Merge pull request #17580 from galaxybot/dev_auto_update_dependencies

Update Python dependencies

lib/galaxy/datatypes/sequence.py

@@ -258,8 +258,8 @@ class Sequence(data.Text):
 
         # These two variables act as an accumulator for consecutive entire blocks that
         # can be copied verbatim (without decompressing)
-        start_chunk = int(-1)
-        end_chunk = int(-1)
+        start_chunk = -1
+        end_chunk = -1
         copy_chunk_cmd = "dd bs=1 skip=%s count=%s if=%s 2> /dev/null >> %s"
 
         while sequence_count > 0 and i < len(sections):

lib/galaxy/dependencies/dev-requirements.txt

@@ -11,8 +11,8 @@ babel==2.14.0 ; python_version >= "3.8" and python_version < "3.13"
 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"
 billiard==4.2.0 ; python_version >= "3.8" and python_version < "3.13"
-black==24.2.0 ; python_version >= "3.8" and python_version < "3.13"
-build==1.0.3 ; python_version >= "3.8" and python_version < "3.13"
+black==24.1.1 ; python_version >= "3.8" and python_version < "3.13"
+build==1.1.1 ; python_version >= "3.8" and python_version < "3.13"
 cachecontrol[filecache]==0.13.1 ; python_version >= "3.8" and python_version < "3.13"
 celery==5.3.6 ; python_version >= "3.8" and python_version < "3.13"
 certifi==2024.2.2 ; python_version >= "3.8" and python_version < "3.13"
@@ -27,15 +27,15 @@ colorama==0.4.6 ; python_version >= "3.8" and python_version < "3.13" and (sys_p
 contourpy==1.1.1 ; python_version >= "3.8" and python_version < "3.13"
 coverage[toml]==7.4.3 ; python_version >= "3.8" and python_version < "3.13"
 cryptography==42.0.5 ; python_version >= "3.8" and python_version < "3.13"
-cwltest==2.4.20240129145612 ; python_version >= "3.8" and python_version < "3.13"
+cwltest==2.5.20240304113812 ; python_version >= "3.8" and python_version < "3.13"
 cycler==0.12.1 ; python_version >= "3.8" and python_version < "3.13"
-darker==1.7.2 ; python_version >= "3.8" and python_version < "3.13"
+darker==1.7.3 ; python_version >= "3.8" and python_version < "3.13"
 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==0.18.1 ; python_version >= "3.8" and python_version < "3.13"
 exceptiongroup==1.2.0 ; python_version >= "3.8" and python_version < "3.11"
 filelock==3.13.1 ; python_version >= "3.8" and python_version < "3.13"
-fluent-logger==0.10.0 ; python_version >= "3.8" and python_version < "3.13"
+fluent-logger==0.11.0 ; python_version >= "3.8" and python_version < "3.13"
 fonttools==4.49.0 ; 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==0.1.7 ; python_version >= "3.8" and python_version < "3.13"
@@ -46,7 +46,7 @@ httpx==0.27.0 ; python_version >= "3.8" and python_version < "3.13"
 idna==3.6 ; python_version >= "3.8" and python_version < "3.13"
 imagesize==1.4.1 ; python_version >= "3.8" and python_version < "3.13"
 importlib-metadata==7.0.1 ; python_version >= "3.8" and python_version < "3.13"
-importlib-resources==6.1.1 ; python_version >= "3.8" and python_version < "3.10"
+importlib-resources==6.1.2 ; python_version >= "3.8" and python_version < "3.10"
 iniconfig==2.0.0 ; python_version >= "3.8" and python_version < "3.13"
 isodate==0.6.1 ; python_version >= "3.8" and python_version < "3.13"
 isort==5.13.2 ; python_version >= "3.8" and python_version < "3.13"
@@ -54,7 +54,7 @@ jaraco-classes==3.3.1 ; python_version >= "3.8" and python_version < "3.13"
 jeepney==0.8.0 ; python_version >= "3.8" and python_version < "3.13" and sys_platform == "linux"
 jinja2==3.1.3 ; python_version >= "3.8" and python_version < "3.13"
 junit-xml==1.9 ; python_version >= "3.8" and python_version < "3.13"
-keyring==24.3.0 ; python_version >= "3.8" and python_version < "3.13"
+keyring==24.3.1 ; python_version >= "3.8" and python_version < "3.13"
 kiwisolver==1.4.5 ; python_version >= "3.8" and python_version < "3.13"
 kombu==5.3.5 ; python_version >= "3.8" and python_version < "3.13"
 lxml==4.9.4 ; python_version >= "3.8" and python_version < "3.13"
@@ -68,7 +68,7 @@ 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"
 mistune==2.0.5 ; python_version >= "3.8" and python_version < "3.13"
 more-itertools==10.2.0 ; python_version >= "3.8" and python_version < "3.13"
-msgpack==1.0.7 ; 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"
 mypy-extensions==1.0.0 ; python_version >= "3.8" and python_version < "3.13"
 myst-parser==2.0.0 ; python_version >= "3.8" and python_version < "3.13"
@@ -80,7 +80,7 @@ packaging==23.2 ; python_version >= "3.8" and python_version < "3.13"
 pathspec==0.12.1 ; python_version >= "3.8" and python_version < "3.13"
 pillow==10.2.0 ; python_version >= "3.8" and python_version < "3.13"
 pkce==1.0.3 ; python_version >= "3.8" and python_version < "3.13"
-pkginfo==1.9.6 ; python_version >= "3.8" and python_version < "3.13"
+pkginfo==1.10.0 ; python_version >= "3.8" and python_version < "3.13"
 platformdirs==4.2.0 ; python_version >= "3.8" and python_version < "3.13"
 playwright==1.41.2 ; python_version >= "3.8" and python_version < "3.13"
 pluggy==1.4.0 ; python_version >= "3.8" and python_version < "3.13"
@@ -111,19 +111,19 @@ pytest-playwright==0.4.4 ; python_version >= "3.8" and python_version < "3.13"
 pytest-postgresql==5.1.0 ; 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"
-python-dateutil==2.8.2 ; 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==2.0.0 ; python_version >= "3.8" and python_version < "3.13"
 python-slugify==8.0.4 ; python_version >= "3.8" and python_version < "3.13"
 pytz==2024.1 ; python_version >= "3.8" and python_version < "3.9"
 pywin32-ctypes==0.2.2 ; python_version >= "3.8" and python_version < "3.13" and sys_platform == "win32"
 pyyaml==6.0.1 ; python_version >= "3.8" and python_version < "3.13"
 rdflib==6.3.2 ; python_version >= "3.8" and python_version < "3.13"
-readme-renderer==42.0 ; python_version >= "3.8" and python_version < "3.13"
+readme-renderer==43.0 ; python_version >= "3.8" and python_version < "3.13"
 requests-toolbelt==1.0.0 ; python_version >= "3.8" and python_version < "3.13"
 requests==2.31.0 ; python_version >= "3.8" and python_version < "3.13"
 responses==0.25.0 ; python_version >= "3.8" and python_version < "3.13"
 rfc3986==2.0.0 ; python_version >= "3.8" and python_version < "3.13"
-rich==13.7.0 ; python_version >= "3.8" and python_version < "3.13"
+rich==13.7.1 ; 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"
 schema-salad==8.5.20240102191335 ; python_version >= "3.8" and python_version < "3.13"
@@ -134,7 +134,7 @@ selenium==4.18.1 ; python_version >= "3.8" and python_version < "3.13"
 seletools==1.4.0 ; python_version >= "3.8" and python_version < "3.13"
 setuptools==69.1.1 ; python_version >= "3.8" and python_version < "3.13"
 six==1.16.0 ; python_version >= "3.8" and python_version < "3.13"
-sniffio==1.3.0 ; 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"
 sortedcontainers==2.4.0 ; python_version >= "3.8" and python_version < "3.13"
 sphinx-rtd-theme==1.3.0 ; python_version >= "3.8" and python_version < "3.13"
@@ -147,7 +147,7 @@ sphinxcontrib-jsmath==1.0.1 ; python_version >= "3.8" and python_version < "3.13
 sphinxcontrib-qthelp==1.0.3 ; python_version >= "3.8" and python_version < "3.13"
 sphinxcontrib-serializinghtml==1.1.5 ; python_version >= "3.8" and python_version < "3.13"
 statsd==4.0.1 ; python_version >= "3.8" and python_version < "3.13"
-testfixtures==8.0.0 ; python_version >= "3.8" and python_version < "3.13"
+testfixtures==8.1.0 ; python_version >= "3.8" and python_version < "3.13"
 text-unidecode==1.3 ; python_version >= "3.8" and python_version < "3.13"
 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"
@@ -157,7 +157,7 @@ trio==0.24.0 ; python_version >= "3.8" and python_version < "3.13"
 tuspy==1.0.3 ; python_version >= "3.8" and python_version < "3.13"
 twill==3.2.2 ; python_version >= "3.8" and python_version < "3.13"
 twine==5.0.0 ; python_version >= "3.8" and python_version < "3.13"
-typing-extensions==4.9.0 ; python_version >= "3.8" and python_version < "3.13"
+typing-extensions==4.10.0 ; python_version >= "3.8" and python_version < "3.13"
 tzdata==2024.1 ; python_version >= "3.8" and python_version < "3.13"
 urllib3==1.26.18 ; python_version >= "3.8" and python_version < "3.13"
 urllib3[socks]==1.26.18 ; python_version >= "3.8" and python_version < "3.13"

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

@@ -4,4 +4,4 @@ flake8-bugbear==24.2.6
 mccabe==0.7.0
 pycodestyle==2.11.1
 pyflakes==3.2.0
-ruff==0.2.2
+ruff==0.3.0

lib/galaxy/dependencies/pinned-requirements.txt

@@ -2,7 +2,7 @@
 
 a2wsgi==1.10.2 ; python_version >= "3.8" and python_version < "3.13"
 adal==1.2.7 ; python_version >= "3.8" and python_version < "3.13"
-aiobotocore==2.11.2 ; python_version >= "3.8" and python_version < "3.13"
+aiobotocore==2.12.0 ; python_version >= "3.8" and python_version < "3.13"
 aiodataloader==0.4.0 ; python_version >= "3.8" and python_version < "3.13"
 aiofiles==23.2.1 ; python_version >= "3.8" and python_version < "3.13"
 aiohttp==3.9.3 ; python_version >= "3.8" and python_version < "3.13"
@@ -13,7 +13,7 @@ amqp==5.2.0 ; python_version >= "3.8" and python_version < "3.13"
 aniso8601==9.0.1 ; python_version >= "3.8" and python_version < "3.13"
 annotated-types==0.6.0 ; python_version >= "3.8" and python_version < "3.13"
 anyio==4.3.0 ; python_version >= "3.8" and python_version < "3.13"
-apispec==6.4.0 ; python_version >= "3.8" and python_version < "3.13"
+apispec==6.5.0 ; python_version >= "3.8" and python_version < "3.13"
 appdirs==1.4.4 ; python_version >= "3.8" and python_version < "3.13"
 arcp==0.2.1 ; python_version >= "3.8" and python_version < "3.13"
 argcomplete==3.2.2 ; python_version >= "3.8" and python_version < "3.13"
@@ -33,7 +33,7 @@ bioblend==1.2.0 ; python_version >= "3.8" and python_version < "3.13"
 bleach==6.1.0 ; python_version >= "3.8" and python_version < "3.13"
 boltons==23.1.1 ; python_version >= "3.8" and python_version < "3.13"
 boto==2.49.0 ; python_version >= "3.8" and python_version < "3.13"
-botocore==1.34.34 ; python_version >= "3.8" and python_version < "3.13"
+botocore==1.34.51 ; python_version >= "3.8" and python_version < "3.13"
 bx-python==0.11.0 ; python_version >= "3.8" and python_version < "3.13"
 cachecontrol[filecache]==0.13.1 ; python_version >= "3.8" and python_version < "3.13"
 celery==5.3.6 ; python_version >= "3.8" and python_version < "3.13"
@@ -65,7 +65,7 @@ docutils==0.18.1 ; python_version >= "3.8" and python_version < "3.13"
 dparse==0.6.3 ; python_version >= "3.8" and python_version < "3.13"
 ecdsa==0.18.0 ; 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==2.1.0.post1 ; python_version >= "3.8" and python_version < "3.13"
+email-validator==2.1.1 ; python_version >= "3.8" and python_version < "3.13"
 exceptiongroup==1.2.0 ; python_version >= "3.8" and python_version < "3.11"
 fastapi==0.110.0 ; python_version >= "3.8" and python_version < "3.13"
 filelock==3.13.1 ; python_version >= "3.8" and python_version < "3.13"
@@ -89,7 +89,7 @@ h5py==3.10.0 ; python_version >= "3.8" and python_version < "3.13"
 humanfriendly==10.0 ; python_version >= "3.8" and python_version < "3.13"
 idna==3.6 ; python_version >= "3.8" and python_version < "3.13"
 importlib-metadata==7.0.1 ; python_version >= "3.8" and python_version < "3.13"
-importlib-resources==6.1.1 ; python_version >= "3.8" and python_version < "3.9"
+importlib-resources==6.1.2 ; python_version >= "3.8" and python_version < "3.9"
 isa-rwval==0.10.10 ; python_version >= "3.8" and python_version < "3.13"
 isal==1.6.0 ; python_version >= "3.8" and python_version < "3.13"
 isodate==0.6.1 ; python_version >= "3.8" and python_version < "3.13"
@@ -110,7 +110,7 @@ mercurial==6.6.3 ; python_version >= "3.8" and python_version < "3.13"
 mistune==2.0.5 ; python_version >= "3.8" and python_version < "3.13"
 mrcfile==1.5.0 ; python_version >= "3.8" and python_version < "3.13"
 msal==1.27.0 ; python_version >= "3.8" and python_version < "3.13"
-msgpack==1.0.7 ; 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"
 mypy-extensions==1.0.0 ; python_version >= "3.8" and python_version < "3.13"
 networkx==2.5 ; python_version >= "3.8" and python_version < "3.13"
@@ -151,7 +151,7 @@ pynacl==1.5.0 ; python_version >= "3.8" and python_version < "3.13"
 pyparsing==3.1.1 ; python_version >= "3.8" and python_version < "3.13"
 pyreadline3==3.4.1 ; sys_platform == "win32" and python_version >= "3.8" and python_version < "3.13"
 pysam==0.22.0 ; python_version >= "3.8" and python_version < "3.13"
-python-dateutil==2.8.2 ; 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-jose==3.3.0 ; python_version >= "3.8" and python_version < "3.13"
 python-magic==0.4.27 ; python_version >= "3.8" and python_version < "3.13"
 python-multipart==0.0.9 ; python_version >= "3.8" and python_version < "3.13"
@@ -168,7 +168,7 @@ requests-oauthlib==1.3.1 ; python_version >= "3.8" and python_version < "3.13"
 requests-toolbelt==1.0.0 ; python_version >= "3.8" and python_version < "3.13"
 requests-unixsocket==0.3.0 ; python_version >= "3.8" and python_version < "3.13"
 requests==2.31.0 ; python_version >= "3.8" and python_version < "3.13"
-rich==13.7.0 ; python_version >= "3.8" and python_version < "3.13"
+rich==13.7.1 ; python_version >= "3.8" and python_version < "3.13"
 rocrate==0.9.0 ; python_version >= "3.8" and python_version < "3.13"
 routes==2.5.1 ; python_version >= "3.8" and python_version < "3.13"
 rpds-py==0.18.0 ; python_version >= "3.8" and python_version < "3.13"
@@ -181,7 +181,7 @@ setuptools-scm==5.0.2 ; python_version >= "3.8" and python_version < "3.13"
 setuptools==69.1.1 ; 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==1.3.0 ; python_version >= "3.8" and python_version < "3.13"
+sniffio==1.3.1 ; python_version >= "3.8" and python_version < "3.13"
 social-auth-core[openidconnect]==4.0.3 ; python_version >= "3.8" and python_version < "3.13"
 sortedcontainers==2.4.0 ; python_version >= "3.8" and python_version < "3.13"
 spython==0.3.13 ; python_version >= "3.8" and python_version < "3.13"
@@ -201,7 +201,7 @@ tornado==6.4 ; python_version >= "3.8" and python_version < "3.13"
 tqdm==4.66.2 ; python_version >= "3.8" and python_version < "3.13"
 tuspy==1.0.3 ; python_version >= "3.8" and python_version < "3.13"
 tuswsgi==0.5.5 ; python_version >= "3.8" and python_version < "3.13"
-typing-extensions==4.9.0 ; python_version >= "3.8" and python_version < "3.13"
+typing-extensions==4.10.0 ; python_version >= "3.8" and python_version < "3.13"
 tzdata==2024.1 ; python_version >= "3.8" and python_version < "3.13"
 tzlocal==5.2 ; python_version >= "3.8" and python_version < "3.13"
 ubiquerg==0.7.0 ; python_version >= "3.8" and python_version < "3.13"

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

@@ -12,14 +12,14 @@ types-bleach==6.1.0.20240222 ; python_version >= "3.8" and python_version < "3.1
 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==0.20.0.20240201 ; python_version >= "3.8" and python_version < "3.13"
-types-html5lib==1.1.11.20240222 ; python_version >= "3.8" and python_version < "3.13"
+types-docutils==0.20.0.20240304 ; 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==3.5.0.20240129 ; python_version >= "3.8" and python_version < "3.13"
 types-paramiko==3.4.0.20240205 ; python_version >= "3.8" and python_version < "3.13"
 types-pkg-resources==0.1.3 ; python_version >= "3.8" and python_version < "3.13"
 types-python-dateutil==2.8.19.20240106 ; python_version >= "3.8" and python_version < "3.13"
 types-pyyaml==6.0.12.12 ; python_version >= "3.8" and python_version < "3.13"
 types-requests==2.31.0.6 ; python_version >= "3.8" and python_version < "3.13"
-types-six==1.16.21.20240106 ; python_version >= "3.8" and python_version < "3.13"
+types-six==1.16.21.20240301 ; python_version >= "3.8" and python_version < "3.13"
 types-urllib3==1.26.25.14 ; python_version >= "3.8" and python_version < "3.13"
-typing-extensions==4.9.0 ; python_version >= "3.8" and python_version < "3.13"
+typing-extensions==4.10.0 ; python_version >= "3.8" and python_version < "3.13"

packages/util/setup.cfg

@@ -51,7 +51,7 @@ python_requires = >=3.7
 jstree =
     dictobj
 template =
-    Cheetah3!=3.2.6.post2
+    Cheetah3
     future>=1.0.0
 
 [options.packages.find]

packages/web_apps/setup.cfg

@@ -42,7 +42,7 @@ install_requires =
     a2wsgi
     apispec
     Babel
-    Cheetah3!=3.2.6.post2
+    Cheetah3
     fastapi>=0.101.0
     gunicorn
     gxformat2

pyproject.toml

@@ -46,7 +46,7 @@ boltons = "*"
 boto = "*"
 bx-python = "*"
 celery = "*"
-Cheetah3 = "!=3.2.6.post2"  # yanked release, https://github.com/python-poetry/poetry/issues/2453
+Cheetah3 = "*"
 cloudauthz = "==0.6.0"
 cloudbridge = "*"
 circus = "*"
@@ -88,7 +88,7 @@ pebble = "*"
 psutil = "*"
 pulsar-galaxy-lib = ">=0.15.0.dev0"
 pycryptodome = "*"
-pydantic = {version = ">=2, !=2.6.0, !=2.6.1, !=2.6.2", extras = ["email"]}  # https://github.com/pydantic/pydantic/issues/8760
+pydantic = {version = ">=2, !=2.6.0, !=2.6.1, !=2.6.2, !=2.6.3", extras = ["email"]}  # https://github.com/pydantic/pydantic/issues/8760
 PyJWT = "*"
 pykwalify = "*"
 pylibmagic = "*"

tox.ini

@@ -16,7 +16,7 @@ skipsdist = True
 [testenv]
 commands =
     first_startup: bash .ci/first_startup.sh
-    lint: ruff .
+    lint: ruff check .
     # Once we are happy to replace flake8 with ruff, we can replace the next line with `black --check --diff`
     # (since ruff delegates to black for checking/fixing many rules).
     lint: bash .ci/flake8_wrapper.sh