From 41458335bf6fda73665bcebcd27cb90b3c1652e4 Mon Sep 17 00:00:00 2001 From: galaxybot Date: Sat, 9 Nov 2024 03:08:36 +0000 Subject: [PATCH 1/2] Update Python dependencies by running `make update-dependencies`. --- lib/galaxy/dependencies/dev-requirements.txt | 21 ++++++------ .../dependencies/pinned-lint-requirements.txt | 4 +-- .../dependencies/pinned-requirements.txt | 32 ++++++++++--------- .../pinned-typecheck-requirements.txt | 8 ++--- 4 files changed, 33 insertions(+), 32 deletions(-) diff --git a/lib/galaxy/dependencies/dev-requirements.txt b/lib/galaxy/dependencies/dev-requirements.txt index 685b1149cd08..4311e90e2096 100644 --- a/lib/galaxy/dependencies/dev-requirements.txt +++ b/lib/galaxy/dependencies/dev-requirements.txt @@ -16,7 +16,7 @@ black==24.8.0 boto3==1.35.36 botocore==1.35.36 build==1.2.2.post1 -cachecontrol==0.14.0 +cachecontrol==0.14.1 certifi==2024.8.30 cffi==1.17.1 charset-normalizer==3.4.0 @@ -83,10 +83,10 @@ myst-parser==3.0.1 nh3==0.2.18 numpy==1.24.4 ; python_full_version < '3.9' numpy==2.0.2 ; python_full_version == '3.9.*' -numpy==2.1.2 ; python_full_version >= '3.10' +numpy==2.1.3 ; python_full_version >= '3.10' onedatafilerestclient==21.2.5.2 outcome==1.3.0.post0 -packaging==24.1 +packaging==24.2 pathspec==0.12.1 pbr==6.1.0 ; python_full_version >= '3.9' pillow==10.4.0 @@ -103,7 +103,7 @@ psutil==6.1.0 ; sys_platform != 'cygwin' psycopg==3.2.3 pycparser==2.22 pyee==12.0.0 -pygithub==2.4.0 +pygithub==2.5.0 pygments==2.18.0 pyjwt==2.9.0 pynacl==1.5.0 @@ -135,20 +135,19 @@ requests==2.32.3 requests-toolbelt==1.0.0 responses==0.25.3 rfc3986==2.0.0 -rich==13.9.3 -rpds-py==0.20.0 ; python_full_version >= '3.9' +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==35.4.1 ; python_full_version >= '3.9' +rucio-clients==35.5.0 ; python_full_version >= '3.9' s3transfer==0.10.3 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' +scipy==1.13.1 ; python_full_version >= '3.9' secretstorage==3.3.3 ; sys_platform == 'linux' -selenium==4.25.0 +selenium==4.26.1 seletools==1.5.0 -setuptools==75.2.0 +setuptools==75.3.0 six==1.16.0 sniffio==1.3.1 snowballstemmer==2.2.0 diff --git a/lib/galaxy/dependencies/pinned-lint-requirements.txt b/lib/galaxy/dependencies/pinned-lint-requirements.txt index 60d87b7dfddb..d063a6f43020 100644 --- a/lib/galaxy/dependencies/pinned-lint-requirements.txt +++ b/lib/galaxy/dependencies/pinned-lint-requirements.txt @@ -1,7 +1,7 @@ attrs==24.2.0 flake8==7.1.1 -flake8-bugbear==24.8.19 +flake8-bugbear==24.10.31 mccabe==0.7.0 pycodestyle==2.12.1 pyflakes==3.2.0 -ruff==0.7.1 +ruff==0.7.3 diff --git a/lib/galaxy/dependencies/pinned-requirements.txt b/lib/galaxy/dependencies/pinned-requirements.txt index 6f4c5cc99496..342ba9da8659 100644 --- a/lib/galaxy/dependencies/pinned-requirements.txt +++ b/lib/galaxy/dependencies/pinned-requirements.txt @@ -9,7 +9,7 @@ aiohappyeyeballs==2.4.3 aiohttp==3.10.10 aioitertools==0.12.0 aiosignal==1.3.1 -alembic==1.13.3 +alembic==1.14.0 amqp==5.2.0 annotated-types==0.7.0 anyio==4.5.2 @@ -28,13 +28,13 @@ bcrypt==4.2.0 bdbag==1.7.3 beaker==1.13.0 billiard==4.2.1 -bioblend==1.3.0 +bioblend==1.4.0 bleach==6.1.0 -boltons==24.0.0 +boltons==24.1.0 boto==2.49.0 botocore==1.35.36 bx-python==0.13.0 -cachecontrol==0.14.0 +cachecontrol==0.14.1 celery==5.4.0 certifi==2024.8.30 cffi==1.17.1 @@ -60,7 +60,7 @@ dictobj==0.4 dnspython==2.6.1 docopt==0.6.2 docutils==0.20.1 -dparse==0.6.3 +dparse==0.6.4 edam-ontology==1.25.2 email-validator==2.2.0 exceptiongroup==1.2.2 ; python_full_version < '3.11' @@ -72,7 +72,7 @@ fs==2.4.16 fsspec==2024.10.0 future==1.0.0 galaxy2cwl==0.1.4 -graphene==3.4.1 +graphene==3.4.3 graphene-sqlalchemy==3.0.0rc1 graphql-core==3.2.5 graphql-relay==3.2.0 @@ -116,11 +116,11 @@ 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==2.1.2 ; python_full_version >= '3.10' +numpy==2.1.3 ; python_full_version >= '3.10' oauthlib==3.2.2 -orjson==3.10.10 +orjson==3.10.11 oyaml==1.0 -packaging==24.1 +packaging==24.2 paramiko==3.5.0 parsley==1.3 paste==3.10.1 @@ -152,7 +152,8 @@ pyreadline3==3.5.4 ; sys_platform == 'win32' pysam==0.22.1 python-dateutil==2.9.0.post0 python-magic==0.4.27 -python-multipart==0.0.16 +python-multipart==0.0.17 +python-slugify==8.0.4 python3-openid==3.2.0 pytz==2024.2 pyyaml==6.0.2 @@ -160,21 +161,21 @@ pyzmq==26.2.0 rdflib==6.3.2 referencing==0.35.1 refgenconf==0.12.2 -regex==2024.9.11 +regex==2024.11.6 repoze-lru==0.7 requests==2.32.3 requests-oauthlib==2.0.0 requests-toolbelt==1.0.0 requests-unixsocket==0.3.0 -rich==13.9.3 +rich==13.9.4 rocrate==0.11.0 routes==2.5.1 -rpds-py==0.20.0 +rpds-py==0.20.1 ruamel-yaml==0.18.6 ruamel-yaml-clib==0.2.8 ; python_full_version < '3.13' and platform_python_implementation == 'CPython' s3fs==2024.10.0 schema-salad==8.7.20241010092723 -setuptools==75.2.0 +setuptools==75.3.0 setuptools-scm==5.0.2 six==1.16.0 sniffio==1.3.1 @@ -190,11 +191,12 @@ starlette-graphene3==0.6.0 supervisor==4.2.5 svgwrite==1.4.3 tenacity==9.0.0 +text-unidecode==1.3 tifffile==2023.7.10 tinydb==4.8.2 tomli==2.0.2 ; python_full_version < '3.11' tornado==6.4.1 -tqdm==4.66.6 +tqdm==4.67.0 tuspy==1.0.3 tuswsgi==0.5.5 typing-extensions==4.12.2 diff --git a/lib/galaxy/dependencies/pinned-typecheck-requirements.txt b/lib/galaxy/dependencies/pinned-typecheck-requirements.txt index 947da8733d03..eee703c6e98c 100644 --- a/lib/galaxy/dependencies/pinned-typecheck-requirements.txt +++ b/lib/galaxy/dependencies/pinned-typecheck-requirements.txt @@ -1,8 +1,8 @@ # This file was autogenerated by uv via the following command: # uv export --frozen --no-hashes --only-group=typecheck annotated-types==0.7.0 -boto3-stubs==1.35.49 -botocore-stubs==1.35.49 +boto3-stubs==1.35.57 +botocore-stubs==1.35.57 cffi==1.17.1 ; platform_python_implementation != 'PyPy' cryptography==43.0.3 lxml-stubs==0.5.1 @@ -27,7 +27,7 @@ types-python-slugify==8.0.2.20240310 types-pyyaml==6.0.12.20240917 types-requests==2.31.0.6 types-s3transfer==0.10.3 -types-setuptools==75.2.0.20241025 -types-six==1.16.21.20241009 +types-setuptools==75.3.0.20241107 +types-six==1.16.21.20241105 types-urllib3==1.26.25.14 typing-extensions==4.12.2 From 94593bd64418e5c56c23635a90773c1cd2ec94e1 Mon Sep 17 00:00:00 2001 From: Nicola Soranzo Date: Sun, 10 Nov 2024 18:08:19 +0000 Subject: [PATCH 2/2] Pin scipy to >=1.14.1 for Python 3.13 support --- lib/galaxy/dependencies/dev-requirements.txt | 3 ++- pyproject.toml | 1 + 2 files changed, 3 insertions(+), 1 deletion(-) diff --git a/lib/galaxy/dependencies/dev-requirements.txt b/lib/galaxy/dependencies/dev-requirements.txt index 4311e90e2096..4d6c7013e924 100644 --- a/lib/galaxy/dependencies/dev-requirements.txt +++ b/lib/galaxy/dependencies/dev-requirements.txt @@ -143,7 +143,8 @@ rucio-clients==35.5.0 ; python_full_version >= '3.9' s3transfer==0.10.3 schema-salad==8.7.20241010092723 scipy==1.10.1 ; python_full_version < '3.9' -scipy==1.13.1 ; python_full_version >= '3.9' +scipy==1.13.1 ; 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 seletools==1.5.0 diff --git a/pyproject.toml b/pyproject.toml index 674528fdc0ce..104425646e30 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -149,6 +149,7 @@ dev = [ "pytest-shard", "responses", "rucio-clients>=33.6.0 ; python_version>='3.9'", # https://github.com/galaxyproject/galaxy/pull/17156 + "scipy>=1.14.1; python_version>='3.10'", # ase dependency, Python 3.13 support "selenium", "seletools", "Sphinx>=4.0", # support docutils 0.17