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Update Python dependencies
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@galaxybot @nsoranzo
galaxybot authored and nsoranzo committed Apr 25, 2024
1 parent 7c143ce commit ad2b49c
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Showing 4 changed files with 36 additions and 27 deletions.
24 changes: 17 additions & 7 deletions lib/galaxy/dependencies/dev-requirements.txt
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Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
aiohttp==3.9.4 ; python_version >= "3.8" and python_version < "3.13"
aiohttp==3.9.5 ; 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==4.3.0 ; python_version >= "3.8" and python_version < "3.13"
Expand All @@ -7,7 +7,7 @@ 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"
backports-tarfile==1.1.0 ; python_version >= "3.8" and python_version < "3.12"
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==24.4.0 ; python_version >= "3.8" and python_version < "3.13"
build==1.2.1 ; python_version >= "3.8" and python_version < "3.13"
Expand All @@ -24,11 +24,13 @@ 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==2.1.1 ; python_version >= "3.8" and python_version < "3.13"
darkgraylib==1.2.0 ; 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"
exceptiongroup==1.2.0 ; python_version >= "3.8" and python_version < "3.11"
dogpile-cache==1.2.2 ; python_version >= "3.9" and python_version < "3.13"
exceptiongroup==1.2.1 ; python_version >= "3.8" and python_version < "3.11"
filelock==3.13.4 ; python_version >= "3.8" and python_version < "3.13"
fluent-logger==0.11.0 ; python_version >= "3.8" and python_version < "3.13"
fonttools==4.51.0 ; python_version >= "3.8" and python_version < "3.13"
Expand All @@ -48,9 +50,11 @@ 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"
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==4.0.0 ; 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"
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==25.1.0 ; python_version >= "3.8" and python_version < "3.13"
kiwisolver==1.4.5 ; python_version >= "3.8" and python_version < "3.13"
Expand All @@ -68,19 +72,20 @@ 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"
mypy-extensions==1.0.0 ; python_version >= "3.8" and python_version < "3.13"
myst-parser==2.0.0 ; python_version >= "3.8" and python_version < "3.13"
myst-parser==3.0.0 ; python_version >= "3.8" and python_version < "3.13"
nh3==0.2.17 ; python_version >= "3.8" and python_version < "3.13"
numpy==1.24.4 ; python_version >= "3.8" and python_version < "3.9"
numpy==1.26.4 ; python_version >= "3.9" and python_version < "3.13"
outcome==1.3.0.post0 ; python_version >= "3.8" and python_version < "3.13"
packaging==24.0 ; 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==10.3.0 ; 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==4.2.0 ; python_version >= "3.8" and python_version < "3.13"
playwright==1.43.0 ; python_version >= "3.8" and python_version < "3.13"
pluggy==1.4.0 ; python_version >= "3.8" and python_version < "3.13"
pluggy==1.5.0 ; python_version >= "3.8" and python_version < "3.13"
port-for==0.7.2 ; 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"
Expand Down Expand Up @@ -114,13 +119,16 @@ pywin32-ctypes==0.2.2 ; python_version >= "3.8" and python_version < "3.13" and
pyyaml==6.0.1 ; python_version >= "3.8" and python_version < "3.13"
rdflib==6.3.2 ; python_version >= "3.8" and python_version < "3.13"
readme-renderer==43.0 ; python_version >= "3.8" and python_version < "3.13"
referencing==0.34.0 ; python_version >= "3.9" and python_version < "3.13"
requests-toolbelt==1.0.0 ; python_version >= "3.8" and python_version < "3.13"
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"
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"
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"
Expand All @@ -142,6 +150,8 @@ 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==8.1.0 ; 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"
Expand Down
4 changes: 2 additions & 2 deletions lib/galaxy/dependencies/pinned-lint-requirements.txt
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
attrs==23.2.0
flake8==7.0.0
flake8-bugbear==24.2.6
flake8-bugbear==24.4.21
mccabe==0.7.0
pycodestyle==2.11.1
pyflakes==3.2.0
ruff==0.3.7
ruff==0.4.1
27 changes: 13 additions & 14 deletions lib/galaxy/dependencies/pinned-requirements.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -5,15 +5,15 @@ adal==1.2.7 ; python_version >= "3.8" and python_version < "3.13"
aiobotocore==2.12.3 ; python_version >= "3.8" and python_version < "3.13"
aiodataloader==0.4.0 ; python_version >= "3.8" and python_version < "3.13"
aiofiles==23.2.1 ; python_version >= "3.8" and python_version < "3.13"
aiohttp==3.9.4 ; python_version >= "3.8" and python_version < "3.13"
aiohttp==3.9.5 ; python_version >= "3.8" and python_version < "3.13"
aioitertools==0.11.0 ; python_version >= "3.8" and python_version < "3.13"
aiosignal==1.3.1 ; python_version >= "3.8" and python_version < "3.13"
alembic==1.13.1 ; 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==0.6.0 ; python_version >= "3.8" and python_version < "3.13"
anyio==4.3.0 ; python_version >= "3.8" and python_version < "3.13"
apispec==6.6.0 ; 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==3.3.0 ; python_version >= "3.8" and python_version < "3.13"
Expand All @@ -36,7 +36,7 @@ boto==2.49.0 ; python_version >= "3.8" and python_version < "3.13"
botocore==1.34.69 ; 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]==0.14.0 ; python_version >= "3.8" and python_version < "3.13"
celery==5.3.6 ; python_version >= "3.8" and python_version < "3.13"
celery==5.4.0 ; 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"
charset-normalizer==3.3.2 ; python_version >= "3.8" and python_version < "3.13"
Expand Down Expand Up @@ -65,8 +65,8 @@ docutils==0.20.1 ; python_version >= "3.8" and python_version < "3.13"
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==2.1.1 ; python_version >= "3.8" and python_version < "3.13"
exceptiongroup==1.2.0 ; python_version >= "3.8" and python_version < "3.11"
fastapi==0.110.1 ; python_version >= "3.8" and python_version < "3.13"
exceptiongroup==1.2.1 ; python_version >= "3.8" and python_version < "3.11"
fastapi==0.110.2 ; python_version >= "3.8" and python_version < "3.13"
filelock==3.13.4 ; 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 @@ -80,10 +80,10 @@ graphql-core==3.2.3 ; python_version >= "3.8" and python_version < "3.13"
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 >= "3.8" and 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")
gunicorn==21.2.0 ; python_version >= "3.8" and python_version < "3.13"
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"
h11==0.14.0 ; python_version >= "3.8" and python_version < "3.13"
h5grove==2.1.0 ; 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"
Expand All @@ -96,7 +96,7 @@ 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"
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==4.21.1 ; 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"
Expand Down Expand Up @@ -126,18 +126,17 @@ paste==3.9.0 ; 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==10.3.0 ; 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==3.0.43 ; python_version >= "3.8" and python_version < "3.13"
prov==1.5.1 ; python_version >= "3.8" and python_version < "3.13"
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==2.22 ; python_version >= "3.8" and python_version < "3.13"
pycryptodome==3.20.0 ; python_version >= "3.8" and python_version < "3.13"
pydantic-core==2.18.1 ; python_version >= "3.8" and python_version < "3.13"
pydantic-core==2.18.2 ; python_version >= "3.8" and python_version < "3.13"
pydantic-tes==0.1.5 ; python_version >= "3.8" and python_version < "3.13"
pydantic==2.7.0 ; python_version >= "3.8" and python_version < "3.13"
pydantic[email]==2.7.0 ; python_version >= "3.8" and python_version < "3.13"
pydantic==2.7.1 ; python_version >= "3.8" and python_version < "3.13"
pydantic[email]==2.7.1 ; 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 @@ -156,11 +155,11 @@ python-multipart==0.0.9 ; python_version >= "3.8" and python_version < "3.13"
python3-openid==3.2.0 ; python_version >= "3.8" and python_version < "3.13"
pytz==2024.1 ; python_version >= "3.8" and python_version < "3.13"
pyyaml==6.0.1 ; python_version >= "3.8" and python_version < "3.13"
pyzmq==26.0.0 ; python_version >= "3.8" and python_version < "3.13"
pyzmq==26.0.2 ; python_version >= "3.8" and python_version < "3.13"
rdflib==6.3.2 ; python_version >= "3.8" and python_version < "3.13"
referencing==0.34.0 ; 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"
regex==2024.4.16 ; 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 Down
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
Expand Up @@ -5,17 +5,17 @@ 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==2.22 ; python_version >= "3.8" and python_version < "3.13" and platform_python_implementation != "PyPy"
pydantic-core==2.18.1 ; python_version >= "3.8" and python_version < "3.13"
pydantic==2.7.0 ; python_version >= "3.8" and python_version < "3.13"
pydantic-core==2.18.2 ; python_version >= "3.8" and python_version < "3.13"
pydantic==2.7.1 ; python_version >= "3.8" and python_version < "3.13"
tomli==2.0.1 ; python_version >= "3.8" and python_version < "3.11"
types-bleach==6.1.0.20240331 ; 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==0.20.0.20240406 ; python_version >= "3.8" and python_version < "3.13"
types-docutils==0.21.0.20240423 ; 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==3.6.0.20240316 ; 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-paramiko==3.4.0.20240423 ; 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==2.9.0.20240316 ; python_version >= "3.8" and python_version < "3.13"
types-pyyaml==6.0.12.20240311 ; python_version >= "3.8" and python_version < "3.13"
Expand Down

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