Absence of lib2to3 on ubuntu server causes role to fail

[jdavcs]

We still use the lib2to3 module in lib/galaxy/util/template.py; however, it is not included in Debian python distributions (at least 3.12+). As a result, running a fresh galaxy install on ubuntu server 24.04 fails:

TASK [galaxyproject.galaxy : Get current Galaxy DB version] ********************************************************************************************************************************************************************************************************************************************************************************************************************************
fatal: [192.168.1.157]: FAILED! => changed=false 
  cmd:
  - /srv/galaxy/venv/bin/python
  - /srv/galaxy/server/scripts/manage_db.py
  - -c
  - /srv/galaxy/config/galaxy.yml
  - db_version
  delta: '0:00:00.760434'
  end: '2025-02-15 19:51:32.313093'
  failed_when_result: true
  msg: non-zero return code
  rc: 1
  start: '2025-02-15 19:51:31.552659'
  stderr: |-
    Traceback (most recent call last):
      File "/srv/galaxy/server/scripts/manage_db.py", line 12, in <module>
        from galaxy.model.migrations.scripts import LegacyManageDb
      File "/srv/galaxy/server/lib/galaxy/model/__init__.py", line 144, in <module>
        from galaxy.files.templates import (
      File "/srv/galaxy/server/lib/galaxy/files/__init__.py", line 16, in <module>
        from galaxy.files.sources import (
      File "/srv/galaxy/server/lib/galaxy/files/sources/__init__.py", line 37, in <module>
        from galaxy.util.template import fill_template
      File "/srv/galaxy/server/lib/galaxy/util/template.py", line 28, in <module>
        from lib2to3.refactor import RefactoringTool
    ModuleNotFoundError: No module named 'lib2to3'

The package is deprecated and scheduled for removal in 3.13. More context:
galaxyproject/galaxy#16796 (comment)
and galaxyproject/galaxy#18449

I'm not sure what's the right way to handle this. One solution is to install the 2to3 package. This could be added to a task within the role, maybe? If not, should we add a note to the readme?

[martenson]

Confirming this issue. It means Galaxy cannot be started out of the box on any ubuntu with newer python (e.g. 24.04 with py 3.12).

cc @TomasVondrak

[nsoranzo]

This affects Debian <=12, Ubuntu <=24.10 and derivative distributions, since we already handle the Python 3.13 removal of lib2to3 in Galaxy >=24.2.

My preferred solution would be to:

• Explain in the "Requirements" section of the README.md that python3-lib2to3 needs to be installed under Debian <=12, Ubuntu <=24.10 and derivative distributions.
• In Galaxy, catch the import error in lib/galaxy/util/template.py and print instructions to fix the issue (I can take care of that part).

[martenson]

I read through the comments I found but did not find an answer to whether we can expand the fissix approach from 3.13 to 3.12. Is there one?

[nsoranzo]

I read through the comments I found but did not find an answer to whether we can expand the fissix approach from 3.13 to 3.12. Is there one?

This may work, but only for Galaxy 24.2, I don't think we want to backport adding fissix as a dependency to older releases.

[nsoranzo]

Ah, and we currently install fissix only Python >=3.13: https://github.com/galaxyproject/galaxy/blob/dev/pyproject.toml#L41

[martenson]

I'd be fine with fixing this just in dev by depending on fissix for Python >=3.12. Then we'd run out of the box again on everything affected. Does that make sense?

[nsoranzo]

I think the split of the python3-lib2to3 package is going on since at least Ubuntu 20.04 (focal, the oldest supported version): https://packages.ubuntu.com/focal/python3-lib2to3
That means we would need to do this for Python >=3.8 (i.e. always).

[nsoranzo]

The following patch should fix it for dev, let me know if I should open a PR with it:

diff --git a/lib/galaxy/dependencies/pinned-requirements.txt b/lib/galaxy/dependencies/pinned-requirements.txt
index 4ab8da70ac..40822e9c41 100644
--- a/lib/galaxy/dependencies/pinned-requirements.txt
+++ b/lib/galaxy/dependencies/pinned-requirements.txt
@@ -65,7 +65,7 @@ email-validator==2.2.0
 exceptiongroup==1.2.2 ; python_full_version < '3.11'
 fastapi-slim==0.115.8
 filelock==3.17.0
-fissix==24.4.24 ; python_full_version >= '3.13'
+fissix==24.4.24
 frozenlist==1.5.0
 fs==2.4.16
 fsspec==2025.2.0
diff --git a/lib/galaxy/util/template.py b/lib/galaxy/util/template.py
index 01a2cd68c8..fcfa99bd2f 100644
--- a/lib/galaxy/util/template.py
+++ b/lib/galaxy/util/template.py
@@ -12,7 +12,11 @@ from packaging.version import Version
 from galaxy.util.tree_dict import TreeDict
 from . import unicodify
 
-if sys.version_info >= (3, 13):
+try:
+    from lib2to3.refactor import RefactoringTool
+except ImportError:
+    # Either Python 3.13 or Debian(<=12)/Ubuntu(<=24.10) without the
+    # python3-lib2to3 package
     import fissix
     from fissix import (
         fixes as fissix_fixes,
@@ -25,7 +29,7 @@ if sys.version_info >= (3, 13):
     sys.modules["lib2to3.pgen2"] = fissix_pgen2
     sys.modules["lib2to3.refactor"] = fissix_refactor
 
-from lib2to3.refactor import RefactoringTool
+    from lib2to3.refactor import RefactoringTool
 
 from past.translation import myfixes
 
diff --git a/pyproject.toml b/pyproject.toml
index 31966ff3cf..2c83aadccb 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -38,7 +38,7 @@ dependencies = [
     "dparse",
     "edam-ontology",
     "fastapi-slim>=0.111.0",
-    "fissix ; python_version>='3.13'",
+    "fissix",
     "fs",
     "future>=1.0.0",  # Python 3.12 support
     "graphene",