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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 Jul 27, 2024
1 parent 543ad8b commit cff7aac
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Showing 4 changed files with 41 additions and 46 deletions.
32 changes: 14 additions & 18 deletions lib/galaxy/dependencies/dev-requirements.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -25,16 +25,14 @@ colorama==0.4.6 ; python_version >= "3.8" and python_version < "3.13" and (sys_p
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]==7.6.0 ; 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"
cryptography==43.0.0 ; python_version >= "3.8" and python_version < "3.13"
cwltest==2.5.20240714110256 ; python_version >= "3.8" and python_version < "3.13"
cycler==0.12.1 ; python_version >= "3.8" and python_version < "3.13"
darker==2.1.1 ; python_version >= "3.8" and python_version < "3.13"
darkgraylib==1.2.1 ; python_version >= "3.8" and python_version < "3.13"
decorator==5.1.1 ; python_version >= "3.9" and python_version < "3.13"
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==1.2.2 ; 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"
Expand All @@ -48,7 +46,7 @@ httpcore==1.0.5 ; python_version >= "3.8" and python_version < "3.13"
httpx==0.27.0 ; python_version >= "3.8" and python_version < "3.13"
idna==3.7 ; python_version >= "3.8" and python_version < "3.13"
imagesize==1.4.1 ; python_version >= "3.8" and python_version < "3.13"
importlib-metadata==8.0.0 ; python_version >= "3.8" and python_version < "3.13"
importlib-metadata==8.2.0 ; python_version >= "3.8" and python_version < "3.13"
importlib-resources==6.4.0 ; python_version >= "3.8" and python_version < "3.10"
iniconfig==2.0.0 ; python_version >= "3.8" and python_version < "3.13"
isodate==0.6.1 ; python_version >= "3.8" and python_version < "3.13"
Expand All @@ -60,7 +58,7 @@ jeepney==0.8.0 ; python_version >= "3.8" and python_version < "3.13" and sys_pla
jinja2==3.1.4 ; python_version >= "3.8" and python_version < "3.13"
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==4.20.0 ; 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==25.2.1 ; python_version >= "3.8" and python_version < "3.13"
kiwisolver==1.4.5 ; python_version >= "3.8" and python_version < "3.13"
Expand All @@ -81,17 +79,16 @@ 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==0.2.18 ; 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"
numpy==2.0.1 ; python_version >= "3.9" and python_version < "3.13"
onedatafilerestclient==21.2.5.1 ; 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"
pathspec==0.12.1 ; python_version >= "3.8" and python_version < "3.13"
pbr==6.0.0 ; 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==4.2.2 ; python_version >= "3.8" and python_version < "3.13"
playwright==1.45.0 ; python_version >= "3.8" and python_version < "3.13"
playwright==1.45.1 ; 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==3.10.2 ; python_version >= "3.8" and python_version < "3.13"
Expand All @@ -106,18 +103,18 @@ pynacl==1.5.0 ; python_version >= "3.8" and python_version < "3.13"
pyparsing==3.1.2 ; python_version >= "3.8" and python_version < "3.13"
pyproject-hooks==1.1.0 ; python_version >= "3.8" and python_version < "3.13"
pysocks==1.7.1 ; python_version >= "3.8" and python_version < "3.13"
pytest-asyncio==0.23.7 ; python_version >= "3.8" and python_version < "3.13"
pytest-asyncio==0.23.8 ; python_version >= "3.8" and python_version < "3.13"
pytest-base-url==2.1.0 ; python_version >= "3.8" and python_version < "3.13"
pytest-cov==5.0.0 ; python_version >= "3.8" and python_version < "3.13"
pytest-html==4.1.1 ; python_version >= "3.8" and python_version < "3.13"
pytest-httpserver==1.0.10 ; python_version >= "3.8" and python_version < "3.13"
pytest-httpserver==1.0.12 ; python_version >= "3.8" and python_version < "3.13"
pytest-json-report==1.5.0 ; python_version >= "3.8" and python_version < "3.13"
pytest-metadata==3.1.1 ; python_version >= "3.8" and python_version < "3.13"
pytest-mock==3.14.0 ; python_version >= "3.8" and python_version < "3.13"
pytest-playwright==0.5.1 ; python_version >= "3.8" and python_version < "3.13"
pytest-postgresql==6.0.0 ; python_version >= "3.8" and python_version < "3.13"
pytest-shard==0.1.2 ; python_version >= "3.8" and python_version < "3.13"
pytest==7.4.4 ; python_version >= "3.8" and python_version < "3.13"
pytest==8.3.2 ; 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-irodsclient==2.0.1 ; python_version >= "3.8" and python_version < "3.13"
python-slugify==8.0.4 ; python_version >= "3.8" and python_version < "3.13"
Expand All @@ -132,19 +129,19 @@ 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==0.19.0 ; python_version >= "3.9" and python_version < "3.13"
rpds-py==0.19.1 ; 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"
rucio-clients==35.0.0rc2 ; python_version >= "3.9" and python_version < "3.13"
s3transfer==0.10.2 ; python_version >= "3.8" and python_version < "3.13"
schema-salad==8.6.20240710082410 ; python_version >= "3.8" and python_version < "3.13"
schema-salad==8.7.20240718183047 ; 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"
selenium==4.23.1 ; python_version >= "3.8" and python_version < "3.13"
seletools==1.5.0 ; python_version >= "3.8" and python_version < "3.13"
setuptools==70.3.0 ; python_version >= "3.8" and python_version < "3.13"
setuptools==71.1.0 ; 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 All @@ -159,7 +156,6 @@ sphinxcontrib-jsmath==1.0.1 ; python_version >= "3.8" and python_version < "3.13
sphinxcontrib-qthelp==1.0.3 ; python_version >= "3.8" and python_version < "3.13"
sphinxcontrib-serializinghtml==1.1.5 ; python_version >= "3.8" and python_version < "3.13"
statsd==4.0.1 ; python_version >= "3.8" and python_version < "3.13"
stevedore==5.2.0 ; 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"
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==24.4.26
mccabe==0.7.0
pycodestyle==2.12.0
pyflakes==3.2.0
ruff==0.5.1
ruff==0.5.5
37 changes: 19 additions & 18 deletions lib/galaxy/dependencies/pinned-requirements.txt
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
--extra-index-url https://wheels.galaxyproject.org/simple

a2wsgi==1.10.6 ; python_version >= "3.8" and python_version < "3.13"
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==2.13.1 ; python_version >= "3.8" and python_version < "3.13"
aiodataloader==0.4.0 ; python_version >= "3.8" and python_version < "3.13"
Expand All @@ -25,7 +25,7 @@ backports-zoneinfo==0.2.1 ; python_version >= "3.8" and python_version < "3.9"
backports-zoneinfo[tzdata]==0.2.1 ; python_version >= "3.8" and python_version < "3.9"
bagit-profile==1.3.1 ; python_version >= "3.8" and python_version < "3.13"
bagit==1.8.1 ; python_version >= "3.8" and python_version < "3.13"
bcrypt==4.1.3 ; python_version >= "3.8" and python_version < "3.13"
bcrypt==4.2.0 ; python_version >= "3.8" and python_version < "3.13"
bdbag==1.7.3 ; python_version >= "3.8" and python_version < "3.13"
beaker==1.13.0 ; python_version >= "3.8" and python_version < "3.13"
billiard==4.2.0 ; python_version >= "3.8" and python_version < "3.13"
Expand All @@ -51,7 +51,7 @@ 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"
cryptography==42.0.8 ; python_version >= "3.8" and python_version < "3.13"
cryptography==43.0.0 ; 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==3.1.20240708091337 ; python_version >= "3.8" and python_version < "3.13"
Expand All @@ -65,7 +65,7 @@ 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==0.111.0 ; python_version >= "3.8" and python_version < "3.13"
fastapi-slim==0.111.1 ; 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"
fs==2.4.16 ; python_version >= "3.8" and python_version < "3.13"
Expand All @@ -80,13 +80,13 @@ graphql-relay==3.2.0 ; python_version >= "3.8" and python_version < "3.13"
gravity==1.0.6 ; python_version >= "3.8" and python_version < "3.13"
greenlet==3.0.3 ; python_version < "3.13" and (platform_machine == "aarch64" or platform_machine == "ppc64le" or platform_machine == "x86_64" or platform_machine == "amd64" or platform_machine == "AMD64" or platform_machine == "win32" or platform_machine == "WIN32") and python_version >= "3.8"
gunicorn==22.0.0 ; python_version >= "3.8" and python_version < "3.13"
gxformat2==0.18.0 ; python_version >= "3.8" and python_version < "3.13"
gxformat2==0.19.0 ; python_version >= "3.8" and python_version < "3.13"
h11==0.14.0 ; python_version >= "3.8" and python_version < "3.13"
h5grove==2.2.0 ; 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==3.7 ; python_version >= "3.8" and python_version < "3.13"
importlib-metadata==8.0.0 ; python_version >= "3.8" and python_version < "3.13"
importlib-metadata==8.2.0 ; python_version >= "3.8" and python_version < "3.13"
importlib-resources==6.4.0 ; 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"
isal==1.6.1 ; python_version >= "3.8" and python_version < "3.13"
Expand All @@ -95,7 +95,7 @@ jinja2==3.1.4 ; python_version >= "3.8" and python_version < "3.13"
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==4.20.0 ; python_version >= "3.8" and python_version < "3.13"
jsonschema==4.23.0 ; python_version >= "3.8" and python_version < "3.13"
kombu==5.3.7 ; python_version >= "3.8" and python_version < "3.13"
lagom==2.6.0 ; python_version >= "3.8" and python_version < "3.13"
lxml==5.2.2 ; python_version >= "3.8" and python_version < "3.13"
Expand All @@ -106,15 +106,15 @@ 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==6.8 ; python_version >= "3.8" and python_version < "3.13"
mistune==3.0.2 ; python_version >= "3.8" and python_version < "3.13"
mrcfile==1.5.1 ; python_version >= "3.8" and python_version < "3.13"
msal==1.29.0 ; python_version >= "3.8" and python_version < "3.13"
mrcfile==1.5.3 ; python_version >= "3.8" and python_version < "3.13"
msal==1.30.0 ; 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"
mypy-extensions==1.0.0 ; python_version >= "3.8" and python_version < "3.13"
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==2.0.0 ; python_version >= "3.9" and python_version < "3.13"
numpy==2.0.1 ; python_version >= "3.9" and python_version < "3.13"
oauthlib==3.2.2 ; python_version >= "3.8" and python_version < "3.13"
orjson==3.10.6 ; python_version >= "3.8" and python_version < "3.13"
oyaml==1.0 ; python_version >= "3.8" and python_version < "3.13"
Expand All @@ -125,6 +125,7 @@ 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"
pebble==5.0.7 ; python_version >= "3.8" and python_version < "3.13"
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==3.0.47 ; python_version >= "3.8" and python_version < "3.13"
prov==1.5.1 ; python_version >= "3.8" and python_version < "3.13"
Expand All @@ -136,7 +137,7 @@ 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==2.8.2 ; 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"
pydot==3.0.1 ; 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"
pygments==2.18.0 ; python_version >= "3.8" and python_version < "3.13"
Expand All @@ -158,7 +159,7 @@ pyzmq==26.0.3 ; python_version >= "3.8" and python_version < "3.13"
rdflib==6.3.2 ; python_version >= "3.8" and python_version < "3.13"
referencing==0.35.1 ; python_version >= "3.8" and python_version < "3.13"
refgenconf==0.12.2 ; python_version >= "3.8" and python_version < "3.13"
regex==2024.5.15 ; python_version >= "3.8" and python_version < "3.13"
regex==2024.7.24 ; python_version >= "3.8" and python_version < "3.13"
repoze-lru==0.7 ; python_version >= "3.8" and python_version < "3.13"
requests-oauthlib==2.0.0 ; python_version >= "3.8" and python_version < "3.13"
requests-toolbelt==1.0.0 ; python_version >= "3.8" and python_version < "3.13"
Expand All @@ -167,13 +168,13 @@ 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==0.19.0 ; python_version >= "3.8" and python_version < "3.13"
rpds-py==0.19.1 ; 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==8.6.20240710082410 ; python_version >= "3.8" and python_version < "3.13"
schema-salad==8.7.20240718183047 ; python_version >= "3.8" and python_version < "3.13"
setuptools-scm==5.0.2 ; python_version >= "3.8" and python_version < "3.13"
setuptools==70.3.0 ; python_version >= "3.8" and python_version < "3.13"
setuptools==71.1.0 ; 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"
Expand All @@ -182,7 +183,7 @@ 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==2.0.31 ; python_version >= "3.8" and python_version < "3.13"
sqlitedict==2.1.0 ; python_version >= "3.8" and python_version < "3.13"
sqlparse==0.5.0 ; 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"
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"
Expand All @@ -201,7 +202,7 @@ tzdata==2024.1 ; 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==1.26.19 ; python_version >= "3.8" and python_version < "3.13"
uvicorn==0.30.1 ; python_version >= "3.8" and python_version < "3.13"
uvicorn==0.30.3 ; python_version >= "3.8" and python_version < "3.13"
uvloop==0.19.0 ; 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 @@ -213,4 +214,4 @@ yacman==0.9.3 ; python_version >= "3.8" and python_version < "3.13"
yarl==1.9.4 ; python_version >= "3.8" and python_version < "3.13"
zipp==3.19.2 ; python_version >= "3.8" and python_version < "3.13"
zipstream-new==1.1.8 ; python_version >= "3.8" and python_version < "3.13"
zstandard==0.22.0 ; python_version >= "3.8" and python_version < "3.13"
zstandard==0.23.0 ; python_version >= "3.8" and python_version < "3.13"
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