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Update Python dependencies
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@galaxybot @nsoranzo
galaxybot authored and nsoranzo committed Apr 16, 2024
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38 changes: 14 additions & 24 deletions lib/galaxy/dependencies/dev-requirements.txt
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Original file line number Diff line number Diff line change
@@ -1,26 +1,20 @@
aiohttp==3.9.3 ; python_version >= "3.8" and python_version < "3.13"
aiohttp==3.9.4 ; 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"
amqp==5.2.0 ; python_version >= "3.8" and python_version < "3.13"
anyio==4.3.0 ; python_version >= "3.8" and python_version < "3.13"
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"
backports-tarfile==1.1.0 ; python_version >= "3.8" and python_version < "3.12"
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==24.3.0 ; python_version >= "3.8" and python_version < "3.13"
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"
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"
charset-normalizer==3.3.2 ; python_version >= "3.8" and python_version < "3.13"
click-didyoumean==0.3.1 ; python_version >= "3.8" and python_version < "3.13"
click-plugins==1.1.1 ; python_version >= "3.8" and python_version < "3.13"
click-repl==0.3.0 ; python_version >= "3.8" and python_version < "3.13"
click==8.1.7 ; python_version >= "3.8" and python_version < "3.13"
codespell==2.2.6 ; 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")
Expand All @@ -29,38 +23,37 @@ 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==2.1.0 ; python_version >= "3.8" and python_version < "3.13"
darkgraylib==1.1.1 ; 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"
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"
filelock==3.13.3 ; python_version >= "3.8" and python_version < "3.13"
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"
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==1.0.1 ; python_version >= "3.8" and python_version < "3.13"
graylint==1.1.1 ; 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==1.0.5 ; python_version >= "3.8" and python_version < "3.13"
httpx==0.27.0 ; python_version >= "3.8" and python_version < "3.13"
idna==3.6 ; 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==7.1.0 ; 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"
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==5.1.0 ; 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"
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"
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"
kombu==5.3.6 ; 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"
Expand All @@ -86,15 +79,14 @@ 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==1.42.0 ; 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"
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"
prompt-toolkit==3.0.43 ; 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"
pycparser==2.22 ; python_version >= "3.8" and python_version < "3.13"
pyee==11.0.1 ; 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"
pygments==2.17.2 ; python_version >= "3.8" and python_version < "3.13"
pyjwt[crypto]==2.8.0 ; python_version >= "3.8" and python_version < "3.13"
Expand All @@ -104,7 +96,6 @@ pyproject-hooks==1.0.0 ; python_version >= "3.8" and python_version < "3.13"
pysocks==1.7.1 ; python_version >= "3.8" and python_version < "3.13"
pytest-asyncio==0.23.6 ; 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-celery==0.0.0 ; 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"
Expand All @@ -130,13 +121,13 @@ 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==8.5.20240311110950 ; python_version >= "3.8" 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==4.19.0 ; python_version >= "3.8" and python_version < "3.13"
seletools==1.4.0 ; python_version >= "3.8" and python_version < "3.13"
setuptools==69.2.0 ; 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"
snowballstemmer==2.2.0 ; python_version >= "3.8" and python_version < "3.13"
Expand All @@ -162,10 +153,9 @@ tuspy==1.0.3 ; python_version >= "3.8" and python_version < "3.13"
twill==3.2.3 ; python_version >= "3.8" and python_version < "3.13"
twine==5.0.0 ; python_version >= "3.8" and python_version < "3.13"
typing-extensions==4.11.0 ; python_version >= "3.8" and python_version < "3.13"
tzdata==2024.1 ; python_version >= "3.8" and python_version < "3.13"
tzdata==2024.1 ; python_version >= "3.8" and python_version < "3.13" and sys_platform == "win32"
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"
vine==5.1.0 ; 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"
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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==0.3.5
ruff==0.3.7
40 changes: 20 additions & 20 deletions lib/galaxy/dependencies/pinned-requirements.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -2,10 +2,10 @@

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==2.12.2 ; 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==3.9.3 ; python_version >= "3.8" and python_version < "3.13"
aiohttp==3.9.4 ; 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"
Expand All @@ -16,7 +16,7 @@ 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"
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"
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"
Expand All @@ -27,13 +27,13 @@ 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==1.7.2 ; python_version >= "3.8" and python_version < "3.13"
beaker==1.12.1 ; 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"
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==1.34.51 ; 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"
Expand All @@ -53,8 +53,8 @@ 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==42.0.5 ; 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==0.32 ; python_version >= "3.8" and python_version < "3.13"
cwltool==3.1.20240112164112 ; 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"
decorator==5.1.1 ; 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"
Expand All @@ -67,7 +67,7 @@ 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"
filelock==3.13.3 ; 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"
fsspec==2023.12.2 ; python_version >= "3.8" and python_version < "3.13"
Expand All @@ -84,9 +84,9 @@ gunicorn==21.2.0 ; 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"
h5py==3.10.0 ; 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==3.6 ; python_version >= "3.8" and python_version < "3.13"
idna==3.7 ; python_version >= "3.8" and python_version < "3.13"
importlib-metadata==7.1.0 ; 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==0.10.10 ; python_version >= "3.8" and python_version < "3.13"
Expand All @@ -97,10 +97,10 @@ 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"
kombu==5.3.6 ; 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==1.3.2 ; python_version >= "3.8" and python_version < "3.13"
mako==1.3.3 ; 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"
Expand All @@ -117,7 +117,7 @@ nodeenv==1.8.0 ; 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"
oauthlib==3.2.2 ; python_version >= "3.8" and python_version < "3.13"
orjson==3.10.0 ; python_version >= "3.8" and python_version < "3.13"
orjson==3.10.1 ; python_version >= "3.8" and python_version < "3.13"
oyaml==1.0 ; python_version >= "3.8" and python_version < "3.13"
packaging==24.0 ; python_version >= "3.8" and python_version < "3.13"
paramiko==3.4.0 ; python_version >= "3.8" and python_version < "3.13"
Expand All @@ -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==2.22 ; python_version >= "3.8" and python_version < "3.13"
pycryptodome==3.20.0 ; python_version >= "3.8" and python_version < "3.13"
pydantic-core==2.14.6 ; python_version >= "3.8" and python_version < "3.13"
pydantic-core==2.18.1 ; python_version >= "3.8" and python_version < "3.13"
pydantic-tes==0.1.5 ; python_version >= "3.8" and python_version < "3.13"
pydantic==2.5.3 ; python_version >= "3.8" and python_version < "3.13"
pydantic[email]==2.5.3 ; python_version >= "3.8" and python_version < "3.13"
pydantic==2.7.0 ; python_version >= "3.8" and python_version < "3.13"
pydantic[email]==2.7.0 ; python_version >= "3.8" and python_version < "3.13"
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 @@ -156,7 +156,7 @@ 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==25.1.2 ; python_version >= "3.8" and python_version < "3.13"
pyzmq==26.0.0 ; 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"
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==8.5.20240311110950 ; python_version >= "3.8" and python_version < "3.13"
schema-salad==8.5.20240410123758 ; python_version >= "3.8" and python_version < "3.13"
setuptools-scm==5.0.2 ; python_version >= "3.8" and python_version < "3.13"
setuptools==69.2.0 ; python_version >= "3.8" and python_version < "3.13"
setuptools==69.5.1 ; 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 @@ -184,7 +184,7 @@ 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==2.0.29 ; python_version >= "3.8" and python_version < "3.13"
sqlitedict==2.1.0 ; python_version >= "3.8" and python_version < "3.13"
sqlparse==0.4.4 ; 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"
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