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Update Python dependencies #17420

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merged 5 commits into from
Feb 15, 2024
Merged

Update Python dependencies #17420

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f9384bb
Disallow pydantic 2.6.0 and 2.6.1
nsoranzo Feb 12, 2024
1efa675
Update Python dependencies
galaxybot Feb 10, 2024
167282f
Update ruff settings for 0.2.0 deprecations
nsoranzo Feb 14, 2024
6250c97
Allow manual dispatch of "Update dependencies" GH workflow
nsoranzo Feb 12, 2024
ca1cf0a
Update ``test_api_meta`` integration test for h5grove 2.0.0
nsoranzo Feb 14, 2024
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1 change: 1 addition & 0 deletions .github/workflows/dependencies.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,7 @@ name: Update dependencies
on:
schedule:
- cron: '0 3 * * 6' # Run every saturday at 3 am.
workflow_dispatch:
jobs:
update_dependencies:
name: Update dependencies
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60 changes: 30 additions & 30 deletions lib/galaxy/dependencies/dev-requirements.txt
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Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
aiohttp==3.9.1 ; python_version >= "3.8" and python_version < "3.13"
aiohttp==3.9.3 ; 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"
amqp==5.2.0 ; python_version >= "3.8" and python_version < "3.13"
Expand All @@ -11,11 +11,11 @@ babel==2.14.0 ; python_version >= "3.8" and python_version < "3.13"
backports-zoneinfo==0.2.1 ; python_version >= "3.8" and python_version < "3.9"
backports-zoneinfo[tzdata]==0.2.1 ; python_version >= "3.8" and python_version < "3.9"
billiard==4.2.0 ; python_version >= "3.8" and python_version < "3.13"
black==24.1.1 ; python_version >= "3.8" and python_version < "3.13"
black==24.2.0 ; python_version >= "3.8" and python_version < "3.13"
build==1.0.3 ; python_version >= "3.8" and python_version < "3.13"
cachecontrol[filecache]==0.13.1 ; python_version >= "3.8" and python_version < "3.13"
celery==5.3.6 ; python_version >= "3.8" and python_version < "3.13"
certifi==2023.11.17 ; python_version >= "3.8" and python_version < "3.13"
certifi==2024.2.2 ; python_version >= "3.8" and python_version < "3.13"
cffi==1.16.0 ; python_version >= "3.8" and python_version < "3.13"
charset-normalizer==3.3.2 ; python_version >= "3.8" and python_version < "3.13"
click-didyoumean==0.3.0 ; python_version >= "3.8" and python_version < "3.13"
Expand All @@ -26,8 +26,8 @@ codespell==2.2.6 ; 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 < "3.13"
coverage[toml]==7.4.1 ; python_version >= "3.8" and python_version < "3.13"
cryptography==42.0.1 ; python_version >= "3.8" and python_version < "3.13"
cwltest==2.4.20231222081524 ; python_version >= "3.8" and python_version < "3.13"
cryptography==42.0.2 ; python_version >= "3.8" and python_version < "3.13"
cwltest==2.4.20240129145612 ; python_version >= "3.8" and python_version < "3.13"
cycler==0.12.1 ; python_version >= "3.8" and python_version < "3.13"
darker==1.7.2 ; python_version >= "3.8" and python_version < "3.13"
defusedxml==0.7.1 ; python_version >= "3.8" and python_version < "3.13"
Expand All @@ -36,7 +36,7 @@ docutils==0.18.1 ; python_version >= "3.8" and python_version < "3.13"
exceptiongroup==1.2.0 ; python_version >= "3.8" and python_version < "3.11"
filelock==3.13.1 ; python_version >= "3.8" and python_version < "3.13"
fluent-logger==0.10.0 ; python_version >= "3.8" and python_version < "3.13"
fonttools==4.47.2 ; python_version >= "3.8" and python_version < "3.13"
fonttools==4.48.1 ; python_version >= "3.8" and python_version < "3.13"
frozenlist==1.4.1 ; python_version >= "3.8" and python_version < "3.13"
galaxy-release-util==0.1.5 ; python_version >= "3.8" and python_version < "3.13"
greenlet==3.0.3 ; python_version >= "3.8" and python_version < "3.13"
Expand All @@ -50,7 +50,7 @@ importlib-resources==6.1.1 ; 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==3.3.0 ; python_version >= "3.8" and python_version < "3.13"
jaraco-classes==3.3.1 ; 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==3.1.3 ; python_version >= "3.8" and python_version < "3.13"
junit-xml==1.9 ; python_version >= "3.8" and python_version < "3.13"
Expand All @@ -60,7 +60,7 @@ kombu==5.3.5 ; python_version >= "3.8" and python_version < "3.13"
lxml==4.9.4 ; 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==2.1.4 ; python_version >= "3.8" and python_version < "3.13"
markupsafe==2.1.5 ; python_version >= "3.8" and python_version < "3.13"
matplotlib==3.7.4 ; python_version >= "3.8" and python_version < "3.9"
matplotlib==3.8.2 ; python_version >= "3.9" and python_version < "3.13"
mdit-py-plugins==0.4.0 ; python_version >= "3.8" and python_version < "3.13"
Expand All @@ -69,70 +69,70 @@ mirakuru==2.5.2 ; python_version >= "3.8" and python_version < "3.13"
mistune==2.0.5 ; python_version >= "3.8" and python_version < "3.13"
more-itertools==10.2.0 ; python_version >= "3.8" and python_version < "3.13"
msgpack==1.0.7 ; python_version >= "3.8" and python_version < "3.13"
multidict==6.0.4 ; python_version >= "3.8" and python_version < "3.13"
multidict==6.0.5 ; 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==2.0.0 ; python_version >= "3.8" and python_version < "3.13"
nh3==0.2.15 ; python_version >= "3.8" and python_version < "3.13"
numpy==1.24.4 ; python_version >= "3.8" and python_version < "3.9"
numpy==1.26.3 ; python_version >= "3.9" and python_version < "3.13"
numpy==1.26.4 ; python_version >= "3.9" and python_version < "3.13"
outcome==1.3.0.post0 ; python_version >= "3.8" and python_version < "3.13"
packaging==23.2 ; python_version >= "3.8" and python_version < "3.13"
pathspec==0.12.1 ; python_version >= "3.8" and python_version < "3.13"
pillow==10.2.0 ; python_version >= "3.8" and python_version < "3.13"
pkce==1.0.3 ; python_version >= "3.8" and python_version < "3.13"
pkginfo==1.9.6 ; python_version >= "3.8" and python_version < "3.13"
platformdirs==4.1.0 ; python_version >= "3.8" and python_version < "3.13"
playwright==1.41.1 ; python_version >= "3.8" and python_version < "3.13"
platformdirs==4.2.0 ; python_version >= "3.8" and python_version < "3.13"
playwright==1.41.2 ; python_version >= "3.8" and python_version < "3.13"
pluggy==1.4.0 ; python_version >= "3.8" and python_version < "3.13"
port-for==0.7.2 ; python_version >= "3.8" and python_version < "3.13"
prettytable==3.9.0 ; python_version >= "3.8" and python_version < "3.13"
prompt-toolkit==3.0.43 ; python_version >= "3.8" and python_version < "3.13"
psutil==5.9.8 ; python_version >= "3.8" and python_version < "3.13" and sys_platform != "cygwin"
psycopg==3.1.17 ; python_version >= "3.8" and python_version < "3.13"
psycopg==3.1.18 ; python_version >= "3.8" and python_version < "3.13"
pycparser==2.21 ; python_version >= "3.8" and python_version < "3.13"
pyee==11.0.1 ; python_version >= "3.8" and python_version < "3.13"
pygithub==2.1.1 ; python_version >= "3.8" and python_version < "3.13"
pygithub==2.2.0 ; python_version >= "3.8" and python_version < "3.13"
pygments==2.17.2 ; python_version >= "3.8" and python_version < "3.13"
pyjwt[crypto]==2.8.0 ; python_version >= "3.8" and python_version < "3.13"
pynacl==1.5.0 ; python_version >= "3.8" and python_version < "3.13"
pyparsing==3.1.1 ; python_version >= "3.8" and python_version < "3.13"
pyproject-hooks==1.0.0 ; python_version >= "3.8" and python_version < "3.13"
pysocks==1.7.1 ; python_version >= "3.8" and python_version < "3.13"
pytest-asyncio==0.23.3 ; python_version >= "3.8" and python_version < "3.13"
pytest-base-url==2.0.0 ; python_version >= "3.8" and python_version < "3.13"
pytest-asyncio==0.23.5 ; 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-celery==0.0.0 ; python_version >= "3.8" and python_version < "3.13"
pytest-cov==4.1.0 ; 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==1.0.8 ; python_version >= "3.8" and python_version < "3.13"
pytest-httpserver==1.0.9 ; 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==3.0.0 ; 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==3.12.0 ; python_version >= "3.8" and python_version < "3.13"
pytest-playwright==0.4.3 ; python_version >= "3.8" and python_version < "3.13"
pytest-postgresql==5.0.0 ; python_version >= "3.8" and python_version < "3.13"
pytest-playwright==0.4.4 ; python_version >= "3.8" and python_version < "3.13"
pytest-postgresql==5.1.0 ; 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==2.8.2 ; python_version >= "3.8" and python_version < "3.13"
python-irodsclient==1.1.9 ; python_version >= "3.8" and python_version < "3.13"
python-slugify==8.0.2 ; python_version >= "3.8" and python_version < "3.13"
pytz==2023.3.post1 ; python_version >= "3.8" and python_version < "3.9"
python-irodsclient==2.0.0 ; python_version >= "3.8" and python_version < "3.13"
python-slugify==8.0.4 ; python_version >= "3.8" and python_version < "3.13"
pytz==2024.1 ; python_version >= "3.8" and python_version < "3.9"
pywin32-ctypes==0.2.2 ; python_version >= "3.8" and python_version < "3.13" and sys_platform == "win32"
pyyaml==6.0.1 ; python_version >= "3.8" and python_version < "3.13"
rdflib==6.3.2 ; python_version >= "3.8" and python_version < "3.13"
readme-renderer==42.0 ; python_version >= "3.8" and python_version < "3.13"
requests-toolbelt==1.0.0 ; python_version >= "3.8" and python_version < "3.13"
requests==2.31.0 ; python_version >= "3.8" and python_version < "3.13"
responses==0.24.1 ; python_version >= "3.8" and python_version < "3.13"
responses==0.25.0 ; python_version >= "3.8" and python_version < "3.13"
rfc3986==2.0.0 ; python_version >= "3.8" and python_version < "3.13"
rich==13.7.0 ; python_version >= "3.8" 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==0.18.5 ; python_version >= "3.8" and python_version < "3.13"
ruamel-yaml==0.18.6 ; python_version >= "3.8" and python_version < "3.13"
schema-salad==8.5.20240102191335 ; python_version >= "3.8" and python_version < "3.13"
scipy==1.10.1 ; python_version >= "3.8" and python_version < "3.9"
scipy==1.12.0 ; python_version >= "3.9" and python_version < "3.13"
secretstorage==3.3.3 ; python_version >= "3.8" and python_version < "3.13" and sys_platform == "linux"
selenium==4.17.2 ; python_version >= "3.8" and python_version < "3.13"
seletools==1.4.0 ; python_version >= "3.8" and python_version < "3.13"
setuptools==69.0.3 ; python_version >= "3.8" and python_version < "3.13"
setuptools==69.1.0 ; python_version >= "3.8" and python_version < "3.13"
six==1.16.0 ; python_version >= "3.8" and python_version < "3.13"
sniffio==1.3.0 ; python_version >= "3.8" and python_version < "3.13"
snowballstemmer==2.2.0 ; python_version >= "3.8" and python_version < "3.13"
Expand All @@ -155,14 +155,14 @@ tomli==2.0.1 ; 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==0.24.0 ; python_version >= "3.8" and python_version < "3.13"
tuspy==1.0.3 ; python_version >= "3.8" and python_version < "3.13"
twill==3.2.1 ; python_version >= "3.8" and python_version < "3.13"
twine==4.0.2 ; python_version >= "3.8" and python_version < "3.13"
twill==3.2.2 ; python_version >= "3.8" and python_version < "3.13"
twine==5.0.0 ; python_version >= "3.8" and python_version < "3.13"
typing-extensions==4.9.0 ; python_version >= "3.8" and python_version < "3.13"
tzdata==2023.4 ; python_version >= "3.8" and python_version < "3.13"
tzdata==2024.1 ; python_version >= "3.8" and python_version < "3.13"
urllib3==1.26.18 ; python_version >= "3.8" and python_version < "3.13"
urllib3[socks]==1.26.18 ; python_version >= "3.8" and python_version < "3.13"
vine==5.1.0 ; python_version >= "3.8" and python_version < "3.13"
watchdog==3.0.0 ; python_version >= "3.8" and python_version < "3.13"
watchdog==4.0.0 ; python_version >= "3.8" and python_version < "3.13"
wcwidth==0.2.13 ; python_version >= "3.8" and python_version < "3.13"
werkzeug==3.0.1 ; python_version >= "3.8" and python_version < "3.13"
wrapt==1.16.0 ; python_version >= "3.8" and python_version < "3.13"
Expand Down
4 changes: 2 additions & 2 deletions lib/galaxy/dependencies/pinned-lint-requirements.txt
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
attrs==23.2.0
flake8==7.0.0
flake8-bugbear==24.1.17
flake8-bugbear==24.2.6
mccabe==0.7.0
pycodestyle==2.11.1
pyflakes==3.2.0
ruff==0.1.14
ruff==0.2.1
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