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[23.0] Add support for Python 3.11 #15487

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merged 2 commits into from Feb 2, 2023
Merged

[23.0] Add support for Python 3.11 #15487

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4ca163b
Add support for Python 3.11
nsoranzo Feb 1, 2023
a7ddf89
Replace 2 `Enum`s with `Literal`s
nsoranzo Feb 1, 2023
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2 changes: 1 addition & 1 deletion .github/workflows/first_startup.yaml
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Expand Up @@ -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}
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2 changes: 1 addition & 1 deletion .github/workflows/lint.yaml
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Expand Up @@ -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'
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2 changes: 1 addition & 1 deletion .github/workflows/reports_startup.yaml
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Expand Up @@ -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}
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2 changes: 1 addition & 1 deletion .github/workflows/test_galaxy_packages.yaml
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Expand Up @@ -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:
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2 changes: 1 addition & 1 deletion .github/workflows/unit.yaml
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Expand Up @@ -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:
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16 changes: 2 additions & 14 deletions client/src/schema/schema.ts
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Expand Up @@ -5066,12 +5066,6 @@ export interface components {
)[];
metadata: components["schemas"]["LibraryFolderMetadata"];
};
/**
* LibraryFolderContentsIndexSortByEnum
* @description An enumeration.
* @enum {string}
*/
LibraryFolderContentsIndexSortByEnum: "name" | "description" | "type" | "size" | "update_time";
/**
* LibraryFolderCurrentPermissions
* @description Base model definition with common configuration used by all derived models.
Expand Down Expand Up @@ -7348,12 +7342,6 @@ export interface components {
[key: string]: number | undefined;
};
};
/**
* WorkflowSortByEnum
* @description An enumeration.
* @enum {string}
*/
WorkflowSortByEnum: "create_time" | "update_time" | "name" | "None";
/**
* WriteInvocationStoreToPayload
* @description Base model definition with common configuration used by all derived models.
Expand Down Expand Up @@ -8655,7 +8643,7 @@ export interface operations {
offset?: number;
search_text?: string;
include_deleted?: boolean;
order_by?: components["schemas"]["LibraryFolderContentsIndexSortByEnum"];
order_by?: "name" | "description" | "type" | "size" | "update_time";
sort_desc?: boolean;
};
/** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
Expand Down Expand Up @@ -14324,7 +14312,7 @@ export interface operations {
missing_tools?: boolean;
show_published?: boolean;
show_shared?: boolean;
sort_by?: components["schemas"]["WorkflowSortByEnum"];
sort_by?: "create_time" | "update_time" | "name";
sort_desc?: boolean;
limit?: number;
offset?: number;
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2 changes: 1 addition & 1 deletion lib/galaxy/dependencies/conditional-requirements.txt
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@@ -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
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270 changes: 136 additions & 134 deletions lib/galaxy/dependencies/dev-requirements.txt
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379 changes: 190 additions & 189 deletions lib/galaxy/dependencies/pinned-requirements.txt
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55 changes: 50 additions & 5 deletions lib/galaxy/dependencies/update.sh
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Expand Up @@ -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=
Expand All @@ -23,7 +26,7 @@ do
;;
esac
done
shift $(($OPTIND - 1))
shift $((OPTIND - 1))

if [ -n "$add" ] && [ $# -eq 0 ]; then
printf "When adding (-a), you must provide at least one package specification.\n" >&2
Expand All @@ -42,6 +45,48 @@ else
poetry add -vv --lock "$@"
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
21 changes: 9 additions & 12 deletions lib/galaxy/managers/folders.py
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Expand Up @@ -37,10 +37,7 @@
RequestParameterInvalidException,
)
from galaxy.model.scoped_session import galaxy_scoped_session
from galaxy.schema.schema import (
LibraryFolderContentsIndexQueryPayload,
LibraryFolderContentsIndexSortByEnum,
)
from galaxy.schema.schema import LibraryFolderContentsIndexQueryPayload
from galaxy.security import RBACAgent
from galaxy.security.idencoding import IdEncodingHelper

Expand All @@ -57,17 +54,17 @@ class SecurityParams:


LDDA_SORT_COLUMN_MAP = {
LibraryFolderContentsIndexSortByEnum.name: lambda ldda, dataset: ldda.name,
LibraryFolderContentsIndexSortByEnum.description: lambda ldda, dataset: ldda.message,
LibraryFolderContentsIndexSortByEnum.type: lambda ldda, dataset: ldda.extension,
LibraryFolderContentsIndexSortByEnum.size: lambda ldda, dataset: dataset.file_size,
LibraryFolderContentsIndexSortByEnum.update_time: lambda ldda, dataset: ldda.update_time,
"name": lambda ldda, dataset: ldda.name,
"description": lambda ldda, dataset: ldda.message,
"type": lambda ldda, dataset: ldda.extension,
"size": lambda ldda, dataset: dataset.file_size,
"update_time": lambda ldda, dataset: ldda.update_time,
}

FOLDER_SORT_COLUMN_MAP = {
LibraryFolderContentsIndexSortByEnum.name: lambda folder: folder.name,
LibraryFolderContentsIndexSortByEnum.description: lambda folder: folder.description,
LibraryFolderContentsIndexSortByEnum.update_time: lambda folder: folder.update_time,
"name": lambda folder: folder.name,
"description": lambda folder: folder.description,
"update_time": lambda folder: folder.update_time,
}


Expand Down
15 changes: 3 additions & 12 deletions lib/galaxy/schema/schema.py
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Expand Up @@ -1093,11 +1093,7 @@ class ExportHistoryArchivePayload(Model):
)


class WorkflowSortByEnum(str, Enum):
create_time = "create_time"
update_time = "update_time"
name = "name"
none = None
WorkflowSortByEnum = Literal["create_time", "update_time", "name"]


class WorkflowIndexQueryPayload(Model):
Expand Down Expand Up @@ -2718,20 +2714,15 @@ class LibraryFolderCurrentPermissions(Model):
)


class LibraryFolderContentsIndexSortByEnum(str, Enum):
name = "name"
description = "description"
type = "type"
size = "size"
update_time = "update_time"
LibraryFolderContentsIndexSortByEnum = Literal["name", "description", "type", "size", "update_time"]


class LibraryFolderContentsIndexQueryPayload(Model):
limit: int = 10
offset: int = 0
search_text: Optional[str] = None
include_deleted: Optional[bool] = None
order_by: LibraryFolderContentsIndexSortByEnum = LibraryFolderContentsIndexSortByEnum.name
order_by: LibraryFolderContentsIndexSortByEnum = "name"
sort_desc: Optional[bool] = False


Expand Down
2 changes: 1 addition & 1 deletion lib/galaxy/webapps/galaxy/api/folder_contents.py
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Expand Up @@ -54,7 +54,7 @@
)

SortByQueryParam: LibraryFolderContentsIndexSortByEnum = Query(
default=LibraryFolderContentsIndexSortByEnum.name,
default="name",
title="Sort By",
description="Sort results by specified field.",
)
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1 change: 1 addition & 0 deletions packages/app/setup.cfg
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Expand Up @@ -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
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1 change: 1 addition & 0 deletions packages/auth/setup.cfg
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Expand Up @@ -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
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1 change: 1 addition & 0 deletions packages/config/setup.cfg
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Expand Up @@ -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
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1 change: 1 addition & 0 deletions packages/data/setup.cfg
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Expand Up @@ -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
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1 change: 1 addition & 0 deletions packages/files/setup.cfg
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Expand Up @@ -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
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1 change: 1 addition & 0 deletions packages/job_execution/setup.cfg
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Expand Up @@ -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
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1 change: 1 addition & 0 deletions packages/job_metrics/setup.cfg
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Expand Up @@ -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
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1 change: 1 addition & 0 deletions packages/meta/setup.cfg
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Expand Up @@ -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
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1 change: 1 addition & 0 deletions packages/navigation/setup.cfg
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Expand Up @@ -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
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1 change: 1 addition & 0 deletions packages/objectstore/setup.cfg
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Expand Up @@ -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
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1 change: 1 addition & 0 deletions packages/selenium/setup.cfg
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Expand Up @@ -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
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1 change: 1 addition & 0 deletions packages/test_api/setup.cfg
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Expand Up @@ -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
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1 change: 1 addition & 0 deletions packages/test_base/setup.cfg
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Expand Up @@ -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
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1 change: 1 addition & 0 deletions packages/test_driver/setup.cfg
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Expand Up @@ -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
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1 change: 1 addition & 0 deletions packages/test_selenium/setup.cfg
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Expand Up @@ -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
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1 change: 1 addition & 0 deletions packages/tool_util/setup.cfg
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Expand Up @@ -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
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1 change: 1 addition & 0 deletions packages/tours/setup.cfg
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Expand Up @@ -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
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1 change: 1 addition & 0 deletions packages/util/setup.cfg
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Expand Up @@ -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
Expand Down