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Update Python dependencies #19190

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merged 2 commits into from
Dec 18, 2024
Merged

Update Python dependencies #19190

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5f7c3ba
Update Python dependencies
galaxybot Dec 16, 2024
3546ae5
Pass ``timeout`` to ``ProcessPool.submit()`` as positional parameter
nsoranzo Dec 17, 2024
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2 changes: 1 addition & 1 deletion lib/galaxy/celery/tasks.py
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Original file line number Diff line number Diff line change
Expand Up @@ -289,7 +289,7 @@ def abort_when_job_stops(function: Callable, session: galaxy_scoped_session, job
if not is_aborted(session, job_id):
future = celery_app.fork_pool.submit(
function,
timeout=None,
None,
**kwargs,
)
while True:
Expand Down
69 changes: 35 additions & 34 deletions lib/galaxy/dependencies/dev-requirements.txt
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Original file line number Diff line number Diff line change
@@ -1,33 +1,33 @@
# This file was autogenerated by uv via the following command:
# uv export --frozen --no-hashes --only-group=dev
aiohappyeyeballs==2.4.3
aiohappyeyeballs==2.4.4
aiohttp==3.10.11
aiosignal==1.3.1
alabaster==0.7.13
anyio==4.5.2
ase==3.23.0
async-timeout==5.0.1 ; python_full_version < '3.11'
attrs==24.2.0
attrs==24.3.0
axe-selenium-python==2.1.6
babel==2.16.0
backports-tarfile==1.2.0 ; python_full_version < '3.12'
backports-tarfile==1.2.0 ; python_full_version < '3.12' and platform_machine != 'ppc64le' and platform_machine != 's390x'
backports-zoneinfo==0.2.1 ; python_full_version < '3.9'
black==24.8.0
boto3==1.35.36
botocore==1.35.36
build==1.2.2.post1
cachecontrol==0.14.1
certifi==2024.8.30
certifi==2024.12.14
cffi==1.17.1
charset-normalizer==3.4.0
click==8.1.7
codespell==2.3.0
colorama==0.4.6 ; (platform_system != 'Windows' and sys_platform == 'win32') or platform_system == 'Windows' or os_name == 'nt'
colorama==0.4.6 ; os_name == 'nt' or (platform_system == 'Windows' and sys_platform != 'win32') or sys_platform == 'win32'
contourpy==1.1.1 ; python_full_version < '3.9'
contourpy==1.3.0 ; python_full_version >= '3.9'
coverage==7.6.1
cryptography==43.0.3
cwltest==2.5.20240906231108
cryptography==44.0.0
cwltest==2.5.20241122133319
cycler==0.12.1
darker==2.1.1
darkgraylib==1.2.1
Expand All @@ -39,59 +39,59 @@ dogpile-cache==1.3.3 ; python_full_version >= '3.9'
exceptiongroup==1.2.2 ; python_full_version < '3.11'
filelock==3.16.1
fluent-logger==0.11.1
fonttools==4.55.0
fonttools==4.55.3
frozenlist==1.5.0
galaxy-release-util==0.1.11
galaxy-release-util==0.2.0
graylint==1.1.1
greenlet==3.1.1
h11==0.14.0
httpcore==1.0.7
httpx==0.27.2
httpx==0.28.1
idna==3.10
imagesize==1.4.1
importlib-metadata==8.5.0
importlib-metadata==8.5.0 ; (python_full_version < '3.10.2' and platform_machine == 'ppc64le') or (python_full_version < '3.10.2' and platform_machine == 's390x') or (python_full_version < '3.12' and platform_machine != 'ppc64le' and platform_machine != 's390x')
importlib-resources==6.4.5 ; python_full_version < '3.10'
iniconfig==2.0.0
isodate==0.6.1
isort==5.13.2
jaraco-classes==3.4.0
jaraco-context==6.0.1
jaraco-functools==4.1.0
jeepney==0.8.0 ; sys_platform == 'linux'
jaraco-classes==3.4.0 ; platform_machine != 'ppc64le' and platform_machine != 's390x'
jaraco-context==6.0.1 ; platform_machine != 'ppc64le' and platform_machine != 's390x'
jaraco-functools==4.1.0 ; platform_machine != 'ppc64le' and platform_machine != 's390x'
jeepney==0.8.0 ; platform_machine != 'ppc64le' and platform_machine != 's390x' and sys_platform == 'linux'
jinja2==3.1.4
jmespath==1.0.1
jsonschema==4.23.0 ; python_full_version >= '3.9'
jsonschema-specifications==2023.12.1 ; python_full_version >= '3.9'
junit-xml==1.9
keyring==25.5.0
keyring==25.5.0 ; platform_machine != 'ppc64le' and platform_machine != 's390x'
kiwisolver==1.4.7
lxml==5.3.0
markdown-it-py==3.0.0
markdown-it-reporter==0.0.2
markupsafe==2.1.5
matplotlib==3.7.5 ; python_full_version < '3.9'
matplotlib==3.9.2 ; python_full_version >= '3.9'
matplotlib==3.9.4 ; python_full_version >= '3.9'
mdit-py-plugins==0.4.2
mdurl==0.1.2
mirakuru==2.5.2
mistune==3.0.2
more-itertools==10.5.0
more-itertools==10.5.0 ; platform_machine != 'ppc64le' and platform_machine != 's390x'
msgpack==1.1.0
multidict==6.1.0
mypy-extensions==1.0.0
myst-parser==3.0.1
nh3==0.2.18
nh3==0.2.19
numpy==1.24.4 ; python_full_version < '3.9'
numpy==2.0.2 ; python_full_version == '3.9.*'
numpy==2.1.3 ; python_full_version >= '3.10'
numpy==2.2.0 ; python_full_version >= '3.10'
onedatafilerestclient==21.2.5.2
outcome==1.3.0.post0
packaging==24.2
pathspec==0.12.1
pbr==6.1.0 ; python_full_version >= '3.9'
pillow==10.4.0
pkce==1.0.3
pkginfo==1.10.0
pkginfo==1.12.0
pkgutil-resolve-name==1.3.10 ; python_version < '0'
platformdirs==4.3.6
playwright==1.48.0
Expand Down Expand Up @@ -126,9 +126,10 @@ python-dateutil==2.9.0.post0
python-irodsclient==2.2.0
python-slugify==8.0.4
pytz==2024.2 ; python_full_version < '3.9'
pywin32-ctypes==0.2.3 ; sys_platform == 'win32'
pywin32-ctypes==0.2.3 ; platform_machine != 'ppc64le' and platform_machine != 's390x' and sys_platform == 'win32'
pyyaml==6.0.2
rdflib==6.3.2
rdflib==6.3.2 ; python_full_version < '3.8.1'
rdflib==7.0.0 ; python_full_version >= '3.8.1'
readme-renderer==43.0
referencing==0.35.1 ; python_full_version >= '3.9'
requests==2.32.3
Expand All @@ -139,17 +140,17 @@ rich==13.9.4
rpds-py==0.20.1 ; python_full_version >= '3.9'
ruamel-yaml==0.18.6
ruamel-yaml-clib==0.2.8 ; python_full_version < '3.13' and platform_python_implementation == 'CPython'
rucio-clients==35.5.0 ; python_full_version >= '3.9'
s3transfer==0.10.3
rucio-clients==36.0.0.post1 ; python_full_version >= '3.9'
s3transfer==0.10.4
schema-salad==8.7.20241010092723
scipy==1.10.1 ; python_full_version < '3.9'
scipy==1.13.1 ; python_full_version == '3.9.*'
scipy==1.14.1 ; python_full_version >= '3.10'
secretstorage==3.3.3 ; sys_platform == 'linux'
selenium==4.26.1
secretstorage==3.3.3 ; platform_machine != 'ppc64le' and platform_machine != 's390x' and sys_platform == 'linux'
selenium==4.27.1
seletools==1.5.0
setuptools==75.3.0
six==1.16.0
six==1.17.0
sniffio==1.3.1
snowballstemmer==2.2.0
sortedcontainers==2.4.0
Expand All @@ -163,26 +164,26 @@ sphinxcontrib-jsmath==1.0.1
sphinxcontrib-qthelp==1.0.3
sphinxcontrib-serializinghtml==1.1.5
statsd==4.0.1
stevedore==5.3.0 ; python_full_version >= '3.9'
stevedore==5.4.0 ; python_full_version >= '3.9'
tabulate==0.9.0 ; python_full_version >= '3.9'
testfixtures==8.3.0
text-unidecode==1.3
tinydb==4.8.2
toml==0.10.2
tomli==2.1.0 ; python_full_version <= '3.11'
tomli==2.2.1 ; python_full_version <= '3.11'
trio==0.27.0
trio-websocket==0.11.1
tuspy==1.0.3
tuspy==1.1.0
twill==3.3
twine==5.1.1
twine==6.0.1
typing-extensions==4.12.2
tzdata==2024.2 ; sys_platform == 'win32'
urllib3==1.26.20
watchdog==4.0.2
wcwidth==0.2.13
websocket-client==1.8.0
werkzeug==3.0.6
wrapt==1.16.0
wrapt==1.17.0
wsproto==1.2.0
yarl==1.15.2
zipp==3.20.2
zipp==3.20.2 ; (python_full_version < '3.10.2' and platform_machine == 'ppc64le') or (python_full_version < '3.10.2' and platform_machine == 's390x') or (python_full_version < '3.12' and platform_machine != 'ppc64le' and platform_machine != 's390x')
6 changes: 3 additions & 3 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==24.2.0
attrs==24.3.0
flake8==7.1.1
flake8-bugbear==24.10.31
flake8-bugbear==24.12.12
mccabe==0.7.0
pycodestyle==2.12.1
pyflakes==3.2.0
ruff==0.8.2
ruff==0.8.3
53 changes: 27 additions & 26 deletions lib/galaxy/dependencies/pinned-requirements.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,7 @@ adal==1.2.7
aiobotocore==2.15.2
aiodataloader==0.4.0
aiofiles==24.1.0
aiohappyeyeballs==2.4.3
aiohappyeyeballs==2.4.4
aiohttp==3.10.11
aioitertools==0.12.0
aiosignal==1.3.1
Expand All @@ -16,15 +16,15 @@ anyio==4.5.2
apispec==6.6.1
appdirs==1.4.4
arcp==0.2.1
argcomplete==3.5.1
argcomplete==3.5.2
async-timeout==5.0.1 ; python_full_version < '3.11'
attmap==0.13.2
attrs==24.2.0
attrs==24.3.0
babel==2.16.0
backports-zoneinfo==0.2.1 ; python_full_version < '3.9'
bagit==1.8.1
bagit-profile==1.3.1
bcrypt==4.2.0
bcrypt==4.2.1
bdbag==1.7.3
beaker==1.13.0
billiard==4.2.1
Expand All @@ -36,7 +36,7 @@ botocore==1.35.36
bx-python==0.13.0
cachecontrol==0.14.1
celery==5.4.0
certifi==2024.8.30
certifi==2024.12.14
cffi==1.17.1
charset-normalizer==3.4.0
circus==0.18.0
Expand All @@ -49,8 +49,8 @@ cloudbridge==3.2.0
colorama==0.4.6 ; platform_system == 'Windows'
coloredlogs==15.0.1
conda-package-streaming==0.11.0
cryptography==43.0.3
ct3==3.3.3.post1
cryptography==44.0.0
ct3==3.4.0
cwl-upgrader==1.2.11
cwl-utils==0.35
cwltool==3.1.20241007082533
Expand All @@ -64,7 +64,7 @@ dparse==0.6.4
edam-ontology==1.25.2
email-validator==2.2.0
exceptiongroup==1.2.2 ; python_full_version < '3.11'
fastapi-slim==0.115.5
fastapi-slim==0.115.6
filelock==3.16.1
fissix==24.4.24 ; python_full_version >= '3.13'
frozenlist==1.5.0
Expand All @@ -73,7 +73,7 @@ fsspec==2024.10.0
future==1.0.0
galaxy2cwl==0.1.4
graphene==3.4.3
graphene-sqlalchemy==3.0.0rc1
graphene-sqlalchemy==3.0.0rc2
graphql-core==3.2.5
graphql-relay==3.2.0
gravity==1.0.6
Expand All @@ -97,35 +97,35 @@ jsonref==1.1.0
jsonschema==4.23.0
jsonschema-specifications==2023.12.1
kombu==5.4.2
lagom==2.6.0
lagom==2.7.5
legacy-cgi==2.6.1 ; python_full_version >= '3.13'
lxml==5.3.0
mako==1.3.6
mako==1.3.8
markdown==3.7
markdown-it-py==3.0.0
markupsafe==2.1.5
mdurl==0.1.2
mercurial==6.8.2
mercurial==6.9
mistune==3.0.2
mrcfile==1.5.3
msal==1.31.0
msal==1.31.1
msgpack==1.1.0
multidict==6.1.0
mypy-extensions==1.0.0
networkx==3.1
nodeenv==1.9.1
numpy==1.24.4 ; python_full_version < '3.9'
numpy==2.0.2 ; python_full_version == '3.9.*'
numpy==2.1.3 ; python_full_version >= '3.10'
numpy==2.2.0 ; python_full_version >= '3.10'
oauthlib==3.2.2
orjson==3.10.11
orjson==3.10.12
oyaml==1.0
packaging==24.2
paramiko==3.5.0
parsley==1.3
paste==3.10.1
pastedeploy==3.1.0
pebble==5.0.7
pebble==5.1.0
pillow==10.4.0
pkgutil-resolve-name==1.3.10 ; python_full_version < '3.9'
promise==2.3
Expand All @@ -152,13 +152,14 @@ pyreadline3==3.5.4 ; sys_platform == 'win32'
pysam==0.22.1
python-dateutil==2.9.0.post0
python-magic==0.4.27
python-multipart==0.0.18
python-multipart==0.0.19
python-slugify==8.0.4
python3-openid==3.2.0
pytz==2024.2
pyyaml==6.0.2
pyzmq==26.2.0
rdflib==6.3.2
rdflib==6.3.2 ; python_full_version < '3.8.1'
rdflib==7.0.0 ; python_full_version >= '3.8.1'
referencing==0.35.1
refgenconf==0.12.2
regex==2024.11.6
Expand All @@ -177,15 +178,15 @@ s3fs==2024.10.0
schema-salad==8.7.20241010092723
setuptools==75.3.0
setuptools-scm==5.0.2
six==1.16.0
six==1.17.0
sniffio==1.3.1
social-auth-core==4.5.4
sortedcontainers==2.4.0
spython==0.3.14
sqlalchemy==2.0.35
sqlitedict==2.1.0
sqlparse==0.5.2
starlette==0.41.2
sqlparse==0.5.3
starlette==0.41.3
starlette-context==0.3.6
starlette-graphene3==0.6.0
supervisor==4.2.5
Expand All @@ -194,24 +195,24 @@ tenacity==9.0.0
text-unidecode==1.3
tifffile==2023.7.10
tinydb==4.8.2
tomli==2.1.0 ; python_full_version < '3.11'
tomli==2.2.1 ; python_full_version < '3.11'
tornado==6.4.2
tqdm==4.67.0
tuspy==1.0.3
tqdm==4.67.1
tuspy==1.1.0
tuswsgi==0.5.5
typing-extensions==4.12.2
tzdata==2024.2
tzlocal==5.2
ubiquerg==0.8.0
urllib3==1.26.20
uvicorn==0.32.0
uvicorn==0.33.0
uvloop==0.21.0
vine==5.1.0
wcwidth==0.2.13
webencodings==0.5.1
webob==1.8.9
whoosh==2.7.4
wrapt==1.16.0
wrapt==1.17.0
yacman==0.9.3
yarl==1.15.2
zipp==3.20.2
Expand Down
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