Merge pull request #18449 from nsoranzo/python3.13

Add Python 3.13 support

Author: nsoranzo

.github/workflows/first_startup.yaml

@@ -23,7 +23,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.8', '3.12']
+        python-version: ['3.8', '3.13']
     defaults:
       run:
         shell: bash -l {0}

.github/workflows/lint.yaml

@@ -22,7 +22,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.8', '3.12']
+        python-version: ['3.8', '3.13']
     env:
       LINT_PATH: 'lib/galaxy/dependencies/pinned-lint-requirements.txt'
       TYPE_PATH: 'lib/galaxy/dependencies/pinned-typecheck-requirements.txt'

.github/workflows/lint_openapi_schema.yml

@@ -20,7 +20,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.8', '3.12']
+        python-version: ['3.8', '3.13']
     steps:
       - uses: actions/checkout@v4
         with:

.github/workflows/osx_startup.yaml

@@ -21,7 +21,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.8', '3.12']
+        python-version: ['3.8', '3.13']
     defaults:
       run:
         shell: bash -l {0}

.github/workflows/reports_startup.yaml

@@ -18,7 +18,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.8', '3.12']
+        python-version: ['3.8', '3.13']
     defaults:
       run:
         shell: bash -l {0}

.github/workflows/test_galaxy_packages.yaml

@@ -18,7 +18,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.8', '3.12']
+        python-version: ['3.8', '3.13']
     steps:
       - uses: actions/checkout@v4
         with:

.github/workflows/toolshed.yaml

@@ -21,7 +21,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.8', '3.12']
+        python-version: ['3.8', '3.13']
         shed-api: ['v1', 'v2']
         test-install-client: ['galaxy_api', 'standalone']
     services:

.github/workflows/unit.yaml

@@ -20,7 +20,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.8', '3.12']
+        python-version: ['3.8', '3.13']
     steps:
       - uses: actions/checkout@v4
         with:

lib/galaxy/dependencies/conditional-requirements.txt

@@ -1,5 +1,5 @@
 # These dependencies are only required when certain config options are set
-psycopg2-binary==2.9.9
+psycopg2-binary==2.9.10
 mysqlclient
 fluent-logger
 sentry-sdk[fastapi]

lib/galaxy/dependencies/pinned-requirements.txt

@@ -39,7 +39,6 @@ celery==5.4.0
 certifi==2024.8.30
 cffi==1.17.1
 charset-normalizer==3.4.0
-cheetah3==3.2.6.post1
 circus==0.18.0
 click==8.1.7
 click-didyoumean==0.3.1
@@ -51,6 +50,7 @@ colorama==0.4.6 ; platform_system == 'Windows'
 coloredlogs==15.0.1
 conda-package-streaming==0.11.0
 cryptography==43.0.3
+ct3==3.3.3.post1
 cwl-upgrader==1.2.11
 cwl-utils==0.35
 cwltool==3.1.20241007082533
@@ -66,6 +66,7 @@ email-validator==2.2.0
 exceptiongroup==1.2.2 ; python_full_version < '3.11'
 fastapi-slim==0.115.4
 filelock==3.16.1
+fissix==24.4.24 ; python_full_version >= '3.13'
 frozenlist==1.5.0
 fs==2.4.16
 fsspec==2024.10.0

lib/galaxy/util/image_util.py

@@ -1,6 +1,5 @@
 """Provides utilities for working with image files."""
 
-import imghdr
 import logging
 from typing import (
     List,
@@ -22,11 +21,7 @@ def image_type(filename: str) -> Optional[str]:
             with Image.open(filename) as im:
                 fmt = im.format
         except Exception:
-            # We continue to try with imghdr, so this is a rare case of an
-            # exception we expect to happen frequently, so we're not logging
             pass
-    if not fmt:
-        fmt = imghdr.what(filename)
     if fmt:
         return fmt.upper()
     else:

lib/galaxy/util/template.py

@@ -1,18 +1,34 @@
 """Entry point for the usage of Cheetah templating within Galaxy."""
 
+import sys
 import traceback
-from lib2to3.refactor import RefactoringTool
 
 from Cheetah.Compiler import Compiler
 from Cheetah.NameMapper import NotFound
 from Cheetah.Parser import ParseError
 from Cheetah.Template import Template
 from packaging.version import Version
-from past.translation import myfixes
 
 from galaxy.util.tree_dict import TreeDict
 from . import unicodify
 
+if sys.version_info >= (3, 13):
+    import fissix
+    from fissix import (
+        fixes as fissix_fixes,
+        pgen2 as fissix_pgen2,
+        refactor as fissix_refactor,
+    )
+
+    sys.modules["lib2to3"] = fissix
+    sys.modules["lib2to3.fixes"] = fissix_fixes
+    sys.modules["lib2to3.pgen2"] = fissix_pgen2
+    sys.modules["lib2to3.refactor"] = fissix_refactor
+
+from lib2to3.refactor import RefactoringTool
+
+from past.translation import myfixes
+
 # Skip libpasteurize fixers, which make sure code is py2 and py3 compatible.
 # This is not needed, we only translate code on py3.
 myfixes = [f for f in myfixes if not f.startswith("libpasteurize")]

packages/app/setup.cfg

@@ -41,7 +41,7 @@ install_requires =
     galaxy-objectstore
     galaxy-tool-util[cwl,edam]
     galaxy-tours
-    galaxy-util
+    galaxy-util[image_util]
     galaxy-web-framework
     galaxy-web-stack
     Beaker
@@ -57,7 +57,7 @@ install_requires =
     Mako
     Markdown
     MarkupSafe
-    mercurial
+    mercurial>=6.8.2
     packaging
     paramiko!=2.9.0,!=2.9.1
     pebble
@@ -74,7 +74,7 @@ install_requires =
     starlette
     svgwrite
     typing-extensions
-    WebOb
+    WebOb>=1.8.9
     Whoosh
 packages = find:
 python_requires = >=3.8

packages/data/setup.cfg

@@ -36,7 +36,7 @@ install_requires =
     galaxy-objectstore
     galaxy-schema
     galaxy-tool-util
-    galaxy-util[template]
+    galaxy-util[image_util,template]
     alembic
     alembic-utils
     bdbag>=1.6.3
@@ -46,7 +46,7 @@ install_requires =
     h5grove>=1.2.1
     h5py
     isa-rwval @ git+https://github.com/nsoranzo/isa-rwval.git@master
-    isal
+    isal>=1.7.0
     MarkupSafe
     msal
     mrcfile
@@ -62,7 +62,6 @@ install_requires =
     SQLAlchemy>=2.0,<2.1,!=2.0.36
     tifffile
     typing-extensions
-    WebOb
 packages = find:
 python_requires = >=3.8
 

packages/files/setup.cfg

@@ -34,7 +34,6 @@ include_package_data = True
 install_requires =
     galaxy-util[config_template]
     fs
-    isal
     typing-extensions
 packages = find:
 python_requires = >=3.8

packages/test.sh

@@ -49,7 +49,7 @@ while read -r package_dir || [ -n "$package_dir" ]; do  # https://stackoverflow.
 
     # Install extras (if needed)
     if [ "$package_dir" = "util" ]; then
-        pip install '.[template,jstree,config_template]'
+        pip install '.[image_util,template,jstree,config_template]'
     elif [ "$package_dir" = "tool_util" ]; then
         pip install '.[cwl,mulled,edam,extended-assertions]'
     else

packages/test_base/setup.cfg

@@ -35,7 +35,7 @@ install_requires =
     galaxy-tool-util
     galaxy-util
     bioblend
-    cwltest
+    cwltest>=2.5.20240906231108
     gxformat2
     pytest
     PyYAML

packages/tool_shed/setup.cfg

@@ -36,7 +36,7 @@ install_requires =
     galaxy-auth
     galaxy-config
     galaxy-data
-    galaxy-util
+    galaxy-util[image_util]
     galaxy-web-framework
     galaxy-web-stack
     galaxy-web-apps
@@ -48,7 +48,7 @@ install_requires =
     graphql-core
     Mako
     MarkupSafe
-    mercurial
+    mercurial>=6.8.2
     Paste
     pydantic>=2.7.4
     Routes

packages/tool_util/setup.cfg

@@ -33,7 +33,7 @@ version = 24.2.dev0
 [options]
 include_package_data = True
 install_requires =
-    galaxy-util>=22.1
+    galaxy-util[image_util]>=22.1
     conda-package-streaming
     lxml!=4.2.2
     MarkupSafe

packages/util/setup.cfg

@@ -48,10 +48,13 @@ packages = find:
 python_requires = >=3.7
 
 [options.extras_require]
+image_util =
+    pillow
 jstree =
     dictobj
 template =
-    Cheetah3
+    CT3>=3.3.3
+    fissix;python_version>='3.13'
     future>=1.0.0
 config_template =
     Jinja2

packages/web_apps/setup.cfg

@@ -42,7 +42,7 @@ install_requires =
     a2wsgi
     apispec
     Babel
-    Cheetah3
+    CT3>=3.3.3
     fastapi>=0.101.0
     gunicorn
     gxformat2
@@ -63,8 +63,8 @@ install_requires =
     tuswsgi
     typing-extensions
     uvicorn
-    uvloop
-    WebOb
+    uvloop>=0.21.0
+    WebOb>=1.8.9
 packages = find:
 python_requires = >=3.8
 

pyproject.toml

@@ -25,18 +25,19 @@ dependencies = [
     "boto",
     "bx-python",
     "celery",
-    "Cheetah3",
     "cloudauthz==0.6.0",
     "cloudbridge",
     "circus",
     "conda-package-streaming",
+    "CT3>=3.3.3",  # Python 3.13 support
     "cwltool>=3.1.20230624081518",  # save time, minimum needed by cwl-1.0 branch
     "dictobj",
     "dnspython",
     "docutils!=0.17,!=0.17.1",
     "dparse",
     "edam-ontology",
     "fastapi-slim>=0.111.0",
+    "fissix ; python_version>='3.13'",
     "fs",
     "future>=1.0.0",  # Python 3.12 support
     "graphene",
@@ -50,14 +51,14 @@ dependencies = [
     "h5py>=3.12 ; python_version>='3.9'",  # Python 3.13 support
     "importlib-resources ; python_version<'3.9'",  # for importlib.{abc.Traversable,resources.{files, Package}}
     "isa-rwval @ git+https://github.com/nsoranzo/isa-rwval.git@master",  # https://github.com/ISA-tools/isa-rwval/pull/17
-    "isal",
+    "isal>=1.7.0",  # Python 3.13 support
     "jinja2",
     "kombu>=5.3",  # for importlib-metadata fix
     "lagom",
     "Mako",
     "Markdown",
     "MarkupSafe",
-    "mercurial",
+    "mercurial>=6.8.2",  # Python 3.13 support
     "mrcfile",
     "msal",
     "nodeenv",
@@ -89,7 +90,7 @@ dependencies = [
     "rocrate",
     "Routes",
     "s3fs>=2023.1.0",
-    "schema-salad!=8.3.20220721194857",  # https://github.com/common-workflow-language/schema_salad/issues/575
+    "schema-salad>=8.7.20240905150001",  # Python 3.13 support
     "social-auth-core>=4.5.0",  # to drop dependency on abandoned python-jose
     "sortedcontainers",
     "SQLAlchemy>=2.0,<2.1,!=2.0.36",  # https://github.com/sqlalchemy/sqlalchemy/issues/12019,
@@ -103,8 +104,8 @@ dependencies = [
     "tuswsgi",
     "typing-extensions",
     "uvicorn!=0.28.0",  # https://github.com/galaxyproject/galaxy/issues/17669
-    "uvloop",
-    "WebOb",
+    "uvloop>=0.21.0",  # Python 3.13 support
+    "WebOb>=1.8.9",  # Python 3.13 support
     "Whoosh",
     "zipstream-new",
 ]
@@ -122,7 +123,7 @@ dev = [
     "black",
     "boto3",
     "codespell",
-    "cwltest",
+    "cwltest>=2.5.20240906231108",  # Python 3.13 support
     "darker",
     "fluent-logger",
     "galaxy-release-util",
@@ -133,7 +134,7 @@ dev = [
     "myst-parser",
     "onedatafilerestclient==21.2.5.2",
     "pkce",
-    "playwright",
+    "playwright>=1.48.0",  # Python 3.13 support
     "pytest<8",  # https://github.com/galaxyproject/galaxy/issues/17561
     "pytest-asyncio",
     "pytest-cov",
@@ -154,7 +155,7 @@ dev = [
     "statsd",
     "testfixtures",
     "tuspy",
-    "twill>=3.2.1",  # https://github.com/twill-tools/twill/issues/18
+    "twill>=3.2.5",  # Python 3.13 support
     "watchdog",
     "Werkzeug",
 ]