Add support for Python 3.11

- Update Python dependencies that didn't have a cp311 wheel: h5py and psycopg2-binary. - For packages for which there is no recent version that works on all Python versions supported by Galaxy (numpy and scipy), replace old requirement with multiple Python-version-specific requirements.
galaxyproject · Feb 2, 2023 · 4ca163b · 4ca163b
1 parent 27cd9bb
commit 4ca163b
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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', '3.10']
+        python-version: ['3.7', '3.11']
     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', '3.10']
+        python-version: ['3.7', '3.11']
     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', '3.10']
+        python-version: ['3.7', '3.11']
     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', '3.10']
+        python-version: ['3.7', '3.11']
     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', '3.10']
+        python-version: ['3.7', '3.11']
     steps:
       - uses: actions/checkout@v3
         with:

diff --git a/lib/galaxy/dependencies/conditional-requirements.txt b/lib/galaxy/dependencies/conditional-requirements.txt
@@ -1,5 +1,5 @@
 # These dependencies are only required when certain config options are set
-psycopg2-binary==2.9.1
+psycopg2-binary==2.9.5
 mysqlclient
 fluent-logger
 sentry-sdk

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/update.sh b/lib/galaxy/dependencies/update.sh
@@ -6,10 +6,13 @@
 
 set -e
 
+SUPPORTED_PYTHON_VERSIONS="3.7 3.8 3.9 3.10 3.11"
+NOT_SUPPORTED_NEXT_PYTHON_VERSION="3.12"
+
 this_directory="$(cd "$(dirname "$0")" > /dev/null && pwd)"
 
 usage() {
-    printf "Usage: %s: [-a] [pkg_spec...]\n" ${0##*/} >&2
+    printf "Usage: %s: [-a] [pkg_spec...]\n" "${0##*/}" >&2
 }
 
 add=
@@ -23,7 +26,7 @@ do
            ;;
     esac
 done
-shift $(($OPTIND - 1))
+shift $((OPTIND - 1))
 
 if [ -n "$add" ] && [ $# -eq 0 ]; then
     printf "When adding (-a), you must provide at least one package specification.\n" >&2
@@ -42,6 +45,48 @@ else
     poetry add -vv --lock "$@"
 fi
 
-# Update pinned requirements.
-poetry export -f requirements.txt --without-hashes --output "$this_directory/pinned-requirements.txt"
-poetry export --only dev -f requirements.txt --without-hashes --output "$this_directory/dev-requirements.txt"
+# Update pinned requirements files.
+PINNED_REQUIREMENTS_FILE=$this_directory/pinned-requirements.txt
+PINNED_DEV_REQUIREMENTS_FILE=$this_directory/dev-requirements.txt
+poetry export -f requirements.txt --without-hashes --output "$PINNED_REQUIREMENTS_FILE"
+poetry export --only dev -f requirements.txt --without-hashes --output "$PINNED_DEV_REQUIREMENTS_FILE"
+
+# Fix requirements
+
+latest_package_version_for_python_version () {
+    PIP_INDEX_OUT=$(pip index versions --python-version "$2" "$1")
+    echo "$PIP_INDEX_OUT" | head -n 1 | sed -e 's/.* (\(.*\)).*/\1/'
+}
+
+split_requirement () {
+    PACKAGE_NAME=$1
+
+    if ! pip index version --help >/dev/null; then
+        echo "pip >= 21.2.1 required for the 'index' command"
+        exit 1
+    fi
+
+    NEW_REQUIREMENTS=
+    PREVIOUS_LATEST_PACKAGE_VERSION=
+    for PYTHON_VERSION in $SUPPORTED_PYTHON_VERSIONS; do
+        LATEST_PACKAGE_VERSION=$(latest_package_version_for_python_version "$PACKAGE_NAME" "$PYTHON_VERSION")
+        if [ -z "$NEW_REQUIREMENTS" ]; then
+            NEW_REQUIREMENTS="$PACKAGE_NAME==$LATEST_PACKAGE_VERSION ; python_version >= \"$PYTHON_VERSION\""
+        elif [ "$LATEST_PACKAGE_VERSION" != "$PREVIOUS_LATEST_PACKAGE_VERSION" ]; then
+            NEW_REQUIREMENTS="$NEW_REQUIREMENTS and python_version < \"$PYTHON_VERSION\"\n$PACKAGE_NAME==$LATEST_PACKAGE_VERSION ; python_version >= \"$PYTHON_VERSION\""
+        fi
+        PREVIOUS_LATEST_PACKAGE_VERSION=$LATEST_PACKAGE_VERSION
+    done
+    if [ -n "$NOT_SUPPORTED_NEXT_PYTHON_VERSION" ]; then
+        NEW_REQUIREMENTS="$NEW_REQUIREMENTS and python_version < \"$NOT_SUPPORTED_NEXT_PYTHON_VERSION\""
+    fi
+
+    sed -i.orig -e "s/^$PACKAGE_NAME==.*/$NEW_REQUIREMENTS/" "$PINNED_REQUIREMENTS_FILE" "$PINNED_DEV_REQUIREMENTS_FILE"
+}
+
+# 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.
+split_requirement numpy
+split_requirement scipy
diff --git a/packages/app/setup.cfg b/packages/app/setup.cfg
@@ -13,6 +13,7 @@ classifiers =
     Programming Language :: Python :: 3.8
     Programming Language :: Python :: 3.9
     Programming Language :: Python :: 3.10
+    Programming Language :: Python :: 3.11
     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 :: 3.8
     Programming Language :: Python :: 3.9
     Programming Language :: Python :: 3.10
+    Programming Language :: Python :: 3.11
     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 :: 3.8
     Programming Language :: Python :: 3.9
     Programming Language :: Python :: 3.10
+    Programming Language :: Python :: 3.11
     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 :: 3.8
     Programming Language :: Python :: 3.9
     Programming Language :: Python :: 3.10
+    Programming Language :: Python :: 3.11
     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 :: 3.8
     Programming Language :: Python :: 3.9
     Programming Language :: Python :: 3.10
+    Programming Language :: Python :: 3.11
     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 :: 3.8
     Programming Language :: Python :: 3.9
     Programming Language :: Python :: 3.10
+    Programming Language :: Python :: 3.11
     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
@@ -13,6 +13,7 @@ classifiers =
     Programming Language :: Python :: 3.8
     Programming Language :: Python :: 3.9
     Programming Language :: Python :: 3.10
+    Programming Language :: Python :: 3.11
     Topic :: Software Development
     Topic :: Software Development :: Code Generators
     Topic :: Software Development :: Testing

diff --git a/packages/meta/setup.cfg b/packages/meta/setup.cfg
@@ -14,6 +14,7 @@ classifiers =
     Programming Language :: Python :: 3.8
     Programming Language :: Python :: 3.9
     Programming Language :: Python :: 3.10
+    Programming Language :: Python :: 3.11
     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 :: 3.8
     Programming Language :: Python :: 3.9
     Programming Language :: Python :: 3.10
+    Programming Language :: Python :: 3.11
     Topic :: Software Development
     Topic :: Software Development :: Code Generators
     Topic :: Software Development :: Testing

diff --git a/packages/objectstore/setup.cfg b/packages/objectstore/setup.cfg
@@ -13,6 +13,7 @@ classifiers =
     Programming Language :: Python :: 3.8
     Programming Language :: Python :: 3.9
     Programming Language :: Python :: 3.10
+    Programming Language :: Python :: 3.11
     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 :: 3.8
     Programming Language :: Python :: 3.9
     Programming Language :: Python :: 3.10
+    Programming Language :: Python :: 3.11
     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 :: 3.8
     Programming Language :: Python :: 3.9
     Programming Language :: Python :: 3.10
+    Programming Language :: Python :: 3.11
     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 :: 3.8
     Programming Language :: Python :: 3.9
     Programming Language :: Python :: 3.10
+    Programming Language :: Python :: 3.11
     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 :: 3.8
     Programming Language :: Python :: 3.9
     Programming Language :: Python :: 3.10
+    Programming Language :: Python :: 3.11
     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 :: 3.8
     Programming Language :: Python :: 3.9
     Programming Language :: Python :: 3.10
+    Programming Language :: Python :: 3.11
     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
@@ -13,6 +13,7 @@ classifiers =
     Programming Language :: Python :: 3.8
     Programming Language :: Python :: 3.9
     Programming Language :: Python :: 3.10
+    Programming Language :: Python :: 3.11
     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 :: 3.8
     Programming Language :: Python :: 3.9
     Programming Language :: Python :: 3.10
+    Programming Language :: Python :: 3.11
     Topic :: Software Development
     Topic :: Software Development :: Code Generators
     Topic :: Software Development :: Testing

diff --git a/packages/util/setup.cfg b/packages/util/setup.cfg
@@ -13,6 +13,7 @@ classifiers =
     Programming Language :: Python :: 3.8
     Programming Language :: Python :: 3.9
     Programming Language :: Python :: 3.10
+    Programming Language :: Python :: 3.11
     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 :: 3.8
     Programming Language :: Python :: 3.9
     Programming Language :: Python :: 3.10
+    Programming Language :: Python :: 3.11
     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 :: 3.8
     Programming Language :: Python :: 3.9
     Programming Language :: Python :: 3.10
+    Programming Language :: Python :: 3.11
     Topic :: Software Development
     Topic :: Software Development :: Code Generators
     Topic :: Software Development :: Testing

diff --git a/packages/webapps/setup.cfg b/packages/webapps/setup.cfg
@@ -13,6 +13,7 @@ classifiers =
     Programming Language :: Python :: 3.8
     Programming Language :: Python :: 3.9
     Programming Language :: Python :: 3.10
+    Programming Language :: Python :: 3.11
     Topic :: Software Development
     Topic :: Software Development :: Code Generators
     Topic :: Software Development :: Testing

diff --git a/pyproject.toml b/pyproject.toml
@@ -84,7 +84,7 @@ pykwalify = "*"
 pylibmagic = "*"
 pyparsing = "*"
 pysam = ">=0.20"
-python = ">=3.7,<3.11"  # Keep maximum version strict to appease numpy and scipy
+python = ">=3.7,<3.12"  # Keep maximum version strict to appease numpy and scipy
 python-dateutil = "*"
 python-magic = "*"
 python-multipart = "*"  # required to support form parsing in FastAPI/Starlette