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Add support for Python 3.12 #16796

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merged 6 commits into from
Jan 22, 2024
Merged

Add support for Python 3.12 #16796

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cc878ba
Update comments
tuncK Oct 6, 2023
76e566d
Fix E231 flake8 error in f-string
nsoranzo Dec 17, 2023
30a6aab
Workaround ``ImportError`` for ``importlib.resources.Anchor``
nsoranzo Dec 17, 2023
4eb94cd
Install `future` from my fork with Python 3.12 patches
nsoranzo Jan 20, 2024
6860c9a
Add support for Python 3.12
tuncK Oct 6, 2023
9978004
Fix tests after Python 3.12 changes for comprehensions
nsoranzo Jan 21, 2024
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2 changes: 1 addition & 1 deletion .github/workflows/first_startup.yaml
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Expand Up @@ -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}
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2 changes: 1 addition & 1 deletion .github/workflows/lint.yaml
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Expand Up @@ -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'
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2 changes: 1 addition & 1 deletion .github/workflows/lint_openapi_schema.yml
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Expand Up @@ -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:
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2 changes: 1 addition & 1 deletion .github/workflows/osx_startup.yaml
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Expand Up @@ -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}
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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: ['3.8', '3.11']
python-version: ['3.8', '3.12']
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: ['3.8', '3.11']
python-version: ['3.8', '3.12']
steps:
- uses: actions/checkout@v3
with:
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2 changes: 1 addition & 1 deletion .github/workflows/toolshed.yaml
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Expand Up @@ -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:
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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: ['3.8', '3.11']
python-version: ['3.8', '3.12']
steps:
- uses: actions/checkout@v3
with:
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322 changes: 161 additions & 161 deletions lib/galaxy/dependencies/dev-requirements.txt
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418 changes: 210 additions & 208 deletions lib/galaxy/dependencies/pinned-requirements.txt
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42 changes: 22 additions & 20 deletions lib/galaxy/dependencies/pinned-typecheck-requirements.txt
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@@ -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"
10 changes: 5 additions & 5 deletions lib/galaxy/dependencies/update.sh
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Expand Up @@ -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)"

Expand Down Expand Up @@ -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
5 changes: 2 additions & 3 deletions lib/galaxy/dependencies/update_lint_requirements.sh
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Expand Up @@ -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)"

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2 changes: 1 addition & 1 deletion lib/galaxy/files/sources/invenio.py
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Expand Up @@ -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:
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15 changes: 6 additions & 9 deletions lib/galaxy/util/resources.py
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Expand Up @@ -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,
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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 :: 3.9
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
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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 :: 3.9
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
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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 :: 3.9
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
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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 :: 3.9
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
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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 :: 3.9
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
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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 :: 3.9
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
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3 changes: 2 additions & 1 deletion packages/job_metrics/setup.cfg
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Expand Up @@ -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
Expand All @@ -38,4 +39,4 @@ python_requires = >=3.7

[options.packages.find]
exclude =
tests*
tests*
1 change: 1 addition & 0 deletions packages/meta/setup.cfg
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Expand Up @@ -14,6 +14,7 @@ classifiers =
Programming Language :: Python :: 3.9
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
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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 :: 3.9
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
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1 change: 1 addition & 0 deletions packages/objectstore/setup.cfg
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Expand Up @@ -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
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2 changes: 2 additions & 0 deletions packages/schema/setup.cfg
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Expand Up @@ -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
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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 :: 3.9
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
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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 :: 3.9
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
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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 :: 3.9
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
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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 :: 3.9
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
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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 :: 3.9
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
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1 change: 1 addition & 0 deletions packages/tool_shed/setup.cfg
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Expand Up @@ -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
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1 change: 1 addition & 0 deletions packages/tool_util/setup.cfg
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Expand Up @@ -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
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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 :: 3.9
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
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3 changes: 2 additions & 1 deletion packages/util/setup.cfg
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Expand Up @@ -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
Expand Down Expand Up @@ -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 =
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1 change: 1 addition & 0 deletions packages/web_apps/setup.cfg
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Expand Up @@ -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
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1 change: 1 addition & 0 deletions packages/web_framework/setup.cfg
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Expand Up @@ -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
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1 change: 1 addition & 0 deletions packages/web_stack/setup.cfg
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Expand Up @@ -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
Expand Down
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