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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 Oct 13, 2024
1 parent fb70217 commit 304c95e
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Showing 3 changed files with 28 additions and 27 deletions.
21 changes: 11 additions & 10 deletions lib/galaxy/dependencies/dev-requirements.txt
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@@ -1,7 +1,7 @@
--extra-index-url https://wheels.galaxyproject.org/simple

aiohappyeyeballs==2.4.3 ; python_version >= "3.8" and python_version < "3.13"
aiohttp==3.10.9 ; python_version >= "3.8" and python_version < "3.13"
aiohttp==3.10.10 ; 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==4.5.0 ; python_version >= "3.8" and python_version < "3.13"
Expand All @@ -13,13 +13,13 @@ 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==1.35.23 ; 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"
boto3==1.35.36 ; python_version >= "3.8" and python_version < "3.13"
botocore==1.35.36 ; python_version >= "3.8" and python_version < "3.13"
build==1.2.2.post1 ; 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"
cffi==1.17.1 ; python_version >= "3.8" and python_version < "3.13"
charset-normalizer==3.3.2 ; python_version >= "3.8" and python_version < "3.13"
charset-normalizer==3.4.0 ; 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")
Expand Down Expand Up @@ -83,7 +83,7 @@ myst-parser==3.0.1 ; 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==2.0.2 ; python_version >= "3.9" and python_version < "3.10"
numpy==2.1.1 ; python_version >= "3.10" and python_version < "3.13"
numpy==2.1.2 ; python_version >= "3.10" and python_version < "3.13"
onedatafilerestclient==21.2.5.2 ; python_version >= "3.8" and python_version < "3.13"
outcome==1.3.0.post0 ; python_version >= "3.8" and python_version < "3.13"
packaging==24.1 ; python_version >= "3.8" and python_version < "3.13"
Expand All @@ -97,6 +97,7 @@ 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"
propcache==0.2.0 ; 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==3.2.3 ; 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 @@ -138,7 +139,7 @@ rpds-py==0.20.0 ; 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==35.4.0 ; python_version >= "3.9" and python_version < "3.13"
s3transfer==0.10.2 ; python_version >= "3.8" and python_version < "3.13"
s3transfer==0.10.3 ; python_version >= "3.8" and python_version < "3.13"
schema-salad==8.7.20240905150001 ; 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"
Expand All @@ -151,7 +152,7 @@ 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"
sortedcontainers==2.4.0 ; python_version >= "3.8" and python_version < "3.13"
sphinx-rtd-theme==2.0.0 ; python_version >= "3.8" and python_version < "3.13"
sphinx-rtd-theme==3.0.1 ; python_version >= "3.8" and python_version < "3.13"
sphinx==7.1.2 ; python_version >= "3.8" and python_version < "3.13"
sphinxcontrib-applehelp==1.0.4 ; python_version >= "3.8" and python_version < "3.13"
sphinxcontrib-devhelp==1.0.2 ; python_version >= "3.8" and python_version < "3.13"
Expand All @@ -165,7 +166,7 @@ stevedore==5.3.0 ; python_version >= "3.9" and python_version < "3.13"
tabulate==0.9.0 ; python_version >= "3.9" and python_version < "3.13"
testfixtures==8.3.0 ; python_version >= "3.8" and python_version < "3.13"
text-unidecode==1.3 ; python_version >= "3.8" and python_version < "3.13"
tinydb==4.8.0 ; python_version >= "3.8" and python_version < "3.13"
tinydb==4.8.1 ; python_version >= "3.8" and python_version < "3.13"
toml==0.10.2 ; python_version >= "3.8" and python_version < "3.13"
tomli==2.0.2 ; 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"
Expand All @@ -183,5 +184,5 @@ websocket-client==1.8.0 ; python_version >= "3.8" and python_version < "3.13"
werkzeug==3.0.4 ; 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==1.13.1 ; python_version >= "3.8" and python_version < "3.13"
yarl==1.15.0 ; python_version >= "3.8" and python_version < "3.13"
zipp==3.20.2 ; python_version >= "3.8" and python_version < "3.13"
26 changes: 13 additions & 13 deletions lib/galaxy/dependencies/pinned-requirements.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -2,11 +2,11 @@

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==2.15.1 ; python_version >= "3.8" and python_version < "3.13"
aiobotocore==2.15.2 ; 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==2.4.3 ; python_version >= "3.8" and python_version < "3.13"
aiohttp==3.10.9 ; python_version >= "3.8" and python_version < "3.13"
aiohttp==3.10.10 ; python_version >= "3.8" and python_version < "3.13"
aioitertools==0.12.0 ; python_version >= "3.8" and python_version < "3.13"
aiosignal==1.3.1 ; python_version >= "3.8" and python_version < "3.13"
alembic==1.13.3 ; python_version >= "3.8" and python_version < "3.13"
Expand All @@ -17,7 +17,7 @@ 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"
argcomplete==3.5.0 ; python_version >= "3.8" and python_version < "3.13"
argcomplete==3.5.1 ; python_version >= "3.8" and python_version < "3.13"
async-timeout==4.0.3 ; python_version >= "3.8" and python_version < "3.11"
attmap==0.13.2 ; python_version >= "3.8" and python_version < "3.13"
attrs==24.2.0 ; python_version >= "3.8" and python_version < "3.13"
Expand All @@ -34,13 +34,13 @@ 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==1.35.23 ; python_version >= "3.8" and python_version < "3.13"
botocore==1.35.36 ; 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"
cffi==1.17.1 ; python_version >= "3.8" and python_version < "3.13"
charset-normalizer==3.3.2 ; python_version >= "3.8" and python_version < "3.13"
charset-normalizer==3.4.0 ; python_version >= "3.8" and python_version < "3.13"
cheetah3==3.2.6.post1 ; python_version >= "3.8" and python_version < "3.13"
circus==0.18.0 ; python_version >= "3.8" and python_version < "3.13"
click-didyoumean==0.3.1 ; python_version >= "3.8" and python_version < "3.13"
Expand All @@ -51,11 +51,11 @@ cloudauthz==0.6.0 ; python_version >= "3.8" and python_version < "3.13"
cloudbridge==3.2.0 ; python_version >= "3.8" and python_version < "3.13"
colorama==0.4.6 ; python_version >= "3.8" and python_version < "3.13" and platform_system == "Windows"
coloredlogs==15.0.1 ; python_version >= "3.8" and python_version < "3.13"
conda-package-streaming==0.10.0 ; python_version >= "3.8" and python_version < "3.13"
conda-package-streaming==0.11.0 ; python_version >= "3.8" and python_version < "3.13"
cryptography==43.0.1 ; 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==0.34 ; python_version >= "3.8" and python_version < "3.13"
cwltool==3.1.20240909164951 ; python_version >= "3.8" and python_version < "3.13"
cwltool==3.1.20241007082533 ; 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 Down Expand Up @@ -116,7 +116,7 @@ networkx==3.1 ; python_version >= "3.8" and python_version < "3.13"
nodeenv==1.9.1 ; python_version >= "3.8" and python_version < "3.13"
numpy==1.24.4 ; python_version >= "3.8" and python_version < "3.9"
numpy==2.0.2 ; python_version >= "3.9" and python_version < "3.10"
numpy==2.1.1 ; python_version >= "3.10" and python_version < "3.13"
numpy==2.1.2 ; python_version >= "3.10" and python_version < "3.13"
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"
Expand All @@ -130,6 +130,7 @@ pillow==10.4.0 ; python_version >= "3.8" and python_version < "3.13"
pkgutil-resolve-name==1.3.10 ; python_version >= "3.8" and python_version < "3.9"
promise==2.3 ; python_version >= "3.8" and python_version < "3.13"
prompt-toolkit==3.0.48 ; python_version >= "3.8" and python_version < "3.13"
propcache==0.2.0 ; python_version >= "3.8" and python_version < "3.13"
prov==1.5.1 ; python_version >= "3.8" and python_version < "3.13"
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"
Expand All @@ -141,7 +142,7 @@ 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"
pyfaidx==0.8.1.3 ; python_version >= "3.8" and python_version < "3.13"
pygments==2.18.0 ; python_version >= "3.8" and python_version < "3.13"
pyjwt==2.9.0 ; python_version >= "3.8" and python_version < "3.13"
pyjwt[crypto]==2.9.0 ; python_version >= "3.8" and python_version < "3.13"
Expand Down Expand Up @@ -177,7 +178,6 @@ 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==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"
Expand All @@ -193,7 +193,7 @@ 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==9.0.0 ; 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"
tinydb==4.8.1 ; python_version >= "3.8" and python_version < "3.13"
tomli==2.0.2 ; python_version >= "3.8" and python_version < "3.11"
tornado==6.4.1 ; python_version >= "3.8" and python_version < "3.13"
tqdm==4.66.5 ; python_version >= "3.8" and python_version < "3.13"
Expand All @@ -204,7 +204,7 @@ tzdata==2024.2 ; 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==1.26.20 ; python_version >= "3.8" and python_version < "3.13"
uvicorn==0.31.0 ; python_version >= "3.8" and python_version < "3.13"
uvicorn==0.31.1 ; python_version >= "3.8" and python_version < "3.13"
uvloop==0.20.0 ; 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"
Expand All @@ -213,7 +213,7 @@ webob==1.8.8 ; 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==1.13.1 ; python_version >= "3.8" and python_version < "3.13"
yarl==1.15.0 ; python_version >= "3.8" and python_version < "3.13"
zipp==3.20.2 ; python_version >= "3.8" and python_version < "3.13"
zipstream-new==1.1.8 ; python_version >= "3.8" and python_version < "3.13"
zstandard==0.23.0 ; python_version >= "3.8" and python_version < "3.13"
8 changes: 4 additions & 4 deletions lib/galaxy/dependencies/pinned-typecheck-requirements.txt
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Original file line number Diff line number Diff line change
@@ -1,8 +1,8 @@
--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]==1.35.34 ; python_version >= "3.8" and python_version < "3.13"
botocore-stubs==1.35.34 ; python_version >= "3.8" and python_version < "3.13"
boto3-stubs[s3]==1.35.39 ; python_version >= "3.8" and python_version < "3.13"
botocore-stubs==1.35.39 ; 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"
Expand All @@ -25,8 +25,8 @@ types-paramiko==3.5.0.20240928 ; python_version >= "3.8" and python_version < "3
types-python-dateutil==2.9.0.20241003 ; 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-s3transfer==0.10.3 ; 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-six==1.16.21.20241009 ; 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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