From e432488e7f86d98232cdc580c6fb17453ee770f6 Mon Sep 17 00:00:00 2001 From: Nicola Soranzo Date: Mon, 30 Sep 2024 13:26:18 +0100 Subject: [PATCH 1/2] Split h5py requirement to support both Python 3.8 and 3.13 --- lib/galaxy/dependencies/update.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/lib/galaxy/dependencies/update.sh b/lib/galaxy/dependencies/update.sh index c7eee2328ad7..8175144aba5d 100755 --- a/lib/galaxy/dependencies/update.sh +++ b/lib/galaxy/dependencies/update.sh @@ -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 From a708ee2329f7273a7559858d7ecd2ea8f9fc2843 Mon Sep 17 00:00:00 2001 From: galaxybot Date: Sat, 28 Sep 2024 03:26:39 +0000 Subject: [PATCH 2/2] Update Python dependencies by running `make update-dependencies`. --- lib/galaxy/dependencies/dev-requirements.txt | 18 ++++++------- .../dependencies/pinned-lint-requirements.txt | 2 +- .../dependencies/pinned-requirements.txt | 25 ++++++++++--------- .../pinned-typecheck-requirements.txt | 6 ++--- 4 files changed, 26 insertions(+), 25 deletions(-) diff --git a/lib/galaxy/dependencies/dev-requirements.txt b/lib/galaxy/dependencies/dev-requirements.txt index 39cf4dca07ca..87bf26b77bae 100644 --- a/lib/galaxy/dependencies/dev-requirements.txt +++ b/lib/galaxy/dependencies/dev-requirements.txt @@ -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" @@ -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" @@ -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" @@ -96,7 +96,7 @@ 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" @@ -104,7 +104,7 @@ 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" @@ -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" @@ -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" @@ -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" diff --git a/lib/galaxy/dependencies/pinned-lint-requirements.txt b/lib/galaxy/dependencies/pinned-lint-requirements.txt index 2b00c5ee134d..200f4e9ea889 100644 --- a/lib/galaxy/dependencies/pinned-lint-requirements.txt +++ b/lib/galaxy/dependencies/pinned-lint-requirements.txt @@ -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 diff --git a/lib/galaxy/dependencies/pinned-requirements.txt b/lib/galaxy/dependencies/pinned-requirements.txt index 518105f7c0ce..eb2c4d9c091d 100644 --- a/lib/galaxy/dependencies/pinned-requirements.txt +++ b/lib/galaxy/dependencies/pinned-requirements.txt @@ -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" @@ -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" @@ -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" @@ -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" @@ -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" @@ -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" @@ -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" @@ -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" diff --git a/lib/galaxy/dependencies/pinned-typecheck-requirements.txt b/lib/galaxy/dependencies/pinned-typecheck-requirements.txt index c23cbbbedc24..44dc87b82b94 100644 --- a/lib/galaxy/dependencies/pinned-typecheck-requirements.txt +++ b/lib/galaxy/dependencies/pinned-typecheck-requirements.txt @@ -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" @@ -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"