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Update Python dependencies
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@galaxybot @nsoranzo
galaxybot authored and nsoranzo committed May 15, 2024
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Showing 4 changed files with 24 additions and 24 deletions.
22 changes: 11 additions & 11 deletions lib/galaxy/dependencies/dev-requirements.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,7 @@ ase==3.22.1 ; python_version >= "3.8" and python_version < "3.13"
async-timeout==4.0.3 ; python_version >= "3.8" and python_version < "3.11"
attrs==23.2.0 ; python_version >= "3.8" and python_version < "3.13"
axe-selenium-python==2.1.6 ; python_version >= "3.8" and python_version < "3.13"
babel==2.14.0 ; python_version >= "3.8" and python_version < "3.13"
babel==2.15.0 ; python_version >= "3.8" and python_version < "3.13"
backports-tarfile==1.1.1 ; python_version >= "3.8" and python_version < "3.12"
backports-zoneinfo==0.2.1 ; python_version >= "3.8" and python_version < "3.9"
black==24.4.2 ; python_version >= "3.8" and python_version < "3.13"
Expand All @@ -20,7 +20,7 @@ codespell==2.2.6 ; 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")
contourpy==1.1.1 ; python_version >= "3.8" and python_version < "3.13"
coverage[toml]==7.5.1 ; python_version >= "3.8" and python_version < "3.13"
cryptography==42.0.6 ; python_version >= "3.8" and python_version < "3.13"
cryptography==42.0.7 ; python_version >= "3.8" and python_version < "3.13"
cwltest==2.5.20240425111257 ; 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"
Expand Down Expand Up @@ -52,19 +52,19 @@ jaraco-classes==3.4.0 ; python_version >= "3.8" and python_version < "3.13"
jaraco-context==5.3.0 ; python_version >= "3.8" and python_version < "3.13"
jaraco-functools==4.0.1 ; python_version >= "3.8" and python_version < "3.13"
jeepney==0.8.0 ; python_version >= "3.8" and python_version < "3.13" and sys_platform == "linux"
jinja2==3.1.3 ; python_version >= "3.8" and python_version < "3.13"
jinja2==3.1.4 ; 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"
junit-xml==1.9 ; python_version >= "3.8" and python_version < "3.13"
keyring==25.2.0 ; 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"
lxml==4.9.4 ; python_version >= "3.8" and python_version < "3.13"
markdown-it-py==3.0.0 ; python_version >= "3.8" and python_version < "3.13"
markdown-it-reporter==0.0.2 ; python_version >= "3.8" and python_version < "3.13"
markupsafe==2.1.5 ; python_version >= "3.8" and python_version < "3.13"
matplotlib==3.7.5 ; python_version >= "3.8" and python_version < "3.9"
matplotlib==3.8.4 ; python_version >= "3.9" and python_version < "3.13"
mdit-py-plugins==0.4.0 ; python_version >= "3.8" and python_version < "3.13"
mdit-py-plugins==0.4.1 ; python_version >= "3.8" and python_version < "3.13"
mdurl==0.1.2 ; python_version >= "3.8" and python_version < "3.13"
mirakuru==2.5.2 ; python_version >= "3.8" and python_version < "3.13"
mistune==3.0.2 ; python_version >= "3.8" and python_version < "3.13"
Expand All @@ -89,7 +89,7 @@ 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==3.10.0 ; python_version >= "3.8" and python_version < "3.13"
psutil==5.9.8 ; python_version >= "3.8" and python_version < "3.13" and sys_platform != "cygwin"
psycopg==3.1.18 ; python_version >= "3.8" and python_version < "3.13"
psycopg==3.1.19 ; python_version >= "3.8" and python_version < "3.13"
pycparser==2.22 ; python_version >= "3.8" and python_version < "3.13"
pyee==11.1.0 ; python_version >= "3.8" and python_version < "3.13"
pygithub==2.3.0 ; python_version >= "3.8" and python_version < "3.13"
Expand All @@ -107,7 +107,7 @@ pytest-httpserver==1.0.10 ; 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==0.4.4 ; python_version >= "3.8" and python_version < "3.13"
pytest-playwright==0.5.0 ; 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"
Expand All @@ -125,16 +125,16 @@ requests==2.31.0 ; python_version >= "3.8" and python_version < "3.13"
responses==0.25.0 ; 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==0.18.0 ; python_version >= "3.9" and python_version < "3.13"
rpds-py==0.18.1 ; 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==34.2.0 ; python_version >= "3.9" and python_version < "3.13"
rucio-clients==34.3.0 ; python_version >= "3.9" and python_version < "3.13"
schema-salad==8.5.20240410123758 ; python_version >= "3.8" and python_version < "3.13"
scipy==1.10.1 ; python_version >= "3.8" and python_version < "3.9"
scipy==1.13.0 ; python_version >= "3.9" and python_version < "3.13"
secretstorage==3.3.3 ; python_version >= "3.8" and python_version < "3.13" and sys_platform == "linux"
selenium==4.20.0 ; python_version >= "3.8" and python_version < "3.13"
seletools==1.4.0 ; python_version >= "3.8" and python_version < "3.13"
seletools==1.5.0 ; python_version >= "3.8" and python_version < "3.13"
setuptools==69.5.1 ; 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 Down Expand Up @@ -168,7 +168,7 @@ urllib3==1.26.18 ; python_version >= "3.8" and python_version < "3.13"
urllib3[socks]==1.26.18 ; python_version >= "3.8" and python_version < "3.13"
watchdog==4.0.0 ; python_version >= "3.8" and python_version < "3.13"
wcwidth==0.2.13 ; python_version >= "3.8" and python_version < "3.13"
werkzeug==3.0.2 ; python_version >= "3.8" and python_version < "3.13"
werkzeug==3.0.3 ; 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==1.9.4 ; 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==2.11.1
pyflakes==3.2.0
ruff==0.4.3
ruff==0.4.4
20 changes: 10 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 @@ -20,7 +20,7 @@ argcomplete==3.3.0 ; 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==23.2.0 ; python_version >= "3.8" and python_version < "3.13"
babel==2.14.0 ; python_version >= "3.8" and python_version < "3.13"
babel==2.15.0 ; python_version >= "3.8" and python_version < "3.13"
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"
Expand All @@ -29,7 +29,7 @@ bcrypt==4.1.3 ; python_version >= "3.8" and python_version < "3.13"
bdbag==1.7.2 ; 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"
bioblend==1.2.0 ; python_version >= "3.8" and python_version < "3.13"
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"
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==0.9.0 ; python_version >= "3.8" and python_version < "3.13"
cryptography==42.0.6 ; python_version >= "3.8" and python_version < "3.13"
cryptography==42.0.7 ; 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==3.1.20240404144621 ; python_version >= "3.8" and python_version < "3.13"
Expand Down Expand Up @@ -92,20 +92,20 @@ importlib-resources==6.4.0 ; python_version >= "3.8" and python_version < "3.9"
isa-rwval==0.10.10 ; python_version >= "3.8" and python_version < "3.13"
isal==1.6.1 ; python_version >= "3.8" and python_version < "3.13"
isodate==0.6.1 ; python_version >= "3.8" and python_version < "3.13"
jinja2==3.1.3 ; python_version >= "3.8" and python_version < "3.13"
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"
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==4.9.4 ; python_version >= "3.8" and python_version < "3.13"
mako==1.3.3 ; python_version >= "3.8" and python_version < "3.13"
mako==1.3.5 ; python_version >= "3.8" and python_version < "3.13"
markdown-it-py==3.0.0 ; python_version >= "3.8" and python_version < "3.13"
markdown==3.6 ; python_version >= "3.8" and python_version < "3.13"
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==6.7.2 ; python_version >= "3.8" and python_version < "3.13"
mercurial==6.7.3 ; python_version >= "3.8" and python_version < "3.13"
mistune==3.0.2 ; python_version >= "3.8" and python_version < "3.13"
mrcfile==1.5.0 ; python_version >= "3.8" and python_version < "3.13"
msal==1.28.0 ; python_version >= "3.8" and python_version < "3.13"
Expand Down Expand Up @@ -159,7 +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==2024.4.28 ; python_version >= "3.8" and python_version < "3.13"
regex==2024.5.10 ; 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 @@ -168,7 +168,7 @@ requests==2.31.0 ; 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==0.18.0 ; python_version >= "3.8" and python_version < "3.13"
rpds-py==0.18.1 ; 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==2024.3.1 ; python_version >= "3.8" and python_version < "3.13"
Expand All @@ -181,15 +181,15 @@ 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==2.0.29 ; python_version >= "3.8" and python_version < "3.13"
sqlalchemy==2.0.30 ; 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"
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"
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==8.2.3 ; python_version >= "3.8" and python_version < "3.13"
tenacity==8.3.0 ; 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"
tomli==2.0.1 ; python_version >= "3.8" and python_version < "3.11"
Expand Down
4 changes: 2 additions & 2 deletions lib/galaxy/dependencies/pinned-typecheck-requirements.txt
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
annotated-types==0.6.0 ; python_version >= "3.8" and python_version < "3.13"
cffi==1.16.0 ; python_version >= "3.8" and python_version < "3.13" and platform_python_implementation != "PyPy"
cryptography==42.0.6 ; python_version >= "3.8" and python_version < "3.13"
cryptography==42.0.7 ; python_version >= "3.8" and python_version < "3.13"
lxml-stubs==0.5.1 ; python_version >= "3.8" and python_version < "3.13"
mypy-extensions==1.0.0 ; python_version >= "3.8" and python_version < "3.13"
mypy==1.10.0 ; python_version >= "3.8" and python_version < "3.13"
Expand All @@ -20,6 +20,6 @@ types-pkg-resources==0.1.3 ; python_version >= "3.8" and python_version < "3.13"
types-python-dateutil==2.9.0.20240316 ; python_version >= "3.8" and python_version < "3.13"
types-pyyaml==6.0.12.20240311 ; 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-six==1.16.21.20240425 ; 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==4.11.0 ; python_version >= "3.8" and python_version < "3.13"

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