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Update Python dependencies #19366

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Update Python dependencies #19366

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151 changes: 98 additions & 53 deletions lib/galaxy/dependencies/dev-requirements.txt
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Original file line number Diff line number Diff line change
@@ -1,31 +1,39 @@
# This file was autogenerated by uv via the following command:
# uv export --frozen --no-hashes --only-group=dev
aiohappyeyeballs==2.4.4
aiohttp==3.10.11
aiosignal==1.3.1
alabaster==0.7.13
anyio==4.5.2
aiohttp==3.10.11 ; python_full_version < '3.9'
aiohttp==3.11.11 ; python_full_version >= '3.9'
aiosignal==1.3.1 ; python_full_version < '3.9'
aiosignal==1.3.2 ; python_full_version >= '3.9'
alabaster==0.7.13 ; python_full_version < '3.9'
alabaster==0.7.16 ; python_full_version == '3.9.*'
alabaster==1.0.0 ; python_full_version >= '3.10'
anyio==4.5.2 ; python_full_version < '3.9'
anyio==4.7.0 ; python_full_version >= '3.9'
ase==3.23.0
async-timeout==5.0.1 ; python_full_version < '3.11'
attrs==24.3.0
axe-selenium-python==2.1.6
babel==2.16.0
backports-tarfile==1.2.0 ; python_full_version < '3.12' and platform_machine != 'ppc64le' and platform_machine != 's390x'
backports-zoneinfo==0.2.1 ; python_full_version < '3.9'
black==24.8.0
boto3==1.35.36
botocore==1.35.36
black==24.8.0 ; python_full_version < '3.9'
black==24.10.0 ; python_full_version >= '3.9'
boto3==1.35.88
botocore==1.35.88
build==1.2.2.post1
cachecontrol==0.14.1
certifi==2024.12.14
cffi==1.17.1
charset-normalizer==3.4.0
click==8.1.7
charset-normalizer==3.4.1
click==8.1.8
codespell==2.3.0
colorama==0.4.6 ; os_name == 'nt' or (platform_system == 'Windows' and sys_platform != 'win32') or sys_platform == 'win32'
colorama==0.4.6 ; os_name == 'nt' or sys_platform == 'win32'
contourpy==1.1.1 ; python_full_version < '3.9'
contourpy==1.3.0 ; python_full_version >= '3.9'
coverage==7.6.1
contourpy==1.3.0 ; python_full_version == '3.9.*'
contourpy==1.3.1 ; python_full_version >= '3.10'
coverage==7.6.1 ; python_full_version < '3.9'
coverage==7.6.10 ; python_full_version >= '3.9'
cryptography==44.0.0
cwltest==2.5.20241122133319
cycler==0.12.1
Expand All @@ -34,7 +42,8 @@ darkgraylib==1.2.1
decorator==5.1.1 ; python_full_version >= '3.9'
defusedxml==0.7.1
deprecated==1.2.15
docutils==0.20.1
docutils==0.20.1 ; python_full_version < '3.9'
docutils==0.21.2 ; python_full_version >= '3.9'
dogpile-cache==1.3.3 ; python_full_version >= '3.9'
exceptiongroup==1.2.2 ; python_full_version < '3.11'
filelock==3.16.1
Expand All @@ -52,7 +61,8 @@ imagesize==1.4.1
importlib-metadata==8.5.0 ; (python_full_version < '3.10.2' and platform_machine == 'ppc64le') or (python_full_version < '3.10.2' and platform_machine == 's390x') or (python_full_version < '3.12' and platform_machine != 'ppc64le' and platform_machine != 's390x')
importlib-resources==6.4.5 ; python_full_version < '3.10'
iniconfig==2.0.0
isodate==0.6.1
isodate==0.6.1 ; python_full_version < '3.9'
isodate==0.7.2 ; python_full_version >= '3.9' and python_full_version < '3.11'
isort==5.13.2
jaraco-classes==3.4.0 ; platform_machine != 'ppc64le' and platform_machine != 's390x'
jaraco-context==6.0.1 ; platform_machine != 'ppc64le' and platform_machine != 's390x'
Expand All @@ -61,108 +71,137 @@ jeepney==0.8.0 ; platform_machine != 'ppc64le' and platform_machine != 's390x' a
jinja2==3.1.5
jmespath==1.0.1
jsonschema==4.23.0 ; python_full_version >= '3.9'
jsonschema-specifications==2023.12.1 ; python_full_version >= '3.9'
jsonschema-specifications==2023.12.1 ; python_version < '0'
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jsonschema-specifications==2024.10.1 ; python_full_version >= '3.9'
junit-xml==1.9
keyring==25.5.0 ; platform_machine != 'ppc64le' and platform_machine != 's390x'
kiwisolver==1.4.7
keyring==25.5.0 ; python_full_version < '3.9' and platform_machine != 'ppc64le' and platform_machine != 's390x'
keyring==25.6.0 ; python_full_version >= '3.9' and platform_machine != 'ppc64le' and platform_machine != 's390x'
kiwisolver==1.4.7 ; python_full_version < '3.10'
kiwisolver==1.4.8 ; python_full_version >= '3.10'
lxml==5.3.0
markdown-it-py==3.0.0
markdown-it-reporter==0.0.2
markupsafe==2.1.5
markupsafe==2.1.5 ; python_full_version < '3.9'
markupsafe==3.0.2 ; python_full_version >= '3.9'
matplotlib==3.7.5 ; python_full_version < '3.9'
matplotlib==3.9.4 ; python_full_version >= '3.9'
matplotlib==3.9.4 ; python_full_version == '3.9.*'
matplotlib==3.10.0 ; python_full_version >= '3.10'
mdit-py-plugins==0.4.2
mdurl==0.1.2
mirakuru==2.5.2
mirakuru==2.5.2 ; python_full_version < '3.9'
mirakuru==2.5.3 ; python_full_version >= '3.9'
mistune==3.0.2
more-itertools==10.5.0 ; platform_machine != 'ppc64le' and platform_machine != 's390x'
msgpack==1.1.0
multidict==6.1.0
mypy-extensions==1.0.0
myst-parser==3.0.1
nh3==0.2.19
myst-parser==3.0.1 ; python_full_version < '3.10'
myst-parser==4.0.0 ; python_full_version >= '3.10'
nh3==0.2.20
numpy==1.24.4 ; python_full_version < '3.9'
numpy==2.0.2 ; python_full_version == '3.9.*'
numpy==2.2.0 ; python_full_version >= '3.10'
numpy==2.2.1 ; python_full_version >= '3.10'
onedatafilerestclient==21.2.5.2
outcome==1.3.0.post0
packaging==24.2
pathspec==0.12.1
pbr==6.1.0 ; python_full_version >= '3.9'
pillow==10.4.0
pillow==10.4.0 ; python_full_version < '3.9'
pillow==11.0.0 ; python_full_version >= '3.9'
pkce==1.0.3
pkginfo==1.12.0
pkgutil-resolve-name==1.3.10 ; python_version < '0'
platformdirs==4.3.6
playwright==1.48.0
playwright==1.48.0 ; python_full_version < '3.9'
playwright==1.49.1 ; python_full_version >= '3.9'
pluggy==1.5.0
port-for==0.7.3
prettytable==3.11.0
propcache==0.2.0
psutil==6.1.0 ; sys_platform != 'cygwin'
port-for==0.7.3 ; python_full_version < '3.9'
port-for==0.7.4 ; python_full_version >= '3.9'
prettytable==3.11.0 ; python_full_version < '3.9'
prettytable==3.12.0 ; python_full_version >= '3.9'
propcache==0.2.0 ; python_full_version < '3.9'
propcache==0.2.1 ; python_full_version >= '3.9'
psutil==6.1.1 ; sys_platform != 'cygwin'
psycopg==3.2.3
pycparser==2.22
pyee==12.0.0
pygithub==2.5.0
pygments==2.18.0
pyjwt==2.9.0
pyjwt==2.9.0 ; python_full_version < '3.9'
pyjwt==2.10.1 ; python_full_version >= '3.9'
pynacl==1.5.0
pyparsing==3.1.4
pyparsing==3.1.4 ; python_full_version < '3.9'
pyparsing==3.2.0 ; python_full_version >= '3.9'
pyproject-hooks==1.2.0
pysocks==1.7.1
pytest==7.4.4
pytest-asyncio==0.23.8
pytest-base-url==2.1.0
pytest-cov==5.0.0
pytest-cov==5.0.0 ; python_full_version < '3.9'
pytest-cov==6.0.0 ; python_full_version >= '3.9'
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-playwright==0.5.2 ; python_full_version < '3.9'
pytest-playwright==0.6.2 ; python_full_version >= '3.9'
pytest-postgresql==6.1.1
pytest-shard==0.1.2
python-dateutil==2.9.0.post0
python-irodsclient==2.2.0
python-irodsclient==3.0.0
python-slugify==8.0.4
pytz==2024.2 ; python_full_version < '3.9'
pywin32-ctypes==0.2.3 ; platform_machine != 'ppc64le' and platform_machine != 's390x' and sys_platform == 'win32'
pyyaml==6.0.2
rdflib==6.3.2 ; python_full_version < '3.8.1'
rdflib==7.0.0 ; python_full_version >= '3.8.1'
readme-renderer==43.0
rdflib==7.0.0 ; python_full_version >= '3.8.1' and python_full_version < '3.9'
rdflib==7.1.1 ; python_full_version >= '3.9'
readme-renderer==43.0 ; python_full_version < '3.9'
readme-renderer==44.0 ; python_full_version >= '3.9'
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==13.9.4
rpds-py==0.20.1 ; python_full_version >= '3.9'
rpds-py==0.20.1 ; python_version < '0'
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This doesn't seem correct.

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I agree. 🦅 👀

rpds-py==0.22.3 ; 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==36.0.0.post1 ; python_full_version >= '3.9'
ruamel-yaml-clib==0.2.8 ; python_full_version < '3.9' and platform_python_implementation == 'CPython'
ruamel-yaml-clib==0.2.12 ; python_full_version >= '3.9' and python_full_version < '3.13' and platform_python_implementation == 'CPython'
rucio-clients==36.0.0.post2 ; python_full_version >= '3.9'
s3transfer==0.10.4
schema-salad==8.7.20241010092723
schema-salad==8.7.20241010092723 ; python_full_version < '3.9'
schema-salad==8.8.20241206093842 ; python_full_version >= '3.9'
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 ; platform_machine != 'ppc64le' and platform_machine != 's390x' and sys_platform == 'linux'
selenium==4.27.1
seletools==1.5.0
setuptools==75.3.0
setuptools==75.3.0 ; python_full_version < '3.9'
setuptools==75.6.0 ; python_full_version >= '3.9'
six==1.17.0
sniffio==1.3.1
snowballstemmer==2.2.0
sortedcontainers==2.4.0
sphinx==7.1.2
sphinx==7.1.2 ; python_full_version < '3.9'
sphinx==7.4.7 ; python_full_version == '3.9.*'
sphinx==8.1.3 ; python_full_version >= '3.10'
sphinx-rtd-theme==3.0.2
sphinxcontrib-applehelp==1.0.4
sphinxcontrib-devhelp==1.0.2
sphinxcontrib-htmlhelp==2.0.1
sphinxcontrib-applehelp==1.0.4 ; python_full_version < '3.9'
sphinxcontrib-applehelp==2.0.0 ; python_full_version >= '3.9'
sphinxcontrib-devhelp==1.0.2 ; python_full_version < '3.9'
sphinxcontrib-devhelp==2.0.0 ; python_full_version >= '3.9'
sphinxcontrib-htmlhelp==2.0.1 ; python_full_version < '3.9'
sphinxcontrib-htmlhelp==2.1.0 ; python_full_version >= '3.9'
sphinxcontrib-jquery==4.1
sphinxcontrib-jsmath==1.0.1
sphinxcontrib-qthelp==1.0.3
sphinxcontrib-serializinghtml==1.1.5
sphinxcontrib-qthelp==1.0.3 ; python_full_version < '3.9'
sphinxcontrib-qthelp==2.0.0 ; python_full_version >= '3.9'
sphinxcontrib-serializinghtml==1.1.5 ; python_full_version < '3.9'
sphinxcontrib-serializinghtml==2.0.0 ; python_full_version >= '3.9'
statsd==4.0.1
stevedore==5.4.0 ; python_full_version >= '3.9'
tabulate==0.9.0 ; python_full_version >= '3.9'
Expand All @@ -171,19 +210,25 @@ text-unidecode==1.3
tinydb==4.8.2
toml==0.10.2
tomli==2.2.1 ; python_full_version <= '3.11'
trio==0.27.0
trio==0.27.0 ; python_full_version < '3.9'
trio==0.28.0 ; python_full_version >= '3.9'
trio-websocket==0.11.1
tuspy==1.1.0
twill==3.3
twine==6.0.1
typing-extensions==4.12.2
tzdata==2024.2 ; sys_platform == 'win32'
urllib3==1.26.20
watchdog==4.0.2
urllib3==1.26.20 ; python_full_version < '3.10'
urllib3==2.3.0 ; python_full_version >= '3.10'
watchdog==4.0.2 ; python_full_version < '3.9'
watchdog==6.0.0 ; python_full_version >= '3.9'
wcwidth==0.2.13
websocket-client==1.8.0
werkzeug==3.0.6
werkzeug==3.0.6 ; python_full_version < '3.9'
werkzeug==3.1.3 ; python_full_version >= '3.9'
wrapt==1.17.0
wsproto==1.2.0
yarl==1.15.2
zipp==3.20.2 ; (python_full_version < '3.10.2' and platform_machine == 'ppc64le') or (python_full_version < '3.10.2' and platform_machine == 's390x') or (python_full_version < '3.12' and platform_machine != 'ppc64le' and platform_machine != 's390x')
yarl==1.15.2 ; python_full_version < '3.9'
yarl==1.18.3 ; python_full_version >= '3.9'
zipp==3.20.2 ; python_full_version < '3.9'
zipp==3.21.0 ; (python_full_version >= '3.9' and python_full_version < '3.10.2' and platform_machine == 'ppc64le') or (python_full_version >= '3.9' and python_full_version < '3.10.2' and platform_machine == 's390x') or (python_full_version >= '3.9' and python_full_version < '3.12' and platform_machine != 'ppc64le' and platform_machine != 's390x')
2 changes: 1 addition & 1 deletion lib/galaxy/dependencies/pinned-lint-requirements.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -4,4 +4,4 @@ flake8-bugbear==24.12.12
mccabe==0.7.0
pycodestyle==2.12.1
pyflakes==3.2.0
ruff==0.8.3
ruff==0.8.4
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