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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 Sep 22, 2024
1 parent 1633c66 commit e768bf5
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Showing 4 changed files with 35 additions and 35 deletions.
20 changes: 10 additions & 10 deletions lib/galaxy/dependencies/dev-requirements.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@ aiohappyeyeballs==2.4.0 ; python_version >= "3.8" and python_version < "3.13"
aiohttp==3.10.5 ; 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==4.4.0 ; python_version >= "3.8" and python_version < "3.13"
anyio==4.5.0 ; 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==24.2.0 ; python_version >= "3.8" and python_version < "3.13"
Expand All @@ -11,8 +11,8 @@ babel==2.16.0 ; python_version >= "3.8" and python_version < "3.13"
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==24.8.0 ; python_version >= "3.8" and python_version < "3.13"
boto3==1.35.16 ; python_version >= "3.8" and python_version < "3.13"
botocore==1.35.16 ; python_version >= "3.8" and python_version < "3.13"
boto3==1.35.23 ; python_version >= "3.8" and python_version < "3.13"
botocore==1.35.23 ; python_version >= "3.8" and python_version < "3.13"
build==1.2.2 ; python_version >= "3.8" and python_version < "3.13"
cachecontrol[filecache]==0.14.0 ; python_version >= "3.8" and python_version < "3.13"
certifi==2024.8.30 ; python_version >= "3.8" and python_version < "3.13"
Expand All @@ -35,7 +35,7 @@ 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==1.3.3 ; python_version >= "3.9" and python_version < "3.13"
exceptiongroup==1.2.2 ; python_version >= "3.8" and python_version < "3.11"
filelock==3.16.0 ; python_version >= "3.8" and python_version < "3.13"
filelock==3.16.1 ; python_version >= "3.8" and python_version < "3.13"
fluent-logger==0.11.1 ; python_version >= "3.8" and python_version < "3.13"
fonttools==4.53.1 ; python_version >= "3.8" and python_version < "3.13"
frozenlist==1.4.1 ; python_version >= "3.8" and python_version < "3.13"
Expand All @@ -45,7 +45,7 @@ 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"
httpcore==1.0.5 ; python_version >= "3.8" and python_version < "3.13"
httpx==0.27.2 ; python_version >= "3.8" and python_version < "3.13"
idna==3.9 ; python_version >= "3.8" and python_version < "3.13"
idna==3.10 ; python_version >= "3.8" and python_version < "3.13"
imagesize==1.4.1 ; python_version >= "3.8" and python_version < "3.13"
importlib-metadata==8.5.0 ; python_version >= "3.8" and python_version < "3.13"
importlib-resources==6.4.5 ; python_version >= "3.8" and python_version < "3.10"
Expand All @@ -61,7 +61,7 @@ jmespath==1.0.1 ; python_version >= "3.8" and python_version < "3.13"
jsonschema-specifications==2023.12.1 ; python_version >= "3.9" and python_version < "3.13"
jsonschema==4.23.0 ; python_version >= "3.9" and python_version < "3.13"
junit-xml==1.9 ; python_version >= "3.8" and python_version < "3.13"
keyring==25.3.0 ; python_version >= "3.8" and python_version < "3.13"
keyring==25.4.1 ; python_version >= "3.8" and python_version < "3.13"
kiwisolver==1.4.7 ; python_version >= "3.8" and python_version < "3.13"
lxml==5.3.0 ; python_version >= "3.8" and python_version < "3.13"
markdown-it-py==3.0.0 ; python_version >= "3.8" and python_version < "3.13"
Expand Down Expand Up @@ -90,13 +90,13 @@ pbr==6.1.0 ; python_version >= "3.9" and python_version < "3.13"
pillow==10.4.0 ; 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"
platformdirs==4.3.3 ; python_version >= "3.8" and python_version < "3.13"
platformdirs==4.3.6 ; python_version >= "3.8" and python_version < "3.13"
playwright==1.47.0 ; python_version >= "3.8" and python_version < "3.13"
pluggy==1.5.0 ; python_version >= "3.8" and python_version < "3.13"
port-for==0.7.3 ; python_version >= "3.8" and python_version < "3.13"
prettytable==3.11.0 ; 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"
psycopg==3.2.2 ; python_version >= "3.8" and python_version < "3.13"
pycparser==2.22 ; python_version >= "3.8" and python_version < "3.13"
pyee==12.0.0 ; python_version >= "3.8" and python_version < "3.13"
pygithub==2.4.0 ; python_version >= "3.8" and python_version < "3.13"
Expand Down Expand Up @@ -142,9 +142,9 @@ 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==1.14.1 ; 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==4.24.0 ; python_version >= "3.8" and python_version < "3.13"
selenium==4.25.0 ; python_version >= "3.8" and python_version < "3.13"
seletools==1.5.0 ; python_version >= "3.8" and python_version < "3.13"
setuptools==74.1.2 ; python_version >= "3.8" and python_version < "3.13"
setuptools==75.1.0 ; python_version >= "3.8" and python_version < "3.13"
six==1.16.0 ; python_version >= "3.8" and python_version < "3.13"
sniffio==1.3.1 ; python_version >= "3.8" and python_version < "3.13"
snowballstemmer==2.2.0 ; python_version >= "3.8" and python_version < "3.13"
Expand Down
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==24.8.19
mccabe==0.7.0
pycodestyle==2.12.1
pyflakes==3.2.0
ruff==0.6.5
ruff==0.6.6
32 changes: 16 additions & 16 deletions lib/galaxy/dependencies/pinned-requirements.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@

a2wsgi==1.10.7 ; python_version >= "3.8" and python_version < "3.13"
adal==1.2.7 ; python_version >= "3.8" and python_version < "3.13"
aiobotocore==2.15.0 ; python_version >= "3.8" and python_version < "3.13"
aiobotocore==2.15.1 ; python_version >= "3.8" and python_version < "3.13"
aiodataloader==0.4.0 ; python_version >= "3.8" and python_version < "3.13"
aiofiles==24.1.0 ; python_version >= "3.8" and python_version < "3.13"
aiohappyeyeballs==2.4.0 ; python_version >= "3.8" and python_version < "3.13"
Expand All @@ -13,7 +13,7 @@ alembic==1.13.2 ; 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==0.7.0 ; python_version >= "3.8" and python_version < "3.13"
anyio==4.4.0 ; python_version >= "3.8" and python_version < "3.13"
anyio==4.5.0 ; 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 @@ -34,8 +34,8 @@ 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==1.35.16 ; python_version >= "3.8" and python_version < "3.13"
bx-python==0.12.0 ; python_version >= "3.8" and python_version < "3.13"
botocore==1.35.23 ; python_version >= "3.8" and python_version < "3.13"
bx-python==0.13.0 ; 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==2024.8.30 ; python_version >= "3.8" and python_version < "3.13"
Expand Down Expand Up @@ -66,8 +66,8 @@ 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==1.2.2 ; python_version >= "3.8" and python_version < "3.11"
fastapi-slim==0.114.2 ; python_version >= "3.8" and python_version < "3.13"
filelock==3.16.0 ; python_version >= "3.8" and python_version < "3.13"
fastapi-slim==0.115.0 ; python_version >= "3.8" and python_version < "3.13"
filelock==3.16.1 ; python_version >= "3.8" and python_version < "3.13"
frozenlist==1.4.1 ; python_version >= "3.8" and python_version < "3.13"
fs==2.4.16 ; python_version >= "3.8" and python_version < "3.13"
fsspec==2024.9.0 ; python_version >= "3.8" and python_version < "3.13"
Expand All @@ -86,7 +86,7 @@ h11==0.14.0 ; python_version >= "3.8" and python_version < "3.13"
h5grove==2.3.0 ; python_version >= "3.8" and python_version < "3.13"
h5py==3.11.0 ; python_version >= "3.8" and python_version < "3.13"
humanfriendly==10.0 ; python_version >= "3.8" and python_version < "3.13"
idna==3.9 ; python_version >= "3.8" and python_version < "3.13"
idna==3.10 ; python_version >= "3.8" and python_version < "3.13"
importlib-metadata==8.5.0 ; python_version >= "3.8" and python_version < "3.13"
importlib-resources==6.4.5 ; python_version >= "3.8" and python_version < "3.9"
isa-rwval @ git+https://github.com/nsoranzo/isa-rwval.git@3d989181058d2765a93cb0e7ca85d6955e0eb6ef ; python_version >= "3.8" and python_version < "3.13"
Expand All @@ -97,7 +97,7 @@ jmespath==1.0.1 ; python_version >= "3.8" and python_version < "3.13"
jsonref==1.1.0 ; python_version >= "3.8" and python_version < "3.13"
jsonschema-specifications==2023.12.1 ; python_version >= "3.8" and python_version < "3.13"
jsonschema==4.23.0 ; python_version >= "3.8" and python_version < "3.13"
kombu==5.4.1 ; python_version >= "3.8" and python_version < "3.13"
kombu==5.4.2 ; python_version >= "3.8" and python_version < "3.13"
lagom==2.6.0 ; python_version >= "3.8" and python_version < "3.13"
lxml==5.3.0 ; python_version >= "3.8" and python_version < "3.13"
mako==1.3.5 ; python_version >= "3.8" and python_version < "3.13"
Expand All @@ -121,7 +121,7 @@ oauthlib==3.2.2 ; python_version >= "3.8" and python_version < "3.13"
orjson==3.10.7 ; python_version >= "3.8" and python_version < "3.13"
oyaml==1.0 ; python_version >= "3.8" and python_version < "3.13"
packaging==24.1 ; python_version >= "3.8" and python_version < "3.13"
paramiko==3.4.1 ; python_version >= "3.8" and python_version < "3.13"
paramiko==3.5.0 ; python_version >= "3.8" and python_version < "3.13"
parsley==1.3 ; python_version >= "3.8" and python_version < "3.13"
paste==3.10.1 ; python_version >= "3.8" and python_version < "3.13"
pastedeploy==3.1.0 ; python_version >= "3.8" and python_version < "3.13"
Expand All @@ -135,10 +135,10 @@ 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==2.23.3 ; python_version >= "3.8" and python_version < "3.13"
pydantic-core==2.23.4 ; python_version >= "3.8" and python_version < "3.13"
pydantic-tes==0.1.5 ; python_version >= "3.8" and python_version < "3.13"
pydantic==2.9.1 ; python_version >= "3.8" and python_version < "3.13"
pydantic[email]==2.9.1 ; python_version >= "3.8" and python_version < "3.13"
pydantic==2.9.2 ; python_version >= "3.8" and python_version < "3.13"
pydantic[email]==2.9.2 ; 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==0.8.1.2 ; python_version >= "3.8" and python_version < "3.13"
Expand All @@ -149,7 +149,7 @@ pykwalify==1.8.0 ; python_version >= "3.8" and python_version < "3.13"
pylibmagic==0.5.0 ; python_version >= "3.8" and python_version < "3.13"
pynacl==1.5.0 ; python_version >= "3.8" and python_version < "3.13"
pyparsing==3.1.4 ; python_version >= "3.8" and python_version < "3.13"
pyreadline3==3.4.3 ; sys_platform == "win32" and python_version >= "3.8" and python_version < "3.13"
pyreadline3==3.5.4 ; sys_platform == "win32" and python_version >= "3.8" and python_version < "3.13"
pysam==0.22.1 ; 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-magic==0.4.27 ; python_version >= "3.8" and python_version < "3.13"
Expand All @@ -176,14 +176,14 @@ ruamel-yaml==0.18.6 ; python_version >= "3.8" and python_version < "3.13"
s3fs==2024.9.0 ; python_version >= "3.8" and python_version < "3.13"
schema-salad==8.7.20240905150001 ; python_version >= "3.8" and python_version < "3.13"
setuptools-scm==5.0.2 ; python_version >= "3.8" and python_version < "3.13"
setuptools==74.1.2 ; python_version >= "3.8" and python_version < "3.13"
setuptools==75.1.0 ; 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"
social-auth-core==4.5.4 ; python_version >= "3.8" and python_version < "3.13"
sortedcontainers==2.4.0 ; python_version >= "3.8" and python_version < "3.13"
spython==0.3.13 ; python_version >= "3.8" and python_version < "3.13"
sqlalchemy==2.0.34 ; python_version >= "3.8" and python_version < "3.13"
spython==0.3.14 ; python_version >= "3.8" and python_version < "3.13"
sqlalchemy==2.0.35 ; python_version >= "3.8" and python_version < "3.13"
sqlitedict==2.1.0 ; python_version >= "3.8" and python_version < "3.13"
sqlparse==0.5.1 ; python_version >= "3.8" and python_version < "3.13"
starlette-context==0.3.6 ; python_version >= "3.8" and python_version < "3.13"
Expand Down
16 changes: 8 additions & 8 deletions lib/galaxy/dependencies/pinned-typecheck-requirements.txt
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Original file line number Diff line number Diff line change
@@ -1,15 +1,15 @@
annotated-types==0.7.0 ; python_version >= "3.8" and python_version < "3.13"
boto3-stubs[s3]==1.35.19 ; python_version >= "3.8" and python_version < "3.13"
botocore-stubs==1.35.19 ; python_version >= "3.8" and python_version < "3.13"
boto3-stubs[s3]==1.35.24 ; python_version >= "3.8" and python_version < "3.13"
botocore-stubs==1.35.24 ; python_version >= "3.8" and python_version < "3.13"
cffi==1.17.1 ; python_version >= "3.8" and python_version < "3.13" and platform_python_implementation != "PyPy"
cryptography==43.0.1 ; 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==1.35.16 ; python_version >= "3.8" and python_version < "3.13"
mypy-boto3-s3==1.35.22 ; python_version >= "3.8" and python_version < "3.13"
mypy-extensions==1.0.0 ; python_version >= "3.8" and python_version < "3.13"
mypy==1.11.2 ; 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==2.23.3 ; python_version >= "3.8" and python_version < "3.13"
pydantic==2.9.1 ; python_version >= "3.8" and python_version < "3.13"
pydantic-core==2.23.4 ; python_version >= "3.8" and python_version < "3.13"
pydantic==2.9.2 ; python_version >= "3.8" and python_version < "3.13"
tomli==2.0.1 ; python_version >= "3.8" and python_version < "3.11"
types-awscrt==0.21.5 ; 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 @@ -19,12 +19,12 @@ types-dataclasses==0.6.6 ; python_version >= "3.8" and python_version < "3.13"
types-docutils==0.21.0.20240907 ; python_version >= "3.8" and python_version < "3.13"
types-html5lib==1.1.11.20240806 ; python_version >= "3.8" and python_version < "3.13"
types-markdown==3.7.0.20240822 ; python_version >= "3.8" and python_version < "3.13"
types-paramiko==3.4.0.20240423 ; python_version >= "3.8" and python_version < "3.13"
types-paramiko==3.5.0.20240918 ; python_version >= "3.8" and python_version < "3.13"
types-python-dateutil==2.9.0.20240906 ; python_version >= "3.8" and python_version < "3.13"
types-pyyaml==6.0.12.20240808 ; python_version >= "3.8" and python_version < "3.13"
types-pyyaml==6.0.12.20240917 ; python_version >= "3.8" and python_version < "3.13"
types-requests==2.31.0.6 ; python_version >= "3.8" and python_version < "3.13"
types-s3transfer==0.10.2 ; python_version >= "3.8" and python_version < "3.13"
types-setuptools==74.1.0.20240907 ; python_version >= "3.8" and python_version < "3.13"
types-setuptools==75.1.0.20240917 ; 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==4.12.2 ; python_version >= "3.8" and python_version < "3.13"

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