diff --git a/lib/galaxy/dependencies/dev-requirements.txt b/lib/galaxy/dependencies/dev-requirements.txt index 2d83fdd2c9f..afb44df79cc 100644 --- a/lib/galaxy/dependencies/dev-requirements.txt +++ b/lib/galaxy/dependencies/dev-requirements.txt @@ -53,7 +53,7 @@ lockfile==0.12.2 ; python_version >= "3.7" and python_version < "3.11" lxml==4.9.2 ; python_version >= "3.7" and python_version < "3.11" markdown-it-reporter==0.0.2 ; python_version >= "3.7" and python_version < "3.11" markdown==3.4.1 ; python_version >= "3.7" and python_version < "3.11" -markupsafe==2.1.1 ; python_version >= "3.7" and python_version < "3.11" +markupsafe==2.1.2 ; python_version >= "3.7" and python_version < "3.11" matplotlib==3.5.3 ; python_version >= "3.7" and python_version < "3.11" mirakuru==2.4.2 ; python_version >= "3.7" and python_version < "3.11" mistune==2.0.4 ; python_version >= "3.7" and python_version < "3.11" @@ -89,10 +89,10 @@ pytest-metadata==2.0.4 ; python_version >= "3.7" and python_version < "3.11" pytest-mock==3.10.0 ; python_version >= "3.7" and python_version < "3.11" pytest-postgresql==4.1.1 ; python_version >= "3.7" and python_version < "3.11" pytest-shard==0.1.2 ; python_version >= "3.7" and python_version < "3.11" -pytest==7.2.0 ; python_version >= "3.7" and python_version < "3.11" +pytest==7.2.1 ; python_version >= "3.7" and python_version < "3.11" python-dateutil==2.8.2 ; python_version >= "3.7" and python_version < "3.11" -python-irodsclient==1.1.5 ; python_version >= "3.7" and python_version < "3.11" -pytz==2022.7 ; python_version >= "3.7" and python_version < "3.11" +python-irodsclient==1.1.6 ; python_version >= "3.7" and python_version < "3.11" +pytz==2022.7.1 ; python_version >= "3.7" and python_version < "3.11" rdflib==6.2.0 ; python_version >= "3.7" and python_version < "3.11" recommonmark==0.7.1 ; python_version >= "3.7" and python_version < "3.11" requests==2.28.2 ; python_version >= "3.7" and python_version < "3.11" @@ -104,7 +104,7 @@ schema-salad==8.3.20230109181936 ; python_version >= "3.7" and python_version < scipy==1.7.3 ; python_version >= "3.7" and python_version < "3.11" selenium==4.7.2 ; python_version >= "3.7" and python_version < "3.11" seletools==1.3.0 ; python_version >= "3.7" and python_version < "3.11" -setuptools==65.7.0 ; python_version >= "3.7" and python_version < "3.11" +setuptools==66.1.1 ; python_version >= "3.7" and python_version < "3.11" six==1.16.0 ; python_version >= "3.7" and python_version < "3.11" sniffio==1.3.0 ; python_version >= "3.7" and python_version < "3.11" snowballstemmer==2.2.0 ; python_version >= "3.7" and python_version < "3.11" @@ -120,7 +120,7 @@ sphinxcontrib-qthelp==1.0.3 ; python_version >= "3.7" and python_version < "3.11 sphinxcontrib-serializinghtml==1.1.5 ; python_version >= "3.7" and python_version < "3.11" statsd==4.0.1 ; python_version >= "3.7" and python_version < "3.11" testfixtures==7.0.4 ; python_version >= "3.7" and python_version < "3.11" -tinydb==4.7.0 ; python_version >= "3.7" and python_version < "3.11" +tinydb==4.7.1 ; python_version >= "3.7" and python_version < "3.11" toml==0.10.2 ; python_version >= "3.7" and python_version < "3.11" tomli==2.0.1 ; python_version >= "3.7" and python_version < "3.11" trio-websocket==0.9.2 ; python_version >= "3.7" and python_version < "3.11" @@ -134,7 +134,7 @@ urllib3==1.26.14 ; python_version >= "3.7" and python_version < "3.11" urllib3[socks]==1.26.14 ; python_version >= "3.7" and python_version < "3.11" vine==5.0.0 ; python_version >= "3.7" and python_version < "3.11" watchdog==2.2.1 ; python_version >= "3.7" and python_version < "3.11" -wcwidth==0.2.5 ; python_version >= "3.7" and python_version < "3.11" +wcwidth==0.2.6 ; python_version >= "3.7" and python_version < "3.11" wrapt==1.14.1 ; python_version >= "3.7" and python_version < "3.11" wsproto==1.2.0 ; python_version >= "3.7" and python_version < "3.11" yarl==1.8.2 ; 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 4cf3961e3dd..e5ca6fafb5d 100644 --- a/lib/galaxy/dependencies/pinned-lint-requirements.txt +++ b/lib/galaxy/dependencies/pinned-lint-requirements.txt @@ -1,10 +1,10 @@ attrs==22.2.0 flake8==5.0.4 -flake8-bugbear==22.12.6 +flake8-bugbear==23.1.20 importlib-metadata==4.2.0 mccabe==0.7.0 pycodestyle==2.9.1 pyflakes==2.5.0 -ruff==0.0.223 +ruff==0.0.228 typing_extensions==4.4.0 zipp==3.11.0 diff --git a/lib/galaxy/dependencies/pinned-requirements.txt b/lib/galaxy/dependencies/pinned-requirements.txt index 3bd0f4ea87b..3cf5b20fd73 100644 --- a/lib/galaxy/dependencies/pinned-requirements.txt +++ b/lib/galaxy/dependencies/pinned-requirements.txt @@ -5,8 +5,8 @@ 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==3.8.3 ; python_version >= "3.7" and python_version < "3.11" aiosignal==1.3.1 ; python_version >= "3.7" and python_version < "3.11" -alembic==1.9.1 ; python_version >= "3.7" and python_version < "3.11" -alembic_utils==0.7.8 ; python_version >= "3.7" and python_version < "3.11" +alembic-utils==0.7.8 ; python_version >= "3.7" and python_version < "3.11" +alembic==1.9.2 ; python_version >= "3.7" and python_version < "3.11" amqp==5.1.1 ; python_version >= "3.7" and python_version < "3.11" anyio==3.6.2 ; python_version >= "3.7" and python_version < "3.11" apispec==6.0.2 ; python_version >= "3.7" and python_version < "3.11" @@ -46,7 +46,6 @@ cloudauthz==0.6.0 ; python_version >= "3.7" and python_version < "3.11" cloudbridge==3.1.0 ; python_version >= "3.7" and python_version < "3.11" colorama==0.4.6 ; python_version >= "3.7" and python_version < "3.11" and platform_system == "Windows" coloredlogs==15.0.1 ; python_version >= "3.7" and python_version < "3.11" -commonmark==0.9.1 ; python_version >= "3.7" and python_version < "3.11" cryptography==39.0.0 ; python_version >= "3.7" and python_version < "3.11" cwl-upgrader==1.2.4 ; python_version >= "3.7" and python_version < "3.11" cwl-utils==0.21 ; python_version >= "3.7" and python_version < "3.11" @@ -55,7 +54,7 @@ decorator==5.1.1 ; python_version >= "3.7" and python_version < "3.11" defusedxml==0.7.1 ; python_version >= "3.7" and python_version < "3.11" deprecation==2.1.0 ; python_version >= "3.7" and python_version < "3.11" dictobj==0.4 ; python_version >= "3.7" and python_version < "3.11" -dnspython==2.2.1 ; python_version >= "3.7" and python_version < "3.11" +dnspython==2.3.0 ; python_version >= "3.7" and python_version < "3.11" docopt==0.6.2 ; python_version >= "3.7" and python_version < "3.11" 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" @@ -63,6 +62,7 @@ edam-ontology==1.25.2 ; python_version >= "3.7" and python_version < "3.11" email-validator==1.3.0 ; python_version >= "3.7" and python_version < "3.11" fastapi-utils==0.2.1 ; python_version >= "3.7" and python_version < "3.11" fastapi==0.89.1 ; python_version >= "3.7" and python_version < "3.11" +flupy==1.2.0 ; python_version >= "3.7" and python_version < "3.11" frozenlist==1.3.3 ; 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" @@ -82,15 +82,17 @@ importlib-resources==5.10.2 ; 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==1.0.1 ; python_version >= "3.7" and python_version < "3.11" +jsonref==1.1.0 ; python_version >= "3.7" and python_version < "3.11" jsonschema==4.17.3 ; python_version >= "3.7" and python_version < "3.11" kombu==5.2.4 ; python_version >= "3.7" and python_version < "3.11" lagom==2.2.0 ; python_version >= "3.7" and python_version < "3.11" lockfile==0.12.2 ; python_version >= "3.7" and python_version < "3.11" lxml==4.9.2 ; python_version >= "3.7" and python_version < "3.11" mako==1.2.4 ; python_version >= "3.7" and python_version < "3.11" +markdown-it-py==2.1.0 ; python_version >= "3.7" and python_version < "3.11" markdown==3.4.1 ; python_version >= "3.7" and python_version < "3.11" -markupsafe==2.1.1 ; python_version >= "3.7" and python_version < "3.11" +markupsafe==2.1.2 ; python_version >= "3.7" and python_version < "3.11" +mdurl==0.1.2 ; python_version >= "3.7" and python_version < "3.11" mercurial==6.3.2 ; python_version >= "3.7" and python_version < "3.11" mistune==2.0.4 ; python_version >= "3.7" and python_version < "3.11" mrcfile==1.4.3 ; python_version >= "3.7" and python_version < "3.11" @@ -103,7 +105,8 @@ numpy==1.21.6 ; python_version >= "3.7" and python_version < "3.11" oauthlib==3.2.2 ; python_version >= "3.7" and python_version < "3.11" oyaml==1.0 ; python_version >= "3.7" and python_version < "3.11" packaging==21.3 ; python_version >= "3.7" and python_version < "3.11" -paramiko==2.12.0 ; python_version >= "3.7" and python_version < "3.11" +paramiko==3.0.0 ; python_version >= "3.7" and python_version < "3.11" +parse==1.19.0 ; python_version >= "3.7" and python_version < "3.11" 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==3.0.1 ; python_version >= "3.7" and python_version < "3.11" @@ -138,7 +141,7 @@ python-jose==3.3.0 ; python_version >= "3.7" and python_version < "3.11" python-magic==0.4.27 ; python_version >= "3.7" and python_version < "3.11" 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==2022.7 ; python_version >= "3.7" and python_version < "3.11" +pytz==2022.7.1 ; python_version >= "3.7" and python_version < "3.11" pyyaml==6.0 ; python_version >= "3.7" and python_version < "3.11" pyzmq==25.0.0 ; python_version >= "3.7" and python_version < "3.11" rdflib==6.2.0 ; python_version >= "3.7" and python_version < "3.11" @@ -148,7 +151,7 @@ requests-oauthlib==1.3.1 ; python_version >= "3.7" and python_version < "3.11" requests-toolbelt==0.10.1 ; python_version >= "3.7" and python_version < "3.11" requests-unixsocket==0.3.0 ; python_version >= "3.7" and python_version < "3.11" requests==2.28.2 ; python_version >= "3.7" and python_version < "3.11" -rich==13.0.1 ; python_version >= "3.7" and python_version < "3.11" +rich==13.2.0 ; python_version >= "3.7" and python_version < "3.11" 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" @@ -156,7 +159,7 @@ ruamel-yaml-clib==0.2.7 ; platform_python_implementation == "CPython" and python ruamel-yaml==0.17.21 ; python_version < "3.11" and python_version >= "3.7" schema-salad==8.3.20230109181936 ; python_version >= "3.7" and python_version < "3.11" setuptools-scm==5.0.2 ; python_version >= "3.7" and python_version < "3.11" -setuptools==65.7.0 ; python_version >= "3.7" and python_version < "3.11" +setuptools==66.1.1 ; python_version >= "3.7" and python_version < "3.11" shellescape==3.8.1 ; python_version >= "3.7" and python_version < "3.11" six==1.16.0 ; python_version >= "3.7" and python_version < "3.11" sniffio==1.3.0 ; python_version >= "3.7" and python_version < "3.11" @@ -173,7 +176,7 @@ 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" tenacity==8.1.0 ; python_version >= "3.7" and python_version < "3.11" tifffile==2021.11.2 ; python_version >= "3.7" and python_version < "3.11" -tinydb==4.7.0 ; python_version >= "3.7" and python_version < "3.11" +tinydb==4.7.1 ; python_version >= "3.7" and python_version < "3.11" tornado==6.2 ; python_version >= "3.7" and python_version < "3.11" tqdm==4.64.1 ; python_version >= "3.7" and python_version < "3.11" tuspy==1.0.0 ; python_version >= "3.7" and python_version < "3.11" @@ -185,7 +188,7 @@ urllib3==1.26.14 ; python_version >= "3.7" and python_version < "3.11" uvicorn==0.20.0 ; 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" +wcwidth==0.2.6 ; python_version >= "3.7" and python_version < "3.11" webencodings==0.5.1 ; python_version >= "3.7" and python_version < "3.11" webob==1.8.7 ; python_version >= "3.7" and python_version < "3.11" whoosh==2.7.4 ; python_version >= "3.7" and python_version < "3.11" diff --git a/lib/galaxy/dependencies/pinned-typecheck-requirements.txt b/lib/galaxy/dependencies/pinned-typecheck-requirements.txt index f1e1c5305b3..5b68529c79c 100644 --- a/lib/galaxy/dependencies/pinned-typecheck-requirements.txt +++ b/lib/galaxy/dependencies/pinned-typecheck-requirements.txt @@ -6,16 +6,16 @@ pycparser==2.21 tomli==2.0.1 typed-ast==1.5.4 types-bleach==5.0.3.1 -types-boto==2.49.18.4 +types-boto==2.49.18.5 types-contextvars==2.4.7 types-dataclasses==0.6.6 -types-docutils==0.19.1.1 -types-Markdown==3.4.2.1 -types-paramiko==2.12.0.2 +types-docutils==0.19.1.2 +types-Markdown==3.4.2.2 +types-paramiko==2.12.0.3 types-pkg-resources==0.1.3 -types-python-dateutil==2.8.19.5 -types-PyYAML==6.0.12.2 -types-requests==2.28.11.7 +types-python-dateutil==2.8.19.6 +types-PyYAML==6.0.12.3 +types-requests==2.28.11.8 types-six==1.16.21.4 types-urllib3==1.26.25.4 typing_extensions==4.4.0