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Update Python dependencies
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by running `make update-dependencies`.
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@galaxybot @nsoranzo
galaxybot authored and nsoranzo committed Jul 13, 2024
1 parent f1a4b56 commit b3b527a
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Showing 4 changed files with 30 additions and 30 deletions.
22 changes: 11 additions & 11 deletions lib/galaxy/dependencies/dev-requirements.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -16,15 +16,15 @@ boto3==1.34.131 ; python_version >= "3.8" and python_version < "3.13"
botocore==1.34.131 ; 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==2024.6.2 ; python_version >= "3.8" and python_version < "3.13"
certifi==2024.7.4 ; 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==2.3.0 ; 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==1.2.1 ; python_version >= "3.9" and python_version < "3.13"
coverage[toml]==7.5.4 ; python_version >= "3.8" and python_version < "3.13"
coverage[toml]==7.6.0 ; python_version >= "3.8" and python_version < "3.13"
cryptography==42.0.8 ; 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 @@ -35,10 +35,10 @@ 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==1.2.2 ; python_version >= "3.9" and python_version < "3.13"
exceptiongroup==1.2.1 ; python_version >= "3.8" and python_version < "3.11"
exceptiongroup==1.2.2 ; python_version >= "3.8" and python_version < "3.11"
filelock==3.15.4 ; python_version >= "3.8" and python_version < "3.13"
fluent-logger==0.11.1 ; python_version >= "3.8" and python_version < "3.13"
fonttools==4.53.0 ; python_version >= "3.8" and python_version < "3.13"
fonttools==4.53.1 ; 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==0.1.11 ; python_version >= "3.8" and python_version < "3.13"
graylint==1.1.1 ; python_version >= "3.8" and python_version < "3.13"
Expand Down Expand Up @@ -69,7 +69,7 @@ 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==3.9.0 ; python_version >= "3.9" and python_version < "3.13"
matplotlib==3.9.1 ; python_version >= "3.9" and python_version < "3.13"
mdit-py-plugins==0.4.1 ; 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"
Expand All @@ -79,7 +79,7 @@ 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"
myst-parser==3.0.1 ; python_version >= "3.8" and python_version < "3.13"
nh3==0.2.17 ; 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==2.0.0 ; python_version >= "3.9" and python_version < "3.13"
onedatafilerestclient==21.2.5.1 ; python_version >= "3.8" and python_version < "3.13"
Expand All @@ -94,7 +94,7 @@ platformdirs==4.2.2 ; python_version >= "3.8" and python_version < "3.13"
playwright==1.45.0 ; python_version >= "3.8" and python_version < "3.13"
pluggy==1.5.0 ; python_version >= "3.8" and python_version < "3.13"
port-for==0.7.2 ; python_version >= "3.8" and python_version < "3.13"
prettytable==3.10.0 ; python_version >= "3.8" and python_version < "3.13"
prettytable==3.10.2 ; python_version >= "3.8" and python_version < "3.13"
psutil==6.0.0 ; python_version >= "3.8" and python_version < "3.13" and sys_platform != "cygwin"
psycopg==3.2.1 ; python_version >= "3.8" and python_version < "3.13"
pycparser==2.22 ; python_version >= "3.8" and python_version < "3.13"
Expand Down Expand Up @@ -132,19 +132,19 @@ 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==13.7.1 ; python_version >= "3.8" and python_version < "3.13"
rpds-py==0.18.1 ; python_version >= "3.9" and python_version < "3.13"
rpds-py==0.19.0 ; 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==34.5.0 ; python_version >= "3.9" and python_version < "3.13"
s3transfer==0.10.2 ; python_version >= "3.8" and python_version < "3.13"
schema-salad==8.5.20240503091721 ; python_version >= "3.8" and python_version < "3.13"
schema-salad==8.6.20240710082410 ; 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==1.14.0 ; 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==4.22.0 ; python_version >= "3.8" and python_version < "3.13"
seletools==1.5.0 ; python_version >= "3.8" and python_version < "3.13"
setuptools==70.2.0 ; python_version >= "3.8" and python_version < "3.13"
setuptools==70.3.0 ; 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 @@ -167,7 +167,7 @@ tinydb==4.8.0 ; python_version >= "3.8" and python_version < "3.13"
toml==0.10.2 ; python_version >= "3.8" and python_version < "3.13"
tomli==2.0.1 ; 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==0.25.1 ; python_version >= "3.8" and python_version < "3.13"
trio==0.26.0 ; python_version >= "3.8" and python_version < "3.13"
tuspy==1.0.3 ; python_version >= "3.8" and python_version < "3.13"
twill==3.2.5 ; python_version >= "3.8" and python_version < "3.13"
twine==5.1.1 ; python_version >= "3.8" and python_version < "3.13"
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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==2.12.0
pyflakes==3.2.0
ruff==0.5.0
ruff==0.5.1
24 changes: 12 additions & 12 deletions lib/galaxy/dependencies/pinned-requirements.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -37,7 +37,7 @@ botocore==1.34.131 ; python_version >= "3.8" and python_version < "3.13"
bx-python==0.12.0 ; 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"
certifi==2024.6.2 ; python_version >= "3.8" and python_version < "3.13"
certifi==2024.7.4 ; 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"
cheetah3==3.2.6.post1 ; python_version >= "3.8" and python_version < "3.13"
Expand All @@ -54,7 +54,7 @@ conda-package-streaming==0.10.0 ; python_version >= "3.8" and python_version < "
cryptography==42.0.8 ; python_version >= "3.8" and python_version < "3.13"
cwl-upgrader==1.2.11 ; python_version >= "3.8" and python_version < "3.13"
cwl-utils==0.33 ; python_version >= "3.8" and python_version < "3.13"
cwltool==3.1.20240508115724 ; python_version >= "3.8" and python_version < "3.13"
cwltool==3.1.20240708091337 ; python_version >= "3.8" and python_version < "3.13"
defusedxml==0.7.1 ; python_version >= "3.8" and python_version < "3.13"
deprecation==2.1.0 ; python_version >= "3.8" and python_version < "3.13"
dictobj==0.4 ; python_version >= "3.8" and python_version < "3.13"
Expand All @@ -64,7 +64,7 @@ docutils==0.20.1 ; python_version >= "3.8" and python_version < "3.13"
dparse==0.6.3 ; python_version >= "3.8" and python_version < "3.13"
edam-ontology==1.25.2 ; python_version >= "3.8" and python_version < "3.13"
email-validator==2.2.0 ; python_version >= "3.8" and python_version < "3.13"
exceptiongroup==1.2.1 ; python_version >= "3.8" and python_version < "3.11"
exceptiongroup==1.2.2 ; python_version >= "3.8" and python_version < "3.11"
fastapi-slim==0.111.0 ; python_version >= "3.8" and python_version < "3.13"
filelock==3.15.4 ; python_version >= "3.8" and python_version < "3.13"
frozenlist==1.4.1 ; python_version >= "3.8" and python_version < "3.13"
Expand Down Expand Up @@ -104,9 +104,9 @@ markdown-it-py==3.0.0 ; python_version >= "3.8" and python_version < "3.13"
markdown==3.6 ; python_version >= "3.8" and python_version < "3.13"
markupsafe==2.1.5 ; python_version >= "3.8" and python_version < "3.13"
mdurl==0.1.2 ; python_version >= "3.8" and python_version < "3.13"
mercurial==6.7.4 ; python_version >= "3.8" and python_version < "3.13"
mercurial==6.8 ; python_version >= "3.8" and python_version < "3.13"
mistune==3.0.2 ; python_version >= "3.8" and python_version < "3.13"
mrcfile==1.5.0 ; python_version >= "3.8" and python_version < "3.13"
mrcfile==1.5.1 ; python_version >= "3.8" and python_version < "3.13"
msal==1.29.0 ; python_version >= "3.8" and python_version < "3.13"
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"
Expand All @@ -132,10 +132,10 @@ psutil==6.0.0 ; 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==2.20.0 ; python_version >= "3.8" and python_version < "3.13"
pydantic-core==2.20.1 ; python_version >= "3.8" and python_version < "3.13"
pydantic-tes==0.1.5 ; python_version >= "3.8" and python_version < "3.13"
pydantic==2.8.0 ; python_version >= "3.8" and python_version < "3.13"
pydantic[email]==2.8.0 ; python_version >= "3.8" and python_version < "3.13"
pydantic==2.8.2 ; python_version >= "3.8" and python_version < "3.13"
pydantic[email]==2.8.2 ; 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 @@ -167,13 +167,13 @@ 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"
rpds-py==0.19.0 ; 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==0.18.6 ; python_version >= "3.8" and python_version < "3.13"
s3fs==2024.6.1 ; python_version >= "3.8" and python_version < "3.13"
schema-salad==8.5.20240503091721 ; python_version >= "3.8" and python_version < "3.13"
schema-salad==8.6.20240710082410 ; python_version >= "3.8" and python_version < "3.13"
setuptools-scm==5.0.2 ; python_version >= "3.8" and python_version < "3.13"
setuptools==70.2.0 ; python_version >= "3.8" and python_version < "3.13"
setuptools==70.3.0 ; 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 @@ -188,7 +188,7 @@ starlette-graphene3==0.6.0 ; python_version >= "3.8" and python_version < "3.13"
starlette==0.37.2 ; python_version >= "3.8" and python_version < "3.13"
supervisor==4.2.5 ; python_version >= "3.8" and python_version < "3.13"
svgwrite==1.4.3 ; python_version >= "3.8" and python_version < "3.13"
tenacity==8.4.2 ; python_version >= "3.8" and python_version < "3.13"
tenacity==8.5.0 ; python_version >= "3.8" and python_version < "3.13"
tifffile==2023.7.10 ; python_version >= "3.8" and python_version < "3.13"
tinydb==4.8.0 ; python_version >= "3.8" and python_version < "3.13"
tomli==2.0.1 ; python_version >= "3.8" and python_version < "3.11"
Expand Down
12 changes: 6 additions & 6 deletions lib/galaxy/dependencies/pinned-typecheck-requirements.txt
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Original file line number Diff line number Diff line change
@@ -1,24 +1,24 @@
--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]==1.34.138 ; python_version >= "3.8" and python_version < "3.13"
botocore-stubs==1.34.138 ; python_version >= "3.8" and python_version < "3.13"
boto3-stubs[s3]==1.34.144 ; python_version >= "3.8" and python_version < "3.13"
botocore-stubs==1.34.144 ; 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==42.0.8 ; python_version >= "3.8" and python_version < "3.13"
lxml-stubs==0.5.1 ; python_version >= "3.8" and python_version < "3.13"
mypy-boto3-s3==1.34.138 ; python_version >= "3.8" and python_version < "3.13"
mypy-extensions==1.0.0 ; python_version >= "3.8" and python_version < "3.13"
mypy==1.10.1 ; 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==2.20.0 ; python_version >= "3.8" and python_version < "3.13"
pydantic==2.8.0 ; python_version >= "3.8" and python_version < "3.13"
pydantic-core==2.20.1 ; python_version >= "3.8" and python_version < "3.13"
pydantic==2.8.2 ; python_version >= "3.8" and python_version < "3.13"
tomli==2.0.1 ; python_version >= "3.8" and python_version < "3.11"
types-awscrt==0.20.12 ; python_version >= "3.8" and python_version < "3.13"
types-awscrt==0.21.0 ; python_version >= "3.8" and python_version < "3.13"
types-bleach==6.1.0.20240331 ; python_version >= "3.8" and python_version < "3.13"
types-boto==2.49.18.20240205 ; python_version >= "3.8" and python_version < "3.13"
types-contextvars==2.4.7.3 ; python_version >= "3.8" and python_version < "3.13"
types-dataclasses==0.6.6 ; python_version >= "3.8" and python_version < "3.13"
types-docutils==0.21.0.20240423 ; python_version >= "3.8" and python_version < "3.13"
types-docutils==0.21.0.20240711 ; python_version >= "3.8" and python_version < "3.13"
types-html5lib==1.1.11.20240228 ; python_version >= "3.8" and python_version < "3.13"
types-markdown==3.6.0.20240316 ; python_version >= "3.8" and python_version < "3.13"
types-paramiko==3.4.0.20240423 ; python_version >= "3.8" and python_version < "3.13"
Expand Down

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