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Update Python dependencies #18904

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merged 2 commits into from
Oct 2, 2024
Merged

Update Python dependencies #18904

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e432488
Split h5py requirement to support both Python 3.8 and 3.13
nsoranzo Sep 30, 2024
a708ee2
Update Python dependencies
galaxybot Sep 28, 2024
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18 changes: 9 additions & 9 deletions lib/galaxy/dependencies/dev-requirements.txt
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Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
aiohappyeyeballs==2.4.0 ; python_version >= "3.8" and python_version < "3.13"
aiohttp==3.10.5 ; python_version >= "3.8" and python_version < "3.13"
aiohappyeyeballs==2.4.2 ; python_version >= "3.8" and python_version < "3.13"
aiohttp==3.10.8 ; 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==4.5.0 ; python_version >= "3.8" and python_version < "3.13"
Expand Down Expand Up @@ -37,7 +37,7 @@ dogpile-cache==1.3.3 ; python_version >= "3.9" and python_version < "3.13"
exceptiongroup==1.2.2 ; python_version >= "3.8" and python_version < "3.11"
filelock==3.16.1 ; python_version >= "3.8" and python_version < "3.13"
fluent-logger==0.11.1 ; python_version >= "3.8" and python_version < "3.13"
fonttools==4.53.1 ; python_version >= "3.8" and python_version < "3.13"
fonttools==4.54.1 ; 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==0.1.11 ; python_version >= "3.8" and python_version < "3.13"
graylint==1.1.1 ; python_version >= "3.8" and python_version < "3.13"
Expand All @@ -54,7 +54,7 @@ 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==6.0.1 ; python_version >= "3.8" and python_version < "3.13"
jaraco-functools==4.0.2 ; python_version >= "3.8" and python_version < "3.13"
jaraco-functools==4.1.0 ; 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==3.1.4 ; python_version >= "3.8" and python_version < "3.13"
jmespath==1.0.1 ; python_version >= "3.8" and python_version < "3.13"
Expand Down Expand Up @@ -96,15 +96,15 @@ pluggy==1.5.0 ; python_version >= "3.8" and python_version < "3.13"
port-for==0.7.3 ; python_version >= "3.8" and python_version < "3.13"
prettytable==3.11.0 ; python_version >= "3.8" and python_version < "3.13"
psutil==6.0.0 ; python_version >= "3.8" and python_version < "3.13" and sys_platform != "cygwin"
psycopg==3.2.2 ; python_version >= "3.8" and python_version < "3.13"
psycopg==3.2.3 ; python_version >= "3.8" and python_version < "3.13"
pycparser==2.22 ; python_version >= "3.8" and python_version < "3.13"
pyee==12.0.0 ; python_version >= "3.8" and python_version < "3.13"
pygithub==2.4.0 ; python_version >= "3.8" and python_version < "3.13"
pygments==2.18.0 ; python_version >= "3.8" and python_version < "3.13"
pyjwt[crypto]==2.9.0 ; python_version >= "3.8" and python_version < "3.13"
pynacl==1.5.0 ; python_version >= "3.8" and python_version < "3.13"
pyparsing==3.1.4 ; python_version >= "3.8" and python_version < "3.13"
pyproject-hooks==1.1.0 ; python_version >= "3.8" and python_version < "3.13"
pyproject-hooks==1.2.0 ; python_version >= "3.8" and python_version < "3.13"
pysocks==1.7.1 ; python_version >= "3.8" and python_version < "3.13"
pytest-asyncio==0.23.8 ; python_version >= "3.8" and python_version < "3.13"
pytest-base-url==2.1.0 ; python_version >= "3.8" and python_version < "3.13"
Expand Down Expand Up @@ -135,7 +135,7 @@ rich==13.8.1 ; python_version >= "3.8" and python_version < "3.13"
rpds-py==0.20.0 ; 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==35.3.0 ; python_version >= "3.9" and python_version < "3.13"
rucio-clients==35.4.0 ; python_version >= "3.9" and python_version < "3.13"
s3transfer==0.10.2 ; python_version >= "3.8" and python_version < "3.13"
schema-salad==8.7.20240905150001 ; python_version >= "3.8" and python_version < "3.13"
scipy==1.10.1 ; python_version >= "3.8" and python_version < "3.9"
Expand Down Expand Up @@ -172,7 +172,7 @@ tuspy==1.0.3 ; python_version >= "3.8" and python_version < "3.13"
twill==3.2.5 ; python_version >= "3.8" and python_version < "3.13"
twine==5.1.1 ; python_version >= "3.8" and python_version < "3.13"
typing-extensions==4.12.2 ; 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"
tzdata==2024.2 ; python_version >= "3.8" and python_version < "3.13" and sys_platform == "win32"
urllib3==1.26.20 ; python_version >= "3.8" and python_version < "3.13"
urllib3[socks]==1.26.20 ; python_version >= "3.8" and python_version < "3.13"
watchdog==4.0.2 ; python_version >= "3.8" and python_version < "3.13"
Expand All @@ -181,5 +181,5 @@ websocket-client==1.8.0 ; python_version >= "3.8" and python_version < "3.13"
werkzeug==3.0.4 ; 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==1.11.1 ; python_version >= "3.8" and python_version < "3.13"
yarl==1.13.1 ; python_version >= "3.8" and python_version < "3.13"
zipp==3.20.2 ; 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==24.8.19
mccabe==0.7.0
pycodestyle==2.12.1
pyflakes==3.2.0
ruff==0.6.6
ruff==0.6.8
25 changes: 13 additions & 12 deletions lib/galaxy/dependencies/pinned-requirements.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -5,11 +5,11 @@ adal==1.2.7 ; python_version >= "3.8" and python_version < "3.13"
aiobotocore==2.15.1 ; python_version >= "3.8" and python_version < "3.13"
aiodataloader==0.4.0 ; python_version >= "3.8" and python_version < "3.13"
aiofiles==24.1.0 ; python_version >= "3.8" and python_version < "3.13"
aiohappyeyeballs==2.4.0 ; python_version >= "3.8" and python_version < "3.13"
aiohttp==3.10.5 ; python_version >= "3.8" and python_version < "3.13"
aiohappyeyeballs==2.4.2 ; python_version >= "3.8" and python_version < "3.13"
aiohttp==3.10.8 ; python_version >= "3.8" and python_version < "3.13"
aioitertools==0.12.0 ; python_version >= "3.8" and python_version < "3.13"
aiosignal==1.3.1 ; python_version >= "3.8" and python_version < "3.13"
alembic==1.13.2 ; python_version >= "3.8" and python_version < "3.13"
alembic==1.13.3 ; 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==0.7.0 ; python_version >= "3.8" and python_version < "3.13"
Expand All @@ -29,7 +29,7 @@ bagit==1.8.1 ; python_version >= "3.8" and python_version < "3.13"
bcrypt==4.2.0 ; python_version >= "3.8" and python_version < "3.13"
bdbag==1.7.3 ; 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"
billiard==4.2.1 ; 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"
Expand Down Expand Up @@ -84,13 +84,14 @@ gunicorn==23.0.0 ; python_version >= "3.8" and python_version < "3.13"
gxformat2==0.20.0 ; python_version >= "3.8" and python_version < "3.13"
h11==0.14.0 ; python_version >= "3.8" and python_version < "3.13"
h5grove==2.3.0 ; python_version >= "3.8" and python_version < "3.13"
h5py==3.11.0 ; python_version >= "3.8" and python_version < "3.13"
h5py==3.11.0 ; python_version >= "3.8" and python_version < "3.9"
h5py==3.12.1 ; python_version >= "3.9" and python_version < "3.13"
humanfriendly==10.0 ; python_version >= "3.8" and python_version < "3.13"
idna==3.10 ; python_version >= "3.8" and python_version < "3.13"
importlib-metadata==8.5.0 ; python_version >= "3.8" and python_version < "3.13"
importlib-resources==6.4.5 ; python_version >= "3.8" and python_version < "3.9"
isa-rwval @ git+https://github.com/nsoranzo/isa-rwval.git@3d989181058d2765a93cb0e7ca85d6955e0eb6ef ; python_version >= "3.8" and python_version < "3.13"
isal==1.7.0 ; python_version >= "3.8" and python_version < "3.13"
isal==1.7.1 ; python_version >= "3.8" and python_version < "3.13"
isodate==0.6.1 ; python_version >= "3.8" and python_version < "3.13"
jinja2==3.1.4 ; python_version >= "3.8" and python_version < "3.13"
jmespath==1.0.1 ; python_version >= "3.8" and python_version < "3.13"
Expand Down Expand Up @@ -129,7 +130,7 @@ pebble==5.0.7 ; python_version >= "3.8" and python_version < "3.13"
pillow==10.4.0 ; 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==3.0.47 ; python_version >= "3.8" and python_version < "3.13"
prompt-toolkit==3.0.48 ; python_version >= "3.8" and python_version < "3.13"
prov==1.5.1 ; python_version >= "3.8" and python_version < "3.13"
psutil==6.0.0 ; python_version >= "3.8" and python_version < "3.13"
pulsar-galaxy-lib==0.15.6 ; python_version >= "3.8" and python_version < "3.13"
Expand All @@ -153,7 +154,7 @@ pyreadline3==3.5.4 ; sys_platform == "win32" and python_version >= "3.8" and pyt
pysam==0.22.1 ; 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-magic==0.4.27 ; python_version >= "3.8" and python_version < "3.13"
python-multipart==0.0.9 ; python_version >= "3.8" and python_version < "3.13"
python-multipart==0.0.12 ; python_version >= "3.8" and python_version < "3.13"
python3-openid==3.2.0 ; python_version >= "3.8" and python_version < "3.13"
pytz==2024.2 ; python_version >= "3.8" and python_version < "3.13"
pyyaml==6.0.2 ; python_version >= "3.8" and python_version < "3.13"
Expand Down Expand Up @@ -188,7 +189,7 @@ sqlitedict==2.1.0 ; python_version >= "3.8" and python_version < "3.13"
sqlparse==0.5.1 ; 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==0.38.5 ; python_version >= "3.8" and python_version < "3.13"
starlette==0.38.6 ; 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==9.0.0 ; python_version >= "3.8" and python_version < "3.13"
Expand All @@ -200,11 +201,11 @@ tqdm==4.66.5 ; python_version >= "3.8" and python_version < "3.13"
tuspy==1.0.3 ; python_version >= "3.8" and python_version < "3.13"
tuswsgi==0.5.5 ; python_version >= "3.8" and python_version < "3.13"
typing-extensions==4.12.2 ; python_version >= "3.8" and python_version < "3.13"
tzdata==2024.1 ; python_version >= "3.8" and python_version < "3.13"
tzdata==2024.2 ; python_version >= "3.8" and python_version < "3.13"
tzlocal==5.2 ; python_version >= "3.8" and python_version < "3.13"
ubiquerg==0.8.0 ; python_version >= "3.8" and python_version < "3.13"
urllib3==1.26.20 ; python_version >= "3.8" and python_version < "3.13"
uvicorn==0.30.6 ; python_version >= "3.8" and python_version < "3.13"
uvicorn==0.31.0 ; python_version >= "3.8" and python_version < "3.13"
uvloop==0.20.0 ; 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 @@ -213,7 +214,7 @@ webob==1.8.8 ; python_version >= "3.8" and python_version < "3.13"
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==1.11.1 ; python_version >= "3.8" and python_version < "3.13"
yarl==1.13.1 ; python_version >= "3.8" and python_version < "3.13"
zipp==3.20.2 ; python_version >= "3.8" and python_version < "3.13"
zipstream-new==1.1.8 ; python_version >= "3.8" and python_version < "3.13"
zstandard==0.23.0 ; python_version >= "3.8" and python_version < "3.13"
6 changes: 3 additions & 3 deletions lib/galaxy/dependencies/pinned-typecheck-requirements.txt
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@@ -1,6 +1,6 @@
annotated-types==0.7.0 ; python_version >= "3.8" and python_version < "3.13"
boto3-stubs[s3]==1.35.24 ; python_version >= "3.8" and python_version < "3.13"
botocore-stubs==1.35.24 ; python_version >= "3.8" and python_version < "3.13"
boto3-stubs[s3]==1.35.29 ; python_version >= "3.8" and python_version < "3.13"
botocore-stubs==1.35.29 ; python_version >= "3.8" and python_version < "3.13"
cffi==1.17.1 ; python_version >= "3.8" and python_version < "3.13" and platform_python_implementation != "PyPy"
cryptography==43.0.1 ; python_version >= "3.8" and python_version < "3.13"
lxml-stubs==0.5.1 ; python_version >= "3.8" and python_version < "3.13"
Expand All @@ -19,7 +19,7 @@ types-dataclasses==0.6.6 ; python_version >= "3.8" and python_version < "3.13"
types-docutils==0.21.0.20240907 ; python_version >= "3.8" and python_version < "3.13"
types-html5lib==1.1.11.20240806 ; python_version >= "3.8" and python_version < "3.13"
types-markdown==3.7.0.20240822 ; python_version >= "3.8" and python_version < "3.13"
types-paramiko==3.5.0.20240918 ; python_version >= "3.8" and python_version < "3.13"
types-paramiko==3.5.0.20240928 ; python_version >= "3.8" and python_version < "3.13"
types-python-dateutil==2.9.0.20240906 ; python_version >= "3.8" and python_version < "3.13"
types-pyyaml==6.0.12.20240917 ; python_version >= "3.8" and python_version < "3.13"
types-requests==2.31.0.6 ; python_version >= "3.8" and python_version < "3.13"
Expand Down
2 changes: 1 addition & 1 deletion lib/galaxy/dependencies/update.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -88,8 +88,8 @@ split_requirement () {
# For some packages there is no recent version that works on all Python versions
# supported by Galaxy, so Poetry resorts to an old version. Here we replace any
# such requirement with multiple Python-version-specific requirements.
# Packages which specify a maximum Python version pin:
split_requirement contourpy
split_requirement h5py
split_requirement matplotlib
split_requirement numpy
split_requirement scipy
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