From 4899a6e3f5a0db80e4ddd6390f72b9b6c214e5de Mon Sep 17 00:00:00 2001 From: galaxybot Date: Sat, 17 Sep 2022 03:58:36 +0000 Subject: [PATCH] Update Python dependencies --- lib/galaxy/dependencies/dev-requirements.txt | 12 ++++---- .../dependencies/pinned-lint-requirements.txt | 6 ++-- .../dependencies/pinned-requirements.txt | 28 ++++++++++--------- 3 files changed, 24 insertions(+), 22 deletions(-) diff --git a/lib/galaxy/dependencies/dev-requirements.txt b/lib/galaxy/dependencies/dev-requirements.txt index 697c946d84b..4c8ffbba7c4 100644 --- a/lib/galaxy/dependencies/dev-requirements.txt +++ b/lib/galaxy/dependencies/dev-requirements.txt @@ -13,10 +13,10 @@ attrs==22.1.0 ; python_version >= "3.7" and python_version < "3.11" babel==2.10.3 ; python_version >= "3.7" and python_version < "3.11" billiard==3.6.4.0 ; python_version >= "3.7" and python_version < "3.11" black==22.8.0 ; python_version >= "3.7" and python_version < "3.11" -cachecontrol==0.12.11 ; python_version >= "3.7" and python_version < "3.11" +cachecontrol[filecache]==0.12.11 ; python_version >= "3.7" and python_version < "3.11" cached-property==1.5.2 ; python_version >= "3.7" and python_version < "3.8" celery==5.2.7 ; python_version >= "3.7" and python_version < "3.11" -certifi==2022.6.15.1 ; python_version >= "3.7" and python_version < "3.11" +certifi==2022.9.14 ; python_version >= "3.7" and python_version < "3.11" cffi==1.15.1 ; python_version >= "3.7" and python_version < "3.11" charset-normalizer==2.1.1 ; python_version >= "3.7" and python_version < "3.11" click-didyoumean==0.3.0 ; python_version >= "3.7" and python_version < "3.11" @@ -28,18 +28,18 @@ commonmark==0.9.1 ; python_version >= "3.7" and python_version < "3.11" coverage[toml]==6.4.4 ; python_version >= "3.7" and python_version < "3.11" cwltest==2.2.20210901154959 ; python_version >= "3.7" and python_version < "3.11" cycler==0.11.0 ; python_version >= "3.7" and python_version < "3.11" -darker==1.5.0 ; python_version >= "3.7" and python_version < "3.11" +darker==1.5.1 ; python_version >= "3.7" and python_version < "3.11" defusedxml==0.7.1 ; python_version >= "3.7" and python_version < "3.11" deprecated==1.2.13 ; python_version >= "3.7" and python_version < "3.11" docutils==0.16 ; python_version >= "3.7" and python_version < "3.11" fluent-logger==0.10.0 ; python_version >= "3.7" and python_version < "3.11" -fonttools==4.37.1 ; python_version >= "3.7" and python_version < "3.11" +fonttools==4.37.2 ; python_version >= "3.7" and python_version < "3.11" frozenlist==1.3.1 ; python_version >= "3.7" and python_version < "3.11" future==0.18.2 ; python_version >= "3.7" and python_version < "3.11" h11==0.12.0 ; python_version >= "3.7" and python_version < "3.11" httpcore==0.15.0 ; python_version >= "3.7" and python_version < "3.11" httpx==0.23.0 ; python_version >= "3.7" and python_version < "3.11" -idna==3.3 ; python_version >= "3.7" and python_version < "3.11" +idna==3.4 ; python_version >= "3.7" and python_version < "3.11" imagesize==1.4.1 ; python_version >= "3.7" and python_version < "3.11" importlib-metadata==4.12.0 ; python_version >= "3.7" and python_version < "3.10" iniconfig==1.1.1 ; python_version >= "3.7" and python_version < "3.11" @@ -101,7 +101,7 @@ responses==0.21.0 ; python_version >= "3.7" and python_version < "3.11" rfc3986[idna2008]==1.5.0 ; python_version >= "3.7" and python_version < "3.11" ruamel-yaml-clib==0.2.6 ; platform_python_implementation == "CPython" and python_version < "3.10" and python_version >= "3.7" ruamel-yaml==0.17.17 ; python_version >= "3.7" and python_version < "3.11" -schema-salad==8.3.20220909144501 ; python_version >= "3.7" and python_version < "3.11" +schema-salad==8.3.20220916115321 ; python_version >= "3.7" and python_version < "3.11" scipy==1.7.3 ; python_version >= "3.7" and python_version < "3.11" selenium==4.4.3 ; python_version >= "3.7" and python_version < "3.11" setuptools-scm==5.0.2 ; python_version >= "3.7" and python_version < "3.11" diff --git a/lib/galaxy/dependencies/pinned-lint-requirements.txt b/lib/galaxy/dependencies/pinned-lint-requirements.txt index b322eaee97a..9ed5c04d422 100644 --- a/lib/galaxy/dependencies/pinned-lint-requirements.txt +++ b/lib/galaxy/dependencies/pinned-lint-requirements.txt @@ -1,6 +1,6 @@ attrs==22.1.0 flake8==5.0.4 -flake8-bugbear==22.8.23 +flake8-bugbear==22.9.11 importlib-metadata==4.2.0 mccabe==0.7.0 mypy==0.971 @@ -14,9 +14,9 @@ types-boto==2.49.17 types-contextvars==2.4.7 types-cryptography==3.3.23 types-dataclasses==0.6.6 -types-docutils==0.19.0 +types-docutils==0.19.1 types-Markdown==3.4.1 -types-paramiko==2.11.5 +types-paramiko==2.11.6 types-pkg-resources==0.1.3 types-python-dateutil==2.8.19 types-PyYAML==6.0.11 diff --git a/lib/galaxy/dependencies/pinned-requirements.txt b/lib/galaxy/dependencies/pinned-requirements.txt index c22527306c1..6f32db7b198 100644 --- a/lib/galaxy/dependencies/pinned-requirements.txt +++ b/lib/galaxy/dependencies/pinned-requirements.txt @@ -1,6 +1,6 @@ --extra-index-url https://wheels.galaxyproject.org/simple -a2wsgi==1.5.0 ; python_version >= "3.7" and python_version < "3.11" +a2wsgi==1.6.0 ; python_version >= "3.7" and python_version < "3.11" adal==1.2.7 ; python_version >= "3.7" and python_version < "3.11" aiofiles==22.1.0 ; python_version >= "3.7" and python_version < "3.11" aiohttp==3.8.1 ; python_version >= "3.7" and python_version < "3.11" @@ -10,7 +10,7 @@ amqp==5.1.1 ; python_version >= "3.7" and python_version < "3.11" anyio==3.6.1 ; python_version >= "3.7" and python_version < "3.11" apispec==5.2.2 ; python_version >= "3.7" and python_version < "3.11" appdirs==1.4.4 ; python_version >= "3.7" and python_version < "3.11" -arcp==0.2.1 +arcp==0.2.1 ; python_version >= "3.7" and python_version < "3.11" argcomplete==2.0.0 ; python_version >= "3.7" and python_version < "3.11" async-timeout==4.0.2 ; python_version >= "3.7" and python_version < "3.11" asynctest==0.13.0 ; python_version >= "3.7" and python_version < "3.8" @@ -28,10 +28,10 @@ bleach==5.0.1 ; python_version >= "3.7" and python_version < "3.11" boltons==21.0.0 ; python_version >= "3.7" and python_version < "3.11" boto==2.49.0 ; python_version >= "3.7" and python_version < "3.11" bx-python==0.9.0 ; python_version >= "3.7" and python_version < "3.11" -cachecontrol==0.12.11 ; python_version >= "3.7" and python_version < "3.11" +cachecontrol[filecache]==0.12.11 ; python_version >= "3.7" and python_version < "3.11" cached-property==1.5.2 ; python_version >= "3.7" and python_version < "3.8" celery==5.2.7 ; python_version >= "3.7" and python_version < "3.11" -certifi==2022.6.15.1 ; python_version >= "3.7" and python_version < "3.11" +certifi==2022.9.14 ; python_version >= "3.7" and python_version < "3.11" cffi==1.15.1 ; python_version >= "3.7" and python_version < "3.11" charset-normalizer==2.1.1 ; python_version >= "3.7" and python_version < "3.11" cheetah3==3.2.6.post1 ; python_version >= "3.7" and python_version < "3.11" @@ -56,24 +56,26 @@ docutils==0.16 ; python_version >= "3.7" and python_version < "3.11" ecdsa==0.18.0 ; python_version >= "3.7" and python_version < "3.11" edam-ontology==1.25.2 ; python_version >= "3.7" and python_version < "3.11" fastapi-utils==0.2.1 ; python_version >= "3.7" and python_version < "3.11" -fastapi==0.82.0 ; python_version >= "3.7" and python_version < "3.11" +fastapi==0.85.0 ; python_version >= "3.7" and python_version < "3.11" frozenlist==1.3.1 ; python_version >= "3.7" and python_version < "3.11" fs==2.4.16 ; python_version >= "3.7" and python_version < "3.11" funcsigs==1.0.2 ; python_version >= "3.7" and python_version < "3.11" future==0.18.2 ; python_version >= "3.7" and python_version < "3.11" galaxy-sequence-utils==1.1.5 ; python_version >= "3.7" and python_version < "3.11" -gravity==0.13.4 ; python_version >= "3.7" and python_version < "3.11" +galaxy2cwl==0.1.4 ; python_version >= "3.7" and python_version < "3.11" +gravity==0.13.5 ; python_version >= "3.7" and python_version < "3.11" greenlet==1.1.3 ; python_version >= "3.7" and (platform_machine == "aarch64" or platform_machine == "ppc64le" or platform_machine == "x86_64" or platform_machine == "amd64" or platform_machine == "AMD64" or platform_machine == "win32" or platform_machine == "WIN32") and python_version < "3.11" gunicorn==20.1.0 ; python_version >= "3.7" and python_version < "3.11" gxformat2==0.15.0 ; python_version >= "3.7" and python_version < "3.11" h11==0.12.0 ; python_version >= "3.7" and python_version < "3.11" h5py==3.7.0 ; python_version >= "3.7" and python_version < "3.11" humanfriendly==10.0 ; python_version >= "3.7" and python_version < "3.11" -idna==3.3 ; python_version >= "3.7" and python_version < "3.11" +idna==3.4 ; python_version >= "3.7" and python_version < "3.11" importlib-metadata==4.12.0 ; python_version >= "3.7" and python_version < "3.10" importlib-resources==5.9.0 ; python_version >= "3.7" and python_version < "3.11" isa-rwval==0.10.10 ; python_version >= "3.7" and python_version < "3.11" isodate==0.6.1 ; python_version >= "3.7" and python_version < "3.11" +jinja2==3.1.2 ; python_version >= "3.7" and python_version < "3.11" jsonref==0.2 ; python_version >= "3.7" and python_version < "3.11" jsonschema==4.16.0 ; python_version >= "3.7" and python_version < "3.11" kombu==5.2.4 ; python_version >= "3.7" and python_version < "3.11" @@ -101,7 +103,7 @@ parsley==1.3 ; python_version >= "3.7" and python_version < "3.11" paste==3.5.2 ; python_version >= "3.7" and python_version < "3.11" pastedeploy==2.1.1 ; python_version >= "3.7" and python_version < "3.11" pbr==5.10.0 ; python_version >= "3.7" and python_version < "3.11" -pebble==4.6.3 ; python_version >= "3.7" and python_version < "3.11" +pebble==5.0.0 ; python_version >= "3.7" and python_version < "3.11" pkgutil-resolve-name==1.3.10 ; python_version >= "3.7" and python_version < "3.9" prompt-toolkit==3.0.31 ; python_version >= "3.7" and python_version < "3.11" prov==1.5.1 ; python_version >= "3.7" and python_version < "3.11" @@ -132,7 +134,7 @@ python-multipart==0.0.5 ; python_version >= "3.7" and python_version < "3.11" python3-openid==3.2.0 ; python_version >= "3.7" and python_version < "3.11" pytz==2022.2.1 ; python_version >= "3.7" and python_version < "3.11" pyyaml==6.0 ; python_version >= "3.7" and python_version < "3.11" -pyzmq==23.2.1 ; python_version >= "3.7" and python_version < "3.11" +pyzmq==24.0.0 ; python_version >= "3.7" and python_version < "3.11" rdflib==6.0.2 ; python_version >= "3.7" and python_version < "3.11" refgenconf==0.12.2 ; python_version >= "3.7" and python_version < "3.11" repoze-lru==0.7 ; python_version >= "3.7" and python_version < "3.11" @@ -140,12 +142,12 @@ requests-oauthlib==1.3.1 ; python_version >= "3.7" and python_version < "3.11" requests-toolbelt==0.9.1 ; python_version >= "3.7" and python_version < "3.11" requests==2.28.1 ; python_version >= "3.7" and python_version < "3.11" rich==12.5.1 ; python_version >= "3.7" and python_version < "3.11" -rocrate==0.6.1 +rocrate==0.7.0 ; python_version >= "3.7" and python_version < "3.11" routes==2.5.1 ; python_version >= "3.7" and python_version < "3.11" rsa==4.9 ; python_version >= "3.7" and python_version < "3.11" ruamel-yaml-clib==0.2.6 ; platform_python_implementation == "CPython" and python_version < "3.10" and python_version >= "3.7" ruamel-yaml==0.17.17 ; python_version >= "3.7" and python_version < "3.11" -schema-salad==8.3.20220909144501 ; python_version >= "3.7" and python_version < "3.11" +schema-salad==8.3.20220916115321 ; python_version >= "3.7" and python_version < "3.11" setuptools-scm==5.0.2 ; python_version >= "3.7" and python_version < "3.11" setuptools==65.3.0 ; python_version >= "3.7" and python_version < "3.11" shellescape==3.8.1 ; python_version >= "3.7" and python_version < "3.11" @@ -158,7 +160,7 @@ sqlalchemy==1.4.41 ; python_version >= "3.7" and python_version < "3.11" sqlitedict==2.0.0 ; python_version >= "3.7" and python_version < "3.11" sqlparse==0.4.2 ; python_version >= "3.7" and python_version < "3.11" starlette-context==0.3.4 ; python_version >= "3.7" and python_version < "3.11" -starlette==0.19.1 ; python_version >= "3.7" and python_version < "3.11" +starlette==0.20.4 ; python_version >= "3.7" and python_version < "3.11" supervisor==4.2.4 ; python_version >= "3.7" and python_version < "3.11" svgwrite==1.4.3 ; python_version >= "3.7" and python_version < "3.11" tempita==0.5.2 ; python_version >= "3.7" and python_version < "3.11" @@ -174,7 +176,7 @@ tzlocal==2.1 ; python_version >= "3.7" and python_version < "3.11" ubiquerg==0.6.2 ; python_version >= "3.7" and python_version < "3.11" urllib3==1.26.12 ; python_version >= "3.7" and python_version < "3.11" uvicorn==0.18.3 ; python_version >= "3.7" and python_version < "3.11" -uvloop==0.16.0 ; python_version >= "3.7" and python_version < "3.11" +uvloop==0.17.0 ; python_version >= "3.7" and python_version < "3.11" vine==5.0.0 ; python_version >= "3.7" and python_version < "3.11" wcwidth==0.2.5 ; python_version >= "3.7" and python_version < "3.11" webencodings==0.5.1 ; python_version >= "3.7" and python_version < "3.11"