From d582d8bce5c19f7038ee484645ded23b06e5da7d Mon Sep 17 00:00:00 2001 From: Ubuntu <19364610+tuncK@users.noreply.github.com> Date: Fri, 6 Oct 2023 10:30:35 +0000 Subject: [PATCH] add support for python3.12 --- .github/workflows/first_startup.yaml | 2 +- .github/workflows/lint.yaml | 2 +- .github/workflows/reports_startup.yaml | 2 +- .github/workflows/test_galaxy_packages.yaml | 2 +- .github/workflows/unit.yaml | 2 +- lib/galaxy/dependencies/dev-requirements.txt | 324 +++++++------- .../dependencies/pinned-lint-requirements.txt | 2 +- .../dependencies/pinned-requirements.txt | 411 +++++++++--------- .../pinned-typecheck-requirements.txt | 40 +- lib/galaxy/dependencies/update.sh | 4 +- packages/app/setup.cfg | 1 + packages/auth/setup.cfg | 3 +- packages/config/setup.cfg | 3 +- packages/data/setup.cfg | 1 + packages/files/setup.cfg | 1 + packages/job_execution/setup.cfg | 3 +- packages/job_metrics/setup.cfg | 3 +- packages/meta/setup.cfg | 1 + packages/navigation/setup.cfg | 3 +- packages/objectstore/setup.cfg | 3 +- packages/schema/setup.cfg | 2 + packages/selenium/setup.cfg | 3 +- packages/test_api/setup.cfg | 3 +- packages/test_base/setup.cfg | 3 +- packages/test_driver/setup.cfg | 3 +- packages/test_selenium/setup.cfg | 1 + packages/tool_shed/setup.cfg | 2 + packages/tool_util/setup.cfg | 1 + packages/tours/setup.cfg | 1 + packages/util/setup.cfg | 1 + packages/web_apps/setup.cfg | 1 + packages/web_framework/setup.cfg | 1 + packages/web_stack/setup.cfg | 3 +- pyproject.toml | 2 +- 34 files changed, 438 insertions(+), 402 deletions(-) diff --git a/.github/workflows/first_startup.yaml b/.github/workflows/first_startup.yaml index 34093cae9605..f55abd7dde6f 100644 --- a/.github/workflows/first_startup.yaml +++ b/.github/workflows/first_startup.yaml @@ -21,7 +21,7 @@ jobs: strategy: fail-fast: false matrix: - python-version: ['3.7', '3.11'] + python-version: ['3.7', '3.12'] defaults: run: shell: bash -l {0} diff --git a/.github/workflows/lint.yaml b/.github/workflows/lint.yaml index 575a6a0f9a31..532ad6a2fec1 100644 --- a/.github/workflows/lint.yaml +++ b/.github/workflows/lint.yaml @@ -21,7 +21,7 @@ jobs: runs-on: ubuntu-latest strategy: matrix: - python-version: ['3.7', '3.11'] + python-version: ['3.7', '3.12'] env: LINT_PATH: 'lib/galaxy/dependencies/pinned-lint-requirements.txt' TYPE_PATH: 'lib/galaxy/dependencies/pinned-typecheck-requirements.txt' diff --git a/.github/workflows/reports_startup.yaml b/.github/workflows/reports_startup.yaml index 805686e3d388..b1bf0be6be0b 100644 --- a/.github/workflows/reports_startup.yaml +++ b/.github/workflows/reports_startup.yaml @@ -18,7 +18,7 @@ jobs: strategy: fail-fast: false matrix: - python-version: ['3.7', '3.11'] + python-version: ['3.7', '3.12'] defaults: run: shell: bash -l {0} diff --git a/.github/workflows/test_galaxy_packages.yaml b/.github/workflows/test_galaxy_packages.yaml index 089d4f45f19e..5b8f3f1d16fb 100644 --- a/.github/workflows/test_galaxy_packages.yaml +++ b/.github/workflows/test_galaxy_packages.yaml @@ -18,7 +18,7 @@ jobs: strategy: fail-fast: false matrix: - python-version: ['3.7', '3.11'] + python-version: ['3.7', '3.12'] steps: - uses: actions/checkout@v3 with: diff --git a/.github/workflows/unit.yaml b/.github/workflows/unit.yaml index 8ade16541a1f..f4d6ea92f17e 100644 --- a/.github/workflows/unit.yaml +++ b/.github/workflows/unit.yaml @@ -20,7 +20,7 @@ jobs: strategy: fail-fast: false matrix: - python-version: ['3.7', '3.11'] + python-version: ['3.7', '3.12'] steps: - uses: actions/checkout@v3 with: diff --git a/lib/galaxy/dependencies/dev-requirements.txt b/lib/galaxy/dependencies/dev-requirements.txt index dd82b1fff80e..61f7f04749ed 100644 --- a/lib/galaxy/dependencies/dev-requirements.txt +++ b/lib/galaxy/dependencies/dev-requirements.txt @@ -1,170 +1,176 @@ -aiohttp==3.8.5 ; 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==3.7.1 ; python_version >= "3.7" and python_version < "3.12" -ase==3.22.1 ; python_version >= "3.7" and python_version < "3.12" -async-timeout==4.0.3 ; python_version >= "3.7" and python_version < "3.12" +aiohttp==3.8.5 ; python_version >= "3.7" and python_version < "3.13" +aiosignal==1.3.1 ; python_version >= "3.7" and python_version < "3.13" +alabaster==0.7.13 ; python_version >= "3.7" and python_version < "3.13" +amqp==5.1.1 ; python_version >= "3.7" and python_version < "3.13" +anyio==3.7.1 ; python_version >= "3.7" and python_version < "3.13" +ase==3.22.1 ; python_version >= "3.7" and python_version < "3.13" +async-timeout==4.0.3 ; python_version >= "3.7" and python_version < "3.13" asynctest==0.13.0 ; python_version >= "3.7" and python_version < "3.8" -attrs==23.1.0 ; python_version >= "3.7" and python_version < "3.12" -axe-selenium-python==2.1.6 ; python_version >= "3.7" and python_version < "3.12" -babel==2.12.1 ; python_version >= "3.7" and python_version < "3.12" -billiard==3.6.4.0 ; python_version >= "3.7" and python_version < "3.12" -black==23.3.0 ; python_version >= "3.7" and python_version < "3.12" -bleach==6.0.0 ; python_version >= "3.7" and python_version < "3.12" -build==1.0.3 ; python_version >= "3.7" and python_version < "3.12" -cachecontrol[filecache]==0.13.1 ; python_version >= "3.7" and python_version < "3.12" +attrs==23.1.0 ; python_version >= "3.7" and python_version < "3.13" +axe-selenium-python==2.1.6 ; python_version >= "3.7" and python_version < "3.13" +babel==2.13.0 ; python_version >= "3.7" and python_version < "3.13" +billiard==3.6.4.0 ; python_version >= "3.7" and python_version < "3.13" +black==23.3.0 ; python_version >= "3.7" and python_version < "3.13" +bleach==6.0.0 ; python_version >= "3.7" and python_version < "3.13" +build==1.0.3 ; python_version >= "3.7" and python_version < "3.13" +cachecontrol[filecache]==0.13.1 ; python_version >= "3.7" and python_version < "3.13" 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==2023.7.22 ; python_version >= "3.7" and python_version < "3.12" -cffi==1.15.1 ; python_version >= "3.7" and python_version < "3.12" -charset-normalizer==3.2.0 ; 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==8.1.7 ; 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==41.0.4 ; python_version >= "3.7" and python_version < "3.12" -cwltest==2.3.20230825125225 ; python_version >= "3.7" and python_version < "3.12" -cycler==0.11.0 ; python_version >= "3.7" and python_version < "3.12" -darker==1.7.2 ; python_version >= "3.7" and python_version < "3.12" -defusedxml==0.7.1 ; python_version >= "3.7" and python_version < "3.12" -deprecated==1.2.14 ; python_version >= "3.7" and python_version < "3.12" -docutils==0.18.1 ; python_version >= "3.7" and python_version < "3.12" +celery==5.2.7 ; python_version >= "3.7" and python_version < "3.13" +certifi==2023.7.22 ; python_version >= "3.7" and python_version < "3.13" +cffi==1.15.1 ; python_version >= "3.7" and python_version < "3.13" +charset-normalizer==3.3.0 ; python_version >= "3.7" and python_version < "3.13" +click-didyoumean==0.3.0 ; python_version >= "3.7" and python_version < "3.13" +click-plugins==1.1.1 ; python_version >= "3.7" and python_version < "3.13" +click-repl==0.3.0 ; python_version >= "3.7" and python_version < "3.13" +click==8.1.7 ; python_version >= "3.7" and python_version < "3.13" +codespell==2.2.5 ; python_version >= "3.7" and python_version < "3.13" +colorama==0.4.6 ; python_version >= "3.7" and python_version < "3.13" and (sys_platform == "win32" or platform_system == "Windows" or os_name == "nt") +coverage[toml]==7.2.7 ; python_version >= "3.7" and python_version < "3.13" +cryptography==41.0.4 ; python_version >= "3.7" and python_version < "3.13" +cwltest==2.3.20230825125225 ; python_version >= "3.7" and python_version < "3.13" +cycler==0.11.0 ; python_version >= "3.7" and python_version < "3.13" +darker==1.7.2 ; python_version >= "3.7" and python_version < "3.13" +defusedxml==0.7.1 ; python_version >= "3.7" and python_version < "3.13" +deprecated==1.2.14 ; python_version >= "3.7" and python_version < "3.13" +docutils==0.18.1 ; python_version >= "3.7" and python_version < "3.13" exceptiongroup==1.1.3 ; python_version >= "3.7" and python_version < "3.11" -filelock==3.12.2 ; python_version >= "3.7" and python_version < "3.12" -fluent-logger==0.10.0 ; python_version >= "3.7" and python_version < "3.12" -fonttools==4.38.0 ; python_version >= "3.7" and python_version < "3.12" -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==0.1.5 ; python_version >= "3.7" and python_version < "3.12" -h11==0.14.0 ; python_version >= "3.7" and python_version < "3.12" -httpcore==0.17.3 ; 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" -importlib-metadata==4.13.0 ; python_version >= "3.7" and python_version < "3.12" -importlib-resources==5.12.0 ; python_version >= "3.7" and python_version < "3.12" -iniconfig==2.0.0 ; python_version >= "3.7" and python_version < "3.12" -isodate==0.6.1 ; python_version >= "3.7" and python_version < "3.12" -isort==5.11.5 ; python_version >= "3.7" and python_version < "3.12" -jaraco-classes==3.2.3 ; python_version >= "3.7" and python_version < "3.12" -jeepney==0.8.0 ; python_version >= "3.7" and python_version < "3.12" and sys_platform == "linux" -jinja2==3.1.2 ; python_version >= "3.7" and python_version < "3.12" -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==1.4.5 ; python_version >= "3.7" and python_version < "3.12" -kombu==5.2.4 ; python_version >= "3.7" and python_version < "3.12" -lxml==4.9.3 ; 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" +filelock==3.12.2 ; python_version >= "3.7" and python_version < "3.13" +fluent-logger==0.10.0 ; python_version >= "3.7" and python_version < "3.13" +fonttools==4.38.0 ; python_version >= "3.7" and python_version < "3.13" +frozenlist==1.3.3 ; python_version >= "3.7" and python_version < "3.13" +future==0.18.3 ; python_version >= "3.7" and python_version < "3.13" +galaxy-release-util==0.1.5 ; python_version >= "3.7" and python_version < "3.13" +greenlet==2.0.2 ; python_version >= "3.7" and python_version < "3.13" +h11==0.14.0 ; python_version >= "3.7" and python_version < "3.13" +httpcore==0.17.3 ; python_version >= "3.7" and python_version < "3.13" +httpx==0.24.1 ; python_version >= "3.7" and python_version < "3.13" +idna==3.4 ; python_version >= "3.7" and python_version < "3.13" +imagesize==1.4.1 ; python_version >= "3.7" and python_version < "3.13" +importlib-metadata==4.13.0 ; python_version >= "3.7" and python_version < "3.13" +importlib-resources==5.12.0 ; python_version >= "3.7" and python_version < "3.13" +iniconfig==2.0.0 ; python_version >= "3.7" and python_version < "3.13" +isodate==0.6.1 ; python_version >= "3.7" and python_version < "3.13" +isort==5.11.5 ; python_version >= "3.7" and python_version < "3.13" +jaraco-classes==3.2.3 ; python_version >= "3.7" and python_version < "3.13" +jeepney==0.8.0 ; python_version >= "3.7" and python_version < "3.13" and sys_platform == "linux" +jinja2==3.1.2 ; python_version >= "3.7" and python_version < "3.13" +junit-xml==1.9 ; python_version >= "3.7" and python_version < "3.13" +keyring==24.1.1 ; python_version >= "3.7" and python_version < "3.13" +kiwisolver==1.4.5 ; python_version >= "3.7" and python_version < "3.13" +kombu==5.2.4 ; python_version >= "3.7" and python_version < "3.13" +lxml==4.9.3 ; python_version >= "3.7" and python_version < "3.13" +markdown-it-py==2.2.0 ; python_version >= "3.7" and python_version < "3.13" +markdown-it-reporter==0.0.2 ; python_version >= "3.7" and python_version < "3.13" +markupsafe==2.1.3 ; python_version >= "3.7" and python_version < "3.13" matplotlib==3.5.3 ; python_version >= "3.7" and python_version < "3.8" matplotlib==3.7.3 ; python_version >= "3.8" and python_version < "3.9" -matplotlib==3.8.0 ; python_version >= "3.9" 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" -mistune==2.0.5 ; python_version >= "3.7" and python_version < "3.12" -more-itertools==9.1.0 ; python_version >= "3.7" and python_version < "3.12" -msgpack==1.0.5 ; python_version >= "3.7" and python_version < "3.12" -multidict==6.0.4 ; python_version >= "3.7" and python_version < "3.12" -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" +matplotlib==3.8.0 ; python_version >= "3.9" and python_version < "3.13" +mdit-py-plugins==0.3.5 ; python_version >= "3.7" and python_version < "3.13" +mdurl==0.1.2 ; python_version >= "3.7" and python_version < "3.13" +mirakuru==2.5.1 ; python_version >= "3.7" and python_version < "3.13" +mistune==2.0.5 ; python_version >= "3.7" and python_version < "3.13" +more-itertools==9.1.0 ; python_version >= "3.7" and python_version < "3.13" +msgpack==1.0.5 ; python_version >= "3.7" and python_version < "3.13" +multidict==6.0.4 ; python_version >= "3.7" and python_version < "3.13" +mypy-extensions==1.0.0 ; python_version >= "3.7" and python_version < "3.13" +myst-parser==1.0.0 ; python_version >= "3.7" and python_version < "3.13" 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==1.26.0 ; 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==0.11.2 ; 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==3.10.0 ; python_version >= "3.7" and python_version < "3.12" -pluggy==1.2.0 ; python_version >= "3.7" and python_version < "3.12" -port-for==0.7.1 ; python_version >= "3.7" and python_version < "3.12" -prettytable==3.7.0 ; python_version >= "3.7" and python_version < "3.12" -prompt-toolkit==3.0.39 ; python_version >= "3.7" and python_version < "3.12" -psutil==5.9.5 ; python_version >= "3.7" and python_version < "3.12" and sys_platform != "cygwin" -py==1.11.0 ; python_version >= "3.7" and python_version < "3.12" -pycparser==2.21 ; python_version >= "3.7" and python_version < "3.12" -pygithub==2.1.1 ; python_version >= "3.7" and python_version < "3.12" -pygments==2.16.1 ; python_version >= "3.7" and python_version < "3.12" -pyjwt[crypto]==2.8.0 ; python_version >= "3.7" and python_version < "3.12" -pynacl==1.5.0 ; python_version >= "3.7" and python_version < "3.12" -pyparsing==3.0.9 ; 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==0.21.1 ; python_version >= "3.7" and python_version < "3.12" -pytest-celery==0.0.0 ; python_version >= "3.7" and python_version < "3.12" -pytest-cov==4.1.0 ; python_version >= "3.7" and python_version < "3.12" -pytest-html==3.2.0 ; python_version >= "3.7" and python_version < "3.12" -pytest-httpserver==1.0.6 ; python_version >= "3.7" and python_version < "3.12" -pytest-json-report==1.5.0 ; python_version >= "3.7" and python_version < "3.12" -pytest-metadata==3.0.0 ; python_version >= "3.7" and python_version < "3.12" -pytest-mock==3.11.1 ; python_version >= "3.7" and python_version < "3.12" -pytest-playwright==0.3.0 ; python_version >= "3.7" and python_version < "3.12" -pytest-postgresql==4.1.1 ; python_version >= "3.7" and python_version < "3.12" -pytest-shard==0.1.2 ; python_version >= "3.7" and python_version < "3.12" -pytest==7.4.2 ; python_version >= "3.7" and python_version < "3.12" -python-dateutil==2.8.2 ; python_version >= "3.7" and python_version < "3.12" -python-irodsclient==1.1.8 ; python_version >= "3.7" and python_version < "3.12" -pytz==2023.3.post1 ; python_version >= "3.7" and python_version < "3.12" -pywin32-ctypes==0.2.2 ; python_version >= "3.7" and python_version < "3.12" and sys_platform == "win32" -pyyaml==6.0.1 ; python_version >= "3.7" and python_version < "3.12" -rdflib==6.2.0 ; python_version >= "3.7" and python_version < "3.12" -readme-renderer==37.3 ; python_version >= "3.7" and python_version < "3.12" -requests-toolbelt==1.0.0 ; python_version >= "3.7" and python_version < "3.12" -requests==2.31.0 ; python_version >= "3.7" and python_version < "3.12" -responses==0.23.3 ; python_version >= "3.7" and python_version < "3.12" -rfc3986==2.0.0 ; python_version >= "3.7" and python_version < "3.12" -rich==13.5.3 ; python_version >= "3.7" and python_version < "3.12" -ruamel-yaml-clib==0.2.7 ; platform_python_implementation == "CPython" and python_version < "3.11" and python_version >= "3.7" -ruamel-yaml==0.17.21 ; python_version >= "3.7" and python_version < "3.12" -schema-salad==8.4.20230808163024 ; python_version >= "3.7" and python_version < "3.12" +numpy==1.26.0 ; python_version >= "3.9" and python_version < "3.13" +outcome==1.2.0 ; python_version >= "3.7" and python_version < "3.13" +packaging==23.2 ; python_version >= "3.7" and python_version < "3.13" +pathspec==0.11.2 ; python_version >= "3.7" and python_version < "3.13" +pillow==9.5.0 ; python_version >= "3.7" and python_version < "3.13" +pkce==1.0.3 ; python_version >= "3.7" and python_version < "3.13" +pkginfo==1.9.6 ; python_version >= "3.7" and python_version < "3.13" +platformdirs==3.11.0 ; python_version >= "3.7" and python_version < "3.13" +playwright==1.35.0 ; python_version >= "3.7" and python_version < "3.13" +pluggy==1.2.0 ; python_version >= "3.7" and python_version < "3.13" +port-for==0.7.1 ; python_version >= "3.7" and python_version < "3.13" +prettytable==3.7.0 ; python_version >= "3.7" and python_version < "3.13" +prompt-toolkit==3.0.39 ; python_version >= "3.7" and python_version < "3.13" +psutil==5.9.5 ; python_version >= "3.7" and python_version < "3.13" and sys_platform != "cygwin" +py==1.11.0 ; python_version >= "3.7" and python_version < "3.13" +pycparser==2.21 ; python_version >= "3.7" and python_version < "3.13" +pyee==9.0.4 ; python_version >= "3.7" and python_version < "3.13" +pygithub==2.1.1 ; python_version >= "3.7" and python_version < "3.13" +pygments==2.16.1 ; python_version >= "3.7" and python_version < "3.13" +pyjwt[crypto]==2.8.0 ; python_version >= "3.7" and python_version < "3.13" +pynacl==1.5.0 ; python_version >= "3.7" and python_version < "3.13" +pyparsing==3.0.9 ; python_version >= "3.7" and python_version < "3.13" +pyproject-hooks==1.0.0 ; python_version >= "3.7" and python_version < "3.13" +pysocks==1.7.1 ; python_version >= "3.7" and python_version < "3.13" +pytest-asyncio==0.21.1 ; python_version >= "3.7" and python_version < "3.13" +pytest-base-url==2.0.0 ; python_version >= "3.7" and python_version < "3.13" +pytest-celery==0.0.0 ; python_version >= "3.7" and python_version < "3.13" +pytest-cov==4.1.0 ; python_version >= "3.7" and python_version < "3.13" +pytest-html==3.2.0 ; python_version >= "3.7" and python_version < "3.13" +pytest-httpserver==1.0.6 ; python_version >= "3.7" and python_version < "3.13" +pytest-json-report==1.5.0 ; python_version >= "3.7" and python_version < "3.13" +pytest-metadata==3.0.0 ; python_version >= "3.7" and python_version < "3.13" +pytest-mock==3.11.1 ; python_version >= "3.7" and python_version < "3.13" +pytest-playwright==0.3.3 ; python_version >= "3.7" and python_version < "3.13" +pytest-postgresql==4.1.1 ; python_version >= "3.7" and python_version < "3.13" +pytest-shard==0.1.2 ; python_version >= "3.7" and python_version < "3.13" +pytest==7.4.2 ; python_version >= "3.7" and python_version < "3.13" +python-dateutil==2.8.2 ; python_version >= "3.7" and python_version < "3.13" +python-irodsclient==1.1.8 ; python_version >= "3.7" and python_version < "3.13" +python-slugify==8.0.1 ; python_version >= "3.7" and python_version < "3.13" +pytz==2023.3.post1 ; python_version >= "3.7" and python_version < "3.13" +pywin32-ctypes==0.2.2 ; python_version >= "3.7" and python_version < "3.13" and sys_platform == "win32" +pyyaml==6.0.1 ; python_version >= "3.7" and python_version < "3.13" +rdflib==6.2.0 ; python_version >= "3.7" and python_version < "3.13" +readme-renderer==37.3 ; python_version >= "3.7" and python_version < "3.13" +requests-toolbelt==1.0.0 ; python_version >= "3.7" and python_version < "3.13" +requests==2.31.0 ; python_version >= "3.7" and python_version < "3.13" +responses==0.23.3 ; python_version >= "3.7" and python_version < "3.13" +rfc3986==2.0.0 ; python_version >= "3.7" and python_version < "3.13" +rich==13.6.0 ; python_version >= "3.7" and python_version < "3.13" +ruamel-yaml-clib==0.2.8 ; platform_python_implementation == "CPython" and python_version < "3.11" and python_version >= "3.7" +ruamel-yaml==0.17.21 ; python_version >= "3.7" and python_version < "3.13" +schema-salad==8.4.20230808163024 ; python_version >= "3.7" and python_version < "3.13" scipy==1.7.3 ; python_version >= "3.7" and python_version < "3.8" scipy==1.10.1 ; python_version >= "3.8" and python_version < "3.9" -scipy==1.11.3 ; python_version >= "3.9" and python_version < "3.12" -secretstorage==3.3.3 ; python_version >= "3.7" and python_version < "3.12" and sys_platform == "linux" -selenium==4.11.2 ; python_version >= "3.7" and python_version < "3.12" -seletools==1.4.0 ; python_version >= "3.7" and python_version < "3.12" -setuptools==68.0.0 ; python_version >= "3.7" and python_version < "3.12" -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" -snowballstemmer==2.2.0 ; python_version >= "3.7" and python_version < "3.12" -sortedcontainers==2.4.0 ; python_version >= "3.7" and python_version < "3.12" -sphinx-rtd-theme==1.3.0 ; python_version >= "3.7" and python_version < "3.12" -sphinx==5.3.0 ; python_version >= "3.7" and python_version < "3.12" -sphinxcontrib-applehelp==1.0.2 ; python_version >= "3.7" and python_version < "3.12" -sphinxcontrib-devhelp==1.0.2 ; python_version >= "3.7" and python_version < "3.12" -sphinxcontrib-htmlhelp==2.0.0 ; python_version >= "3.7" and python_version < "3.12" -sphinxcontrib-jquery==4.1 ; python_version >= "3.7" and python_version < "3.12" -sphinxcontrib-jsmath==1.0.1 ; python_version >= "3.7" and python_version < "3.12" -sphinxcontrib-qthelp==1.0.3 ; python_version >= "3.7" and python_version < "3.12" -sphinxcontrib-serializinghtml==1.1.5 ; python_version >= "3.7" and python_version < "3.12" -statsd==4.0.1 ; python_version >= "3.7" and python_version < "3.12" -testfixtures==7.2.0 ; python_version >= "3.7" and python_version < "3.12" -tinydb==4.8.0 ; python_version >= "3.7" and python_version < "3.12" -toml==0.10.2 ; python_version >= "3.7" and python_version < "3.12" +scipy==1.11.3 ; python_version >= "3.9" and python_version < "3.13" +secretstorage==3.3.3 ; python_version >= "3.7" and python_version < "3.13" and sys_platform == "linux" +selenium==4.11.2 ; python_version >= "3.7" and python_version < "3.13" +seletools==1.4.0 ; python_version >= "3.7" and python_version < "3.13" +setuptools==68.0.0 ; python_version >= "3.7" and python_version < "3.13" +six==1.16.0 ; python_version >= "3.7" and python_version < "3.13" +sniffio==1.3.0 ; python_version >= "3.7" and python_version < "3.13" +snowballstemmer==2.2.0 ; python_version >= "3.7" and python_version < "3.13" +sortedcontainers==2.4.0 ; python_version >= "3.7" and python_version < "3.13" +sphinx-rtd-theme==1.3.0 ; python_version >= "3.7" and python_version < "3.13" +sphinx==5.3.0 ; python_version >= "3.7" and python_version < "3.13" +sphinxcontrib-applehelp==1.0.2 ; python_version >= "3.7" and python_version < "3.13" +sphinxcontrib-devhelp==1.0.2 ; python_version >= "3.7" and python_version < "3.13" +sphinxcontrib-htmlhelp==2.0.0 ; python_version >= "3.7" and python_version < "3.13" +sphinxcontrib-jquery==4.1 ; python_version >= "3.7" and python_version < "3.13" +sphinxcontrib-jsmath==1.0.1 ; python_version >= "3.7" and python_version < "3.13" +sphinxcontrib-qthelp==1.0.3 ; python_version >= "3.7" and python_version < "3.13" +sphinxcontrib-serializinghtml==1.1.5 ; python_version >= "3.7" and python_version < "3.13" +statsd==4.0.1 ; python_version >= "3.7" and python_version < "3.13" +testfixtures==7.2.0 ; python_version >= "3.7" and python_version < "3.13" +text-unidecode==1.3 ; python_version >= "3.7" and python_version < "3.13" +tinydb==4.8.0 ; python_version >= "3.7" and python_version < "3.13" +toml==0.10.2 ; python_version >= "3.7" and python_version < "3.13" tomli==2.0.1 ; python_version >= "3.7" and python_full_version <= "3.11.0a6" -trio-websocket==0.11.1 ; python_version >= "3.7" and python_version < "3.12" -trio==0.22.2 ; python_version >= "3.7" and python_version < "3.12" -tuspy==1.0.1 ; python_version >= "3.7" and python_version < "3.12" -twill==3.1 ; python_version >= "3.7" and python_version < "3.12" -twine==4.0.2 ; python_version >= "3.7" and python_version < "3.12" +trio-websocket==0.11.1 ; python_version >= "3.7" and python_version < "3.13" +trio==0.22.2 ; python_version >= "3.7" and python_version < "3.13" +tuspy==1.0.1 ; python_version >= "3.7" and python_version < "3.13" +twill==3.1 ; python_version >= "3.7" and python_version < "3.13" +twine==4.0.2 ; python_version >= "3.7" and python_version < "3.13" typed-ast==1.5.5 ; python_version < "3.8" and implementation_name == "cpython" and python_version >= "3.7" -types-pyyaml==6.0.12.12 ; python_version >= "3.7" and python_version < "3.12" -typing-extensions==4.7.1 ; python_version >= "3.7" and python_version < "3.12" -urllib3==1.26.16 ; python_version >= "3.7" and python_version < "3.12" -urllib3[socks]==1.26.16 ; python_version >= "3.7" and python_version < "3.12" -vine==5.0.0 ; python_version >= "3.7" and python_version < "3.12" -watchdog==3.0.0 ; python_version >= "3.7" and python_version < "3.12" -wcwidth==0.2.7 ; python_version >= "3.7" and python_version < "3.12" -webencodings==0.5.1 ; python_version >= "3.7" and python_version < "3.12" -werkzeug==2.2.3 ; python_version >= "3.7" and python_version < "3.12" -wrapt==1.15.0 ; python_version >= "3.7" and python_version < "3.12" -wsproto==1.2.0 ; python_version >= "3.7" and python_version < "3.12" -yarl==1.9.2 ; python_version >= "3.7" and python_version < "3.12" -zipp==3.15.0 ; python_version >= "3.7" and python_version < "3.12" +types-pyyaml==6.0.12.12 ; python_version >= "3.7" and python_version < "3.13" +typing-extensions==4.7.1 ; python_version >= "3.7" and python_version < "3.13" +urllib3==1.26.17 ; python_version >= "3.7" and python_version < "3.13" +urllib3[socks]==1.26.17 ; python_version >= "3.7" and python_version < "3.13" +vine==5.0.0 ; python_version >= "3.7" and python_version < "3.13" +watchdog==3.0.0 ; python_version >= "3.7" and python_version < "3.13" +wcwidth==0.2.8 ; python_version >= "3.7" and python_version < "3.13" +webencodings==0.5.1 ; python_version >= "3.7" and python_version < "3.13" +werkzeug==2.2.3 ; python_version >= "3.7" and python_version < "3.13" +wrapt==1.15.0 ; python_version >= "3.7" and python_version < "3.13" +wsproto==1.2.0 ; python_version >= "3.7" and python_version < "3.13" +yarl==1.9.2 ; python_version >= "3.7" and python_version < "3.13" +zipp==3.15.0 ; python_version >= "3.7" and python_version < "3.13" diff --git a/lib/galaxy/dependencies/pinned-lint-requirements.txt b/lib/galaxy/dependencies/pinned-lint-requirements.txt index f63b2768119c..08d44e583e9b 100644 --- a/lib/galaxy/dependencies/pinned-lint-requirements.txt +++ b/lib/galaxy/dependencies/pinned-lint-requirements.txt @@ -5,6 +5,6 @@ importlib-metadata==4.2.0 mccabe==0.7.0 pycodestyle==2.9.1 pyflakes==2.5.0 -ruff==0.0.291 +ruff==0.0.292 typing_extensions==4.7.1 zipp==3.15.0 diff --git a/lib/galaxy/dependencies/pinned-requirements.txt b/lib/galaxy/dependencies/pinned-requirements.txt index 5707ebb1c20f..c5df9e09f496 100644 --- a/lib/galaxy/dependencies/pinned-requirements.txt +++ b/lib/galaxy/dependencies/pinned-requirements.txt @@ -1,212 +1,217 @@ -a2wsgi==1.7.0 ; python_version >= "3.7" and python_version < "3.12" -adal==1.2.7 ; python_version >= "3.7" and python_version < "3.12" -aiobotocore==2.4.2 ; python_version >= "3.7" and python_version < "3.12" -aiofiles==23.2.1 ; python_version >= "3.7" and python_version < "3.12" -aiohttp==3.8.5 ; python_version >= "3.7" and python_version < "3.12" -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==1.12.0 ; python_version >= "3.7" and python_version < "3.12" -amqp==5.1.1 ; python_version >= "3.7" and python_version < "3.12" -anyio==3.7.1 ; 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" -argcomplete==3.1.2 ; python_version >= "3.7" and python_version < "3.12" -async-timeout==4.0.3 ; python_version >= "3.7" and python_version < "3.12" +a2wsgi==1.7.0 ; python_version >= "3.7" and python_version < "3.13" +adal==1.2.7 ; python_version >= "3.7" and python_version < "3.13" +aiobotocore==2.4.2 ; python_version >= "3.7" and python_version < "3.13" +aiodataloader==0.4.0 ; python_version >= "3.7" and python_version < "3.13" +aiofiles==23.2.1 ; python_version >= "3.7" and python_version < "3.13" +aiohttp==3.8.5 ; python_version >= "3.7" and python_version < "3.13" +aioitertools==0.11.0 ; python_version >= "3.7" and python_version < "3.13" +aiosignal==1.3.1 ; python_version >= "3.7" and python_version < "3.13" +alembic==1.12.0 ; python_version >= "3.7" and python_version < "3.13" +amqp==5.1.1 ; python_version >= "3.7" and python_version < "3.13" +aniso8601==9.0.1 ; python_version >= "3.7" and python_version < "3.13" +anyio==3.7.1 ; python_version >= "3.7" and python_version < "3.13" +apispec==6.3.0 ; python_version >= "3.7" and python_version < "3.13" +appdirs==1.4.4 ; python_version >= "3.7" and python_version < "3.13" +arcp==0.2.1 ; python_version >= "3.7" and python_version < "3.13" +argcomplete==3.1.2 ; python_version >= "3.7" and python_version < "3.13" +async-timeout==4.0.3 ; python_version >= "3.7" and python_version < "3.13" asynctest==0.13.0 ; python_version >= "3.7" and python_version < "3.8" -attmap==0.13.2 ; python_version >= "3.7" and python_version < "3.12" -attrs==23.1.0 ; python_version >= "3.7" and python_version < "3.12" -babel==2.12.1 ; python_version >= "3.7" and python_version < "3.12" +attmap==0.13.2 ; python_version >= "3.7" and python_version < "3.13" +attrs==23.1.0 ; python_version >= "3.7" and python_version < "3.13" +babel==2.13.0 ; python_version >= "3.7" and python_version < "3.13" backports-zoneinfo==0.2.1 ; python_version >= "3.7" and python_version < "3.9" -bagit-profile==1.3.1 ; python_version >= "3.7" and python_version < "3.12" -bagit==1.8.1 ; python_version >= "3.7" and python_version < "3.12" -bcrypt==4.0.1 ; python_version >= "3.7" and python_version < "3.12" -bdbag==1.7.1 ; python_version >= "3.7" and python_version < "3.12" -beaker==1.12.1 ; python_version >= "3.7" and python_version < "3.12" -billiard==3.6.4.0 ; python_version >= "3.7" and python_version < "3.12" -bioblend==1.2.0 ; python_version >= "3.7" and python_version < "3.12" -bleach==6.0.0 ; python_version >= "3.7" and python_version < "3.12" -boltons==23.0.0 ; python_version >= "3.7" and python_version < "3.12" -boto==2.49.0 ; python_version >= "3.7" and python_version < "3.12" -botocore==1.27.59 ; python_version >= "3.7" and python_version < "3.12" -bx-python==0.10.0 ; python_version >= "3.7" and python_version < "3.12" -cachecontrol[filecache]==0.13.1 ; python_version >= "3.7" and python_version < "3.12" +bagit-profile==1.3.1 ; python_version >= "3.7" and python_version < "3.13" +bagit==1.8.1 ; python_version >= "3.7" and python_version < "3.13" +bcrypt==4.0.1 ; python_version >= "3.7" and python_version < "3.13" +bdbag==1.7.1 ; python_version >= "3.7" and python_version < "3.13" +beaker==1.12.1 ; python_version >= "3.7" and python_version < "3.13" +billiard==3.6.4.0 ; python_version >= "3.7" and python_version < "3.13" +bioblend==1.2.0 ; python_version >= "3.7" and python_version < "3.13" +bleach==6.0.0 ; python_version >= "3.7" and python_version < "3.13" +boltons==23.0.0 ; python_version >= "3.7" and python_version < "3.13" +boto==2.49.0 ; python_version >= "3.7" and python_version < "3.13" +botocore==1.27.59 ; python_version >= "3.7" and python_version < "3.13" +bx-python==0.10.0 ; python_version >= "3.7" and python_version < "3.13" +cachecontrol[filecache]==0.13.1 ; python_version >= "3.7" and python_version < "3.13" 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==2023.7.22 ; python_version >= "3.7" and python_version < "3.12" -cffi==1.15.1 ; python_version >= "3.7" and python_version < "3.12" -charset-normalizer==3.2.0 ; 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==8.1.7 ; python_version >= "3.7" and python_version < "3.12" -cloudauthz==0.6.0 ; python_version >= "3.7" and python_version < "3.12" -cloudbridge==3.2.0 ; 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==0.9.0 ; python_version >= "3.7" and python_version < "3.12" -cryptography==41.0.4 ; 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" -cython==3.0.2 ; python_version >= "3.7" and python_version < "3.12" -decorator==5.1.1 ; python_version >= "3.7" and python_version < "3.12" -defusedxml==0.7.1 ; python_version >= "3.7" and python_version < "3.12" -deprecation==2.1.0 ; python_version >= "3.7" and python_version < "3.12" -dictobj==0.4 ; python_version >= "3.7" and python_version < "3.12" -dnspython==2.3.0 ; python_version >= "3.7" and python_version < "3.12" -docopt==0.6.2 ; python_version >= "3.7" and python_version < "3.12" -docutils==0.18.1 ; python_version >= "3.7" and python_version < "3.12" -dparse==0.6.3 ; python_version >= "3.7" and python_version < "3.12" -ecdsa==0.18.0 ; python_version >= "3.7" and python_version < "3.12" -edam-ontology==1.25.2 ; python_version >= "3.7" and python_version < "3.12" -email-validator==2.0.0.post2 ; python_version >= "3.7" and python_version < "3.12" +celery==5.2.7 ; python_version >= "3.7" and python_version < "3.13" +certifi==2023.7.22 ; python_version >= "3.7" and python_version < "3.13" +cffi==1.15.1 ; python_version >= "3.7" and python_version < "3.13" +charset-normalizer==3.3.0 ; python_version >= "3.7" and python_version < "3.13" +cheetah3==3.2.6.post1 ; python_version >= "3.7" and python_version < "3.13" +circus==0.18.0 ; python_version >= "3.7" and python_version < "3.13" +click-didyoumean==0.3.0 ; python_version >= "3.7" and python_version < "3.13" +click-plugins==1.1.1 ; python_version >= "3.7" and python_version < "3.13" +click-repl==0.3.0 ; python_version >= "3.7" and python_version < "3.13" +click==8.1.7 ; python_version >= "3.7" and python_version < "3.13" +cloudauthz==0.6.0 ; python_version >= "3.7" and python_version < "3.13" +cloudbridge==3.2.0 ; python_version >= "3.7" and python_version < "3.13" +colorama==0.4.6 ; python_version >= "3.7" and python_version < "3.13" and platform_system == "Windows" +coloredlogs==15.0.1 ; python_version >= "3.7" and python_version < "3.13" +conda-package-streaming==0.9.0 ; python_version >= "3.7" and python_version < "3.13" +cryptography==41.0.4 ; python_version >= "3.7" and python_version < "3.13" +cwl-upgrader==1.2.8 ; python_version >= "3.7" and python_version < "3.13" +cwl-utils==0.28 ; python_version >= "3.7" and python_version < "3.13" +cwltool==3.1.20221109155812 ; python_version >= "3.7" and python_version < "3.13" +decorator==5.1.1 ; python_version >= "3.7" and python_version < "3.13" +defusedxml==0.7.1 ; python_version >= "3.7" and python_version < "3.13" +deprecation==2.1.0 ; python_version >= "3.7" and python_version < "3.13" +dictobj==0.4 ; python_version >= "3.7" and python_version < "3.13" +dnspython==2.3.0 ; python_version >= "3.7" and python_version < "3.13" +docopt==0.6.2 ; python_version >= "3.7" and python_version < "3.13" +docutils==0.18.1 ; python_version >= "3.7" and python_version < "3.13" +dparse==0.6.3 ; python_version >= "3.7" and python_version < "3.13" +ecdsa==0.18.0 ; python_version >= "3.7" and python_version < "3.13" +edam-ontology==1.25.2 ; python_version >= "3.7" and python_version < "3.13" +email-validator==2.0.0.post2 ; python_version >= "3.7" and python_version < "3.13" exceptiongroup==1.1.3 ; python_version >= "3.7" and python_version < "3.11" -fastapi-utils==0.2.1 ; python_version >= "3.7" and python_version < "3.12" -fastapi==0.98.0 ; python_version >= "3.7" and python_version < "3.12" -filelock==3.12.2 ; python_version >= "3.7" and python_version < "3.12" -frozenlist==1.3.3 ; python_version >= "3.7" and python_version < "3.12" -fs==2.4.16 ; python_version >= "3.7" and python_version < "3.12" -fsspec==2023.1.0 ; python_version >= "3.7" and python_version < "3.12" -future==0.18.3 ; python_version >= "3.7" and python_version < "3.12" -galaxy-sequence-utils==1.1.5 ; python_version >= "3.7" and python_version < "3.12" -galaxy2cwl==0.1.4 ; python_version >= "3.7" and python_version < "3.12" -graphene-sqlalchemy==3.0.0b3 ; python_version >= "3.7" and python_version < "3.12" -gravity==1.0.3 ; python_version >= "3.7" and python_version < "3.12" -greenlet==2.0.2 ; python_version >= "3.7" and (platform_machine == "aarch64" or platform_machine == "ppc64le" or platform_machine == "x86_64" or platform_machine == "amd64" or platform_machine == "AMD64" or platform_machine == "win32" or platform_machine == "WIN32") and python_version < "3.12" -gunicorn==21.2.0 ; python_version >= "3.7" and python_version < "3.12" -gxformat2==0.18.0 ; python_version >= "3.7" and python_version < "3.12" -h11==0.14.0 ; python_version >= "3.7" and python_version < "3.12" -h5grove==1.3.0 ; python_version >= "3.7" and python_version < "3.12" -h5py==3.8.0 ; python_version >= "3.7" and python_version < "3.12" -humanfriendly==10.0 ; python_version >= "3.7" and python_version < "3.12" -idna==3.4 ; python_version >= "3.7" and python_version < "3.12" -importlib-metadata==4.13.0 ; python_version >= "3.7" and python_version < "3.12" -importlib-resources==5.12.0 ; python_version >= "3.7" and python_version < "3.12" -isa-rwval==0.10.10 ; python_version >= "3.7" and python_version < "3.12" -isodate==0.6.1 ; python_version >= "3.7" and python_version < "3.12" -jinja2==3.1.2 ; python_version >= "3.7" and python_version < "3.12" -jmespath==1.0.1 ; python_version >= "3.7" and python_version < "3.12" -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==2.5.0 ; 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==3.4.4 ; 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==6.5.2 ; 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==1.24.1 ; python_version >= "3.7" and python_version < "3.12" -msgpack==1.0.5 ; python_version >= "3.7" and python_version < "3.12" -multidict==6.0.4 ; python_version >= "3.7" and python_version < "3.12" -mypy-extensions==1.0.0 ; python_version >= "3.7" and python_version < "3.12" -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" +fastapi-utils==0.2.1 ; python_version >= "3.7" and python_version < "3.13" +fastapi==0.98.0 ; python_version >= "3.7" and python_version < "3.13" +filelock==3.12.2 ; python_version >= "3.7" and python_version < "3.13" +frozenlist==1.3.3 ; python_version >= "3.7" and python_version < "3.13" +fs==2.4.16 ; python_version >= "3.7" and python_version < "3.13" +fsspec==2023.1.0 ; python_version >= "3.7" and python_version < "3.13" +future==0.18.3 ; python_version >= "3.7" and python_version < "3.13" +galaxy-sequence-utils==1.1.5 ; python_version >= "3.7" and python_version < "3.13" +galaxy2cwl==0.1.4 ; python_version >= "3.7" and python_version < "3.13" +graphene-sqlalchemy==3.0.0b3 ; python_version >= "3.7" and python_version < "3.13" +graphene==3.3 ; python_version >= "3.7" and python_version < "3.13" +graphql-core==3.2.3 ; python_version >= "3.7" and python_version < "3.13" +graphql-relay==3.2.0 ; python_version >= "3.7" and python_version < "3.13" +gravity==1.0.3 ; python_version >= "3.7" and python_version < "3.13" +greenlet==2.0.2 ; python_version >= "3.7" and (platform_machine == "aarch64" or platform_machine == "ppc64le" or platform_machine == "x86_64" or platform_machine == "amd64" or platform_machine == "AMD64" or platform_machine == "win32" or platform_machine == "WIN32") and python_version < "3.13" +gunicorn==21.2.0 ; python_version >= "3.7" and python_version < "3.13" +gxformat2==0.18.0 ; python_version >= "3.7" and python_version < "3.13" +h11==0.14.0 ; python_version >= "3.7" and python_version < "3.13" +h5grove==1.3.0 ; python_version >= "3.7" and python_version < "3.13" +h5py==3.8.0 ; python_version >= "3.7" and python_version < "3.13" +humanfriendly==10.0 ; python_version >= "3.7" and python_version < "3.13" +idna==3.4 ; python_version >= "3.7" and python_version < "3.13" +importlib-metadata==4.13.0 ; python_version >= "3.7" and python_version < "3.13" +importlib-resources==5.12.0 ; python_version >= "3.7" and python_version < "3.13" +isa-rwval==0.10.10 ; python_version >= "3.7" and python_version < "3.13" +isodate==0.6.1 ; python_version >= "3.7" and python_version < "3.13" +jinja2==3.1.2 ; python_version >= "3.7" and python_version < "3.13" +jmespath==1.0.1 ; python_version >= "3.7" and python_version < "3.13" +jsonref==1.1.0 ; python_version >= "3.7" and python_version < "3.13" +jsonschema==4.17.3 ; python_version >= "3.7" and python_version < "3.13" +kombu==5.2.4 ; python_version >= "3.7" and python_version < "3.13" +lagom==2.5.0 ; python_version >= "3.7" and python_version < "3.13" +lxml==4.9.3 ; python_version >= "3.7" and python_version < "3.13" +mako==1.2.4 ; python_version >= "3.7" and python_version < "3.13" +markdown-it-py==2.2.0 ; python_version >= "3.7" and python_version < "3.13" +markdown==3.4.4 ; python_version >= "3.7" and python_version < "3.13" +markupsafe==2.1.3 ; python_version >= "3.7" and python_version < "3.13" +mdurl==0.1.2 ; python_version >= "3.7" and python_version < "3.13" +mercurial==6.5.2 ; python_version >= "3.7" and python_version < "3.13" +mistune==2.0.5 ; python_version >= "3.7" and python_version < "3.13" +mrcfile==1.4.3 ; python_version >= "3.7" and python_version < "3.13" +msal==1.24.1 ; python_version >= "3.7" and python_version < "3.13" +msgpack==1.0.5 ; python_version >= "3.7" and python_version < "3.13" +multidict==6.0.4 ; python_version >= "3.7" and python_version < "3.13" +mypy-extensions==1.0.0 ; python_version >= "3.7" and python_version < "3.13" +networkx==2.5 ; python_version >= "3.7" and python_version < "3.13" +nodeenv==1.8.0 ; python_version >= "3.7" and python_version < "3.13" 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==1.26.0 ; python_version >= "3.9" and python_version < "3.12" -oauthlib==3.2.2 ; python_version >= "3.7" and python_version < "3.12" -orjson==3.9.7 ; 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==3.3.1 ; python_version >= "3.7" and python_version < "3.12" -parsley==1.3 ; python_version >= "3.7" and python_version < "3.12" -paste==3.5.3 ; python_version >= "3.7" and python_version < "3.12" -pastedeploy==3.0.1 ; python_version >= "3.7" and python_version < "3.12" -pebble==5.0.3 ; python_version >= "3.7" and python_version < "3.12" +numpy==1.26.0 ; python_version >= "3.9" and python_version < "3.13" +oauthlib==3.2.2 ; python_version >= "3.7" and python_version < "3.13" +orjson==3.9.7 ; python_version >= "3.7" and python_version < "3.13" +oyaml==1.0 ; python_version >= "3.7" and python_version < "3.13" +packaging==23.2 ; python_version >= "3.7" and python_version < "3.13" +paramiko==3.3.1 ; python_version >= "3.7" and python_version < "3.13" +parsley==1.3 ; python_version >= "3.7" and python_version < "3.13" +paste==3.6.0 ; python_version >= "3.7" and python_version < "3.13" +pastedeploy==3.0.1 ; python_version >= "3.7" and python_version < "3.13" +pebble==5.0.3 ; python_version >= "3.7" and python_version < "3.13" pkgutil-resolve-name==1.3.10 ; python_version >= "3.7" and python_version < "3.9" -prompt-toolkit==3.0.39 ; python_version >= "3.7" and python_version < "3.12" -prov==1.5.1 ; python_version >= "3.7" and python_version < "3.12" -psutil==5.9.5 ; python_version >= "3.7" and python_version < "3.12" -pulsar-galaxy-lib==0.15.5 ; python_version >= "3.7" and python_version < "3.12" -pyasn1==0.5.0 ; python_version >= "3.7" and python_version < "3.12" -pycparser==2.21 ; python_version >= "3.7" and python_version < "3.12" -pycryptodome==3.19.0 ; python_version >= "3.7" and python_version < "3.12" -pydantic-tes==0.1.5 ; python_version >= "3.7" and python_version < "3.12" -pydantic==1.10.13 ; python_version >= "3.7" and python_version < "3.12" -pydantic[email]==1.10.13 ; python_version >= "3.7" and python_version < "3.12" -pydot==1.4.2 ; python_version >= "3.7" and python_version < "3.12" -pyeventsystem==0.1.0 ; python_version >= "3.7" and python_version < "3.12" -pyfaidx==0.7.2.2 ; python_version >= "3.7" and python_version < "3.12" -pygments==2.16.1 ; python_version >= "3.7" and python_version < "3.12" -pyjwt==2.8.0 ; python_version >= "3.7" and python_version < "3.12" -pyjwt[crypto]==2.8.0 ; 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==3.0.9 ; 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" +promise==2.3 ; python_version >= "3.7" and python_version < "3.13" +prompt-toolkit==3.0.39 ; python_version >= "3.7" and python_version < "3.13" +prov==1.5.1 ; python_version >= "3.7" and python_version < "3.13" +psutil==5.9.5 ; python_version >= "3.7" and python_version < "3.13" +pulsar-galaxy-lib==0.15.5 ; python_version >= "3.7" and python_version < "3.13" +pyasn1==0.5.0 ; python_version >= "3.7" and python_version < "3.13" +pycparser==2.21 ; python_version >= "3.7" and python_version < "3.13" +pycryptodome==3.19.0 ; python_version >= "3.7" and python_version < "3.13" +pydantic-tes==0.1.5 ; python_version >= "3.7" and python_version < "3.13" +pydantic==1.10.13 ; python_version >= "3.7" and python_version < "3.13" +pydantic[email]==1.10.13 ; python_version >= "3.7" and python_version < "3.13" +pydot==1.4.2 ; python_version >= "3.7" and python_version < "3.13" +pyeventsystem==0.1.0 ; python_version >= "3.7" and python_version < "3.13" +pyfaidx==0.7.2.2 ; python_version >= "3.7" and python_version < "3.13" +pygments==2.16.1 ; python_version >= "3.7" and python_version < "3.13" +pyjwt==2.8.0 ; python_version >= "3.7" and python_version < "3.13" +pyjwt[crypto]==2.8.0 ; python_version >= "3.7" and python_version < "3.13" +pykwalify==1.8.0 ; python_version >= "3.7" and python_version < "3.13" +pylibmagic==0.4.0 ; python_version >= "3.7" and python_version < "3.13" +pynacl==1.5.0 ; python_version >= "3.7" and python_version < "3.13" +pyparsing==3.0.9 ; python_version >= "3.7" and python_version < "3.13" +pyreadline3==3.4.1 ; sys_platform == "win32" and python_version >= "3.8" and python_version < "3.13" 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" -pysam==0.21.0 ; python_version >= "3.7" and python_version < "3.12" -python-dateutil==2.8.2 ; python_version >= "3.7" and python_version < "3.12" -python-jose==3.3.0 ; python_version >= "3.7" and python_version < "3.12" -python-magic==0.4.27 ; python_version >= "3.7" and python_version < "3.12" -python-multipart==0.0.6 ; python_version >= "3.7" and python_version < "3.12" -python3-openid==3.2.0 ; python_version >= "3.7" and python_version < "3.12" -pytz==2023.3.post1 ; python_version >= "3.7" and python_version < "3.12" -pyyaml==6.0.1 ; python_version >= "3.7" and python_version < "3.12" -pyzmq==25.1.1 ; python_version >= "3.7" and python_version < "3.12" -rdflib==6.2.0 ; python_version >= "3.7" and python_version < "3.12" -refgenconf==0.12.2 ; python_version >= "3.7" and python_version < "3.12" -regex==2023.8.8 ; python_version >= "3.7" and python_version < "3.12" -repoze-lru==0.7 ; python_version >= "3.7" and python_version < "3.12" -requests-oauthlib==1.3.1 ; python_version >= "3.7" and python_version < "3.12" -requests-toolbelt==1.0.0 ; python_version >= "3.7" and python_version < "3.12" -requests-unixsocket==0.3.0 ; python_version >= "3.7" and python_version < "3.12" -requests==2.31.0 ; python_version >= "3.7" and python_version < "3.12" -rich==13.5.3 ; python_version >= "3.7" and python_version < "3.12" -rocrate==0.8.0 ; python_version >= "3.7" and python_version < "3.12" -routes==2.5.1 ; python_version >= "3.7" and python_version < "3.12" -rsa==4.9 ; python_version >= "3.7" and python_version < "3.12" -ruamel-yaml-clib==0.2.7 ; platform_python_implementation == "CPython" and python_version < "3.11" and python_version >= "3.7" -ruamel-yaml==0.17.21 ; python_version >= "3.7" and python_version < "3.12" -s3fs==2023.1.0 ; python_version >= "3.7" and python_version < "3.12" -schema-salad==8.4.20230808163024 ; python_version >= "3.7" and python_version < "3.12" -setuptools-scm==5.0.2 ; python_version >= "3.7" and python_version < "3.12" -setuptools==68.0.0 ; python_version >= "3.7" and python_version < "3.12" -shellescape==3.8.1 ; python_version >= "3.7" and python_version < "3.12" -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==1.4.49 ; 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" -starlette_graphene3==0.6.0 ; python_version >= "3.7" and python_version < "3.12" -starlette==0.27.0 ; python_version >= "3.7" and python_version < "3.12" -supervisor==4.2.5 ; python_version >= "3.7" and python_version < "3.12" -svgwrite==1.4.3 ; python_version >= "3.7" and python_version < "3.12" -tenacity==8.2.3 ; python_version >= "3.7" and python_version < "3.12" -tifffile==2021.11.2 ; python_version >= "3.7" and python_version < "3.12" -tinydb==4.8.0 ; python_version >= "3.7" and python_version < "3.12" +pyrsistent==0.19.3 ; python_version >= "3.7" and python_version < "3.13" +pysam==0.22.0 ; python_version >= "3.7" and python_version < "3.13" +python-dateutil==2.8.2 ; python_version >= "3.7" and python_version < "3.13" +python-jose==3.3.0 ; python_version >= "3.7" and python_version < "3.13" +python-magic==0.4.27 ; python_version >= "3.7" and python_version < "3.13" +python-multipart==0.0.6 ; python_version >= "3.7" and python_version < "3.13" +python3-openid==3.2.0 ; python_version >= "3.7" and python_version < "3.13" +pytz==2023.3.post1 ; python_version >= "3.7" and python_version < "3.13" +pyyaml==6.0.1 ; python_version >= "3.7" and python_version < "3.13" +pyzmq==25.1.1 ; python_version >= "3.7" and python_version < "3.13" +rdflib==6.2.0 ; python_version >= "3.7" and python_version < "3.13" +refgenconf==0.12.2 ; python_version >= "3.7" and python_version < "3.13" +regex==2023.10.3 ; python_version >= "3.7" and python_version < "3.13" +repoze-lru==0.7 ; python_version >= "3.7" and python_version < "3.13" +requests-oauthlib==1.3.1 ; python_version >= "3.7" and python_version < "3.13" +requests-toolbelt==1.0.0 ; python_version >= "3.7" and python_version < "3.13" +requests-unixsocket==0.3.0 ; python_version >= "3.7" and python_version < "3.13" +requests==2.31.0 ; python_version >= "3.7" and python_version < "3.13" +rich==13.6.0 ; python_version >= "3.7" and python_version < "3.13" +rocrate==0.8.0 ; python_version >= "3.7" and python_version < "3.13" +routes==2.5.1 ; python_version >= "3.7" and python_version < "3.13" +rsa==4.9 ; python_version >= "3.7" and python_version < "3.13" +ruamel-yaml-clib==0.2.8 ; platform_python_implementation == "CPython" and python_version < "3.11" and python_version >= "3.7" +ruamel-yaml==0.17.21 ; python_version >= "3.7" and python_version < "3.13" +s3fs==2023.1.0 ; python_version >= "3.7" and python_version < "3.13" +schema-salad==8.4.20230808163024 ; python_version >= "3.7" and python_version < "3.13" +setuptools-scm==5.0.2 ; python_version >= "3.7" and python_version < "3.13" +setuptools==68.0.0 ; python_version >= "3.7" and python_version < "3.13" +shellescape==3.8.1 ; python_version >= "3.7" and python_version < "3.13" +six==1.16.0 ; python_version >= "3.7" and python_version < "3.13" +sniffio==1.3.0 ; python_version >= "3.7" and python_version < "3.13" +social-auth-core[openidconnect]==4.0.3 ; python_version >= "3.7" and python_version < "3.13" +sortedcontainers==2.4.0 ; python_version >= "3.7" and python_version < "3.13" +sqlalchemy==1.4.49 ; python_version >= "3.7" and python_version < "3.13" +sqlitedict==2.1.0 ; python_version >= "3.7" and python_version < "3.13" +sqlparse==0.4.4 ; python_version >= "3.7" and python_version < "3.13" +starlette-context==0.3.5 ; python_version >= "3.7" and python_version < "3.13" +starlette-graphene3==0.6.0 ; python_version >= "3.7" and python_version < "3.13" +starlette==0.27.0 ; python_version >= "3.7" and python_version < "3.13" +supervisor==4.2.5 ; python_version >= "3.7" and python_version < "3.13" +svgwrite==1.4.3 ; python_version >= "3.7" and python_version < "3.13" +tenacity==8.2.3 ; python_version >= "3.7" and python_version < "3.13" +tifffile==2021.11.2 ; python_version >= "3.7" and python_version < "3.13" +tinydb==4.8.0 ; python_version >= "3.7" and python_version < "3.13" tomli==2.0.1 ; python_version >= "3.7" and python_version < "3.11" -tornado==6.2 ; python_version >= "3.7" and python_version < "3.12" -tqdm==4.66.1 ; python_version >= "3.7" and python_version < "3.12" -tuspy==1.0.1 ; python_version >= "3.7" and python_version < "3.12" -tuswsgi==0.5.5 ; python_version >= "3.7" and python_version < "3.12" -typing-extensions==4.7.1 ; python_version >= "3.7" and python_version < "3.12" -tzdata==2023.3 ; python_version >= "3.7" and python_version < "3.12" and platform_system == "Windows" -tzlocal==5.0.1 ; python_version >= "3.7" and python_version < "3.12" -ubiquerg==0.6.3 ; python_version >= "3.7" and python_version < "3.12" -urllib3==1.26.16 ; python_version >= "3.7" and python_version < "3.12" -uvicorn==0.22.0 ; python_version >= "3.7" and python_version < "3.12" -uvloop==0.17.0 ; python_version >= "3.7" and python_version < "3.12" -vine==5.0.0 ; python_version >= "3.7" and python_version < "3.12" -wcwidth==0.2.7 ; python_version >= "3.7" and python_version < "3.12" -webencodings==0.5.1 ; python_version >= "3.7" and python_version < "3.12" -webob==1.8.7 ; python_version >= "3.7" and python_version < "3.12" -whoosh==2.7.4 ; python_version >= "3.7" and python_version < "3.12" -wrapt==1.15.0 ; python_version >= "3.7" and python_version < "3.12" -yacman==0.9.1 ; python_version >= "3.7" and python_version < "3.12" -yarl==1.9.2 ; python_version >= "3.7" and python_version < "3.12" -zipp==3.15.0 ; python_version >= "3.7" and python_version < "3.12" -zipstream-new==1.1.8 ; python_version >= "3.7" and python_version < "3.12" -zstandard==0.21.0 ; python_version >= "3.7" and python_version < "3.12" +tornado==6.2 ; python_version >= "3.7" and python_version < "3.13" +tqdm==4.66.1 ; python_version >= "3.7" and python_version < "3.13" +tuspy==1.0.1 ; python_version >= "3.7" and python_version < "3.13" +tuswsgi==0.5.5 ; python_version >= "3.7" and python_version < "3.13" +typing-extensions==4.7.1 ; python_version >= "3.7" and python_version < "3.13" +tzdata==2023.3 ; python_version >= "3.7" and python_version < "3.13" and platform_system == "Windows" +tzlocal==5.1 ; python_version >= "3.7" and python_version < "3.13" +ubiquerg==0.6.3 ; python_version >= "3.7" and python_version < "3.13" +urllib3==1.26.17 ; python_version >= "3.7" and python_version < "3.13" +uvicorn==0.22.0 ; python_version >= "3.7" and python_version < "3.13" +uvloop==0.17.0 ; python_version >= "3.7" and python_version < "3.13" +vine==5.0.0 ; python_version >= "3.7" and python_version < "3.13" +wcwidth==0.2.8 ; python_version >= "3.7" and python_version < "3.13" +webencodings==0.5.1 ; python_version >= "3.7" and python_version < "3.13" +webob==1.8.7 ; python_version >= "3.7" and python_version < "3.13" +whoosh==2.7.4 ; python_version >= "3.7" and python_version < "3.13" +wrapt==1.15.0 ; python_version >= "3.7" and python_version < "3.13" +yacman==0.9.2 ; python_version >= "3.7" and python_version < "3.13" +yarl==1.9.2 ; python_version >= "3.7" and python_version < "3.13" +zipp==3.15.0 ; python_version >= "3.7" and python_version < "3.13" +zipstream-new==1.1.8 ; python_version >= "3.7" and python_version < "3.13" +zstandard==0.21.0 ; python_version >= "3.7" and python_version < "3.13" diff --git a/lib/galaxy/dependencies/pinned-typecheck-requirements.txt b/lib/galaxy/dependencies/pinned-typecheck-requirements.txt index bd28fe6209bf..74d50158e43d 100644 --- a/lib/galaxy/dependencies/pinned-typecheck-requirements.txt +++ b/lib/galaxy/dependencies/pinned-typecheck-requirements.txt @@ -1,22 +1,22 @@ -cffi==1.15.1 ; python_version >= "3.7" and python_version < "3.12" -cryptography==41.0.4 ; python_version >= "3.7" and python_version < "3.12" -mypy-extensions==1.0.0 ; python_version >= "3.7" and python_version < "3.12" -mypy==1.4.1 ; python_version >= "3.7" and python_version < "3.12" -pycparser==2.21 ; python_version >= "3.7" and python_version < "3.12" -pydantic==1.10.13 ; python_version >= "3.7" and python_version < "3.12" +cffi==1.15.1 ; python_version >= "3.7" and python_version < "3.13" +cryptography==41.0.4 ; python_version >= "3.7" and python_version < "3.13" +mypy-extensions==1.0.0 ; python_version >= "3.7" and python_version < "3.13" +mypy==1.4.1 ; python_version >= "3.7" and python_version < "3.13" +pycparser==2.21 ; python_version >= "3.7" and python_version < "3.13" +pydantic==1.10.13 ; python_version >= "3.7" and python_version < "3.13" tomli==2.0.1 ; python_version >= "3.7" and python_version < "3.11" typed-ast==1.5.5 ; python_version >= "3.7" and python_version < "3.8" -types-bleach==6.0.0.4 ; python_version >= "3.7" and python_version < "3.12" -types-boto==2.49.18.9 ; python_version >= "3.7" and python_version < "3.12" -types-contextvars==2.4.7.3 ; python_version >= "3.7" and python_version < "3.12" -types-dataclasses==0.6.6 ; python_version >= "3.7" and python_version < "3.12" -types-docutils==0.20.0.3 ; python_version >= "3.7" and python_version < "3.12" -types-markdown==3.4.2.10 ; python_version >= "3.7" and python_version < "3.12" -types-paramiko==3.3.0.0 ; python_version >= "3.7" and python_version < "3.12" -types-pkg-resources==0.1.3 ; python_version >= "3.7" and python_version < "3.12" -types-python-dateutil==2.8.19.14 ; python_version >= "3.7" and python_version < "3.12" -types-pyyaml==6.0.12.12 ; python_version >= "3.7" and python_version < "3.12" -types-requests==2.31.0.6 ; python_version >= "3.7" and python_version < "3.12" -types-six==1.16.21.9 ; python_version >= "3.7" and python_version < "3.12" -types-urllib3==1.26.25.14 ; python_version >= "3.7" and python_version < "3.12" -typing-extensions==4.7.1 ; python_version >= "3.7" and python_version < "3.12" +types-bleach==6.0.0.5 ; python_version >= "3.7" and python_version < "3.13" +types-boto==2.49.18.9 ; python_version >= "3.7" and python_version < "3.13" +types-contextvars==2.4.7.3 ; python_version >= "3.7" and python_version < "3.13" +types-dataclasses==0.6.6 ; python_version >= "3.7" and python_version < "3.13" +types-docutils==0.20.0.3 ; python_version >= "3.7" and python_version < "3.13" +types-markdown==3.4.2.10 ; python_version >= "3.7" and python_version < "3.13" +types-paramiko==3.3.0.0 ; python_version >= "3.7" and python_version < "3.13" +types-pkg-resources==0.1.3 ; python_version >= "3.7" and python_version < "3.13" +types-python-dateutil==2.8.19.14 ; python_version >= "3.7" and python_version < "3.13" +types-pyyaml==6.0.12.12 ; python_version >= "3.7" and python_version < "3.13" +types-requests==2.31.0.6 ; python_version >= "3.7" and python_version < "3.13" +types-six==1.16.21.9 ; python_version >= "3.7" and python_version < "3.13" +types-urllib3==1.26.25.14 ; python_version >= "3.7" and python_version < "3.13" +typing-extensions==4.7.1 ; python_version >= "3.7" and python_version < "3.13" diff --git a/lib/galaxy/dependencies/update.sh b/lib/galaxy/dependencies/update.sh index 7771ea30791e..c294d7652eef 100755 --- a/lib/galaxy/dependencies/update.sh +++ b/lib/galaxy/dependencies/update.sh @@ -6,8 +6,8 @@ set -e -SUPPORTED_PYTHON_VERSIONS="3.7 3.8 3.9 3.10 3.11" -NOT_SUPPORTED_NEXT_PYTHON_VERSION="3.12" +SUPPORTED_PYTHON_VERSIONS="3.7 3.8 3.9 3.10 3.11 3.12" +NOT_SUPPORTED_NEXT_PYTHON_VERSION="3.13" this_directory="$(cd "$(dirname "$0")" > /dev/null && pwd)" diff --git a/packages/app/setup.cfg b/packages/app/setup.cfg index c8cc845deed1..3869d9db2d2d 100644 --- a/packages/app/setup.cfg +++ b/packages/app/setup.cfg @@ -14,6 +14,7 @@ classifiers = Programming Language :: Python :: 3.9 Programming Language :: Python :: 3.10 Programming Language :: Python :: 3.11 + Programming Language :: Python :: 3.12 Topic :: Software Development Topic :: Software Development :: Code Generators Topic :: Software Development :: Testing diff --git a/packages/auth/setup.cfg b/packages/auth/setup.cfg index cca3a9b7ad7c..7dd09257f05b 100644 --- a/packages/auth/setup.cfg +++ b/packages/auth/setup.cfg @@ -14,6 +14,7 @@ classifiers = Programming Language :: Python :: 3.9 Programming Language :: Python :: 3.10 Programming Language :: Python :: 3.11 + Programming Language :: Python :: 3.12 Topic :: Software Development Topic :: Software Development :: Code Generators Topic :: Software Development :: Testing @@ -39,4 +40,4 @@ python_requires = >=3.7 [options.packages.find] exclude = - tests* \ No newline at end of file + tests* diff --git a/packages/config/setup.cfg b/packages/config/setup.cfg index 16d2815d2a2e..8c9854d0e555 100644 --- a/packages/config/setup.cfg +++ b/packages/config/setup.cfg @@ -14,6 +14,7 @@ classifiers = Programming Language :: Python :: 3.9 Programming Language :: Python :: 3.10 Programming Language :: Python :: 3.11 + Programming Language :: Python :: 3.12 Topic :: Software Development Topic :: Software Development :: Code Generators Topic :: Software Development :: Testing @@ -46,4 +47,4 @@ console_scripts = [options.packages.find] exclude = - tests* \ No newline at end of file + tests* diff --git a/packages/data/setup.cfg b/packages/data/setup.cfg index 02f74386b9d5..11f9c26a9f94 100644 --- a/packages/data/setup.cfg +++ b/packages/data/setup.cfg @@ -14,6 +14,7 @@ classifiers = Programming Language :: Python :: 3.9 Programming Language :: Python :: 3.10 Programming Language :: Python :: 3.11 + Programming Language :: Python :: 3.12 Topic :: Software Development Topic :: Software Development :: Code Generators Topic :: Software Development :: Testing diff --git a/packages/files/setup.cfg b/packages/files/setup.cfg index 9f89c257b476..56f3e60eec31 100644 --- a/packages/files/setup.cfg +++ b/packages/files/setup.cfg @@ -14,6 +14,7 @@ classifiers = Programming Language :: Python :: 3.9 Programming Language :: Python :: 3.10 Programming Language :: Python :: 3.11 + Programming Language :: Python :: 3.12 Topic :: Software Development Topic :: Software Development :: Code Generators Topic :: Software Development :: Testing diff --git a/packages/job_execution/setup.cfg b/packages/job_execution/setup.cfg index ea1943235b8a..47b15dea2ed8 100644 --- a/packages/job_execution/setup.cfg +++ b/packages/job_execution/setup.cfg @@ -14,6 +14,7 @@ classifiers = Programming Language :: Python :: 3.9 Programming Language :: Python :: 3.10 Programming Language :: Python :: 3.11 + Programming Language :: Python :: 3.12 Topic :: Software Development Topic :: Software Development :: Code Generators Topic :: Software Development :: Testing @@ -49,4 +50,4 @@ console_scripts = [options.packages.find] exclude = - tests* \ No newline at end of file + tests* diff --git a/packages/job_metrics/setup.cfg b/packages/job_metrics/setup.cfg index d9576a25c86d..4d16b381adcc 100644 --- a/packages/job_metrics/setup.cfg +++ b/packages/job_metrics/setup.cfg @@ -14,6 +14,7 @@ classifiers = Programming Language :: Python :: 3.9 Programming Language :: Python :: 3.10 Programming Language :: Python :: 3.11 + Programming Language :: Python :: 3.12 Topic :: Software Development Topic :: Software Development :: Code Generators Topic :: Software Development :: Testing @@ -38,4 +39,4 @@ python_requires = >=3.7 [options.packages.find] exclude = - tests* \ No newline at end of file + tests* diff --git a/packages/meta/setup.cfg b/packages/meta/setup.cfg index 516107f5088d..3a32a5e137b6 100644 --- a/packages/meta/setup.cfg +++ b/packages/meta/setup.cfg @@ -15,6 +15,7 @@ classifiers = Programming Language :: Python :: 3.9 Programming Language :: Python :: 3.10 Programming Language :: Python :: 3.11 + Programming Language :: Python :: 3.12 Topic :: Scientific/Engineering :: Bio-Informatics Topic :: Software Development Topic :: Software Development :: Code Generators diff --git a/packages/navigation/setup.cfg b/packages/navigation/setup.cfg index 3b16102ad68c..b3ee2fea2e0d 100644 --- a/packages/navigation/setup.cfg +++ b/packages/navigation/setup.cfg @@ -14,6 +14,7 @@ classifiers = Programming Language :: Python :: 3.9 Programming Language :: Python :: 3.10 Programming Language :: Python :: 3.11 + Programming Language :: Python :: 3.12 Topic :: Software Development Topic :: Software Development :: Code Generators Topic :: Software Development :: Testing @@ -39,4 +40,4 @@ python_requires = >=3.7 [options.packages.find] exclude = - tests* \ No newline at end of file + tests* diff --git a/packages/objectstore/setup.cfg b/packages/objectstore/setup.cfg index 69fc1352966c..b83e74a8c6d3 100644 --- a/packages/objectstore/setup.cfg +++ b/packages/objectstore/setup.cfg @@ -14,6 +14,7 @@ classifiers = Programming Language :: Python :: 3.9 Programming Language :: Python :: 3.10 Programming Language :: Python :: 3.11 + Programming Language :: Python :: 3.12 Topic :: Software Development Topic :: Software Development :: Code Generators Topic :: Software Development :: Testing @@ -40,4 +41,4 @@ python_requires = >=3.7 [options.packages.find] exclude = - tests* \ No newline at end of file + tests* diff --git a/packages/schema/setup.cfg b/packages/schema/setup.cfg index 507f563909ea..1fdec2328835 100644 --- a/packages/schema/setup.cfg +++ b/packages/schema/setup.cfg @@ -13,6 +13,8 @@ classifiers = Programming Language :: Python :: 3.8 Programming Language :: Python :: 3.9 Programming Language :: Python :: 3.10 + Programming Language :: Python :: 3.11 + Programming Language :: Python :: 3.12 Topic :: Software Development Topic :: Software Development :: Code Generators Topic :: Software Development :: Testing diff --git a/packages/selenium/setup.cfg b/packages/selenium/setup.cfg index a95b3a449dfa..8f351396bed7 100644 --- a/packages/selenium/setup.cfg +++ b/packages/selenium/setup.cfg @@ -14,6 +14,7 @@ classifiers = Programming Language :: Python :: 3.9 Programming Language :: Python :: 3.10 Programming Language :: Python :: 3.11 + Programming Language :: Python :: 3.12 Topic :: Software Development Topic :: Software Development :: Code Generators Topic :: Software Development :: Testing @@ -47,4 +48,4 @@ console_scripts = [options.packages.find] exclude = - tests* \ No newline at end of file + tests* diff --git a/packages/test_api/setup.cfg b/packages/test_api/setup.cfg index 2a09121053d3..5ba684fff4b2 100644 --- a/packages/test_api/setup.cfg +++ b/packages/test_api/setup.cfg @@ -14,6 +14,7 @@ classifiers = Programming Language :: Python :: 3.9 Programming Language :: Python :: 3.10 Programming Language :: Python :: 3.11 + Programming Language :: Python :: 3.12 Topic :: Software Development Topic :: Software Development :: Code Generators Topic :: Software Development :: Testing @@ -46,4 +47,4 @@ driver = [options.packages.find] exclude = - tests* \ No newline at end of file + tests* diff --git a/packages/test_base/setup.cfg b/packages/test_base/setup.cfg index a1eec0ef392e..b370c2c55db1 100644 --- a/packages/test_base/setup.cfg +++ b/packages/test_base/setup.cfg @@ -14,6 +14,7 @@ classifiers = Programming Language :: Python :: 3.9 Programming Language :: Python :: 3.10 Programming Language :: Python :: 3.11 + Programming Language :: Python :: 3.12 Topic :: Software Development Topic :: Software Development :: Code Generators Topic :: Software Development :: Testing @@ -45,4 +46,4 @@ python_requires = >=3.7 [options.packages.find] exclude = - tests* \ No newline at end of file + tests* diff --git a/packages/test_driver/setup.cfg b/packages/test_driver/setup.cfg index cd64afd37a8c..9542bd8fbd2f 100644 --- a/packages/test_driver/setup.cfg +++ b/packages/test_driver/setup.cfg @@ -14,6 +14,7 @@ classifiers = Programming Language :: Python :: 3.9 Programming Language :: Python :: 3.10 Programming Language :: Python :: 3.11 + Programming Language :: Python :: 3.12 Topic :: Software Development Topic :: Software Development :: Code Generators Topic :: Software Development :: Testing @@ -47,4 +48,4 @@ python_requires = >=3.7 [options.packages.find] exclude = - tests* \ No newline at end of file + tests* diff --git a/packages/test_selenium/setup.cfg b/packages/test_selenium/setup.cfg index dca41568d040..5cc9fd6ff879 100644 --- a/packages/test_selenium/setup.cfg +++ b/packages/test_selenium/setup.cfg @@ -14,6 +14,7 @@ classifiers = Programming Language :: Python :: 3.9 Programming Language :: Python :: 3.10 Programming Language :: Python :: 3.11 + Programming Language :: Python :: 3.12 Topic :: Software Development Topic :: Software Development :: Code Generators Topic :: Software Development :: Testing diff --git a/packages/tool_shed/setup.cfg b/packages/tool_shed/setup.cfg index 4c5cc82377d2..df5b81d2c36a 100644 --- a/packages/tool_shed/setup.cfg +++ b/packages/tool_shed/setup.cfg @@ -13,6 +13,8 @@ classifiers = Programming Language :: Python :: 3.8 Programming Language :: Python :: 3.9 Programming Language :: Python :: 3.10 + Programming Language :: Python :: 3.11 + Programming Language :: Python :: 3.12 Topic :: Software Development Topic :: Software Development :: Code Generators Topic :: Software Development :: Testing diff --git a/packages/tool_util/setup.cfg b/packages/tool_util/setup.cfg index 817bd9080842..2f8d1a538d62 100644 --- a/packages/tool_util/setup.cfg +++ b/packages/tool_util/setup.cfg @@ -14,6 +14,7 @@ classifiers = Programming Language :: Python :: 3.9 Programming Language :: Python :: 3.10 Programming Language :: Python :: 3.11 + Programming Language :: Python :: 3.12 Topic :: Software Development Topic :: Software Development :: Code Generators Topic :: Software Development :: Testing diff --git a/packages/tours/setup.cfg b/packages/tours/setup.cfg index 1186d0ad6ccf..f9d9eb8a4668 100644 --- a/packages/tours/setup.cfg +++ b/packages/tours/setup.cfg @@ -14,6 +14,7 @@ classifiers = Programming Language :: Python :: 3.9 Programming Language :: Python :: 3.10 Programming Language :: Python :: 3.11 + Programming Language :: Python :: 3.12 Topic :: Software Development Topic :: Software Development :: Code Generators Topic :: Software Development :: Testing diff --git a/packages/util/setup.cfg b/packages/util/setup.cfg index 03afa41b853b..db3c2e9c1c54 100644 --- a/packages/util/setup.cfg +++ b/packages/util/setup.cfg @@ -14,6 +14,7 @@ classifiers = Programming Language :: Python :: 3.9 Programming Language :: Python :: 3.10 Programming Language :: Python :: 3.11 + Programming Language :: Python :: 3.12 Topic :: Software Development Topic :: Software Development :: Code Generators Topic :: Software Development :: Testing diff --git a/packages/web_apps/setup.cfg b/packages/web_apps/setup.cfg index f2468f577aba..613e94b61df6 100644 --- a/packages/web_apps/setup.cfg +++ b/packages/web_apps/setup.cfg @@ -14,6 +14,7 @@ classifiers = Programming Language :: Python :: 3.9 Programming Language :: Python :: 3.10 Programming Language :: Python :: 3.11 + Programming Language :: Python :: 3.12 Topic :: Software Development Topic :: Software Development :: Code Generators Topic :: Software Development :: Testing diff --git a/packages/web_framework/setup.cfg b/packages/web_framework/setup.cfg index 6919f2c9b07c..496aefc1f1da 100644 --- a/packages/web_framework/setup.cfg +++ b/packages/web_framework/setup.cfg @@ -14,6 +14,7 @@ classifiers = Programming Language :: Python :: 3.9 Programming Language :: Python :: 3.10 Programming Language :: Python :: 3.11 + Programming Language :: Python :: 3.12 Topic :: Software Development Topic :: Software Development :: Code Generators Topic :: Software Development :: Testing diff --git a/packages/web_stack/setup.cfg b/packages/web_stack/setup.cfg index 54b91dfad20c..5a1ba7de0156 100644 --- a/packages/web_stack/setup.cfg +++ b/packages/web_stack/setup.cfg @@ -14,6 +14,7 @@ classifiers = Programming Language :: Python :: 3.9 Programming Language :: Python :: 3.10 Programming Language :: Python :: 3.11 + Programming Language :: Python :: 3.12 Topic :: Software Development Topic :: Software Development :: Code Generators Topic :: Software Development :: Testing @@ -39,4 +40,4 @@ python_requires = >=3.7 [options.packages.find] exclude = - tests* \ No newline at end of file + tests* diff --git a/pyproject.toml b/pyproject.toml index 4794d781629d..6ee0d2732135 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -95,7 +95,7 @@ pykwalify = "*" pylibmagic = "*" 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 = ">=3.7,<3.13" # Keep maximum version strict to appease numpy and scipy python-dateutil = "*" python-magic = "*" python-multipart = "*" # required to support form parsing in FastAPI/Starlette