Merge pull request galaxyproject#17486 from galaxybot/dev_auto_update…

…_dependencies

Update Python dependencies

lib/galaxy/dependencies/dev-requirements.txt

@@ -2,7 +2,7 @@ aiohttp==3.9.3 ; python_version >= "3.8" and python_version < "3.13"
 aiosignal==1.3.1 ; python_version >= "3.8" and python_version < "3.13"
 alabaster==0.7.13 ; python_version >= "3.8" and python_version < "3.13"
 amqp==5.2.0 ; python_version >= "3.8" and python_version < "3.13"
-anyio==4.2.0 ; python_version >= "3.8" and python_version < "3.13"
+anyio==4.3.0 ; python_version >= "3.8" and python_version < "3.13"
 ase==3.22.1 ; python_version >= "3.8" and python_version < "3.13"
 async-timeout==4.0.3 ; python_version >= "3.8" and python_version < "3.11"
 attrs==23.2.0 ; python_version >= "3.8" and python_version < "3.13"
@@ -25,8 +25,8 @@ click==8.1.7 ; python_version >= "3.8" and python_version < "3.13"
 codespell==2.2.6 ; 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 < "3.13"
-coverage[toml]==7.4.1 ; python_version >= "3.8" and python_version < "3.13"
-cryptography==42.0.2 ; python_version >= "3.8" and python_version < "3.13"
+coverage[toml]==7.4.2 ; python_version >= "3.8" and python_version < "3.13"
+cryptography==42.0.4 ; python_version >= "3.8" and python_version < "3.13"
 cwltest==2.4.20240129145612 ; 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"
@@ -36,13 +36,13 @@ 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"
-fonttools==4.48.1 ; 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==0.1.5 ; python_version >= "3.8" and python_version < "3.13"
+galaxy-release-util==0.1.7 ; python_version >= "3.8" and python_version < "3.13"
 greenlet==3.0.3 ; python_version >= "3.8" and python_version < "3.13"
 h11==0.14.0 ; python_version >= "3.8" and python_version < "3.13"
-httpcore==1.0.2 ; python_version >= "3.8" and python_version < "3.13"
-httpx==0.26.0 ; python_version >= "3.8" and python_version < "3.13"
+httpcore==1.0.4 ; python_version >= "3.8" and python_version < "3.13"
+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"
@@ -61,8 +61,8 @@ lxml==4.9.4 ; python_version >= "3.8" and python_version < "3.13"
 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==3.7.4 ; python_version >= "3.8" and python_version < "3.9"
-matplotlib==3.8.2 ; python_version >= "3.9" and python_version < "3.13"
+matplotlib==3.7.5 ; python_version >= "3.8" and python_version < "3.9"
+matplotlib==3.8.3 ; python_version >= "3.9" and python_version < "3.13"
 mdit-py-plugins==0.4.0 ; 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"
@@ -85,7 +85,7 @@ 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"
 port-for==0.7.2 ; python_version >= "3.8" and python_version < "3.13"
-prettytable==3.9.0 ; python_version >= "3.8" and python_version < "3.13"
+prettytable==3.10.0 ; python_version >= "3.8" and python_version < "3.13"
 prompt-toolkit==3.0.43 ; python_version >= "3.8" and python_version < "3.13"
 psutil==5.9.8 ; python_version >= "3.8" and python_version < "3.13" and sys_platform != "cygwin"
 psycopg==3.1.18 ; python_version >= "3.8" and python_version < "3.13"
@@ -130,7 +130,7 @@ schema-salad==8.5.20240102191335 ; python_version >= "3.8" and python_version <
 scipy==1.10.1 ; python_version >= "3.8" and python_version < "3.9"
 scipy==1.12.0 ; python_version >= "3.9" and python_version < "3.13"
 secretstorage==3.3.3 ; python_version >= "3.8" and python_version < "3.13" and sys_platform == "linux"
-selenium==4.17.2 ; python_version >= "3.8" and python_version < "3.13"
+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==69.1.0 ; python_version >= "3.8" and python_version < "3.13"
 six==1.16.0 ; 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==7.2.2 ; python_version >= "3.8" and python_version < "3.13"
+testfixtures==8.0.0 ; 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"

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==0.2.1
+ruff==0.2.2

lib/galaxy/dependencies/pinned-requirements.txt

@@ -1,4 +1,4 @@
-a2wsgi==1.10.0 ; python_version >= "3.8" and python_version < "3.13"
+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"
 aiodataloader==0.4.0 ; python_version >= "3.8" and python_version < "3.13"
@@ -10,7 +10,7 @@ alembic==1.13.1 ; python_version >= "3.8" and python_version < "3.13"
 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==4.2.0 ; 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"
 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"
@@ -49,15 +49,15 @@ cloudbridge==3.2.0 ; python_version >= "3.8" and python_version < "3.13"
 colorama==0.4.6 ; python_version >= "3.8" and python_version < "3.13" and platform_system == "Windows"
 coloredlogs==15.0.1 ; python_version >= "3.8" and python_version < "3.13"
 conda-package-streaming==0.9.0 ; python_version >= "3.8" and python_version < "3.13"
-cryptography==42.0.2 ; python_version >= "3.8" and python_version < "3.13"
+cryptography==42.0.4 ; 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==0.32 ; python_version >= "3.8" and python_version < "3.13"
 cwltool==3.1.20240112164112 ; python_version >= "3.8" and python_version < "3.13"
 decorator==5.1.1 ; 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"
-dnspython==2.5.0 ; python_version >= "3.8" and python_version < "3.13"
+dnspython==2.6.1 ; python_version >= "3.8" and python_version < "3.13"
 docopt==0.6.2 ; python_version >= "3.8" and python_version < "3.13"
 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"
@@ -70,7 +70,7 @@ filelock==3.13.1 ; python_version >= "3.8" and python_version < "3.13"
 frozenlist==1.4.1 ; python_version >= "3.8" and python_version < "3.13"
 fs==2.4.16 ; python_version >= "3.8" and python_version < "3.13"
 fsspec==2023.12.2 ; python_version >= "3.8" and python_version < "3.13"
-future @ git+https://github.com/nsoranzo/python-future.git@9ef05b386ce45dd40d2dab5915aec3ed78d81ed9 ; python_version >= "3.8" and python_version < "3.13"
+future==1.0.0 ; python_version >= "3.8" and python_version < "3.13"
 galaxy-sequence-utils==1.1.5 ; python_version >= "3.8" and python_version < "3.13"
 galaxy2cwl==0.1.4 ; python_version >= "3.8" and python_version < "3.13"
 graphene-sqlalchemy==3.0.0rc1 ; python_version >= "3.8" and python_version < "3.13"
@@ -89,7 +89,7 @@ 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"
 isa-rwval==0.10.10 ; python_version >= "3.8" and python_version < "3.13"
-isal==1.5.3 ; 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"
 jinja2==3.1.3 ; python_version >= "3.8" and python_version < "3.13"
 jmespath==1.0.1 ; python_version >= "3.8" and python_version < "3.13"
@@ -116,7 +116,7 @@ nodeenv==1.8.0 ; python_version >= "3.8" and python_version < "3.13"
 numpy==1.24.4 ; python_version >= "3.8" and python_version < "3.9"
 numpy==1.26.4 ; python_version >= "3.9" and python_version < "3.13"
 oauthlib==3.2.2 ; python_version >= "3.8" and python_version < "3.13"
-orjson==3.9.13 ; python_version >= "3.8" and python_version < "3.13"
+orjson==3.9.14 ; python_version >= "3.8" and python_version < "3.13"
 oyaml==1.0 ; python_version >= "3.8" and python_version < "3.13"
 packaging==23.2 ; python_version >= "3.8" and python_version < "3.13"
 paramiko==3.4.0 ; python_version >= "3.8" and python_version < "3.13"
@@ -169,7 +169,7 @@ 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"
 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==0.17.1 ; python_version >= "3.8" and python_version < "3.13"
+rpds-py==0.18.0 ; python_version >= "3.8" and python_version < "3.13"
 rsa==4.9 ; 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"

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

@@ -1,18 +1,19 @@
 annotated-types==0.6.0 ; 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==42.0.2 ; python_version >= "3.8" and python_version < "3.13"
+cryptography==42.0.4 ; python_version >= "3.8" and python_version < "3.13"
 lxml-stubs==0.5.1 ; python_version >= "3.8" and python_version < "3.13"
 mypy-extensions==1.0.0 ; python_version >= "3.8" and python_version < "3.13"
 mypy==1.8.0 ; python_version >= "3.8" and python_version < "3.13"
 pycparser==2.21 ; python_version >= "3.8" and python_version < "3.13" and platform_python_implementation != "PyPy"
 pydantic-core==2.14.6 ; python_version >= "3.8" and python_version < "3.13"
 pydantic==2.5.3 ; python_version >= "3.8" and python_version < "3.13"
 tomli==2.0.1 ; python_version >= "3.8" and python_version < "3.11"
-types-bleach==6.1.0.1 ; python_version >= "3.8" and python_version < "3.13"
+types-bleach==6.1.0.20240222 ; 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==0.20.0.20240201 ; 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-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"

packages/util/setup.cfg

@@ -52,7 +52,7 @@ jstree =
     dictobj
 template =
     Cheetah3!=3.2.6.post2
-    future @ git+https://github.com/nsoranzo/python-future.git@python312-imp-module_past
+    future>=1.0.0
 
 [options.packages.find]
 exclude =

pyproject.toml

@@ -59,7 +59,7 @@ dparse = "*"
 edam-ontology = "*"
 fastapi = ">=0.108"
 fs = "*"
-future = { git = "https://github.com/nsoranzo/python-future.git", branch = "python312-imp-module_past" }
+future = ">=1.0.0"  # Python 3.12 support
 galaxy_sequence_utils = "*"
 graphene-sqlalchemy = "3.0.0rc1"  # need a beta release to be compat. with starlette plugin
 gravity = ">=1.0.4"