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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 Feb 15, 2025
1 parent 5cf48dc commit 2a1dd86
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Showing 4 changed files with 29 additions and 26 deletions.
18 changes: 9 additions & 9 deletions lib/galaxy/dependencies/dev-requirements.txt
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Expand Up @@ -35,8 +35,8 @@ contourpy==1.1.1 ; python_full_version < '3.9'
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
coverage==7.6.12 ; python_full_version >= '3.9'
cryptography==44.0.1
cwltest==2.5.20241122133319
cycler==0.12.1
darker==2.1.1
Expand Down Expand Up @@ -85,7 +85,7 @@ keyring==25.5.0 ; python_full_version < '3.9' and platform_machine != 'ppc64le'
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
lxml==5.3.1
markdown-it-py==3.0.0
markdown-it-reporter==0.0.2
markupsafe==2.1.5 ; python_full_version < '3.9'
Expand All @@ -104,11 +104,11 @@ msgpack==1.1.0
multidict==6.1.0
mypy-extensions==1.0.0
myst-parser==3.0.1 ; python_full_version < '3.10'
myst-parser==4.0.0 ; python_full_version >= '3.10'
myst-parser==4.0.1 ; 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==2.2.2 ; python_full_version >= '3.10'
numpy==2.2.3 ; python_full_version >= '3.10'
onedatafilerestclient==21.2.5.2
outcome==1.3.0.post0
packaging==24.2
Expand All @@ -128,7 +128,7 @@ prettytable==3.11.0 ; python_full_version < '3.9'
prettytable==3.14.0 ; 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'
psutil==7.0.0 ; sys_platform != 'cygwin'
psycopg==3.2.4
pycparser==2.22
pyee==12.0.0 ; python_full_version < '3.9'
Expand Down Expand Up @@ -179,10 +179,10 @@ rpds-py==0.22.3 ; python_full_version >= '3.9'
ruamel-yaml==0.18.10
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==36.2.0 ; python_full_version >= '3.9'
rucio-clients==36.3.0 ; python_full_version >= '3.9'
s3transfer==0.11.2
schema-salad==8.7.20241010092723 ; python_full_version < '3.9'
schema-salad==8.8.20241206093842 ; python_full_version >= '3.9'
schema-salad==8.8.20250205075315 ; python_full_version >= '3.9'
scipy==1.10.1 ; python_full_version < '3.9'
scipy==1.13.1 ; python_full_version == '3.9.*'
scipy==1.15.1 ; python_full_version >= '3.10'
Expand Down Expand Up @@ -221,7 +221,7 @@ tinydb==4.8.2
toml==0.10.2
tomli==2.2.1 ; python_full_version <= '3.11'
trio==0.27.0 ; python_full_version < '3.9'
trio==0.28.0 ; python_full_version >= '3.9'
trio==0.29.0 ; python_full_version >= '3.9'
trio-websocket==0.11.1
tuspy==1.1.0
twill==3.3
Expand Down
2 changes: 1 addition & 1 deletion lib/galaxy/dependencies/pinned-lint-requirements.txt
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Expand Up @@ -4,4 +4,4 @@ flake8-bugbear==24.12.12
mccabe==0.7.0
pycodestyle==2.12.1
pyflakes==3.2.0
ruff==0.9.5
ruff==0.9.6
22 changes: 12 additions & 10 deletions lib/galaxy/dependencies/pinned-requirements.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -45,7 +45,7 @@ celery==5.4.0
certifi==2025.1.31
cffi==1.17.1
charset-normalizer==3.4.1
circus==0.18.0
circus==0.19.0
click==8.1.8
click-didyoumean==0.3.1
click-plugins==1.1.1
Expand All @@ -55,12 +55,12 @@ cloudbridge==3.2.0
colorama==0.4.6 ; sys_platform == 'win32'
coloredlogs==15.0.1
conda-package-streaming==0.11.0
cryptography==44.0.0
cryptography==44.0.1
ct3==3.4.0
cwl-upgrader==1.2.11 ; python_full_version < '3.9'
cwl-upgrader==1.2.12 ; python_full_version >= '3.9'
cwl-utils==0.35 ; python_full_version < '3.9'
cwl-utils==0.36 ; python_full_version >= '3.9'
cwl-utils==0.37 ; python_full_version >= '3.9'
cwltool==3.1.20241007082533 ; python_full_version < '3.9'
cwltool==3.1.20250110105449 ; python_full_version >= '3.9'
defusedxml==0.7.1
Expand Down Expand Up @@ -116,7 +116,7 @@ jsonschema-specifications==2024.10.1 ; python_full_version >= '3.9'
kombu==5.4.2
lagom==2.7.5
legacy-cgi==2.6.2 ; python_full_version >= '3.13'
lxml==5.3.0
lxml==5.3.1
mako==1.3.9
markdown==3.7
markdown-it-py==3.0.0
Expand All @@ -136,7 +136,7 @@ networkx==3.4.2 ; python_full_version >= '3.10'
nodeenv==1.9.1
numpy==1.24.4 ; python_full_version < '3.9'
numpy==2.0.2 ; python_full_version == '3.9.*'
numpy==2.2.2 ; python_full_version >= '3.10'
numpy==2.2.3 ; python_full_version >= '3.10'
oauthlib==3.2.2
orjson==3.10.15
oyaml==1.0
Expand All @@ -154,7 +154,7 @@ prompt-toolkit==3.0.50
propcache==0.2.0 ; python_full_version < '3.9'
propcache==0.2.1 ; python_full_version >= '3.9'
prov==1.5.1
psutil==6.1.1
psutil==7.0.0
pulsar-galaxy-lib==0.15.6
pycparser==2.22
pycryptodome==3.21.0
Expand Down Expand Up @@ -195,7 +195,7 @@ requests-oauthlib==2.0.0
requests-toolbelt==1.0.0
requests-unixsocket==0.3.0
rich==13.9.4
rich-argparse==1.6.0 ; python_full_version >= '3.9'
rich-argparse==1.7.0 ; python_full_version >= '3.9'
rocrate==0.11.0 ; python_full_version < '3.9'
rocrate==0.13.0 ; python_full_version >= '3.9'
routes==2.5.1
Expand All @@ -207,13 +207,14 @@ ruamel-yaml-clib==0.2.12 ; python_full_version >= '3.9' and python_full_version
s3fs==2024.10.0 ; python_full_version < '3.9'
s3fs==2025.2.0 ; python_full_version >= '3.9'
schema-salad==8.7.20241010092723 ; python_full_version < '3.9'
schema-salad==8.8.20241206093842 ; python_full_version >= '3.9'
schema-salad==8.8.20250205075315 ; python_full_version >= '3.9'
setuptools==75.3.0 ; python_full_version < '3.9'
setuptools==75.8.0 ; python_full_version >= '3.9'
setuptools-scm==5.0.2
six==1.17.0
sniffio==1.3.1
social-auth-core==4.5.4
social-auth-core==4.5.4 ; python_full_version < '3.9'
social-auth-core==4.5.6 ; python_full_version >= '3.9'
sortedcontainers==2.4.0
spython==0.3.14
sqlalchemy==2.0.38
Expand All @@ -238,7 +239,8 @@ tuspy==1.1.0
tuswsgi==0.5.5
typing-extensions==4.12.2
tzdata==2025.1
tzlocal==5.2
tzlocal==5.2 ; python_full_version < '3.9'
tzlocal==5.3 ; python_full_version >= '3.9'
ubiquerg==0.8.0
urllib3==1.26.20 ; python_full_version < '3.10'
urllib3==2.3.0 ; python_full_version >= '3.10'
Expand Down
13 changes: 7 additions & 6 deletions lib/galaxy/dependencies/pinned-typecheck-requirements.txt
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@@ -1,20 +1,20 @@
# This file was autogenerated by uv via the following command:
# uv export --frozen --no-hashes --only-group=typecheck
annotated-types==0.7.0
boto3-stubs==1.36.16
botocore-stubs==1.36.16
boto3-stubs==1.36.21
botocore-stubs==1.36.21
cffi==1.17.1 ; platform_python_implementation != 'PyPy'
cryptography==44.0.0
cryptography==44.0.1
lxml-stubs==0.5.1
mypy==1.14.1 ; python_full_version < '3.9'
mypy==1.15.0 ; python_full_version >= '3.9'
mypy-boto3-s3==1.36.15
mypy-boto3-s3==1.36.21
mypy-extensions==1.0.0
pycparser==2.22 ; platform_python_implementation != 'PyPy'
pydantic==2.10.6
pydantic-core==2.27.2
tomli==2.2.1 ; python_full_version < '3.11'
types-awscrt==0.23.9
types-awscrt==0.23.10
types-bleach==6.2.0.20241123
types-boto==2.49.18.20241019
types-contextvars==2.4.7.3
Expand All @@ -29,7 +29,8 @@ types-pyyaml==6.0.12.20241230
types-requests==2.31.0.6 ; python_full_version < '3.10'
types-requests==2.32.0.20241016 ; python_full_version >= '3.10'
types-s3transfer==0.11.2
types-setuptools==75.8.0.20250110
types-setuptools==75.8.0.20250110 ; python_full_version < '3.9'
types-setuptools==75.8.0.20250210 ; python_full_version >= '3.9'
types-six==1.17.0.20241205
types-urllib3==1.26.25.14 ; python_full_version < '3.10'
typing-extensions==4.12.2
Expand Down

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