Add support for Python 3.12

galaxyproject · Jan 21, 2024 · 6860c9a · 6860c9a
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commit 6860c9a
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diff --git a/.github/workflows/first_startup.yaml b/.github/workflows/first_startup.yaml
@@ -23,7 +23,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.8', '3.11']
+        python-version: ['3.8', '3.12']
     defaults:
       run:
         shell: bash -l {0}

diff --git a/.github/workflows/lint.yaml b/.github/workflows/lint.yaml
@@ -22,7 +22,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.8', '3.11']
+        python-version: ['3.8', '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/lint_openapi_schema.yml b/.github/workflows/lint_openapi_schema.yml
@@ -20,7 +20,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.8', '3.11']
+        python-version: ['3.8', '3.12']
     steps:
       - uses: actions/checkout@v3
         with:

diff --git a/.github/workflows/osx_startup.yaml b/.github/workflows/osx_startup.yaml
@@ -21,7 +21,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.8', '3.11']
+        python-version: ['3.8', '3.12']
     defaults:
       run:
         shell: bash -l {0}

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: ['3.8', '3.11']
+        python-version: ['3.8', '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: ['3.8', '3.11']
+        python-version: ['3.8', '3.12']
     steps:
       - uses: actions/checkout@v3
         with:

diff --git a/.github/workflows/toolshed.yaml b/.github/workflows/toolshed.yaml
@@ -21,7 +21,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.8', '3.11']
+        python-version: ['3.8', '3.12']
         shed-api: ['v1', 'v2']
         test-install-client: ['galaxy_api', 'standalone']
     services:

diff --git a/.github/workflows/unit.yaml b/.github/workflows/unit.yaml
@@ -20,7 +20,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.8', '3.11']
+        python-version: ['3.8', '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-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
@@ -1,21 +1,23 @@
-cffi==1.16.0 ; python_version >= "3.8" and python_version < "3.12"
-cryptography==41.0.7 ; python_version >= "3.8" and python_version < "3.12"
-mypy-extensions==1.0.0 ; python_version >= "3.8" and python_version < "3.12"
-mypy==1.8.0 ; python_version >= "3.8" and python_version < "3.12"
-pycparser==2.21 ; python_version >= "3.8" and python_version < "3.12"
-pydantic==2.5.3 ; python_version >= "3.8" and python_version < "3.12"
+annotated-types==0.6.0 ; python_version >= "3.8" and python_version < "3.13"
+cffi==1.16.0 ; python_version >= "3.8" and python_version < "3.13"
+cryptography==41.0.7 ; python_version >= "3.8" and python_version < "3.13"
+mypy-extensions==1.0.0 ; python_version >= "3.8" and python_version < "3.13"
+mypy==1.8.0 ; python_version >= "3.8" and python_version < "3.13"
+pycparser==2.21 ; python_version >= "3.8" and python_version < "3.13"
+pydantic-core==2.14.6 ; python_version >= "3.8" and python_version < "3.13"
+pydantic==2.5.3 ; python_version >= "3.8" and python_version < "3.13"
 tomli==2.0.1 ; python_version >= "3.8" and python_version < "3.11"
-types-bleach==6.1.0.1 ; python_version >= "3.8" and python_version < "3.12"
-types-boto==2.49.18.9 ; python_version >= "3.8" and python_version < "3.12"
-types-contextvars==2.4.7.3 ; python_version >= "3.8" and python_version < "3.12"
-types-dataclasses==0.6.6 ; python_version >= "3.8" and python_version < "3.12"
-types-docutils==0.20.0.20240106 ; python_version >= "3.8" and python_version < "3.12"
-types-markdown==3.5.0.20240106 ; python_version >= "3.8" and python_version < "3.12"
-types-paramiko==3.4.0.20240106 ; python_version >= "3.8" and python_version < "3.12"
-types-pkg-resources==0.1.3 ; python_version >= "3.8" and python_version < "3.12"
-types-python-dateutil==2.8.19.20240106 ; python_version >= "3.8" and python_version < "3.12"
-types-pyyaml==6.0.12.12 ; python_version >= "3.8" and python_version < "3.12"
-types-requests==2.31.0.6 ; python_version >= "3.8" and python_version < "3.12"
-types-six==1.16.21.20240106 ; python_version >= "3.8" and python_version < "3.12"
-types-urllib3==1.26.25.14 ; python_version >= "3.8" and python_version < "3.12"
-typing-extensions==4.9.0 ; python_version >= "3.8" and python_version < "3.12"
+types-bleach==6.1.0.1 ; python_version >= "3.8" and python_version < "3.13"
+types-boto==2.49.18.9 ; python_version >= "3.8" and python_version < "3.13"
+types-contextvars==2.4.7.3 ; python_version >= "3.8" and python_version < "3.13"
+types-dataclasses==0.6.6 ; python_version >= "3.8" and python_version < "3.13"
+types-docutils==0.20.0.20240106 ; python_version >= "3.8" and python_version < "3.13"
+types-markdown==3.5.0.20240106 ; python_version >= "3.8" and python_version < "3.13"
+types-paramiko==3.4.0.20240106 ; python_version >= "3.8" and python_version < "3.13"
+types-pkg-resources==0.1.3 ; python_version >= "3.8" and python_version < "3.13"
+types-python-dateutil==2.8.19.20240106 ; python_version >= "3.8" and python_version < "3.13"
+types-pyyaml==6.0.12.12 ; python_version >= "3.8" and python_version < "3.13"
+types-requests==2.31.0.6 ; python_version >= "3.8" and python_version < "3.13"
+types-six==1.16.21.20240106 ; python_version >= "3.8" and python_version < "3.13"
+types-urllib3==1.26.25.14 ; python_version >= "3.8" and python_version < "3.13"
+typing-extensions==4.9.0 ; python_version >= "3.8" and python_version < "3.13"
diff --git a/lib/galaxy/dependencies/update.sh b/lib/galaxy/dependencies/update.sh
@@ -6,8 +6,8 @@
 
 set -e
 
-SUPPORTED_PYTHON_VERSIONS="3.8 3.9 3.10 3.11"
-NOT_SUPPORTED_NEXT_PYTHON_VERSION="3.12"
+SUPPORTED_PYTHON_VERSIONS="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
@@ -13,6 +13,7 @@ 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
@@ -13,6 +13,7 @@ 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/config/setup.cfg b/packages/config/setup.cfg
@@ -13,6 +13,7 @@ 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/data/setup.cfg b/packages/data/setup.cfg
@@ -13,6 +13,7 @@ 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
@@ -13,6 +13,7 @@ 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
@@ -13,6 +13,7 @@ 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_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
@@ -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 :: Scientific/Engineering :: Bio-Informatics
     Topic :: Software Development
     Topic :: Software Development :: Code Generators

diff --git a/packages/navigation/setup.cfg b/packages/navigation/setup.cfg
@@ -13,6 +13,7 @@ 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/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

diff --git a/packages/schema/setup.cfg b/packages/schema/setup.cfg
@@ -12,6 +12,8 @@ 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
@@ -13,6 +13,7 @@ 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/test_api/setup.cfg b/packages/test_api/setup.cfg
@@ -13,6 +13,7 @@ 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/test_base/setup.cfg b/packages/test_base/setup.cfg
@@ -13,6 +13,7 @@ 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/test_driver/setup.cfg b/packages/test_driver/setup.cfg
@@ -13,6 +13,7 @@ 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/test_selenium/setup.cfg b/packages/test_selenium/setup.cfg
@@ -13,6 +13,7 @@ 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 +13,7 @@ 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_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
@@ -13,6 +13,7 @@ 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
@@ -13,6 +13,7 @@ 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
@@ -13,6 +13,7 @@ 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
@@ -13,6 +13,7 @@ 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/pyproject.toml b/pyproject.toml
@@ -93,7 +93,7 @@ pykwalify = "*"
 pylibmagic = "*"
 pyparsing = "*"
 pysam = ">=0.21"  # for Python 3.11 support on macOS
-python = ">=3.8,<3.12"  # Keep maximum version strict to appease numpy and scipy
+python = ">=3.8,<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