From 65f163308bb2a38bc6df2a1821893d06ef0a8d9e Mon Sep 17 00:00:00 2001 From: galaxybot Date: Sat, 9 Dec 2023 03:12:35 +0000 Subject: [PATCH] Update Python dependencies --- lib/galaxy/dependencies/dev-requirements.txt | 19 ++++++------ .../dependencies/pinned-lint-requirements.txt | 4 +-- .../dependencies/pinned-requirements.txt | 31 ++++++++++--------- 3 files changed, 27 insertions(+), 27 deletions(-) diff --git a/lib/galaxy/dependencies/dev-requirements.txt b/lib/galaxy/dependencies/dev-requirements.txt index 0be0caf9a3fd..b55d2289c810 100644 --- a/lib/galaxy/dependencies/dev-requirements.txt +++ b/lib/galaxy/dependencies/dev-requirements.txt @@ -36,9 +36,8 @@ docutils==0.18.1 ; python_version >= "3.8" and python_version < "3.12" exceptiongroup==1.2.0 ; python_version >= "3.8" and python_version < "3.11" filelock==3.13.1 ; python_version >= "3.8" and python_version < "3.12" fluent-logger==0.10.0 ; python_version >= "3.8" and python_version < "3.12" -fonttools==4.45.1 ; python_version >= "3.8" and python_version < "3.12" +fonttools==4.46.0 ; python_version >= "3.8" and python_version < "3.12" frozenlist==1.4.0 ; python_version >= "3.8" and python_version < "3.12" -future==0.18.3 ; python_version >= "3.8" and python_version < "3.12" galaxy-release-util==0.1.5 ; python_version >= "3.8" and python_version < "3.12" greenlet==3.0.1 ; python_version >= "3.8" and python_version < "3.12" h11==0.14.0 ; python_version >= "3.8" and python_version < "3.12" @@ -46,7 +45,7 @@ httpcore==1.0.2 ; python_version >= "3.8" and python_version < "3.12" httpx==0.25.2 ; python_version >= "3.8" and python_version < "3.12" idna==3.6 ; python_version >= "3.8" and python_version < "3.12" imagesize==1.4.1 ; python_version >= "3.8" and python_version < "3.12" -importlib-metadata==6.9.0 ; python_version >= "3.8" and python_version < "3.12" +importlib-metadata==7.0.0 ; python_version >= "3.8" and python_version < "3.12" importlib-resources==6.1.1 ; python_version >= "3.8" and python_version < "3.10" iniconfig==2.0.0 ; python_version >= "3.8" and python_version < "3.12" isodate==0.6.1 ; python_version >= "3.8" and python_version < "3.12" @@ -73,7 +72,7 @@ msgpack==1.0.7 ; python_version >= "3.8" and python_version < "3.12" multidict==6.0.4 ; python_version >= "3.8" and python_version < "3.12" mypy-extensions==1.0.0 ; python_version >= "3.8" and python_version < "3.12" myst-parser==2.0.0 ; python_version >= "3.8" and python_version < "3.12" -nh3==0.2.14 ; python_version >= "3.8" and python_version < "3.12" +nh3==0.2.15 ; python_version >= "3.8" and python_version < "3.12" numpy==1.24.4 ; python_version >= "3.8" and python_version < "3.9" numpy==1.26.2 ; python_version >= "3.9" and python_version < "3.12" outcome==1.3.0.post0 ; python_version >= "3.8" and python_version < "3.12" @@ -82,14 +81,14 @@ pathspec==0.11.2 ; python_version >= "3.8" and python_version < "3.12" pillow==10.1.0 ; python_version >= "3.8" and python_version < "3.12" pkce==1.0.3 ; python_version >= "3.8" and python_version < "3.12" pkginfo==1.9.6 ; python_version >= "3.8" and python_version < "3.12" -platformdirs==4.0.0 ; python_version >= "3.8" and python_version < "3.12" +platformdirs==4.1.0 ; python_version >= "3.8" and python_version < "3.12" playwright==1.40.0 ; python_version >= "3.8" and python_version < "3.12" pluggy==1.3.0 ; python_version >= "3.8" and python_version < "3.12" port-for==0.7.2 ; python_version >= "3.8" and python_version < "3.12" prettytable==3.9.0 ; python_version >= "3.8" and python_version < "3.12" prompt-toolkit==3.0.41 ; python_version >= "3.8" and python_version < "3.12" psutil==5.9.6 ; python_version >= "3.8" and python_version < "3.12" and sys_platform != "cygwin" -psycopg==3.1.13 ; python_version >= "3.8" and python_version < "3.12" +psycopg==3.1.14 ; python_version >= "3.8" and python_version < "3.12" pycparser==2.21 ; python_version >= "3.8" and python_version < "3.12" pyee==11.0.1 ; python_version >= "3.8" and python_version < "3.12" pygithub==2.1.1 ; python_version >= "3.8" and python_version < "3.12" @@ -99,7 +98,7 @@ pynacl==1.5.0 ; python_version >= "3.8" and python_version < "3.12" pyparsing==3.1.1 ; python_version >= "3.8" and python_version < "3.12" pyproject-hooks==1.0.0 ; python_version >= "3.8" and python_version < "3.12" pysocks==1.7.1 ; python_version >= "3.8" and python_version < "3.12" -pytest-asyncio==0.21.1 ; python_version >= "3.8" and python_version < "3.12" +pytest-asyncio==0.23.2 ; python_version >= "3.8" and python_version < "3.12" pytest-base-url==2.0.0 ; python_version >= "3.8" and python_version < "3.12" pytest-celery==0.0.0 ; python_version >= "3.8" and python_version < "3.12" pytest-cov==4.1.0 ; python_version >= "3.8" and python_version < "3.12" @@ -131,7 +130,7 @@ schema-salad==8.5.20231201181309 ; python_version >= "3.8" and python_version < scipy==1.10.1 ; python_version >= "3.8" and python_version < "3.9" scipy==1.11.4 ; python_version >= "3.9" and python_version < "3.12" secretstorage==3.3.3 ; python_version >= "3.8" and python_version < "3.12" and sys_platform == "linux" -selenium==4.15.2 ; python_version >= "3.8" and python_version < "3.12" +selenium==4.16.0 ; python_version >= "3.8" and python_version < "3.12" seletools==1.4.0 ; python_version >= "3.8" and python_version < "3.12" setuptools==69.0.2 ; python_version >= "3.8" and python_version < "3.12" six==1.16.0 ; python_version >= "3.8" and python_version < "3.12" @@ -155,7 +154,7 @@ toml==0.10.2 ; python_version >= "3.8" and python_version < "3.12" tomli==2.0.1 ; python_version >= "3.8" and python_full_version <= "3.11.0a6" trio-websocket==0.11.1 ; python_version >= "3.8" and python_version < "3.12" trio==0.23.1 ; python_version >= "3.8" and python_version < "3.12" -tuspy==1.0.1 ; python_version >= "3.8" and python_version < "3.12" +tuspy==1.0.2 ; python_version >= "3.8" and python_version < "3.12" twill==3.2.1 ; python_version >= "3.8" and python_version < "3.12" twine==4.0.2 ; python_version >= "3.8" and python_version < "3.12" typing-extensions==4.8.0 ; python_version >= "3.8" and python_version < "3.12" @@ -168,5 +167,5 @@ wcwidth==0.2.12 ; python_version >= "3.8" and python_version < "3.12" werkzeug==3.0.1 ; python_version >= "3.8" and python_version < "3.12" wrapt==1.16.0 ; python_version >= "3.8" and python_version < "3.12" wsproto==1.2.0 ; python_version >= "3.8" and python_version < "3.12" -yarl==1.9.3 ; python_version >= "3.8" and python_version < "3.12" +yarl==1.9.4 ; python_version >= "3.8" and python_version < "3.12" zipp==3.17.0 ; python_version >= "3.8" and python_version < "3.12" diff --git a/lib/galaxy/dependencies/pinned-lint-requirements.txt b/lib/galaxy/dependencies/pinned-lint-requirements.txt index 95966290773c..18619fe4d38f 100644 --- a/lib/galaxy/dependencies/pinned-lint-requirements.txt +++ b/lib/galaxy/dependencies/pinned-lint-requirements.txt @@ -1,7 +1,7 @@ attrs==23.1.0 flake8==6.1.0 -flake8-bugbear==23.11.28 +flake8-bugbear==23.12.2 mccabe==0.7.0 pycodestyle==2.11.1 pyflakes==3.1.0 -ruff==0.1.6 +ruff==0.1.7 diff --git a/lib/galaxy/dependencies/pinned-requirements.txt b/lib/galaxy/dependencies/pinned-requirements.txt index 87940aa7e3ed..b262a3faf2cc 100644 --- a/lib/galaxy/dependencies/pinned-requirements.txt +++ b/lib/galaxy/dependencies/pinned-requirements.txt @@ -1,6 +1,6 @@ -a2wsgi==1.8.0 ; python_version >= "3.8" and python_version < "3.12" +a2wsgi==1.9.0 ; python_version >= "3.8" and python_version < "3.12" adal==1.2.7 ; python_version >= "3.8" and python_version < "3.12" -aiobotocore==2.7.0 ; python_version >= "3.8" and python_version < "3.12" +aiobotocore==2.8.0 ; python_version >= "3.8" and python_version < "3.12" aiodataloader==0.4.0 ; python_version >= "3.8" and python_version < "3.12" aiofiles==23.2.1 ; python_version >= "3.8" and python_version < "3.12" aiohttp==3.9.1 ; python_version >= "3.8" and python_version < "3.12" @@ -30,7 +30,7 @@ bioblend==1.2.0 ; python_version >= "3.8" and python_version < "3.12" bleach==6.1.0 ; python_version >= "3.8" and python_version < "3.12" boltons==23.1.1 ; python_version >= "3.8" and python_version < "3.12" boto==2.49.0 ; python_version >= "3.8" and python_version < "3.12" -botocore==1.31.64 ; python_version >= "3.8" and python_version < "3.12" +botocore==1.33.1 ; python_version >= "3.8" and python_version < "3.12" bx-python==0.10.0 ; python_version >= "3.8" and python_version < "3.12" cachecontrol[filecache]==0.13.1 ; python_version >= "3.8" and python_version < "3.12" celery==5.3.6 ; python_version >= "3.8" and python_version < "3.12" @@ -51,7 +51,7 @@ conda-package-streaming==0.9.0 ; python_version >= "3.8" and python_version < "3 cryptography==41.0.7 ; python_version >= "3.8" and python_version < "3.12" cwl-upgrader==1.2.10 ; python_version >= "3.8" and python_version < "3.12" cwl-utils==0.32 ; python_version >= "3.8" and python_version < "3.12" -cwltool==3.1.20231114134824 ; python_version >= "3.8" and python_version < "3.12" +cwltool==3.1.20231207110929 ; python_version >= "3.8" and python_version < "3.12" decorator==5.1.1 ; python_version >= "3.8" and python_version < "3.12" defusedxml==0.7.1 ; python_version >= "3.8" and python_version < "3.12" deprecation==2.1.0 ; python_version >= "3.8" and python_version < "3.12" @@ -69,7 +69,7 @@ fastapi==0.98.0 ; python_version >= "3.8" and python_version < "3.12" filelock==3.13.1 ; python_version >= "3.8" and python_version < "3.12" frozenlist==1.4.0 ; python_version >= "3.8" and python_version < "3.12" fs==2.4.16 ; python_version >= "3.8" and python_version < "3.12" -fsspec==2023.10.0 ; python_version >= "3.8" and python_version < "3.12" +fsspec==2023.12.1 ; python_version >= "3.8" and python_version < "3.12" future==0.18.3 ; python_version >= "3.8" and python_version < "3.12" galaxy-sequence-utils==1.1.5 ; python_version >= "3.8" and python_version < "3.12" galaxy2cwl==0.1.4 ; python_version >= "3.8" and python_version < "3.12" @@ -86,8 +86,8 @@ h5grove==1.3.0 ; python_version >= "3.8" and python_version < "3.12" h5py==3.10.0 ; python_version >= "3.8" and python_version < "3.12" humanfriendly==10.0 ; python_version >= "3.8" and python_version < "3.12" idna==3.6 ; python_version >= "3.8" and python_version < "3.12" -importlib-metadata==6.9.0 ; python_version >= "3.8" and python_version < "3.12" -importlib-resources==6.1.1 ; python_version >= "3.8" and python_version < "3.12" +importlib-metadata==7.0.0 ; python_version >= "3.8" and python_version < "3.12" +importlib-resources==6.1.1 ; python_version >= "3.8" and python_version < "3.9" isa-rwval==0.10.10 ; python_version >= "3.8" and python_version < "3.12" isodate==0.6.1 ; python_version >= "3.8" and python_version < "3.12" jinja2==3.1.2 ; python_version >= "3.8" and python_version < "3.12" @@ -103,10 +103,10 @@ markdown-it-py==3.0.0 ; python_version >= "3.8" and python_version < "3.12" markdown==3.5.1 ; python_version >= "3.8" and python_version < "3.12" markupsafe==2.1.3 ; python_version >= "3.8" and python_version < "3.12" mdurl==0.1.2 ; python_version >= "3.8" and python_version < "3.12" -mercurial==6.6 ; python_version >= "3.8" and python_version < "3.12" +mercurial==6.6.1 ; python_version >= "3.8" and python_version < "3.12" mistune==2.0.5 ; python_version >= "3.8" and python_version < "3.12" mrcfile==1.4.3 ; python_version >= "3.8" and python_version < "3.12" -msal==1.25.0 ; python_version >= "3.8" and python_version < "3.12" +msal==1.26.0 ; python_version >= "3.8" and python_version < "3.12" msgpack==1.0.7 ; python_version >= "3.8" and python_version < "3.12" multidict==6.0.4 ; python_version >= "3.8" and python_version < "3.12" mypy-extensions==1.0.0 ; python_version >= "3.8" and python_version < "3.12" @@ -122,7 +122,7 @@ paramiko==3.3.1 ; python_version >= "3.8" and python_version < "3.12" parsley==1.3 ; python_version >= "3.8" and python_version < "3.12" paste==3.7.1 ; python_version >= "3.8" and python_version < "3.12" pastedeploy==3.1.0 ; python_version >= "3.8" and python_version < "3.12" -pebble==5.0.4 ; python_version >= "3.8" and python_version < "3.12" +pebble==5.0.5 ; python_version >= "3.8" and python_version < "3.12" 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 < "3.12" prompt-toolkit==3.0.41 ; python_version >= "3.8" and python_version < "3.12" @@ -154,9 +154,9 @@ python-multipart==0.0.6 ; python_version >= "3.8" and python_version < "3.12" python3-openid==3.2.0 ; python_version >= "3.8" and python_version < "3.12" pytz==2023.3.post1 ; python_version >= "3.8" and python_version < "3.12" pyyaml==6.0.1 ; python_version >= "3.8" and python_version < "3.12" -pyzmq==25.1.1 ; python_version >= "3.8" and python_version < "3.12" +pyzmq==25.1.2 ; python_version >= "3.8" and python_version < "3.12" rdflib==6.3.2 ; python_version >= "3.8" and python_version < "3.12" -referencing==0.31.1 ; python_version >= "3.8" and python_version < "3.12" +referencing==0.32.0 ; python_version >= "3.8" and python_version < "3.12" refgenconf==0.12.2 ; python_version >= "3.8" and python_version < "3.12" regex==2023.10.3 ; python_version >= "3.8" and python_version < "3.12" repoze-lru==0.7 ; python_version >= "3.8" and python_version < "3.12" @@ -171,7 +171,7 @@ rpds-py==0.13.2 ; python_version >= "3.8" and python_version < "3.12" rsa==4.9 ; python_version >= "3.8" and python_version < "3.12" ruamel-yaml-clib==0.2.8 ; platform_python_implementation == "CPython" and python_version < "3.12" and python_version >= "3.8" ruamel-yaml==0.18.5 ; python_version >= "3.8" and python_version < "3.12" -s3fs==2023.10.0 ; python_version >= "3.8" and python_version < "3.12" +s3fs==2023.12.1 ; python_version >= "3.8" and python_version < "3.12" schema-salad==8.5.20231201181309 ; python_version >= "3.8" and python_version < "3.12" setuptools-scm==5.0.2 ; python_version >= "3.8" and python_version < "3.12" setuptools==69.0.2 ; python_version >= "3.8" and python_version < "3.12" @@ -180,6 +180,7 @@ six==1.16.0 ; python_version >= "3.8" and python_version < "3.12" sniffio==1.3.0 ; python_version >= "3.8" and python_version < "3.12" social-auth-core[openidconnect]==4.0.3 ; python_version >= "3.8" and python_version < "3.12" sortedcontainers==2.4.0 ; python_version >= "3.8" and python_version < "3.12" +spython==0.3.11 ; python_version >= "3.8" and python_version < "3.12" sqlalchemy==1.4.50 ; python_version >= "3.8" and python_version < "3.12" sqlitedict==2.1.0 ; python_version >= "3.8" and python_version < "3.12" sqlparse==0.4.4 ; python_version >= "3.8" and python_version < "3.12" @@ -194,7 +195,7 @@ tinydb==4.8.0 ; python_version >= "3.8" and python_version < "3.12" tomli==2.0.1 ; python_version >= "3.8" and python_version < "3.11" tornado==6.4 ; python_version >= "3.8" and python_version < "3.12" tqdm==4.66.1 ; python_version >= "3.8" and python_version < "3.12" -tuspy==1.0.1 ; python_version >= "3.8" and python_version < "3.12" +tuspy==1.0.2 ; python_version >= "3.8" and python_version < "3.12" tuswsgi==0.5.5 ; python_version >= "3.8" and python_version < "3.12" typing-extensions==4.8.0 ; python_version >= "3.8" and python_version < "3.12" tzdata==2023.3 ; python_version >= "3.8" and python_version < "3.12" @@ -210,7 +211,7 @@ webob==1.8.7 ; python_version >= "3.8" and python_version < "3.12" whoosh==2.7.4 ; python_version >= "3.8" and python_version < "3.12" wrapt==1.16.0 ; python_version >= "3.8" and python_version < "3.12" yacman==0.9.2 ; python_version >= "3.8" and python_version < "3.12" -yarl==1.9.3 ; python_version >= "3.8" and python_version < "3.12" +yarl==1.9.4 ; python_version >= "3.8" and python_version < "3.12" zipp==3.17.0 ; python_version >= "3.8" and python_version < "3.12" zipstream-new==1.1.8 ; python_version >= "3.8" and python_version < "3.12" zstandard==0.22.0 ; python_version >= "3.8" and python_version < "3.12"