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Update Python dependencies
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by running `make update-dependencies`.
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@galaxybot @github-actions
galaxybot authored and github-actions[bot] committed Jun 1, 2024
1 parent 9753a0b commit fe5efbe
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38 changes: 20 additions & 18 deletions lib/galaxy/dependencies/dev-requirements.txt
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Original file line number Diff line number Diff line change
@@ -1,27 +1,29 @@
--extra-index-url https://wheels.galaxyproject.org/simple

aiohttp==3.9.5 ; 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==4.3.0 ; python_version >= "3.8" and python_version < "3.13"
ase==3.22.1 ; python_version >= "3.8" and python_version < "3.13"
anyio==4.4.0 ; 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==23.2.0 ; 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==2.15.0 ; python_version >= "3.8" and python_version < "3.13"
backports-tarfile==1.1.1 ; python_version >= "3.8" and python_version < "3.12"
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==24.4.2 ; python_version >= "3.8" and python_version < "3.13"
boto3==1.34.106 ; python_version >= "3.8" and python_version < "3.13"
botocore==1.34.106 ; python_version >= "3.8" and python_version < "3.13"
boto3==1.34.117 ; python_version >= "3.8" and python_version < "3.13"
botocore==1.34.117 ; python_version >= "3.8" and python_version < "3.13"
build==1.2.1 ; python_version >= "3.8" and python_version < "3.13"
cachecontrol[filecache]==0.14.0 ; python_version >= "3.8" and python_version < "3.13"
certifi==2024.2.2 ; 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==8.1.7 ; python_version >= "3.8" and python_version < "3.13"
codespell==2.2.6 ; 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 < "3.13"
coverage[toml]==7.5.1 ; python_version >= "3.8" and python_version < "3.13"
coverage[toml]==7.5.3 ; python_version >= "3.8" and python_version < "3.13"
cryptography==42.0.7 ; python_version >= "3.8" and python_version < "3.13"
cwltest==2.5.20240425111257 ; python_version >= "3.8" and python_version < "3.13"
cycler==0.12.1 ; python_version >= "3.8" and python_version < "3.13"
Expand All @@ -35,9 +37,9 @@ dogpile-cache==1.2.2 ; python_version >= "3.9" and python_version < "3.13"
exceptiongroup==1.2.1 ; python_version >= "3.8" and python_version < "3.11"
filelock==3.14.0 ; python_version >= "3.8" and python_version < "3.13"
fluent-logger==0.11.0 ; python_version >= "3.8" and python_version < "3.13"
fonttools==4.51.0 ; python_version >= "3.8" and python_version < "3.13"
fonttools==4.53.0 ; 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==0.1.9 ; 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==3.0.3 ; python_version >= "3.8" and python_version < "3.13"
h11==0.14.0 ; python_version >= "3.8" and python_version < "3.13"
Expand Down Expand Up @@ -86,7 +88,7 @@ pathspec==0.12.1 ; python_version >= "3.8" and python_version < "3.13"
pbr==6.0.0 ; python_version >= "3.9" and python_version < "3.13"
pillow==10.3.0 ; 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"
pkginfo==1.11.0 ; python_version >= "3.8" and python_version < "3.13"
platformdirs==4.2.2 ; python_version >= "3.8" and python_version < "3.13"
playwright==1.44.0 ; python_version >= "3.8" and python_version < "3.13"
pluggy==1.5.0 ; python_version >= "3.8" and python_version < "3.13"
Expand Down Expand Up @@ -114,7 +116,7 @@ pytest-mock==3.14.0 ; python_version >= "3.8" and python_version < "3.13"
pytest-playwright==0.5.0 ; python_version >= "3.8" and python_version < "3.13"
pytest-postgresql==6.0.0 ; 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"
pytest==8.2.1 ; 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==2.0.1 ; python_version >= "3.8" and python_version < "3.13"
python-slugify==8.0.4 ; python_version >= "3.8" and python_version < "3.13"
Expand All @@ -125,22 +127,22 @@ 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==2.31.0 ; python_version >= "3.8" and python_version < "3.13"
requests==2.32.3 ; python_version >= "3.8" and python_version < "3.13"
responses==0.25.0 ; python_version >= "3.8" and python_version < "3.13"
rfc3986==2.0.0 ; python_version >= "3.8" and python_version < "3.13"
rich==13.7.1 ; python_version >= "3.8" and python_version < "3.13"
rpds-py==0.18.1 ; 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==34.3.0 ; python_version >= "3.9" and python_version < "3.13"
rucio-clients==34.4.1 ; python_version >= "3.9" and python_version < "3.13"
s3transfer==0.10.1 ; python_version >= "3.8" and python_version < "3.13"
schema-salad==8.5.20240503091721 ; python_version >= "3.8" and python_version < "3.13"
scipy==1.10.1 ; python_version >= "3.8" and python_version < "3.9"
scipy==1.13.0 ; python_version >= "3.9" and python_version < "3.13"
scipy==1.13.1 ; 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==4.21.0 ; python_version >= "3.8" and python_version < "3.13"
seletools==1.5.0 ; python_version >= "3.8" and python_version < "3.13"
setuptools==69.5.1 ; python_version >= "3.8" and python_version < "3.13"
setuptools==70.0.0 ; 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"
Expand All @@ -167,14 +169,14 @@ trio==0.25.1 ; python_version >= "3.8" and python_version < "3.13"
tuspy==1.0.3 ; python_version >= "3.8" and python_version < "3.13"
twill==3.2.4 ; python_version >= "3.8" and python_version < "3.13"
twine==5.1.0 ; python_version >= "3.8" and python_version < "3.13"
typing-extensions==4.11.0 ; python_version >= "3.8" and python_version < "3.13"
typing-extensions==4.12.0 ; python_version >= "3.8" and python_version < "3.13"
tzdata==2024.1 ; python_version >= "3.8" and python_version < "3.13" and sys_platform == "win32"
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"
watchdog==4.0.0 ; python_version >= "3.8" and python_version < "3.13"
watchdog==4.0.1 ; python_version >= "3.8" and python_version < "3.13"
wcwidth==0.2.13 ; python_version >= "3.8" and python_version < "3.13"
werkzeug==3.0.3 ; 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==1.9.4 ; python_version >= "3.8" and python_version < "3.13"
zipp==3.18.2 ; python_version >= "3.8" and python_version < "3.13"
zipp==3.19.1 ; python_version >= "3.8" and python_version < "3.13"
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==24.4.26
mccabe==0.7.0
pycodestyle==2.11.1
pyflakes==3.2.0
ruff==0.4.4
ruff==0.4.7
31 changes: 14 additions & 17 deletions lib/galaxy/dependencies/pinned-requirements.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -2,17 +2,15 @@

a2wsgi==1.10.4 ; python_version >= "3.8" and python_version < "3.13"
adal==1.2.7 ; python_version >= "3.8" and python_version < "3.13"
aiobotocore==2.13.0 ; python_version >= "3.8" and python_version < "3.13"
aiodataloader==0.4.0 ; python_version >= "3.8" and python_version < "3.13"
aiofiles==23.2.1 ; python_version >= "3.8" and python_version < "3.13"
aiohttp==3.9.5 ; python_version >= "3.8" and python_version < "3.13"
aioitertools==0.11.0 ; python_version >= "3.8" and python_version < "3.13"
aiosignal==1.3.1 ; python_version >= "3.8" and python_version < "3.13"
alembic==1.13.1 ; python_version >= "3.8" and python_version < "3.13"
amqp==5.2.0 ; python_version >= "3.8" and python_version < "3.13"
aniso8601==9.0.1 ; python_version >= "3.8" and python_version < "3.13"
annotated-types==0.6.0 ; python_version >= "3.8" and python_version < "3.13"
anyio==4.3.0 ; python_version >= "3.8" and python_version < "3.13"
annotated-types==0.7.0 ; python_version >= "3.8" and python_version < "3.13"
anyio==4.4.0 ; python_version >= "3.8" and python_version < "3.13"
apispec==6.6.1 ; python_version >= "3.8" and python_version < "3.13"
appdirs==1.4.4 ; python_version >= "3.8" and python_version < "3.13"
arcp==0.2.1 ; python_version >= "3.8" and python_version < "3.13"
Expand All @@ -33,7 +31,7 @@ bioblend==1.3.0 ; python_version >= "3.8" and python_version < "3.13"
bleach==6.1.0 ; python_version >= "3.8" and python_version < "3.13"
boltons==24.0.0 ; python_version >= "3.8" and python_version < "3.13"
boto==2.49.0 ; python_version >= "3.8" and python_version < "3.13"
botocore==1.34.106 ; python_version >= "3.8" and python_version < "3.13"
botocore==1.34.117 ; python_version >= "3.8" and python_version < "3.13"
bx-python==0.11.0 ; python_version >= "3.8" and python_version < "3.13"
cachecontrol[filecache]==0.14.0 ; python_version >= "3.8" and python_version < "3.13"
celery==5.4.0 ; python_version >= "3.8" and python_version < "3.13"
Expand Down Expand Up @@ -113,7 +111,7 @@ msgpack==1.0.8 ; 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"
networkx==2.5 ; python_version >= "3.8" and python_version < "3.13"
nodeenv==1.8.0 ; python_version >= "3.8" and python_version < "3.13"
nodeenv==1.9.0 ; python_version >= "3.8" and python_version < "3.13"
numpy==1.24.4 ; python_version >= "3.8" and python_version < "3.9"
numpy==1.26.4 ; python_version >= "3.9" and python_version < "3.13"
oauthlib==3.2.2 ; python_version >= "3.8" and python_version < "3.13"
Expand All @@ -127,16 +125,16 @@ pastedeploy==3.1.0 ; python_version >= "3.8" and python_version < "3.13"
pebble==5.0.7 ; python_version >= "3.8" and python_version < "3.13"
pillow==10.3.0 ; python_version >= "3.8" and python_version < "3.13"
promise==2.3 ; python_version >= "3.8" and python_version < "3.13"
prompt-toolkit==3.0.43 ; python_version >= "3.8" and python_version < "3.13"
prompt-toolkit==3.0.45 ; python_version >= "3.8" and python_version < "3.13"
prov==1.5.1 ; python_version >= "3.8" and python_version < "3.13"
psutil==5.9.8 ; python_version >= "3.8" and python_version < "3.13"
pulsar-galaxy-lib==0.15.6 ; python_version >= "3.8" and python_version < "3.13"
pycparser==2.22 ; python_version >= "3.8" and python_version < "3.13"
pycryptodome==3.20.0 ; python_version >= "3.8" and python_version < "3.13"
pydantic-core==2.18.2 ; python_version >= "3.8" and python_version < "3.13"
pydantic-core==2.18.3 ; python_version >= "3.8" and python_version < "3.13"
pydantic-tes==0.1.5 ; python_version >= "3.8" and python_version < "3.13"
pydantic==2.7.1 ; python_version >= "3.8" and python_version < "3.13"
pydantic[email]==2.7.1 ; python_version >= "3.8" and python_version < "3.13"
pydantic==2.7.2 ; python_version >= "3.8" and python_version < "3.13"
pydantic[email]==2.7.2 ; python_version >= "3.8" and python_version < "3.13"
pydot==2.0.0 ; python_version >= "3.8" and python_version < "3.13"
pyeventsystem==0.1.0 ; python_version >= "3.8" and python_version < "3.13"
pyfaidx==0.8.1.1 ; python_version >= "3.8" and python_version < "3.13"
Expand Down Expand Up @@ -164,17 +162,17 @@ repoze-lru==0.7 ; python_version >= "3.8" and python_version < "3.13"
requests-oauthlib==2.0.0 ; python_version >= "3.8" and python_version < "3.13"
requests-toolbelt==1.0.0 ; python_version >= "3.8" and python_version < "3.13"
requests-unixsocket==0.3.0 ; python_version >= "3.8" and python_version < "3.13"
requests==2.31.0 ; python_version >= "3.8" and python_version < "3.13"
requests==2.32.3 ; python_version >= "3.8" and python_version < "3.13"
rich==13.7.1 ; python_version >= "3.8" and python_version < "3.13"
rocrate==0.10.0 ; python_version >= "3.8" and python_version < "3.13"
routes==2.5.1 ; python_version >= "3.8" and python_version < "3.13"
rpds-py==0.18.1 ; 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==0.18.6 ; python_version >= "3.8" and python_version < "3.13"
s3fs==2024.5.0 ; python_version >= "3.8" and python_version < "3.13"
s3fs==0.4.2 ; python_version >= "3.8" and python_version < "3.13"
schema-salad==8.5.20240503091721 ; python_version >= "3.8" and python_version < "3.13"
setuptools-scm==5.0.2 ; python_version >= "3.8" and python_version < "3.13"
setuptools==69.5.1 ; python_version >= "3.8" and python_version < "3.13"
setuptools==70.0.0 ; python_version >= "3.8" and python_version < "3.13"
shellescape==3.8.1 ; 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"
Expand All @@ -197,21 +195,20 @@ tornado==6.4 ; python_version >= "3.8" and python_version < "3.13"
tqdm==4.66.4 ; python_version >= "3.8" and python_version < "3.13"
tuspy==1.0.3 ; python_version >= "3.8" and python_version < "3.13"
tuswsgi==0.5.5 ; python_version >= "3.8" and python_version < "3.13"
typing-extensions==4.11.0 ; python_version >= "3.8" and python_version < "3.13"
typing-extensions==4.12.0 ; python_version >= "3.8" and python_version < "3.13"
tzdata==2024.1 ; python_version >= "3.8" and python_version < "3.13"
tzlocal==5.2 ; python_version >= "3.8" and python_version < "3.13"
ubiquerg==0.8.0 ; python_version >= "3.8" and python_version < "3.13"
urllib3==1.26.18 ; python_version >= "3.8" and python_version < "3.13"
uvicorn==0.29.0 ; python_version >= "3.8" and python_version < "3.13"
uvicorn==0.30.0 ; python_version >= "3.8" and python_version < "3.13"
uvloop==0.19.0 ; python_version >= "3.8" and python_version < "3.13"
vine==5.1.0 ; python_version >= "3.8" and python_version < "3.13"
wcwidth==0.2.13 ; python_version >= "3.8" and python_version < "3.13"
webencodings==0.5.1 ; python_version >= "3.8" and python_version < "3.13"
webob==1.8.7 ; python_version >= "3.8" and python_version < "3.13"
whoosh==2.7.4 ; python_version >= "3.8" and python_version < "3.13"
wrapt==1.16.0 ; python_version >= "3.8" and python_version < "3.13"
yacman==0.9.3 ; python_version >= "3.8" and python_version < "3.13"
yarl==1.9.4 ; python_version >= "3.8" and python_version < "3.13"
zipp==3.18.2 ; python_version >= "3.8" and python_version < "3.13"
zipp==3.19.1 ; python_version >= "3.8" and python_version < "3.13"
zipstream-new==1.1.8 ; python_version >= "3.8" and python_version < "3.13"
zstandard==0.22.0 ; python_version >= "3.8" and python_version < "3.13"
12 changes: 7 additions & 5 deletions lib/galaxy/dependencies/pinned-typecheck-requirements.txt
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Original file line number Diff line number Diff line change
@@ -1,5 +1,7 @@
annotated-types==0.6.0 ; python_version >= "3.8" and python_version < "3.13"
boto3-stubs[s3]==1.34.108 ; python_version >= "3.8" and python_version < "3.13"
--extra-index-url https://wheels.galaxyproject.org/simple

annotated-types==0.7.0 ; python_version >= "3.8" and python_version < "3.13"
boto3-stubs[s3]==1.34.117 ; python_version >= "3.8" and python_version < "3.13"
botocore-stubs==1.34.94 ; python_version >= "3.8" and python_version < "3.13"
cffi==1.16.0 ; python_version >= "3.8" and python_version < "3.13" and platform_python_implementation != "PyPy"
cryptography==42.0.7 ; python_version >= "3.8" and python_version < "3.13"
Expand All @@ -8,8 +10,8 @@ mypy-boto3-s3==1.34.105 ; python_version >= "3.8" and python_version < "3.13"
mypy-extensions==1.0.0 ; python_version >= "3.8" and python_version < "3.13"
mypy==1.10.0 ; python_version >= "3.8" and python_version < "3.13"
pycparser==2.22 ; python_version >= "3.8" and python_version < "3.13" and platform_python_implementation != "PyPy"
pydantic-core==2.18.2 ; python_version >= "3.8" and python_version < "3.13"
pydantic==2.7.1 ; python_version >= "3.8" and python_version < "3.13"
pydantic-core==2.18.3 ; python_version >= "3.8" and python_version < "3.13"
pydantic==2.7.2 ; python_version >= "3.8" and python_version < "3.13"
tomli==2.0.1 ; python_version >= "3.8" and python_version < "3.11"
types-awscrt==0.20.9 ; python_version >= "3.8" and python_version < "3.13"
types-bleach==6.1.0.20240331 ; python_version >= "3.8" and python_version < "3.13"
Expand All @@ -27,4 +29,4 @@ types-requests==2.31.0.6 ; python_version >= "3.8" and python_version < "3.13"
types-s3transfer==0.10.1 ; python_version >= "3.8" and python_version < "3.13"
types-six==1.16.21.20240513 ; python_version >= "3.8" and python_version < "3.13"
types-urllib3==1.26.25.14 ; python_version >= "3.8" and python_version < "3.13"
typing-extensions==4.11.0 ; python_version >= "3.8" and python_version < "3.13"
typing-extensions==4.12.0 ; python_version >= "3.8" and python_version < "3.13"

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