add support for python3.12

galaxyproject · Oct 6, 2023 · d582d8b · d582d8b
1 parent bdcd16e
commit d582d8b
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diff --git 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
@@ -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
@@ -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
@@ -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
@@ -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
diff --git 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
diff --git 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
@@ -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
@@ -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
@@ -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*
+    tests*
diff --git 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*
+    tests*
diff --git 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
@@ -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
@@ -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*
+    tests*
diff --git 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*
+    tests*
diff --git 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
@@ -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*
+    tests*
diff --git 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*
+    tests*
diff --git 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
@@ -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*
+    tests*
diff --git 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*
+    tests*
diff --git 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*
+    tests*
diff --git 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*
+    tests*
diff --git 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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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*
+    tests*
diff --git 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