Merge pull request #16796 from tuncK/py3_12

Add support for Python 3.12
galaxyproject · Jan 22, 2024 · 6d58253 · 6d58253
2 parents 5f25a48 + 9978004
commit 6d58253
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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)"
 
@@ -86,9 +86,9 @@ split_requirement () {
 }
 
 # For some packages there is no recent version that works on all Python versions
-# supported by Galaxy, so Poetry resorts to an old version that didn't have a
-# maximum Python version pin. Here we replace any such requirement with multiple
-# Python-version-specific requirements.
+# supported by Galaxy, so Poetry resorts to an old version. Here we replace any
+# such requirement with multiple Python-version-specific requirements.
+# Packages which specify a maximum Python version pin:
 split_requirement matplotlib
 split_requirement numpy
 split_requirement scipy
diff --git a/lib/galaxy/dependencies/update_lint_requirements.sh b/lib/galaxy/dependencies/update_lint_requirements.sh
@@ -3,9 +3,8 @@
 set -e
 
 # This script updates the pinned requirements for linting.
-# The lint requirements are split from the other ones due to incompatible
-# dependencies: flake8 requires importlib-metadata 4.2, while the Galaxy's core
-# dependencies depend on importlib-metadata 4.13.
+# The lint requirements are split from the other ones since they often have
+# incompatible dependencies.
 
 THIS_DIRECTORY="$(cd "$(dirname "$0")" > /dev/null && pwd)"
 

diff --git a/lib/galaxy/files/sources/invenio.py b/lib/galaxy/files/sources/invenio.py
@@ -294,7 +294,7 @@ def _get_download_file_url(self, record_id: str, filename: str, user_context: Op
             # TODO: This is a temporary workaround for the fact that the "content" API
             # does not support downloading files from S3 or other remote storage classes.
             # More info: https://inveniordm.docs.cern.ch/reference/file_storage/#remote-files-r
-            download_file_content_url = f"{file_details_url.replace('/api','')}?download=1"
+            download_file_content_url = f"{file_details_url.replace('/api', '')}?download=1"
         return download_file_content_url
 
     def _is_api_url(self, url: str) -> bool:

diff --git a/lib/galaxy/util/resources.py b/lib/galaxy/util/resources.py
@@ -2,20 +2,17 @@
 """
 import sys
 
-if sys.version_info >= (3, 12):
-    from importlib.resources import (
-        Anchor,
-        as_file,
-        files,
-    )
-    from importlib.resources.abc import Traversable
-elif sys.version_info >= (3, 9):
-    from importlib.abc import Traversable
+if sys.version_info >= (3, 9):
     from importlib.resources import (
         as_file,
         files,
         Package as Anchor,
     )
+
+    if sys.version_info >= (3, 12):
+        from importlib.resources.abc import Traversable
+    else:
+        from importlib.abc import Traversable
 else:
     from importlib_resources import (
         as_file,

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
@@ -51,7 +52,7 @@ jstree =
     dictobj
 template =
     Cheetah3!=3.2.6.post2
-    future
+    future @ git+https://github.com/nsoranzo/python-future.git@python312-imp-module_past
 
 [options.packages.find]
 exclude =

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