diff --git a/lib/galaxy/dependencies/dev-requirements.txt b/lib/galaxy/dependencies/dev-requirements.txt index 8c4bb177cba5..0be0caf9a3fd 100644 --- a/lib/galaxy/dependencies/dev-requirements.txt +++ b/lib/galaxy/dependencies/dev-requirements.txt @@ -26,7 +26,7 @@ codespell==2.2.6 ; python_version >= "3.8" and python_version < "3.12" colorama==0.4.6 ; python_version >= "3.8" and python_version < "3.12" and (sys_platform == "win32" or platform_system == "Windows" or os_name == "nt") contourpy==1.1.1 ; python_version >= "3.8" and python_version < "3.12" coverage[toml]==7.3.2 ; python_version >= "3.8" and python_version < "3.12" -cryptography==41.0.5 ; python_version >= "3.8" and python_version < "3.12" +cryptography==41.0.7 ; python_version >= "3.8" and python_version < "3.12" cwltest==2.4.20231031143732 ; python_version >= "3.8" and python_version < "3.12" cycler==0.12.1 ; python_version >= "3.8" and python_version < "3.12" darker==1.7.2 ; python_version >= "3.8" and python_version < "3.12" @@ -46,8 +46,8 @@ 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==6.8.0 ; 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==6.9.0 ; python_version >= "3.8" and python_version < "3.12" +importlib-resources==6.1.1 ; python_version >= "3.8" and python_version < "3.10" 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" isort==5.12.0 ; python_version >= "3.8" and python_version < "3.12" @@ -127,7 +127,7 @@ rfc3986==2.0.0 ; python_version >= "3.8" and python_version < "3.12" rich==13.7.0 ; 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" -schema-salad==8.4.20231117150958 ; python_version >= "3.8" and python_version < "3.12" +schema-salad==8.5.20231201181309 ; python_version >= "3.8" and python_version < "3.12" 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" diff --git a/lib/galaxy/dependencies/pinned-lint-requirements.txt b/lib/galaxy/dependencies/pinned-lint-requirements.txt index 6663da463581..95966290773c 100644 --- a/lib/galaxy/dependencies/pinned-lint-requirements.txt +++ b/lib/galaxy/dependencies/pinned-lint-requirements.txt @@ -1,6 +1,6 @@ attrs==23.1.0 flake8==6.1.0 -flake8-bugbear==23.9.16 +flake8-bugbear==23.11.28 mccabe==0.7.0 pycodestyle==2.11.1 pyflakes==3.1.0 diff --git a/lib/galaxy/dependencies/pinned-requirements.txt b/lib/galaxy/dependencies/pinned-requirements.txt index 35c59dfd9e7f..87940aa7e3ed 100644 --- a/lib/galaxy/dependencies/pinned-requirements.txt +++ b/lib/galaxy/dependencies/pinned-requirements.txt @@ -6,7 +6,7 @@ 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" aioitertools==0.11.0 ; python_version >= "3.8" and python_version < "3.12" aiosignal==1.3.1 ; python_version >= "3.8" and python_version < "3.12" -alembic==1.12.1 ; python_version >= "3.8" and python_version < "3.12" +alembic==1.13.0 ; python_version >= "3.8" and python_version < "3.12" amqp==5.2.0 ; python_version >= "3.8" and python_version < "3.12" aniso8601==9.0.1 ; python_version >= "3.8" and python_version < "3.12" anyio==4.1.0 ; python_version >= "3.8" and python_version < "3.12" @@ -22,7 +22,7 @@ backports-zoneinfo==0.2.1 ; python_version >= "3.8" and python_version < "3.9" backports-zoneinfo[tzdata]==0.2.1 ; python_version >= "3.8" and python_version < "3.9" bagit-profile==1.3.1 ; python_version >= "3.8" and python_version < "3.12" bagit==1.8.1 ; python_version >= "3.8" and python_version < "3.12" -bcrypt==4.0.1 ; python_version >= "3.8" and python_version < "3.12" +bcrypt==4.1.1 ; python_version >= "3.8" and python_version < "3.12" bdbag==1.7.1 ; python_version >= "3.8" and python_version < "3.12" beaker==1.12.1 ; python_version >= "3.8" and python_version < "3.12" billiard==4.2.0 ; python_version >= "3.8" and python_version < "3.12" @@ -48,9 +48,9 @@ cloudbridge==3.2.0 ; python_version >= "3.8" and python_version < "3.12" colorama==0.4.6 ; python_version >= "3.8" and python_version < "3.12" and platform_system == "Windows" coloredlogs==15.0.1 ; python_version >= "3.8" and python_version < "3.12" conda-package-streaming==0.9.0 ; python_version >= "3.8" and python_version < "3.12" -cryptography==41.0.5 ; python_version >= "3.8" and python_version < "3.12" +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==0.31 ; 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" 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" @@ -86,14 +86,14 @@ 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==6.8.0 ; 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" 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" jmespath==1.0.1 ; python_version >= "3.8" and python_version < "3.12" jsonref==1.1.0 ; python_version >= "3.8" and python_version < "3.12" -jsonschema-specifications==2023.11.1 ; python_version >= "3.8" and python_version < "3.12" +jsonschema-specifications==2023.11.2 ; python_version >= "3.8" and python_version < "3.12" jsonschema==4.20.0 ; python_version >= "3.8" and python_version < "3.12" kombu==5.3.4 ; python_version >= "3.8" and python_version < "3.12" lagom==2.6.0 ; python_version >= "3.8" and python_version < "3.12" @@ -156,7 +156,7 @@ 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" rdflib==6.3.2 ; python_version >= "3.8" and python_version < "3.12" -referencing==0.31.0 ; python_version >= "3.8" and python_version < "3.12" +referencing==0.31.1 ; 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" @@ -167,12 +167,12 @@ requests==2.31.0 ; python_version >= "3.8" and python_version < "3.12" rich==13.7.0 ; python_version >= "3.8" and python_version < "3.12" rocrate==0.9.0 ; python_version >= "3.8" and python_version < "3.12" routes==2.5.1 ; python_version >= "3.8" and python_version < "3.12" -rpds-py==0.13.1 ; python_version >= "3.8" and python_version < "3.12" +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" -schema-salad==8.4.20231117150958 ; 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" shellescape==3.8.1 ; python_version >= "3.8" and python_version < "3.12" @@ -192,7 +192,7 @@ tenacity==8.2.3 ; python_version >= "3.8" and python_version < "3.12" tifffile==2023.7.10 ; python_version >= "3.8" and python_version < "3.12" 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==6.3.3 ; python_version >= "3.8" and python_version < "3.12" +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" tuswsgi==0.5.5 ; python_version >= "3.8" and python_version < "3.12" diff --git a/lib/galaxy/dependencies/pinned-typecheck-requirements.txt b/lib/galaxy/dependencies/pinned-typecheck-requirements.txt index f25703f5524c..83876770d945 100644 --- a/lib/galaxy/dependencies/pinned-typecheck-requirements.txt +++ b/lib/galaxy/dependencies/pinned-typecheck-requirements.txt @@ -1,5 +1,5 @@ cffi==1.16.0 ; python_version >= "3.8" and python_version < "3.12" -cryptography==41.0.5 ; python_version >= "3.8" and python_version < "3.12" +cryptography==41.0.7 ; python_version >= "3.8" and python_version < "3.12" mypy-extensions==1.0.0 ; python_version >= "3.8" and python_version < "3.12" mypy==1.7.1 ; python_version >= "3.8" and python_version < "3.12" pycparser==2.21 ; python_version >= "3.8" and python_version < "3.12"