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Update Python dependencies
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@galaxybot
galaxybot authored Mar 16, 2024
1 parent af376f2 commit 8a0e255
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26 changes: 14 additions & 12 deletions lib/galaxy/dependencies/dev-requirements.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -11,9 +11,9 @@ babel==2.14.0 ; 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"
billiard==4.2.0 ; python_version >= "3.8" and python_version < "3.13"
black==24.1.1 ; python_version >= "3.8" and python_version < "3.13"
black==24.3.0 ; python_version >= "3.8" and python_version < "3.13"
build==1.1.1 ; python_version >= "3.8" and python_version < "3.13"
cachecontrol[filecache]==0.13.1 ; python_version >= "3.8" and python_version < "3.13"
cachecontrol[filecache]==0.14.0 ; python_version >= "3.8" and python_version < "3.13"
celery==5.3.6 ; python_version >= "3.8" and python_version < "3.13"
certifi==2024.2.2 ; python_version >= "3.8" and python_version < "3.13"
cffi==1.16.0 ; python_version >= "3.8" and python_version < "3.13"
Expand All @@ -25,28 +25,30 @@ click==8.1.7 ; python_version >= "3.8" and python_version < "3.13"
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]==7.4.3 ; python_version >= "3.8" and python_version < "3.13"
coverage[toml]==7.4.4 ; python_version >= "3.8" and python_version < "3.13"
cryptography==42.0.5 ; python_version >= "3.8" and python_version < "3.13"
cwltest==2.5.20240304113812 ; python_version >= "3.8" and python_version < "3.13"
cycler==0.12.1 ; python_version >= "3.8" and python_version < "3.13"
darker==1.7.3 ; python_version >= "3.8" and python_version < "3.13"
darker==2.0.0 ; python_version >= "3.8" and python_version < "3.13"
darkgraylib==1.0.0 ; python_version >= "3.8" 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==0.18.1 ; python_version >= "3.8" and python_version < "3.13"
exceptiongroup==1.2.0 ; python_version >= "3.8" and python_version < "3.11"
filelock==3.13.1 ; python_version >= "3.8" and python_version < "3.13"
fluent-logger==0.11.0 ; python_version >= "3.8" and python_version < "3.13"
fonttools==4.49.0 ; python_version >= "3.8" and python_version < "3.13"
fonttools==4.50.0 ; python_version >= "3.8" and python_version < "3.13"
frozenlist==1.4.1 ; python_version >= "3.8" and python_version < "3.13"
galaxy-release-util==0.1.7 ; python_version >= "3.8" and python_version < "3.13"
graylint==1.0.0 ; python_version >= "3.8" and python_version < "3.13"
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==1.0.4 ; python_version >= "3.8" and python_version < "3.13"
httpx==0.27.0 ; python_version >= "3.8" and python_version < "3.13"
idna==3.6 ; python_version >= "3.8" and python_version < "3.13"
imagesize==1.4.1 ; python_version >= "3.8" and python_version < "3.13"
importlib-metadata==7.0.2 ; python_version >= "3.8" and python_version < "3.13"
importlib-resources==6.1.3 ; python_version >= "3.8" and python_version < "3.10"
importlib-resources==6.3.0 ; 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"
isort==5.13.2 ; python_version >= "3.8" and python_version < "3.13"
Expand All @@ -66,7 +68,7 @@ matplotlib==3.8.3 ; python_version >= "3.9" and python_version < "3.13"
mdit-py-plugins==0.4.0 ; 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==2.0.5 ; python_version >= "3.8" and python_version < "3.13"
mistune==3.0.2 ; python_version >= "3.8" and python_version < "3.13"
more-itertools==10.2.0 ; 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"
Expand Down Expand Up @@ -108,9 +110,9 @@ 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==3.12.0 ; python_version >= "3.8" and python_version < "3.13"
pytest-playwright==0.4.4 ; python_version >= "3.8" and python_version < "3.13"
pytest-postgresql==5.1.1 ; 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==8.1.1 ; 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-irodsclient==2.0.0 ; 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 @@ -126,13 +128,13 @@ 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"
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"
schema-salad==8.5.20240102191335 ; python_version >= "3.8" and python_version < "3.13"
schema-salad==8.5.20240311110950 ; python_version >= "3.8" and python_version < "3.13"
scipy==1.10.1 ; python_version >= "3.8" and python_version < "3.9"
scipy==1.12.0 ; 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==4.18.1 ; python_version >= "3.8" and python_version < "3.13"
seletools==1.4.0 ; python_version >= "3.8" and python_version < "3.13"
setuptools==69.1.1 ; python_version >= "3.8" and python_version < "3.13"
setuptools==69.2.0 ; 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 Expand Up @@ -168,4 +170,4 @@ werkzeug==3.0.1 ; 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"
zipp==3.17.0 ; python_version >= "3.8" and python_version < "3.13"
zipp==3.18.1 ; python_version >= "3.8" and python_version < "3.13"
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==24.2.6
mccabe==0.7.0
pycodestyle==2.11.1
pyflakes==3.2.0
ruff==0.3.2
ruff==0.3.3
36 changes: 18 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
--index-url https://wheels.galaxyproject.org/simple

a2wsgi==1.10.2 ; python_version >= "3.8" and python_version < "3.13"
a2wsgi==1.10.4 ; python_version >= "3.8" and python_version < "3.13"
adal==1.2.7 ; python_version >= "3.8" and python_version < "3.13"
aiobotocore==2.12.1 ; python_version >= "3.8" and python_version < "3.13"
aiodataloader==0.4.0 ; python_version >= "3.8" and python_version < "3.13"
Expand All @@ -13,7 +13,7 @@ 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==0.6.0 ; python_version >= "3.8" and python_version < "3.13"
anyio==4.3.0 ; python_version >= "3.8" and python_version < "3.13"
apispec==6.5.0 ; python_version >= "3.8" and python_version < "3.13"
apispec==6.6.0 ; 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==3.2.3 ; python_version >= "3.8" and python_version < "3.13"
Expand All @@ -26,7 +26,7 @@ backports-zoneinfo[tzdata]==0.2.1 ; python_version >= "3.8" and python_version <
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==4.1.2 ; python_version >= "3.8" and python_version < "3.13"
bdbag==1.7.1 ; python_version >= "3.8" and python_version < "3.13"
bdbag==1.7.2 ; python_version >= "3.8" and python_version < "3.13"
beaker==1.12.1 ; 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"
Expand All @@ -35,7 +35,7 @@ boltons==23.1.1 ; python_version >= "3.8" and python_version < "3.13"
boto==2.49.0 ; python_version >= "3.8" and python_version < "3.13"
botocore==1.34.51 ; python_version >= "3.8" and python_version < "3.13"
bx-python==0.11.0 ; python_version >= "3.8" and python_version < "3.13"
cachecontrol[filecache]==0.13.1 ; python_version >= "3.8" and python_version < "3.13"
cachecontrol[filecache]==0.14.0 ; python_version >= "3.8" and python_version < "3.13"
celery==5.3.6 ; python_version >= "3.8" and python_version < "3.13"
certifi==2024.2.2 ; python_version >= "3.8" and python_version < "3.13"
cffi==1.16.0 ; python_version >= "3.8" and python_version < "3.13"
Expand Down Expand Up @@ -88,9 +88,9 @@ h5py==3.10.0 ; python_version >= "3.8" and python_version < "3.13"
humanfriendly==10.0 ; python_version >= "3.8" and python_version < "3.13"
idna==3.6 ; python_version >= "3.8" and python_version < "3.13"
importlib-metadata==7.0.2 ; python_version >= "3.8" and python_version < "3.13"
importlib-resources==6.1.3 ; python_version >= "3.8" and python_version < "3.9"
importlib-resources==6.3.0 ; python_version >= "3.8" and python_version < "3.9"
isa-rwval==0.10.10 ; python_version >= "3.8" and python_version < "3.13"
isal==1.6.0 ; 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"
jmespath==1.0.1 ; python_version >= "3.8" and python_version < "3.13"
Expand All @@ -102,11 +102,11 @@ 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==1.3.2 ; 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==3.5.2 ; 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==6.6.3 ; python_version >= "3.8" and python_version < "3.13"
mistune==2.0.5 ; python_version >= "3.8" and python_version < "3.13"
mercurial==6.7 ; 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==1.27.0 ; python_version >= "3.8" and python_version < "3.13"
msgpack==1.0.8 ; python_version >= "3.8" and python_version < "3.13"
Expand Down Expand Up @@ -134,10 +134,10 @@ psutil==5.9.8 ; 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==2.21 ; python_version >= "3.8" and python_version < "3.13"
pycryptodome==3.20.0 ; python_version >= "3.8" and python_version < "3.13"
pydantic-core==2.14.6 ; python_version >= "3.8" and python_version < "3.13"
pydantic-core==2.16.3 ; python_version >= "3.8" and python_version < "3.13"
pydantic-tes==0.1.5 ; python_version >= "3.8" and python_version < "3.13"
pydantic==2.5.3 ; python_version >= "3.8" and python_version < "3.13"
pydantic[email]==2.5.3 ; python_version >= "3.8" and python_version < "3.13"
pydantic==2.6.4 ; python_version >= "3.8" and python_version < "3.13"
pydantic[email]==2.6.4 ; 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==0.8.1.1 ; python_version >= "3.8" and python_version < "3.13"
Expand All @@ -162,7 +162,7 @@ referencing==0.33.0 ; python_version >= "3.8" and python_version < "3.13"
refgenconf==0.12.2 ; python_version >= "3.8" and python_version < "3.13"
regex==2023.12.25 ; python_version >= "3.8" and python_version < "3.13"
repoze-lru==0.7 ; python_version >= "3.8" and python_version < "3.13"
requests-oauthlib==1.3.1 ; python_version >= "3.8" and python_version < "3.13"
requests-oauthlib==1.4.0 ; python_version >= "3.8" and python_version < "3.13"
requests-toolbelt==1.0.0 ; python_version >= "3.8" and python_version < "3.13"
requests-unixsocket==0.3.0 ; python_version >= "3.8" and python_version < "3.13"
requests==2.31.0 ; python_version >= "3.8" and python_version < "3.13"
Expand All @@ -173,9 +173,9 @@ rpds-py==0.18.0 ; 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==2023.12.2 ; python_version >= "3.8" and python_version < "3.13"
schema-salad==8.5.20240102191335 ; python_version >= "3.8" and python_version < "3.13"
schema-salad==8.5.20240311110950 ; python_version >= "3.8" and python_version < "3.13"
setuptools-scm==5.0.2 ; python_version >= "3.8" and python_version < "3.13"
setuptools==69.1.1 ; python_version >= "3.8" and python_version < "3.13"
setuptools==69.2.0 ; 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 Down Expand Up @@ -203,7 +203,7 @@ 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==0.7.0 ; python_version >= "3.8" and python_version < "3.13"
urllib3==1.26.18 ; python_version >= "3.8" and python_version < "3.13"
uvicorn==0.27.1 ; python_version >= "3.8" and python_version < "3.13"
uvicorn==0.28.0 ; 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 @@ -213,6 +213,6 @@ 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==1.9.4 ; python_version >= "3.8" and python_version < "3.13"
zipp==3.17.0 ; python_version >= "3.8" and python_version < "3.13"
zipp==3.18.1 ; 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"
18 changes: 9 additions & 9 deletions lib/galaxy/dependencies/pinned-typecheck-requirements.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -5,21 +5,21 @@ 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==1.9.0 ; python_version >= "3.8" and python_version < "3.13"
pycparser==2.21 ; python_version >= "3.8" and python_version < "3.13" and platform_python_implementation != "PyPy"
pydantic-core==2.14.6 ; python_version >= "3.8" and python_version < "3.13"
pydantic==2.5.3 ; python_version >= "3.8" and python_version < "3.13"
pydantic-core==2.16.3 ; python_version >= "3.8" and python_version < "3.13"
pydantic==2.6.4 ; python_version >= "3.8" and python_version < "3.13"
tomli==2.0.1 ; python_version >= "3.8" and python_version < "3.11"
types-bleach==6.1.0.20240222 ; python_version >= "3.8" and python_version < "3.13"
types-bleach==6.1.0.20240311 ; python_version >= "3.8" and python_version < "3.13"
types-boto==2.49.18.20240205 ; python_version >= "3.8" and python_version < "3.13"
types-contextvars==2.4.7.3 ; python_version >= "3.8" and python_version < "3.13"
types-dataclasses==0.6.6 ; python_version >= "3.8" and python_version < "3.13"
types-docutils==0.20.0.20240310 ; python_version >= "3.8" and python_version < "3.13"
types-docutils==0.20.0.20240316 ; python_version >= "3.8" and python_version < "3.13"
types-html5lib==1.1.11.20240228 ; python_version >= "3.8" and python_version < "3.13"
types-markdown==3.5.0.20240129 ; python_version >= "3.8" and python_version < "3.13"
types-paramiko==3.4.0.20240205 ; python_version >= "3.8" and python_version < "3.13"
types-markdown==3.6.0.20240316 ; python_version >= "3.8" and python_version < "3.13"
types-paramiko==3.4.0.20240311 ; python_version >= "3.8" and python_version < "3.13"
types-pkg-resources==0.1.3 ; python_version >= "3.8" and python_version < "3.13"
types-python-dateutil==2.8.19.20240106 ; python_version >= "3.8" and python_version < "3.13"
types-pyyaml==6.0.12.12 ; 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==1.16.21.20240310 ; python_version >= "3.8" and python_version < "3.13"
types-six==1.16.21.20240311 ; 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==4.10.0 ; python_version >= "3.8" and python_version < "3.13"

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