From 2a41350596a81892475edfc4a9e00d8f99a4af75 Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
Date: Wed, 23 Oct 2024 11:57:55 +0100
Subject: [PATCH] Use fissix to replace lib2to3 under Python >=3.13

Add entries to `sys.modules` so that `future`/`past` can find
lib2to3 modules.
---
 .../dependencies/pinned-requirements.txt       |  1 +
 lib/galaxy/util/template.py                    | 18 ++++++++++++++++--
 packages/util/setup.cfg                        |  1 +
 pyproject.toml                                 |  1 +
 4 files changed, 19 insertions(+), 2 deletions(-)

diff --git a/lib/galaxy/dependencies/pinned-requirements.txt b/lib/galaxy/dependencies/pinned-requirements.txt
index 55078397df8c..593e014fa0b2 100644
--- a/lib/galaxy/dependencies/pinned-requirements.txt
+++ b/lib/galaxy/dependencies/pinned-requirements.txt
@@ -67,6 +67,7 @@ email-validator==2.2.0 ; python_version >= "3.8" and python_version < "3.14"
 exceptiongroup==1.2.2 ; python_version >= "3.8" and python_version < "3.11"
 fastapi-slim==0.115.2 ; python_version >= "3.8" and python_version < "3.14"
 filelock==3.16.1 ; python_version >= "3.8" and python_version < "3.14"
+fissix==24.4.24 ; python_version >= "3.13" and python_version < "3.14"
 frozenlist==1.4.1 ; python_version >= "3.8" and python_version < "3.14"
 fs==2.4.16 ; python_version >= "3.8" and python_version < "3.14"
 fsspec==2024.9.0 ; python_version >= "3.8" and python_version < "3.14"
diff --git a/lib/galaxy/util/template.py b/lib/galaxy/util/template.py
index 9b7f7965592e..d7872691cb60 100644
--- a/lib/galaxy/util/template.py
+++ b/lib/galaxy/util/template.py
@@ -1,18 +1,32 @@
 """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")]
diff --git a/packages/util/setup.cfg b/packages/util/setup.cfg
index ad9dff07b28d..7865c54eb421 100644
--- a/packages/util/setup.cfg
+++ b/packages/util/setup.cfg
@@ -54,6 +54,7 @@ jstree =
     dictobj
 template =
     CT3
+    fissix;python>=3.13
     future>=1.0.0
 config_template =
     Jinja2
diff --git a/pyproject.toml b/pyproject.toml
index c83ef32abc89..ac2cc7b90eeb 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -58,6 +58,7 @@ docutils = "!=0.17, !=0.17.1"
 dparse = "*"
 edam-ontology = "*"
 fastapi-slim = ">=0.111.0"
+fissix = { version = "*", python = ">=3.13" }
 fs = "*"
 future = ">=1.0.0"  # Python 3.12 support
 graphene = "*"