= "3.8" and python_version < "3.13"
-ase==3.23.0 ; python_version >= "3.8" and python_version < "3.13"
-async-timeout==4.0.3 ; python_version >= "3.8" and python_version < "3.11"
-attrs==24.2.0 ; python_version >= "3.8" and python_version < "3.13"
-axe-selenium-python==2.1.6 ; python_version >= "3.8" and python_version < "3.13"
-babel==2.16.0 ; python_version >= "3.8" and python_version < "3.13"
-backports-tarfile==1.2.0 ; python_version >= "3.8" and python_version < "3.12"
-backports-zoneinfo==0.2.1 ; python_version >= "3.8" and python_version < "3.9"
-black==24.8.0 ; python_version >= "3.8" and python_version < "3.13"
-boto3==1.35.36 ; python_version >= "3.8" and python_version < "3.13"
-botocore==1.35.36 ; python_version >= "3.8" and python_version < "3.13"
-build==1.2.2.post1 ; python_version >= "3.8" and python_version < "3.13"
-cachecontrol[filecache]==0.14.0 ; python_version >= "3.8" and python_version < "3.13"
-certifi==2024.8.30 ; python_version >= "3.8" and python_version < "3.13"
-cffi==1.17.1 ; python_version >= "3.8" and python_version < "3.13"
-charset-normalizer==3.4.0 ; python_version >= "3.8" and python_version < "3.13"
-click==8.1.7 ; python_version >= "3.8" and python_version < "3.13"
-codespell==2.3.0 ; python_version >= "3.8" and python_version < "3.13"
-colorama==0.4.6 ; python_version >= "3.8" and python_version < "3.13" and (sys_platform == "win32" or platform_system == "Windows" or os_name == "nt")
-contourpy==1.1.1 ; python_version >= "3.8" and python_version < "3.9"
-contourpy==1.3.0 ; python_version >= "3.9" and python_version < "3.13"
-coverage[toml]==7.6.1 ; python_version >= "3.8" and python_version < "3.13"
-cryptography==43.0.3 ; python_version >= "3.8" and python_version < "3.13"
-cwltest==2.5.20240906231108 ; python_version >= "3.8" and python_version < "3.13"
-cycler==0.12.1 ; python_version >= "3.8" and python_version < "3.13"
-darker==2.1.1 ; python_version >= "3.8" and python_version < "3.13"
-darkgraylib==1.2.1 ; python_version >= "3.8" and python_version < "3.13"
-decorator==5.1.1 ; python_version >= "3.9" and python_version < "3.13"
-defusedxml==0.7.1 ; python_version >= "3.8" and python_version < "3.13"
-deprecated==1.2.14 ; python_version >= "3.8" and python_version < "3.13"
-docutils==0.20.1 ; python_version >= "3.8" and python_version < "3.13"
-dogpile-cache==1.3.3 ; python_version >= "3.9" and python_version < "3.13"
-exceptiongroup==1.2.2 ; python_version >= "3.8" and python_version < "3.11"
-filelock==3.16.1 ; python_version >= "3.8" and python_version < "3.13"
-fluent-logger==0.11.1 ; python_version >= "3.8" and python_version < "3.13"
-fonttools==4.54.1 ; python_version >= "3.8" and python_version < "3.13"
-frozenlist==1.5.0 ; python_version >= "3.8" and python_version < "3.13"
-galaxy-release-util==0.1.11 ; python_version >= "3.8" and python_version < "3.13"
-graylint==1.1.1 ; python_version >= "3.8" and python_version < "3.13"
-greenlet==3.1.1 ; python_version >= "3.8" and python_version < "3.13"
-h11==0.14.0 ; python_version >= "3.8" and python_version < "3.13"
-httpcore==1.0.6 ; python_version >= "3.8" and python_version < "3.13"
-httpx==0.27.2 ; python_version >= "3.8" and python_version < "3.13"
-idna==3.10 ; python_version >= "3.8" and python_version < "3.13"
-imagesize==1.4.1 ; python_version >= "3.8" and python_version < "3.13"
-importlib-metadata==8.5.0 ; python_version >= "3.8" and python_version < "3.13"
-importlib-resources==6.4.5 ; python_version >= "3.8" and python_version < "3.10"
-iniconfig==2.0.0 ; python_version >= "3.8" and python_version < "3.13"
-isodate==0.6.1 ; python_version >= "3.8" and python_version < "3.13"
-isort==5.13.2 ; python_version >= "3.8" and python_version < "3.13"
-jaraco-classes==3.4.0 ; python_version >= "3.8" and python_version < "3.13"
-jaraco-context==6.0.1 ; python_version >= "3.8" and python_version < "3.13"
-jaraco-functools==4.1.0 ; python_version >= "3.8" and python_version < "3.13"
-jeepney==0.8.0 ; python_version >= "3.8" and python_version < "3.13" and sys_platform == "linux"
-jinja2==3.1.4 ; python_version >= "3.8" and python_version < "3.13"
-jmespath==1.0.1 ; python_version >= "3.8" and python_version < "3.13"
-jsonschema-specifications==2023.12.1 ; python_version >= "3.9" and python_version < "3.13"
-jsonschema==4.23.0 ; python_version >= "3.9" and python_version < "3.13"
-junit-xml==1.9 ; python_version >= "3.8" and python_version < "3.13"
-keyring==25.4.1 ; python_version >= "3.8" and python_version < "3.13"
-kiwisolver==1.4.7 ; python_version >= "3.8" and python_version < "3.13"
-lxml==5.3.0 ; python_version >= "3.8" and python_version < "3.13"
-markdown-it-py==3.0.0 ; python_version >= "3.8" and python_version < "3.13"
-markdown-it-reporter==0.0.2 ; python_version >= "3.8" and python_version < "3.13"
-markupsafe==2.1.5 ; python_version >= "3.8" and python_version < "3.13"
-matplotlib==3.7.5 ; python_version >= "3.8" and python_version < "3.9"
-matplotlib==3.9.2 ; python_version >= "3.9" and python_version < "3.13"
-mdit-py-plugins==0.4.2 ; python_version >= "3.8" and python_version < "3.13"
-mdurl==0.1.2 ; python_version >= "3.8" and python_version < "3.13"
-mirakuru==2.5.2 ; python_version >= "3.8" and python_version < "3.13"
-mistune==3.0.2 ; python_version >= "3.8" and python_version < "3.13"
-more-itertools==10.5.0 ; python_version >= "3.8" and python_version < "3.13"
-msgpack==1.1.0 ; python_version >= "3.8" and python_version < "3.13"
-multidict==6.1.0 ; python_version >= "3.8" and python_version < "3.13"
-mypy-extensions==1.0.0 ; python_version >= "3.8" and python_version < "3.13"
-myst-parser==3.0.1 ; python_version >= "3.8" and python_version < "3.13"
-nh3==0.2.18 ; python_version >= "3.8" and python_version < "3.13"
-numpy==1.24.4 ; python_version >= "3.8" and python_version < "3.9"
-numpy==2.0.2 ; python_version >= "3.9" and python_version < "3.10"
-numpy==2.1.2 ; python_version >= "3.10" and python_version < "3.13"
-onedatafilerestclient==21.2.5.2 ; python_version >= "3.8" and python_version < "3.13"
-outcome==1.3.0.post0 ; python_version >= "3.8" and python_version < "3.13"
-packaging==24.1 ; python_version >= "3.8" and python_version < "3.13"
-pathspec==0.12.1 ; python_version >= "3.8" and python_version < "3.13"
-pbr==6.1.0 ; python_version >= "3.9" and python_version < "3.13"
-pillow==10.4.0 ; python_version >= "3.8" and python_version < "3.13"
-pkce==1.0.3 ; python_version >= "3.8" and python_version < "3.13"
-pkginfo==1.10.0 ; python_version >= "3.8" and python_version < "3.13"
-platformdirs==4.3.6 ; python_version >= "3.8" and python_version < "3.13"
-playwright==1.48.0 ; python_version >= "3.8" and python_version < "3.13"
-pluggy==1.5.0 ; python_version >= "3.8" and python_version < "3.13"
-port-for==0.7.3 ; python_version >= "3.8" and python_version < "3.13"
-prettytable==3.11.0 ; python_version >= "3.8" and python_version < "3.13"
-propcache==0.2.0 ; python_version >= "3.8" and python_version < "3.13"
-psutil==6.1.0 ; python_version >= "3.8" and python_version < "3.13" and sys_platform != "cygwin"
-psycopg==3.2.3 ; python_version >= "3.8" and python_version < "3.13"
-pycparser==2.22 ; python_version >= "3.8" and python_version < "3.13"
-pyee==12.0.0 ; python_version >= "3.8" and python_version < "3.13"
-pygithub==2.4.0 ; python_version >= "3.8" and python_version < "3.13"
-pygments==2.18.0 ; python_version >= "3.8" and python_version < "3.13"
-pyjwt[crypto]==2.9.0 ; python_version >= "3.8" and python_version < "3.13"
-pynacl==1.5.0 ; python_version >= "3.8" and python_version < "3.13"
-pyparsing==3.1.4 ; python_version >= "3.8" and python_version < "3.13"
-pyproject-hooks==1.2.0 ; python_version >= "3.8" and python_version < "3.13"
-pysocks==1.7.1 ; python_version >= "3.8" and python_version < "3.13"
-pytest-asyncio==0.23.8 ; python_version >= "3.8" and python_version < "3.13"
-pytest-base-url==2.1.0 ; python_version >= "3.8" and python_version < "3.13"
-pytest-cov==5.0.0 ; python_version >= "3.8" and python_version < "3.13"
-pytest-html==4.1.1 ; python_version >= "3.8" and python_version < "3.13"
-pytest-httpserver==1.1.0 ; python_version >= "3.8" and python_version < "3.13"
-pytest-json-report==1.5.0 ; python_version >= "3.8" and python_version < "3.13"
-pytest-metadata==3.1.1 ; python_version >= "3.8" and python_version < "3.13"
-pytest-mock==3.14.0 ; python_version >= "3.8" and python_version < "3.13"
-pytest-playwright==0.5.2 ; python_version >= "3.8" and python_version < "3.13"
-pytest-postgresql==6.1.1 ; python_version >= "3.8" and python_version < "3.13"
-pytest-shard==0.1.2 ; python_version >= "3.8" and python_version < "3.13"
-pytest==7.4.4 ; python_version >= "3.8" and python_version < "3.13"
-python-dateutil==2.9.0.post0 ; python_version >= "3.8" and python_version < "3.13"
-python-irodsclient==2.2.0 ; python_version >= "3.8" and python_version < "3.13"
-python-slugify==8.0.4 ; python_version >= "3.8" and python_version < "3.13"
-pytz==2024.2 ; python_version >= "3.8" and python_version < "3.9"
-pywin32-ctypes==0.2.3 ; python_version >= "3.8" and python_version < "3.13" and sys_platform == "win32"
-pyyaml==6.0.2 ; python_version >= "3.8" and python_version < "3.13"
-rdflib==6.3.2 ; python_version >= "3.8" and python_version < "3.13"
-readme-renderer==43.0 ; python_version >= "3.8" and python_version < "3.13"
-referencing==0.35.1 ; python_version >= "3.9" and python_version < "3.13"
-requests-toolbelt==1.0.0 ; python_version >= "3.8" and python_version < "3.13"
-requests==2.32.3 ; python_version >= "3.8" and python_version < "3.13"
-responses==0.25.3 ; python_version >= "3.8" and python_version < "3.13"
-rfc3986==2.0.0 ; python_version >= "3.8" and python_version < "3.13"
-rich==13.9.3 ; python_version >= "3.8" and python_version < "3.13"
-rpds-py==0.20.0 ; python_version >= "3.9" and python_version < "3.13"
-ruamel-yaml-clib==0.2.8 ; platform_python_implementation == "CPython" and python_version < "3.13" and python_version >= "3.8"
-ruamel-yaml==0.18.6 ; python_version >= "3.8" and python_version < "3.13"
-rucio-clients==35.4.1 ; python_version >= "3.9" and python_version < "3.13"
-s3transfer==0.10.3 ; python_version >= "3.8" and python_version < "3.13"
-schema-salad==8.7.20241010092723 ; python_version >= "3.8" and python_version < "3.13"
-scipy==1.10.1 ; python_version >= "3.8" and python_version < "3.9"
-scipy==1.13.1 ; python_version >= "3.9" and python_version < "3.10"
-scipy==1.14.1 ; python_version >= "3.10" and python_version < "3.13"
-secretstorage==3.3.3 ; python_version >= "3.8" and python_version < "3.13" and sys_platform == "linux"
-selenium==4.25.0 ; python_version >= "3.8" and python_version < "3.13"
-seletools==1.5.0 ; python_version >= "3.8" and python_version < "3.13"
-setuptools==75.2.0 ; python_version >= "3.8" and python_version < "3.13"
-six==1.16.0 ; python_version >= "3.8" and python_version < "3.13"
-sniffio==1.3.1 ; python_version >= "3.8" and python_version < "3.13"
-snowballstemmer==2.2.0 ; python_version >= "3.8" and python_version < "3.13"
-sortedcontainers==2.4.0 ; python_version >= "3.8" and python_version < "3.13"
-sphinx-rtd-theme==3.0.1 ; python_version >= "3.8" and python_version < "3.13"
-sphinx==7.1.2 ; python_version >= "3.8" and python_version < "3.13"
-sphinxcontrib-applehelp==1.0.4 ; python_version >= "3.8" and python_version < "3.13"
-sphinxcontrib-devhelp==1.0.2 ; python_version >= "3.8" and python_version < "3.13"
-sphinxcontrib-htmlhelp==2.0.1 ; python_version >= "3.8" and python_version < "3.13"
-sphinxcontrib-jquery==4.1 ; python_version >= "3.8" and python_version < "3.13"
-sphinxcontrib-jsmath==1.0.1 ; python_version >= "3.8" and python_version < "3.13"
-sphinxcontrib-qthelp==1.0.3 ; python_version >= "3.8" and python_version < "3.13"
-sphinxcontrib-serializinghtml==1.1.5 ; python_version >= "3.8" and python_version < "3.13"
-statsd==4.0.1 ; python_version >= "3.8" and python_version < "3.13"
-stevedore==5.3.0 ; python_version >= "3.9" and python_version < "3.13"
-tabulate==0.9.0 ; python_version >= "3.9" and python_version < "3.13"
-testfixtures==8.3.0 ; python_version >= "3.8" and python_version < "3.13"
-text-unidecode==1.3 ; python_version >= "3.8" and python_version < "3.13"
-tinydb==4.8.2 ; python_version >= "3.8" and python_version < "3.13"
-toml==0.10.2 ; python_version >= "3.8" and python_version < "3.13"
-tomli==2.0.2 ; python_version >= "3.8" and python_full_version <= "3.11.0a6"
-trio-websocket==0.11.1 ; python_version >= "3.8" and python_version < "3.13"
-trio==0.27.0 ; python_version >= "3.8" and python_version < "3.13"
-tuspy==1.0.3 ; python_version >= "3.8" and python_version < "3.13"
-twill==3.3 ; python_version >= "3.8" and python_version < "3.13"
-twine==5.1.1 ; python_version >= "3.8" and python_version < "3.13"
-typing-extensions==4.12.2 ; python_version >= "3.8" and python_version < "3.13"
-tzdata==2024.2 ; python_version >= "3.8" and python_version < "3.13" and sys_platform == "win32"
-urllib3==1.26.20 ; python_version >= "3.8" and python_version < "3.13"
-urllib3[socks]==1.26.20 ; python_version >= "3.8" and python_version < "3.13"
-watchdog==4.0.2 ; python_version >= "3.8" and python_version < "3.13"
-wcwidth==0.2.13 ; python_version >= "3.8" and python_version < "3.13"
-websocket-client==1.8.0 ; python_version >= "3.8" and python_version < "3.13"
-werkzeug==3.0.6 ; python_version >= "3.8" and python_version < "3.13"
-wrapt==1.16.0 ; python_version >= "3.8" and python_version < "3.13"
-wsproto==1.2.0 ; python_version >= "3.8" and python_version < "3.13"
-yarl==1.15.2 ; python_version >= "3.8" and python_version < "3.13"
-zipp==3.20.2 ; python_version >= "3.8" and python_version < "3.13"
+# This file was autogenerated by uv via the following command:
+#    uv export --no-hashes --only-group=dev
+aiohappyeyeballs==2.4.3
+aiohttp==3.10.10
+aiosignal==1.3.1
+alabaster==0.7.13
+anyio==4.5.2
+ase==3.23.0
+async-timeout==4.0.3 ; python_full_version < '3.11'
+attrs==24.2.0
+axe-selenium-python==2.1.6
+babel==2.16.0
+backports-tarfile==1.2.0 ; python_full_version < '3.12'
+backports-zoneinfo==0.2.1 ; python_full_version < '3.9'
+black==24.8.0
+boto3==1.35.36
+botocore==1.35.36
+build==1.2.2.post1
+cachecontrol==0.14.0
+certifi==2024.8.30
+cffi==1.17.1
+charset-normalizer==3.4.0
+click==8.1.7
+codespell==2.3.0
+colorama==0.4.6 ; (platform_system != 'Windows' and sys_platform == 'win32') or platform_system == 'Windows' or os_name == 'nt'
+contourpy==1.1.1 ; python_full_version < '3.9'
+contourpy==1.3.0 ; python_full_version >= '3.9'
+coverage==7.6.1
+cryptography==43.0.3
+cwltest==2.5.20240906231108
+cycler==0.12.1
+darker==2.1.1
+darkgraylib==1.2.1
+decorator==5.1.1 ; python_full_version >= '3.9'
+defusedxml==0.7.1
+deprecated==1.2.14
+docutils==0.20.1
+dogpile-cache==1.3.3 ; python_full_version >= '3.9'
+exceptiongroup==1.2.2 ; python_full_version < '3.11'
+filelock==3.16.1
+fluent-logger==0.11.1
+fonttools==4.54.1
+frozenlist==1.5.0
+galaxy-release-util==0.1.11
+graylint==1.1.1
+greenlet==3.1.1
+h11==0.14.0
+httpcore==1.0.6
+httpx==0.27.2
+idna==3.10
+imagesize==1.4.1
+importlib-metadata==8.5.0
+importlib-resources==6.4.5 ; python_full_version < '3.10'
+iniconfig==2.0.0
+isodate==0.6.1
+isort==5.13.2
+jaraco-classes==3.4.0
+jaraco-context==6.0.1
+jaraco-functools==4.1.0
+jeepney==0.8.0 ; sys_platform == 'linux'
+jinja2==3.1.4
+jmespath==1.0.1
+jsonschema==4.23.0 ; python_full_version >= '3.9'
+jsonschema-specifications==2023.12.1 ; python_full_version >= '3.9'
+junit-xml==1.9
+keyring==25.5.0
+kiwisolver==1.4.7
+lxml==5.3.0
+markdown-it-py==3.0.0
+markdown-it-reporter==0.0.2
+markupsafe==2.1.5
+matplotlib==3.7.5 ; python_full_version < '3.9'
+matplotlib==3.9.2 ; python_full_version >= '3.9'
+mdit-py-plugins==0.4.2
+mdurl==0.1.2
+mirakuru==2.5.2
+mistune==3.0.2
+more-itertools==10.5.0
+msgpack==1.1.0
+multidict==6.1.0
+mypy-extensions==1.0.0
+myst-parser==3.0.1
+nh3==0.2.18
+numpy==1.24.4 ; python_full_version < '3.9'
+numpy==2.0.2 ; python_full_version == '3.9.*'
+numpy==2.1.2 ; python_full_version >= '3.10'
+onedatafilerestclient==21.2.5.2
+outcome==1.3.0.post0
+packaging==24.1
+pathspec==0.12.1
+pbr==6.1.0 ; python_full_version >= '3.9'
+pillow==10.4.0
+pkce==1.0.3
+pkginfo==1.10.0
+pkgutil-resolve-name==1.3.10 ; python_version < '0'
+platformdirs==4.3.6
+playwright==1.48.0
+pluggy==1.5.0
+port-for==0.7.3
+prettytable==3.11.0
+propcache==0.2.0
+psutil==6.1.0 ; sys_platform != 'cygwin'
+psycopg==3.2.3
+pycparser==2.22
+pyee==12.0.0
+pygithub==2.4.0
+pygments==2.18.0
+pyjwt==2.9.0
+pynacl==1.5.0
+pyparsing==3.1.4
+pyproject-hooks==1.2.0
+pysocks==1.7.1
+pytest==8.3.3
+pytest-asyncio==0.24.0
+pytest-base-url==2.1.0
+pytest-cov==5.0.0
+pytest-html==4.1.1
+pytest-httpserver==1.1.0
+pytest-json-report==1.5.0
+pytest-metadata==3.1.1
+pytest-mock==3.14.0
+pytest-playwright==0.5.2
+pytest-postgresql==6.1.1
+pytest-shard==0.1.2
+python-dateutil==2.9.0.post0
+python-irodsclient==2.2.0
+python-slugify==8.0.4
+pytz==2024.2 ; python_full_version < '3.9'
+pywin32-ctypes==0.2.3 ; sys_platform == 'win32'
+pyyaml==6.0.2
+rdflib==6.3.2
+readme-renderer==43.0
+referencing==0.35.1 ; python_full_version >= '3.9'
+requests==2.32.3
+requests-toolbelt==1.0.0
+responses==0.25.3
+rfc3986==2.0.0
+rich==13.9.3
+rpds-py==0.20.0 ; python_full_version >= '3.9'
+ruamel-yaml==0.18.6
+ruamel-yaml-clib==0.2.8 ; python_full_version < '3.13' and platform_python_implementation == 'CPython'
+rucio-clients==35.4.1
+s3transfer==0.10.3
+schema-salad==8.7.20241010092723
+scipy==1.10.1 ; python_full_version < '3.9'
+scipy==1.13.1 ; python_full_version == '3.9.*'
+scipy==1.14.1 ; python_full_version >= '3.10'
+secretstorage==3.3.3 ; sys_platform == 'linux'
+selenium==4.25.0
+seletools==1.5.0
+setuptools==75.2.0
+six==1.16.0
+sniffio==1.3.1
+snowballstemmer==2.2.0
+sortedcontainers==2.4.0
+sphinx==7.1.2
+sphinx-rtd-theme==3.0.1
+sphinxcontrib-applehelp==1.0.4
+sphinxcontrib-devhelp==1.0.2
+sphinxcontrib-htmlhelp==2.0.1
+sphinxcontrib-jquery==4.1
+sphinxcontrib-jsmath==1.0.1
+sphinxcontrib-qthelp==1.0.3
+sphinxcontrib-serializinghtml==1.1.5
+statsd==4.0.1
+stevedore==5.3.0 ; python_full_version >= '3.9'
+tabulate==0.9.0 ; python_full_version >= '3.9'
+testfixtures==8.3.0
+text-unidecode==1.3
+tinydb==4.8.2
+toml==0.10.2
+tomli==2.0.2 ; python_full_version <= '3.11'
+trio==0.27.0
+trio-websocket==0.11.1
+tuspy==1.0.3
+twill==3.3
+twine==5.1.1
+typing-extensions==4.12.2
+tzdata==2024.2 ; sys_platform == 'win32'
+urllib3==1.26.20
+watchdog==4.0.2
+wcwidth==0.2.13
+websocket-client==1.8.0
+werkzeug==3.0.6
+wrapt==1.16.0
+wsproto==1.2.0
+yarl==1.15.2
+zipp==3.20.2