Merge pull request #19123 from galaxybot/dev_auto_update_dependencies

Update Python dependencies

lib/galaxy/dependencies/dev-requirements.txt

@@ -16,7 +16,7 @@ black==24.8.0
 boto3==1.35.36
 botocore==1.35.36
 build==1.2.2.post1
-cachecontrol==0.14.0
+cachecontrol==0.14.1
 certifi==2024.8.30
 cffi==1.17.1
 charset-normalizer==3.4.0
@@ -83,10 +83,10 @@ myst-parser==3.0.1
 nh3==0.2.18
 numpy==1.24.4 ; python_full_version < '3.9'
 numpy==2.0.2 ; python_full_version == '3.9.*'
-numpy==2.1.2 ; python_full_version >= '3.10'
+numpy==2.1.3 ; python_full_version >= '3.10'
 onedatafilerestclient==21.2.5.2
 outcome==1.3.0.post0
-packaging==24.1
+packaging==24.2
 pathspec==0.12.1
 pbr==6.1.0 ; python_full_version >= '3.9'
 pillow==10.4.0
@@ -103,7 +103,7 @@ psutil==6.1.0 ; sys_platform != 'cygwin'
 psycopg==3.2.3
 pycparser==2.22
 pyee==12.0.0
-pygithub==2.4.0
+pygithub==2.5.0
 pygments==2.18.0
 pyjwt==2.9.0
 pynacl==1.5.0
@@ -135,20 +135,20 @@ requests==2.32.3
 requests-toolbelt==1.0.0
 responses==0.25.3
 rfc3986==2.0.0
-rich==13.9.3
-rpds-py==0.20.0 ; python_full_version >= '3.9'
+rich==13.9.4
+rpds-py==0.20.1 ; python_full_version >= '3.9'
 ruamel-yaml==0.18.6
 ruamel-yaml-clib==0.2.8 ; python_full_version < '3.13' and platform_python_implementation == 'CPython'
-rucio-clients==35.4.1 ; python_full_version >= '3.9'
+rucio-clients==35.5.0 ; python_full_version >= '3.9'
 s3transfer==0.10.3
 schema-salad==8.7.20241010092723
 scipy==1.10.1 ; python_full_version < '3.9'
 scipy==1.13.1 ; python_full_version == '3.9.*'
 scipy==1.14.1 ; python_full_version >= '3.10'
 secretstorage==3.3.3 ; sys_platform == 'linux'
-selenium==4.25.0
+selenium==4.26.1
 seletools==1.5.0
-setuptools==75.2.0
+setuptools==75.3.0
 six==1.16.0
 sniffio==1.3.1
 snowballstemmer==2.2.0

lib/galaxy/dependencies/pinned-lint-requirements.txt

@@ -1,7 +1,7 @@
 attrs==24.2.0
 flake8==7.1.1
-flake8-bugbear==24.8.19
+flake8-bugbear==24.10.31
 mccabe==0.7.0
 pycodestyle==2.12.1
 pyflakes==3.2.0
-ruff==0.7.1
+ruff==0.7.3

lib/galaxy/dependencies/pinned-requirements.txt

@@ -9,7 +9,7 @@ aiohappyeyeballs==2.4.3
 aiohttp==3.10.10
 aioitertools==0.12.0
 aiosignal==1.3.1
-alembic==1.13.3
+alembic==1.14.0
 amqp==5.2.0
 annotated-types==0.7.0
 anyio==4.5.2
@@ -28,13 +28,13 @@ bcrypt==4.2.0
 bdbag==1.7.3
 beaker==1.13.0
 billiard==4.2.1
-bioblend==1.3.0
+bioblend==1.4.0
 bleach==6.1.0
-boltons==24.0.0
+boltons==24.1.0
 boto==2.49.0
 botocore==1.35.36
 bx-python==0.13.0
-cachecontrol==0.14.0
+cachecontrol==0.14.1
 celery==5.4.0
 certifi==2024.8.30
 cffi==1.17.1
@@ -60,7 +60,7 @@ dictobj==0.4
 dnspython==2.6.1
 docopt==0.6.2
 docutils==0.20.1
-dparse==0.6.3
+dparse==0.6.4
 edam-ontology==1.25.2
 email-validator==2.2.0
 exceptiongroup==1.2.2 ; python_full_version < '3.11'
@@ -72,7 +72,7 @@ fs==2.4.16
 fsspec==2024.10.0
 future==1.0.0
 galaxy2cwl==0.1.4
-graphene==3.4.1
+graphene==3.4.3
 graphene-sqlalchemy==3.0.0rc1
 graphql-core==3.2.5
 graphql-relay==3.2.0
@@ -116,11 +116,11 @@ networkx==3.1
 nodeenv==1.9.1
 numpy==1.24.4 ; python_full_version < '3.9'
 numpy==2.0.2 ; python_full_version == '3.9.*'
-numpy==2.1.2 ; python_full_version >= '3.10'
+numpy==2.1.3 ; python_full_version >= '3.10'
 oauthlib==3.2.2
-orjson==3.10.10
+orjson==3.10.11
 oyaml==1.0
-packaging==24.1
+packaging==24.2
 paramiko==3.5.0
 parsley==1.3
 paste==3.10.1
@@ -152,29 +152,30 @@ pyreadline3==3.5.4 ; sys_platform == 'win32'
 pysam==0.22.1
 python-dateutil==2.9.0.post0
 python-magic==0.4.27
-python-multipart==0.0.16
+python-multipart==0.0.17
+python-slugify==8.0.4
 python3-openid==3.2.0
 pytz==2024.2
 pyyaml==6.0.2
 pyzmq==26.2.0
 rdflib==6.3.2
 referencing==0.35.1
 refgenconf==0.12.2
-regex==2024.9.11
+regex==2024.11.6
 repoze-lru==0.7
 requests==2.32.3
 requests-oauthlib==2.0.0
 requests-toolbelt==1.0.0
 requests-unixsocket==0.3.0
-rich==13.9.3
+rich==13.9.4
 rocrate==0.11.0
 routes==2.5.1
-rpds-py==0.20.0
+rpds-py==0.20.1
 ruamel-yaml==0.18.6
 ruamel-yaml-clib==0.2.8 ; python_full_version < '3.13' and platform_python_implementation == 'CPython'
 s3fs==2024.10.0
 schema-salad==8.7.20241010092723
-setuptools==75.2.0
+setuptools==75.3.0
 setuptools-scm==5.0.2
 six==1.16.0
 sniffio==1.3.1
@@ -190,11 +191,12 @@ starlette-graphene3==0.6.0
 supervisor==4.2.5
 svgwrite==1.4.3
 tenacity==9.0.0
+text-unidecode==1.3
 tifffile==2023.7.10
 tinydb==4.8.2
 tomli==2.0.2 ; python_full_version < '3.11'
 tornado==6.4.1
-tqdm==4.66.6
+tqdm==4.67.0
 tuspy==1.0.3
 tuswsgi==0.5.5
 typing-extensions==4.12.2

lib/galaxy/dependencies/pinned-typecheck-requirements.txt

@@ -1,8 +1,8 @@
 # This file was autogenerated by uv via the following command:
 #    uv export --frozen --no-hashes --only-group=typecheck
 annotated-types==0.7.0
-boto3-stubs==1.35.49
-botocore-stubs==1.35.49
+boto3-stubs==1.35.57
+botocore-stubs==1.35.57
 cffi==1.17.1 ; platform_python_implementation != 'PyPy'
 cryptography==43.0.3
 lxml-stubs==0.5.1
@@ -27,7 +27,7 @@ types-python-slugify==8.0.2.20240310
 types-pyyaml==6.0.12.20240917
 types-requests==2.31.0.6
 types-s3transfer==0.10.3
-types-setuptools==75.2.0.20241025
-types-six==1.16.21.20241009
+types-setuptools==75.3.0.20241107
+types-six==1.16.21.20241105
 types-urllib3==1.26.25.14
 typing-extensions==4.12.2

pyproject.toml

@@ -149,6 +149,7 @@ dev = [
     "pytest-shard",
     "responses",
     "rucio-clients>=33.6.0 ; python_version>='3.9'",  # https://github.com/galaxyproject/galaxy/pull/17156
+    "scipy>=1.14.1; python_version>='3.10'",  # ase dependency, Python 3.13 support
     "selenium",
     "seletools",
     "Sphinx>=4.0",  # support docutils 0.17