Merge pull request #16389 from galaxybot/dev_auto_update_dependencies

Update Python dependencies

lib/galaxy/dependencies/dev-requirements.txt

@@ -2,7 +2,7 @@ aiohttp==3.8.4 ; python_version >= "3.7" and python_version < "3.12"
 aiosignal==1.3.1 ; python_version >= "3.7" and python_version < "3.12"
 alabaster==0.7.13 ; python_version >= "3.7" and python_version < "3.12"
 amqp==5.1.1 ; python_version >= "3.7" and python_version < "3.12"
-anyio==3.7.0 ; python_version >= "3.7" and python_version < "3.12"
+anyio==3.7.1 ; python_version >= "3.7" and python_version < "3.12"
 ase==3.22.1 ; python_version >= "3.7" and python_version < "3.12"
 async-timeout==4.0.2 ; python_version >= "3.7" and python_version < "3.12"
 asynctest==0.13.0 ; python_version >= "3.7" and python_version < "3.8"
@@ -18,15 +18,15 @@ cached-property==1.5.2 ; python_version >= "3.7" and python_version < "3.8"
 celery==5.2.7 ; python_version >= "3.7" and python_version < "3.12"
 certifi==2023.5.7 ; python_version >= "3.7" and python_version < "3.12"
 cffi==1.15.1 ; python_version >= "3.7" and python_version < "3.12"
-charset-normalizer==3.1.0 ; python_version >= "3.7" and python_version < "3.12"
+charset-normalizer==3.2.0 ; python_version >= "3.7" and python_version < "3.12"
 click-didyoumean==0.3.0 ; python_version >= "3.7" and python_version < "3.12"
 click-plugins==1.1.1 ; python_version >= "3.7" and python_version < "3.12"
 click-repl==0.3.0 ; python_version >= "3.7" and python_version < "3.12"
-click==8.1.3 ; python_version >= "3.7" and python_version < "3.12"
+click==8.1.4 ; python_version >= "3.7" and python_version < "3.12"
 codespell==2.2.5 ; python_version >= "3.7" and python_version < "3.12"
 colorama==0.4.6 ; python_version >= "3.7" and python_version < "3.12" and (sys_platform == "win32" or platform_system == "Windows" or os_name == "nt")
 coverage[toml]==7.2.7 ; python_version >= "3.7" and python_version < "3.12"
-cryptography==41.0.1 ; python_version >= "3.7" and python_version < "3.12" and sys_platform == "linux"
+cryptography==41.0.2 ; python_version >= "3.7" and python_version < "3.12" and sys_platform == "linux"
 cwltest==2.3.20230527113600 ; python_version >= "3.7" and python_version < "3.12"
 cycler==0.11.0 ; python_version >= "3.7" and python_version < "3.12"
 darker==1.7.1 ; python_version >= "3.7" and python_version < "3.12"
@@ -41,7 +41,7 @@ frozenlist==1.3.3 ; python_version >= "3.7" and python_version < "3.12"
 future==0.18.3 ; python_version >= "3.7" and python_version < "3.12"
 galaxy-release-util==0.1.4 ; python_version >= "3.7" and python_version < "3.12"
 h11==0.14.0 ; python_version >= "3.7" and python_version < "3.12"
-httpcore==0.17.2 ; python_version >= "3.7" and python_version < "3.12"
+httpcore==0.17.3 ; python_version >= "3.7" and python_version < "3.12"
 httpx==0.24.1 ; python_version >= "3.7" and python_version < "3.12"
 idna==3.4 ; python_version >= "3.7" and python_version < "3.12"
 imagesize==1.4.1 ; python_version >= "3.7" and python_version < "3.12"
@@ -57,12 +57,12 @@ junit-xml==1.9 ; python_version >= "3.7" and python_version < "3.12"
 keyring==24.1.1 ; python_version >= "3.7" and python_version < "3.12"
 kiwisolver==1.4.4 ; python_version >= "3.7" and python_version < "3.12"
 kombu==5.2.4 ; python_version >= "3.7" and python_version < "3.12"
-lxml==4.9.2 ; python_version >= "3.7" and python_version < "3.12"
+lxml==4.9.3 ; python_version >= "3.7" and python_version < "3.12"
 markdown-it-py==2.2.0 ; python_version >= "3.7" and python_version < "3.12"
 markdown-it-reporter==0.0.2 ; python_version >= "3.7" and python_version < "3.12"
 markupsafe==2.1.3 ; python_version >= "3.7" and python_version < "3.12"
 matplotlib==3.5.3 ; python_version >= "3.7" and python_version < "3.8"
-matplotlib==3.7.1 ; python_version >= "3.8" and python_version < "3.12"
+matplotlib==3.7.2 ; python_version >= "3.8" and python_version < "3.12"
 mdit-py-plugins==0.3.5 ; python_version >= "3.7" and python_version < "3.12"
 mdurl==0.1.2 ; python_version >= "3.7" and python_version < "3.12"
 mirakuru==2.5.1 ; python_version >= "3.7" and python_version < "3.12"
@@ -74,14 +74,14 @@ mypy-extensions==1.0.0 ; python_version >= "3.7" and python_version < "3.12"
 myst-parser==1.0.0 ; python_version >= "3.7" and python_version < "3.12"
 numpy==1.21.6 ; python_version >= "3.7" and python_version < "3.8"
 numpy==1.24.4 ; python_version >= "3.8" and python_version < "3.9"
-numpy==1.25.0 ; python_version >= "3.9" and python_version < "3.12"
+numpy==1.25.1 ; python_version >= "3.9" and python_version < "3.12"
 outcome==1.2.0 ; python_version >= "3.7" and python_version < "3.12"
 packaging==23.1 ; python_version >= "3.7" and python_version < "3.12"
 pathspec==0.11.1 ; python_version >= "3.7" and python_version < "3.12"
 pillow==9.5.0 ; python_version >= "3.7" and python_version < "3.12"
 pkce==1.0.3 ; python_version >= "3.7" and python_version < "3.12"
 pkginfo==1.9.6 ; python_version >= "3.7" and python_version < "3.12"
-platformdirs==3.8.0 ; python_version >= "3.7" and python_version < "3.12"
+platformdirs==3.8.1 ; python_version >= "3.7" and python_version < "3.12"
 pluggy==1.2.0 ; python_version >= "3.7" and python_version < "3.12"
 port-for==0.7.0 ; python_version >= "3.7" and python_version < "3.12"
 prettytable==3.7.0 ; python_version >= "3.7" and python_version < "3.12"
@@ -93,7 +93,7 @@ pygithub==1.59.0 ; python_version >= "3.7" and python_version < "3.12"
 pygments==2.15.1 ; python_version >= "3.7" and python_version < "3.12"
 pyjwt[crypto]==2.7.0 ; python_version >= "3.7" and python_version < "3.12"
 pynacl==1.5.0 ; python_version >= "3.7" and python_version < "3.12"
-pyparsing==3.1.0 ; python_version >= "3.7" and python_version < "3.12"
+pyparsing==3.0.9 ; python_version >= "3.7" and python_version < "3.12"
 pyproject-hooks==1.0.0 ; python_version >= "3.7" and python_version < "3.12"
 pysocks==1.7.1 ; python_version >= "3.7" and python_version < "3.12"
 pytest-asyncio==0.21.0 ; python_version >= "3.7" and python_version < "3.12"

lib/galaxy/dependencies/pinned-requirements.txt

@@ -9,7 +9,7 @@ aioitertools==0.11.0 ; python_version >= "3.7" and python_version < "3.12"
 aiosignal==1.3.1 ; python_version >= "3.7" and python_version < "3.12"
 alembic==1.11.1 ; python_version >= "3.7" and python_version < "3.12"
 amqp==5.1.1 ; python_version >= "3.7" and python_version < "3.12"
-anyio==3.7.0 ; python_version >= "3.7" and python_version < "3.12"
+anyio==3.7.1 ; python_version >= "3.7" and python_version < "3.12"
 apispec==6.3.0 ; python_version >= "3.7" and python_version < "3.12"
 appdirs==1.4.4 ; python_version >= "3.7" and python_version < "3.12"
 arcp==0.2.1 ; python_version >= "3.7" and python_version < "3.12"
@@ -36,19 +36,19 @@ cached-property==1.5.2 ; python_version >= "3.7" and python_version < "3.8"
 celery==5.2.7 ; python_version >= "3.7" and python_version < "3.12"
 certifi==2023.5.7 ; python_version >= "3.7" and python_version < "3.12"
 cffi==1.15.1 ; python_version >= "3.7" and python_version < "3.12"
-charset-normalizer==3.1.0 ; python_version >= "3.7" and python_version < "3.12"
+charset-normalizer==3.2.0 ; python_version >= "3.7" and python_version < "3.12"
 cheetah3==3.2.6.post1 ; python_version >= "3.7" and python_version < "3.12"
 circus==0.18.0 ; python_version >= "3.7" and python_version < "3.12"
 click-didyoumean==0.3.0 ; python_version >= "3.7" and python_version < "3.12"
 click-plugins==1.1.1 ; python_version >= "3.7" and python_version < "3.12"
 click-repl==0.3.0 ; python_version >= "3.7" and python_version < "3.12"
-click==8.1.3 ; python_version >= "3.7" and python_version < "3.12"
+click==8.1.4 ; python_version >= "3.7" and python_version < "3.12"
 cloudauthz==0.6.0 ; python_version >= "3.7" and python_version < "3.12"
 cloudbridge==3.1.0 ; python_version >= "3.7" and python_version < "3.12"
 colorama==0.4.6 ; python_version >= "3.7" and python_version < "3.12" and platform_system == "Windows"
 coloredlogs==15.0.1 ; python_version >= "3.7" and python_version < "3.12"
 conda-package-streaming==0.8.0 ; python_version >= "3.7" and python_version < "3.12"
-cryptography==41.0.1 ; python_version >= "3.7" and python_version < "3.12"
+cryptography==41.0.2 ; python_version >= "3.7" and python_version < "3.12"
 cwl-upgrader==1.2.8 ; python_version >= "3.7" and python_version < "3.12"
 cwl-utils==0.28 ; python_version >= "3.7" and python_version < "3.12"
 cwltool==3.1.20221109155812 ; python_version >= "3.7" and python_version < "3.12"
@@ -92,13 +92,13 @@ jsonref==1.1.0 ; python_version >= "3.7" and python_version < "3.12"
 jsonschema==4.17.3 ; python_version >= "3.7" and python_version < "3.12"
 kombu==5.2.4 ; python_version >= "3.7" and python_version < "3.12"
 lagom==2.4.1 ; python_version >= "3.7" and python_version < "3.12"
-lxml==4.9.2 ; python_version >= "3.7" and python_version < "3.12"
+lxml==4.9.3 ; python_version >= "3.7" and python_version < "3.12"
 mako==1.2.4 ; python_version >= "3.7" and python_version < "3.12"
 markdown-it-py==2.2.0 ; python_version >= "3.7" and python_version < "3.12"
 markdown==3.4.3 ; python_version >= "3.7" and python_version < "3.12"
 markupsafe==2.1.3 ; python_version >= "3.7" and python_version < "3.12"
 mdurl==0.1.2 ; python_version >= "3.7" and python_version < "3.12"
-mercurial==6.4.5 ; python_version >= "3.7" and python_version < "3.12"
+mercurial==6.5 ; python_version >= "3.7" and python_version < "3.12"
 mistune==2.0.5 ; python_version >= "3.7" and python_version < "3.12"
 mrcfile==1.4.3 ; python_version >= "3.7" and python_version < "3.12"
 msal==1.22.0 ; python_version >= "3.7" and python_version < "3.12"
@@ -109,9 +109,9 @@ networkx==2.5 ; python_version >= "3.7" and python_version < "3.12"
 nodeenv==1.8.0 ; python_version >= "3.7" and python_version < "3.12"
 numpy==1.21.6 ; python_version >= "3.7" and python_version < "3.8"
 numpy==1.24.4 ; python_version >= "3.8" and python_version < "3.9"
-numpy==1.25.0 ; python_version >= "3.9" and python_version < "3.12"
+numpy==1.25.1 ; python_version >= "3.9" and python_version < "3.12"
 oauthlib==3.2.2 ; python_version >= "3.7" and python_version < "3.12"
-orjson==3.9.1 ; python_version >= "3.7" and python_version < "3.12"
+orjson==3.9.2 ; python_version >= "3.7" and python_version < "3.12"
 oyaml==1.0 ; python_version >= "3.7" and python_version < "3.12"
 packaging==23.1 ; python_version >= "3.7" and python_version < "3.12"
 paramiko==3.2.0 ; python_version >= "3.7" and python_version < "3.12"
@@ -139,7 +139,7 @@ pyjwt[crypto]==2.7.0 ; python_version >= "3.7" and python_version < "3.12"
 pykwalify==1.8.0 ; python_version >= "3.7" and python_version < "3.12"
 pylibmagic==0.4.0 ; python_version >= "3.7" and python_version < "3.12"
 pynacl==1.5.0 ; python_version >= "3.7" and python_version < "3.12"
-pyparsing==3.1.0 ; python_version >= "3.7" and python_version < "3.12"
+pyparsing==3.0.9 ; python_version >= "3.7" and python_version < "3.12"
 pyreadline3==3.4.1 ; sys_platform == "win32" and python_version >= "3.8" and python_version < "3.12"
 pyreadline==2.1 ; sys_platform == "win32" and python_version < "3.8" and python_version >= "3.7"
 pyrsistent==0.19.3 ; python_version >= "3.7" and python_version < "3.12"
@@ -174,7 +174,7 @@ six==1.16.0 ; python_version >= "3.7" and python_version < "3.12"
 sniffio==1.3.0 ; python_version >= "3.7" and python_version < "3.12"
 social-auth-core[openidconnect]==4.0.3 ; python_version >= "3.7" and python_version < "3.12"
 sortedcontainers==2.4.0 ; python_version >= "3.7" and python_version < "3.12"
-sqlalchemy==1.4.48 ; python_version >= "3.7" and python_version < "3.12"
+sqlalchemy==1.4.49 ; python_version >= "3.7" and python_version < "3.12"
 sqlitedict==2.1.0 ; python_version >= "3.7" and python_version < "3.12"
 sqlparse==0.4.4 ; python_version >= "3.7" and python_version < "3.12"
 starlette-context==0.3.5 ; python_version >= "3.7" and python_version < "3.12"

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

@@ -1,5 +1,5 @@
 cffi==1.15.1
-cryptography==41.0.1
+cryptography==41.0.2
 mypy==1.4.1
 mypy-extensions==1.0.0
 pycparser==2.21
@@ -8,7 +8,7 @@ tomli==2.0.1
 typed-ast==1.5.5
 types-bleach==6.0.0.3
 types-boto==2.49.18.8
-types-contextvars==2.4.7.2
+types-contextvars==2.4.7.3
 types-dataclasses==0.6.6
 types-docutils==0.20.0.1
 types-Markdown==3.4.2.9

pyproject.toml

@@ -85,7 +85,7 @@ pydantic = {version = "<2", extras = ["email"]}
 PyJWT = "*"
 pykwalify = "*"
 pylibmagic = "*"
-pyparsing = "*"
+pyparsing = "<3.1"  # Needed by matplotlib on Python >=3.8 https://github.com/matplotlib/matplotlib/issues/26152
 pysam = ">=0.21"  # for Python 3.11 support on macOS
 python = ">=3.7,<3.12"  # Keep maximum version strict to appease numpy and scipy
 python-dateutil = "*"