Use fissix to replace lib2to3 under Python >=3.13

Add entries to `sys.modules` so that `future`/`past` can find
lib2to3 modules.

Author: nsoranzo

lib/galaxy/dependencies/pinned-requirements.txt

@@ -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/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/util/setup.cfg

@@ -54,6 +54,7 @@ jstree =
     dictobj
 template =
     CT3>=3.3.3
+    fissix;python_version>='3.13'
     future>=1.0.0
 config_template =
     Jinja2

pyproject.toml

@@ -37,6 +37,7 @@ dependencies = [
     "dparse",
     "edam-ontology",
     "fastapi-slim>=0.111.0",
+    "fissix ; python_version>='3.13'",
     "fs",
     "future>=1.0.0",  # Python 3.12 support
     "graphene",