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Update Python dependencies #21229

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b86ee75
Disallow also fastapi 0.120.3 and 0.120.4
nsoranzo Nov 1, 2025
9237864
Disallow mirakuru 3.0.0
nsoranzo Nov 1, 2025
13abf87
Update Python dependencies
galaxybot Nov 1, 2025
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17 changes: 9 additions & 8 deletions lib/galaxy/dependencies/dev-requirements.txt
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@@ -1,7 +1,7 @@
# This file was autogenerated by uv via the following command:
# uv export --frozen --no-annotate --no-hashes --only-group=dev
aiohappyeyeballs==2.6.1
aiohttp==3.13.1
aiohttp==3.13.2
aiosignal==1.4.0
alabaster==0.7.16 ; python_full_version < '3.10'
alabaster==1.0.0 ; python_full_version >= '3.10'
Expand All @@ -14,8 +14,8 @@ babel==2.17.0
backports-asyncio-runner==1.2.0 ; python_full_version < '3.11'
backports-tarfile==1.2.0 ; python_full_version < '3.12' and platform_machine != 'ppc64le' and platform_machine != 's390x'
black==25.9.0
boto3==1.40.49
botocore==1.40.49
boto3==1.40.61
botocore==1.40.61
build==1.3.0
cachecontrol==0.14.3
cachetools==6.2.1
Expand Down Expand Up @@ -100,7 +100,7 @@ mypy==1.18.2
mypy-extensions==1.1.0
myst-parser==3.0.1 ; python_full_version < '3.10'
myst-parser==4.0.1 ; python_full_version >= '3.10'
nh3==0.3.1
nh3==0.3.2
numpy==2.0.2 ; python_full_version < '3.10'
numpy==2.2.6 ; python_full_version == '3.10.*'
numpy==2.3.4 ; python_full_version >= '3.11'
Expand Down Expand Up @@ -174,12 +174,12 @@ rpds-py==0.27.1 ; python_full_version < '3.10'
rpds-py==0.28.0 ; python_full_version >= '3.10'
ruamel-yaml==0.18.16
ruamel-yaml-clib==0.2.14 ; python_full_version < '3.14' and platform_python_implementation == 'CPython'
rucio-clients==38.4.0
rucio-clients==38.5.0
s3transfer==0.14.0
schema-salad==8.9.20250723145140
scipy==1.13.1 ; python_full_version < '3.10'
scipy==1.15.3 ; python_full_version == '3.10.*'
scipy==1.16.2 ; python_full_version >= '3.11'
scipy==1.16.3 ; python_full_version >= '3.11'
secretstorage==3.3.3 ; python_full_version < '3.10' and platform_machine != 'ppc64le' and platform_machine != 's390x' and sys_platform == 'linux'
secretstorage==3.4.0 ; python_full_version >= '3.10' and platform_machine != 'ppc64le' and platform_machine != 's390x' and sys_platform == 'linux'
selenium==4.32.0 ; python_full_version < '3.10'
Expand All @@ -204,13 +204,14 @@ statsd==4.0.1
stevedore==5.5.0
tabulate==0.9.0
testfixtures==8.3.0 ; python_full_version < '3.11'
testfixtures==9.2.0 ; python_full_version >= '3.11'
testfixtures==10.0.0 ; python_full_version >= '3.11'
text-unidecode==1.3
tinydb==4.8.2
toml==0.10.2
tomli==2.3.0 ; python_full_version <= '3.11'
total-perspective-vortex==3.1.2
trio==0.31.0
trio==0.31.0 ; python_full_version < '3.10'
trio==0.32.0 ; python_full_version >= '3.10'
trio-websocket==0.12.2
tuspy==1.1.0
twill==3.3.1
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==2.14.0
pyflakes==3.4.0
ruff==0.14.2
ruff==0.14.3
27 changes: 14 additions & 13 deletions lib/galaxy/dependencies/pinned-requirements.txt
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Expand Up @@ -2,14 +2,14 @@
# uv export --frozen --no-annotate --no-hashes --no-dev
a2wsgi==1.10.10
adal==1.2.7
aiobotocore==2.25.0
aiobotocore==2.25.1
aiofiles==25.1.0
aiohappyeyeballs==2.6.1
aiohttp==3.13.1
aiohttp==3.13.2
aioitertools==0.12.0
aiosignal==1.4.0
alembic==1.16.5 ; python_full_version < '3.10'
alembic==1.17.0 ; python_full_version >= '3.10'
alembic==1.17.1 ; python_full_version >= '3.10'
amqp==5.3.1
annotated-types==0.7.0
anyio==4.11.0
Expand All @@ -28,10 +28,11 @@ bdbag==1.8.0
beaker==1.13.0
billiard==4.2.2
bioblend==1.6.0
bleach==6.2.0
bleach==6.2.0 ; python_full_version < '3.10'
bleach==6.3.0 ; python_full_version >= '3.10'
boltons==25.0.0
boto==2.49.0
botocore==1.40.49
botocore==1.40.61
bx-python==0.14.0
cachecontrol==0.14.3
cachetools==6.2.1
Expand All @@ -56,15 +57,15 @@ cwl-upgrader==1.2.12
cwl-utils==0.40
cwltool==3.1.20250925164626
defusedxml==0.7.1
deprecated==1.2.18
deprecated==1.3.1
deprecation==2.1.0
dictobj==0.4
dnspython==2.7.0 ; python_full_version < '3.10'
dnspython==2.8.0 ; python_full_version >= '3.10'
docopt==0.6.2
docutils==0.21.2
dparse==0.6.4
edam-ontology==1.25.2
edam-ontology==1.25.3
email-validator==2.3.0
et-xmlfile==2.0.0
exceptiongroup==1.3.0 ; python_full_version < '3.11'
Expand All @@ -74,10 +75,10 @@ filelock==3.20.0 ; python_full_version >= '3.10'
fissix==24.4.24
frozenlist==1.8.0
fs==2.4.16
fsspec==2025.9.0
fsspec==2025.10.0
future==1.0.0
google-api-core==2.27.0
google-auth==2.41.1
google-api-core==2.28.1
google-auth==2.42.1
google-cloud-batch==0.18.0
googleapis-common-protos==1.71.0
gravity==1.1.1
Expand Down Expand Up @@ -191,15 +192,15 @@ requests-oauthlib==2.0.0
requests-toolbelt==1.0.0
requests-unixsocket==0.4.1
rich==13.9.4
rich-argparse==1.7.1
rich-argparse==1.7.2
rocrate==0.14.2
routes==2.5.1
rpds-py==0.27.1 ; python_full_version < '3.10'
rpds-py==0.28.0 ; python_full_version >= '3.10'
rsa==4.9.1
ruamel-yaml==0.18.16
ruamel-yaml-clib==0.2.14 ; python_full_version < '3.14' and platform_python_implementation == 'CPython'
s3fs==2025.9.0
s3fs==2025.10.0
schema-salad==8.9.20250723145140
setuptools==80.9.0
six==1.17.0
Expand All @@ -225,7 +226,7 @@ tomli==2.3.0 ; python_full_version < '3.11'
tornado==6.5.2
tqdm==4.67.1
tuspy==1.1.0
tuspyserver==4.2.0
tuspyserver==4.2.1
typing-extensions==4.15.0
typing-inspection==0.4.2
tzdata==2025.2
Expand Down
15 changes: 8 additions & 7 deletions lib/galaxy/dependencies/pinned-test-requirements.txt
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Original file line number Diff line number Diff line change
@@ -1,16 +1,16 @@
# This file was autogenerated by uv via the following command:
# uv export --frozen --no-annotate --no-hashes --only-group=test
aiohappyeyeballs==2.6.1
aiohttp==3.13.1
aiohttp==3.13.2
aiosignal==1.4.0
anyio==4.11.0
ase==3.26.0
async-timeout==5.0.1 ; python_full_version < '3.11'
attrs==25.4.0
axe-selenium-python==2.1.6
backports-asyncio-runner==1.2.0 ; python_full_version < '3.11'
boto3==1.40.49
botocore==1.40.49
boto3==1.40.61
botocore==1.40.61
cachecontrol==0.14.3
cachetools==6.2.1
cattrs==25.3.0
Expand Down Expand Up @@ -136,12 +136,12 @@ rpds-py==0.27.1 ; python_full_version < '3.10'
rpds-py==0.28.0 ; python_full_version >= '3.10'
ruamel-yaml==0.18.16
ruamel-yaml-clib==0.2.14 ; python_full_version < '3.14' and platform_python_implementation == 'CPython'
rucio-clients==38.4.0
rucio-clients==38.5.0
s3transfer==0.14.0
schema-salad==8.9.20250723145140
scipy==1.13.1 ; python_full_version < '3.10'
scipy==1.15.3 ; python_full_version == '3.10.*'
scipy==1.16.2 ; python_full_version >= '3.11'
scipy==1.16.3 ; python_full_version >= '3.11'
selenium==4.32.0 ; python_full_version < '3.10'
selenium==4.38.0 ; python_full_version >= '3.10'
seletools==1.5.0
Expand All @@ -152,13 +152,14 @@ statsd==4.0.1
stevedore==5.5.0
tabulate==0.9.0
testfixtures==8.3.0 ; python_full_version < '3.11'
testfixtures==9.2.0 ; python_full_version >= '3.11'
testfixtures==10.0.0 ; python_full_version >= '3.11'
text-unidecode==1.3
tinydb==4.8.2
toml==0.10.2
tomli==2.3.0 ; python_full_version <= '3.11'
total-perspective-vortex==3.1.2
trio==0.31.0
trio==0.31.0 ; python_full_version < '3.10'
trio==0.32.0 ; python_full_version >= '3.10'
trio-websocket==0.12.2
tuspy==1.1.0
twill==3.3.1
Expand Down
8 changes: 4 additions & 4 deletions lib/galaxy/dependencies/pinned-typecheck-requirements.txt
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@@ -1,21 +1,21 @@
# This file was autogenerated by uv via the following command:
# uv export --frozen --no-annotate --no-hashes --only-group=typecheck
annotated-types==0.7.0
boto3-stubs==1.40.59
botocore-stubs==1.40.59
boto3-stubs==1.40.64
botocore-stubs==1.40.64
cffi==2.0.0 ; platform_python_implementation != 'PyPy'
cryptography==46.0.3
lxml-stubs==0.5.1
mypy==1.18.2
mypy-boto3-s3==1.40.26
mypy-boto3-s3==1.40.61
mypy-extensions==1.1.0
pathspec==0.12.1
pycparser==2.23 ; implementation_name != 'PyPy' and platform_python_implementation != 'PyPy'
pydantic==2.12.3
pydantic-core==2.41.4
tomli==2.3.0 ; python_full_version < '3.11'
types-awscrt==0.28.2
types-bleach==6.2.0.20250809
types-bleach==6.3.0.20251029
types-boto==2.49.18.20241019
types-contextvars==2.4.7.3
types-dataclasses==0.6.6
Expand Down
2 changes: 1 addition & 1 deletion packages/tool_shed/setup.cfg
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Expand Up @@ -42,7 +42,7 @@ install_requires =
galaxy-web-apps
a2wsgi
alembic
fastapi>=0.111.0,!=0.119.*,!=0.120.0,!=0.120.1,!=0.120.2
fastapi>=0.111.0,!=0.119.*,!=0.120.0,!=0.120.1,!=0.120.2,!=0.120.3,!=0.120.4
Mako
MarkupSafe
mercurial>=6.8.2
Expand Down
2 changes: 1 addition & 1 deletion packages/web_apps/setup.cfg
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Expand Up @@ -43,7 +43,7 @@ install_requires =
apispec
Babel
CT3>=3.3.3
fastapi>=0.111.0,!=0.119.*,!=0.120.0,!=0.120.1,!=0.120.2
fastapi>=0.111.0,!=0.119.*,!=0.120.0,!=0.120.1,!=0.120.2,!=0.120.3,!=0.120.4
gunicorn
httpx
gxformat2
Expand Down
3 changes: 2 additions & 1 deletion pyproject.toml
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Expand Up @@ -37,7 +37,7 @@ dependencies = [
"docutils!=0.17,!=0.17.1",
"dparse",
"edam-ontology",
"fastapi>=0.111.0,!=0.119.*,!=0.120.0,!=0.120.1,!=0.120.2", # https://github.com/fastapi/fastapi/pull/13918
"fastapi>=0.111.0,!=0.119.*,!=0.120.0,!=0.120.1,!=0.120.2,!=0.120.3,!=0.120.4", # https://github.com/fastapi/fastapi/pull/13918
"fissix",
"fs",
"future>=1.0.0", # Python 3.12 support
Expand Down Expand Up @@ -256,6 +256,7 @@ keep-runtime-typing = true
[tool.uv]
constraint-dependencies = [
"limits>=2.5.0", # prefer not downgrading this to upgrading packaging
"mirakuru!=3.0.0", # https://github.com/dbfixtures/mirakuru/pull/949
"scipy>=1.14.1; python_version>='3.10'", # Python 3.13 support
]
default-groups = []
Expand Down
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