Update Python dependencies

by running `make update-dependencies`.
galaxyproject · Jul 13, 2024 · 9d40d1f · 9d40d1f
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diff --git a/lib/galaxy/dependencies/dev-requirements.txt b/lib/galaxy/dependencies/dev-requirements.txt
@@ -16,15 +16,15 @@ boto3==1.34.131 ; python_version >= "3.8" and python_version < "3.13"
 botocore==1.34.131 ; python_version >= "3.8" and python_version < "3.13"
 build==1.2.1 ; python_version >= "3.8" and python_version < "3.13"
 cachecontrol[filecache]==0.14.0 ; python_version >= "3.8" and python_version < "3.13"
-certifi==2024.6.2 ; python_version >= "3.8" and python_version < "3.13"
+certifi==2024.7.4 ; python_version >= "3.8" and python_version < "3.13"
 cffi==1.16.0 ; python_version >= "3.8" and python_version < "3.13"
 charset-normalizer==3.3.2 ; python_version >= "3.8" and python_version < "3.13"
 click==8.1.7 ; python_version >= "3.8" and python_version < "3.13"
 codespell==2.3.0 ; python_version >= "3.8" and python_version < "3.13"
 colorama==0.4.6 ; python_version >= "3.8" and python_version < "3.13" and (sys_platform == "win32" or platform_system == "Windows" or os_name == "nt")
 contourpy==1.1.1 ; python_version >= "3.8" and python_version < "3.9"
 contourpy==1.2.1 ; python_version >= "3.9" and python_version < "3.13"
-coverage[toml]==7.5.4 ; python_version >= "3.8" and python_version < "3.13"
+coverage[toml]==7.6.0 ; python_version >= "3.8" and python_version < "3.13"
 cryptography==42.0.8 ; python_version >= "3.8" and python_version < "3.13"
 cwltest==2.5.20240425111257 ; python_version >= "3.8" and python_version < "3.13"
 cycler==0.12.1 ; python_version >= "3.8" and python_version < "3.13"
@@ -35,10 +35,10 @@ defusedxml==0.7.1 ; python_version >= "3.8" and python_version < "3.13"
 deprecated==1.2.14 ; python_version >= "3.8" and python_version < "3.13"
 docutils==0.20.1 ; python_version >= "3.8" and python_version < "3.13"
 dogpile-cache==1.2.2 ; python_version >= "3.9" and python_version < "3.13"
-exceptiongroup==1.2.1 ; python_version >= "3.8" and python_version < "3.11"
+exceptiongroup==1.2.2 ; python_version >= "3.8" and python_version < "3.11"
 filelock==3.15.4 ; python_version >= "3.8" and python_version < "3.13"
 fluent-logger==0.11.1 ; python_version >= "3.8" and python_version < "3.13"
-fonttools==4.53.0 ; python_version >= "3.8" and python_version < "3.13"
+fonttools==4.53.1 ; python_version >= "3.8" and python_version < "3.13"
 frozenlist==1.4.1 ; python_version >= "3.8" and python_version < "3.13"
 galaxy-release-util==0.1.11 ; python_version >= "3.8" and python_version < "3.13"
 graylint==1.1.1 ; python_version >= "3.8" and python_version < "3.13"
@@ -69,7 +69,7 @@ markdown-it-py==3.0.0 ; python_version >= "3.8" and python_version < "3.13"
 markdown-it-reporter==0.0.2 ; python_version >= "3.8" and python_version < "3.13"
 markupsafe==2.1.5 ; python_version >= "3.8" and python_version < "3.13"
 matplotlib==3.7.5 ; python_version >= "3.8" and python_version < "3.9"
-matplotlib==3.9.0 ; python_version >= "3.9" and python_version < "3.13"
+matplotlib==3.9.1 ; python_version >= "3.9" and python_version < "3.13"
 mdit-py-plugins==0.4.1 ; python_version >= "3.8" and python_version < "3.13"
 mdurl==0.1.2 ; python_version >= "3.8" and python_version < "3.13"
 mirakuru==2.5.2 ; python_version >= "3.8" and python_version < "3.13"
@@ -79,7 +79,7 @@ msgpack==1.0.8 ; python_version >= "3.8" and python_version < "3.13"
 multidict==6.0.5 ; python_version >= "3.8" and python_version < "3.13"
 mypy-extensions==1.0.0 ; python_version >= "3.8" and python_version < "3.13"
 myst-parser==3.0.1 ; python_version >= "3.8" and python_version < "3.13"
-nh3==0.2.17 ; python_version >= "3.8" and python_version < "3.13"
+nh3==0.2.18 ; python_version >= "3.8" and python_version < "3.13"
 numpy==1.24.4 ; python_version >= "3.8" and python_version < "3.9"
 numpy==2.0.0 ; python_version >= "3.9" and python_version < "3.13"
 onedatafilerestclient==21.2.5.1 ; python_version >= "3.8" and python_version < "3.13"
@@ -94,7 +94,7 @@ platformdirs==4.2.2 ; python_version >= "3.8" and python_version < "3.13"
 playwright==1.45.0 ; python_version >= "3.8" and python_version < "3.13"
 pluggy==1.5.0 ; python_version >= "3.8" and python_version < "3.13"
 port-for==0.7.2 ; python_version >= "3.8" and python_version < "3.13"
-prettytable==3.10.0 ; python_version >= "3.8" and python_version < "3.13"
+prettytable==3.10.2 ; python_version >= "3.8" and python_version < "3.13"
 psutil==6.0.0 ; python_version >= "3.8" and python_version < "3.13" and sys_platform != "cygwin"
 psycopg==3.2.1 ; python_version >= "3.8" and python_version < "3.13"
 pycparser==2.22 ; python_version >= "3.8" and python_version < "3.13"
@@ -117,7 +117,7 @@ pytest-mock==3.14.0 ; python_version >= "3.8" and python_version < "3.13"
 pytest-playwright==0.5.1 ; python_version >= "3.8" and python_version < "3.13"
 pytest-postgresql==6.0.0 ; python_version >= "3.8" and python_version < "3.13"
 pytest-shard==0.1.2 ; python_version >= "3.8" and python_version < "3.13"
-pytest==7.4.4 ; python_version >= "3.8" and python_version < "3.13"
+pytest==8.2.2 ; python_version >= "3.8" and python_version < "3.13"
 python-dateutil==2.9.0.post0 ; python_version >= "3.8" and python_version < "3.13"
 python-irodsclient==2.0.1 ; python_version >= "3.8" and python_version < "3.13"
 python-slugify==8.0.4 ; python_version >= "3.8" and python_version < "3.13"
@@ -132,19 +132,19 @@ requests==2.32.3 ; python_version >= "3.8" and python_version < "3.13"
 responses==0.25.3 ; python_version >= "3.8" and python_version < "3.13"
 rfc3986==2.0.0 ; python_version >= "3.8" and python_version < "3.13"
 rich==13.7.1 ; python_version >= "3.8" and python_version < "3.13"
-rpds-py==0.18.1 ; python_version >= "3.9" and python_version < "3.13"
+rpds-py==0.19.0 ; python_version >= "3.9" and python_version < "3.13"
 ruamel-yaml-clib==0.2.8 ; platform_python_implementation == "CPython" and python_version < "3.13" and python_version >= "3.8"
 ruamel-yaml==0.18.6 ; python_version >= "3.8" and python_version < "3.13"
 rucio-clients==34.5.0 ; python_version >= "3.9" and python_version < "3.13"
 s3transfer==0.10.2 ; python_version >= "3.8" and python_version < "3.13"
-schema-salad==8.5.20240503091721 ; python_version >= "3.8" and python_version < "3.13"
+schema-salad==8.6.20240710082410 ; python_version >= "3.8" and python_version < "3.13"
 scipy==1.10.1 ; python_version >= "3.8" and python_version < "3.9"
 scipy==1.13.1 ; python_version >= "3.9" and python_version < "3.10"
 scipy==1.14.0 ; python_version >= "3.10" and python_version < "3.13"
 secretstorage==3.3.3 ; python_version >= "3.8" and python_version < "3.13" and sys_platform == "linux"
 selenium==4.22.0 ; python_version >= "3.8" and python_version < "3.13"
 seletools==1.5.0 ; python_version >= "3.8" and python_version < "3.13"
-setuptools==70.2.0 ; python_version >= "3.8" and python_version < "3.13"
+setuptools==70.3.0 ; python_version >= "3.8" and python_version < "3.13"
 six==1.16.0 ; python_version >= "3.8" and python_version < "3.13"
 sniffio==1.3.1 ; python_version >= "3.8" and python_version < "3.13"
 snowballstemmer==2.2.0 ; python_version >= "3.8" and python_version < "3.13"
@@ -167,7 +167,7 @@ tinydb==4.8.0 ; python_version >= "3.8" and python_version < "3.13"
 toml==0.10.2 ; python_version >= "3.8" and python_version < "3.13"
 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 < "3.13"
-trio==0.25.1 ; python_version >= "3.8" and python_version < "3.13"
+trio==0.26.0 ; python_version >= "3.8" and python_version < "3.13"
 tuspy==1.0.3 ; python_version >= "3.8" and python_version < "3.13"
 twill==3.2.5 ; python_version >= "3.8" and python_version < "3.13"
 twine==5.1.1 ; python_version >= "3.8" and python_version < "3.13"

diff --git a/lib/galaxy/dependencies/pinned-lint-requirements.txt b/lib/galaxy/dependencies/pinned-lint-requirements.txt
@@ -4,4 +4,4 @@ flake8-bugbear==24.4.26
 mccabe==0.7.0
 pycodestyle==2.12.0
 pyflakes==3.2.0
-ruff==0.5.0
+ruff==0.5.1
diff --git a/lib/galaxy/dependencies/pinned-requirements.txt b/lib/galaxy/dependencies/pinned-requirements.txt
@@ -37,7 +37,7 @@ botocore==1.34.131 ; python_version >= "3.8" and python_version < "3.13"
 bx-python==0.12.0 ; python_version >= "3.8" and python_version < "3.13"
 cachecontrol[filecache]==0.14.0 ; python_version >= "3.8" and python_version < "3.13"
 celery==5.4.0 ; python_version >= "3.8" and python_version < "3.13"
-certifi==2024.6.2 ; python_version >= "3.8" and python_version < "3.13"
+certifi==2024.7.4 ; python_version >= "3.8" and python_version < "3.13"
 cffi==1.16.0 ; python_version >= "3.8" and python_version < "3.13"
 charset-normalizer==3.3.2 ; python_version >= "3.8" and python_version < "3.13"
 cheetah3==3.2.6.post1 ; python_version >= "3.8" and python_version < "3.13"
@@ -54,7 +54,7 @@ conda-package-streaming==0.10.0 ; python_version >= "3.8" and python_version < "
 cryptography==42.0.8 ; python_version >= "3.8" and python_version < "3.13"
 cwl-upgrader==1.2.11 ; python_version >= "3.8" and python_version < "3.13"
 cwl-utils==0.33 ; python_version >= "3.8" and python_version < "3.13"
-cwltool==3.1.20240508115724 ; python_version >= "3.8" and python_version < "3.13"
+cwltool==3.1.20240708091337 ; python_version >= "3.8" and python_version < "3.13"
 defusedxml==0.7.1 ; python_version >= "3.8" and python_version < "3.13"
 deprecation==2.1.0 ; python_version >= "3.8" and python_version < "3.13"
 dictobj==0.4 ; python_version >= "3.8" and python_version < "3.13"
@@ -64,7 +64,7 @@ docutils==0.20.1 ; python_version >= "3.8" and python_version < "3.13"
 dparse==0.6.3 ; python_version >= "3.8" and python_version < "3.13"
 edam-ontology==1.25.2 ; python_version >= "3.8" and python_version < "3.13"
 email-validator==2.2.0 ; python_version >= "3.8" and python_version < "3.13"
-exceptiongroup==1.2.1 ; python_version >= "3.8" and python_version < "3.11"
+exceptiongroup==1.2.2 ; python_version >= "3.8" and python_version < "3.11"
 fastapi-slim==0.111.0 ; python_version >= "3.8" and python_version < "3.13"
 filelock==3.15.4 ; python_version >= "3.8" and python_version < "3.13"
 frozenlist==1.4.1 ; python_version >= "3.8" and python_version < "3.13"
@@ -104,9 +104,9 @@ markdown-it-py==3.0.0 ; python_version >= "3.8" and python_version < "3.13"
 markdown==3.6 ; python_version >= "3.8" and python_version < "3.13"
 markupsafe==2.1.5 ; python_version >= "3.8" and python_version < "3.13"
 mdurl==0.1.2 ; python_version >= "3.8" and python_version < "3.13"
-mercurial==6.7.4 ; python_version >= "3.8" and python_version < "3.13"
+mercurial==6.8 ; python_version >= "3.8" and python_version < "3.13"
 mistune==3.0.2 ; python_version >= "3.8" and python_version < "3.13"
-mrcfile==1.5.0 ; python_version >= "3.8" and python_version < "3.13"
+mrcfile==1.5.1 ; python_version >= "3.8" and python_version < "3.13"
 msal==1.29.0 ; python_version >= "3.8" and python_version < "3.13"
 msgpack==1.0.8 ; python_version >= "3.8" and python_version < "3.13"
 multidict==6.0.5 ; python_version >= "3.8" and python_version < "3.13"
@@ -132,10 +132,10 @@ psutil==6.0.0 ; python_version >= "3.8" and python_version < "3.13"
 pulsar-galaxy-lib==0.15.6 ; python_version >= "3.8" and python_version < "3.13"
 pycparser==2.22 ; python_version >= "3.8" and python_version < "3.13"
 pycryptodome==3.20.0 ; python_version >= "3.8" and python_version < "3.13"
-pydantic-core==2.20.0 ; python_version >= "3.8" and python_version < "3.13"
+pydantic-core==2.20.1 ; python_version >= "3.8" and python_version < "3.13"
 pydantic-tes==0.1.5 ; python_version >= "3.8" and python_version < "3.13"
-pydantic==2.8.0 ; python_version >= "3.8" and python_version < "3.13"
-pydantic[email]==2.8.0 ; python_version >= "3.8" and python_version < "3.13"
+pydantic==2.8.2 ; python_version >= "3.8" and python_version < "3.13"
+pydantic[email]==2.8.2 ; python_version >= "3.8" and python_version < "3.13"
 pydot==2.0.0 ; python_version >= "3.8" and python_version < "3.13"
 pyeventsystem==0.1.0 ; python_version >= "3.8" and python_version < "3.13"
 pyfaidx==0.8.1.1 ; python_version >= "3.8" and python_version < "3.13"
@@ -167,13 +167,13 @@ requests==2.32.3 ; python_version >= "3.8" and python_version < "3.13"
 rich==13.7.1 ; python_version >= "3.8" and python_version < "3.13"
 rocrate==0.10.0 ; python_version >= "3.8" and python_version < "3.13"
 routes==2.5.1 ; python_version >= "3.8" and python_version < "3.13"
-rpds-py==0.18.1 ; python_version >= "3.8" and python_version < "3.13"
+rpds-py==0.19.0 ; python_version >= "3.8" and python_version < "3.13"
 ruamel-yaml-clib==0.2.8 ; platform_python_implementation == "CPython" and python_version < "3.13" and python_version >= "3.8"
 ruamel-yaml==0.18.6 ; python_version >= "3.8" and python_version < "3.13"
 s3fs==2024.6.1 ; python_version >= "3.8" and python_version < "3.13"
-schema-salad==8.5.20240503091721 ; python_version >= "3.8" and python_version < "3.13"
+schema-salad==8.6.20240710082410 ; python_version >= "3.8" and python_version < "3.13"
 setuptools-scm==5.0.2 ; python_version >= "3.8" and python_version < "3.13"
-setuptools==70.2.0 ; python_version >= "3.8" and python_version < "3.13"
+setuptools==70.3.0 ; python_version >= "3.8" and python_version < "3.13"
 shellescape==3.8.1 ; python_version >= "3.8" and python_version < "3.13"
 six==1.16.0 ; python_version >= "3.8" and python_version < "3.13"
 sniffio==1.3.1 ; python_version >= "3.8" and python_version < "3.13"
@@ -188,7 +188,7 @@ starlette-graphene3==0.6.0 ; python_version >= "3.8" and python_version < "3.13"
 starlette==0.37.2 ; python_version >= "3.8" and python_version < "3.13"
 supervisor==4.2.5 ; python_version >= "3.8" and python_version < "3.13"
 svgwrite==1.4.3 ; python_version >= "3.8" and python_version < "3.13"
-tenacity==8.4.2 ; python_version >= "3.8" and python_version < "3.13"
+tenacity==8.5.0 ; python_version >= "3.8" and python_version < "3.13"
 tifffile==2023.7.10 ; python_version >= "3.8" and python_version < "3.13"
 tinydb==4.8.0 ; python_version >= "3.8" and python_version < "3.13"
 tomli==2.0.1 ; python_version >= "3.8" and python_version < "3.11"

diff --git a/lib/galaxy/dependencies/pinned-typecheck-requirements.txt b/lib/galaxy/dependencies/pinned-typecheck-requirements.txt
@@ -1,24 +1,24 @@
 --extra-index-url https://wheels.galaxyproject.org/simple
 
 annotated-types==0.7.0 ; python_version >= "3.8" and python_version < "3.13"
-boto3-stubs[s3]==1.34.138 ; python_version >= "3.8" and python_version < "3.13"
-botocore-stubs==1.34.138 ; python_version >= "3.8" and python_version < "3.13"
+boto3-stubs[s3]==1.34.144 ; python_version >= "3.8" and python_version < "3.13"
+botocore-stubs==1.34.144 ; python_version >= "3.8" and python_version < "3.13"
 cffi==1.16.0 ; python_version >= "3.8" and python_version < "3.13" and platform_python_implementation != "PyPy"
 cryptography==42.0.8 ; python_version >= "3.8" and python_version < "3.13"
 lxml-stubs==0.5.1 ; python_version >= "3.8" and python_version < "3.13"
 mypy-boto3-s3==1.34.138 ; python_version >= "3.8" and python_version < "3.13"
 mypy-extensions==1.0.0 ; python_version >= "3.8" and python_version < "3.13"
 mypy==1.10.1 ; python_version >= "3.8" and python_version < "3.13"
 pycparser==2.22 ; python_version >= "3.8" and python_version < "3.13" and platform_python_implementation != "PyPy"
-pydantic-core==2.20.0 ; python_version >= "3.8" and python_version < "3.13"
-pydantic==2.8.0 ; python_version >= "3.8" and python_version < "3.13"
+pydantic-core==2.20.1 ; python_version >= "3.8" and python_version < "3.13"
+pydantic==2.8.2 ; python_version >= "3.8" and python_version < "3.13"
 tomli==2.0.1 ; python_version >= "3.8" and python_version < "3.11"
-types-awscrt==0.20.12 ; python_version >= "3.8" and python_version < "3.13"
+types-awscrt==0.21.0 ; python_version >= "3.8" and python_version < "3.13"
 types-bleach==6.1.0.20240331 ; python_version >= "3.8" and python_version < "3.13"
 types-boto==2.49.18.20240205 ; python_version >= "3.8" and python_version < "3.13"
 types-contextvars==2.4.7.3 ; python_version >= "3.8" and python_version < "3.13"
 types-dataclasses==0.6.6 ; python_version >= "3.8" and python_version < "3.13"
-types-docutils==0.21.0.20240423 ; python_version >= "3.8" and python_version < "3.13"
+types-docutils==0.21.0.20240711 ; python_version >= "3.8" and python_version < "3.13"
 types-html5lib==1.1.11.20240228 ; python_version >= "3.8" and python_version < "3.13"
 types-markdown==3.6.0.20240316 ; python_version >= "3.8" and python_version < "3.13"
 types-paramiko==3.4.0.20240423 ; python_version >= "3.8" and python_version < "3.13"