Add Python 3.13 support

[nsoranzo]

xref. #16854

Standard library issues:

• imghdr has been removed
• lib2to3 has been removed, which we use in lib/galaxy/util/template.py and is also used by future Compatibility with Python-3.13 PythonCharmers/python-future#640 . https://github.com/amyreese/fissix could be a drop-in replacement for lib2to3, but unit tests break unless also future uses it.

Package issues:

• cwltest cannot be installed under Python 3.13 Python 3.13 support common-workflow-language/cwltest#223 . Fixed in cwltest 2.5.20240906231108
• greenlet 3.0.3 fails to build under Python 3.13. Fixed in greenlet 3.1.0
• playwright 1.47.0 depends on greenlet 3.0.3 [Bug]: Won't install in Windows in Python 3.13 due to pinning to an obsolete version of greenlet microsoft/playwright-python#2564 . Fixed in playwright 1.48.0
• h5py 3.11.0 fails to build under Python 3.13. Fixed in h5py 3.12.1, but this version dropped support for Python 3.8, so we split the requirement in commit e432488
• lxml doesn't currently have a 3.13 wheel on PyPI and it fails to build on the CI due to missing libxml2 and libxslt development packages Add recipe for lxml for Python 3.13 wheels wheelforge#42
• mercurial 6.8.1: hg script breaks under Python 3.13 https://bz.mercurial-scm.org/show_bug.cgi?id=6926 Repo . Fixed in mercurial 6.8.2
• psycopg2 2.9.9 cannot be installed under Python 3.13 Psycopg2 doesn't install on Python 3.13 alpha psycopg/psycopg2#1692 . Fixed in psycopg2 2.9.10
• schema-salad cannot be installed under Python 3.13 Python 3.13 support common-workflow-language/schema_salad#864 . Fixed in schema-salad 8.7.20240905150001
• twill 3.2.4 depends on lxml <5 Release with updated lxml dep twill-tools/twill#23 . Fixed in twill 3.2.5
• uvloop fails to build under Python 3.13 uvloop fails to build with Python 3.13-rc1 MagicStack/uvloop#622 . Fixed in uvloop 0.21.0
• WebOb uses removed standard library module cgi DeprecationWarning: 'cgi' is deprecated and slated for removal in Python 3.13 Pylons/webob#437 . Fixed in WebOb 1.8.9

How to test the changes?

(Select all options that apply)

• I've included appropriate automated tests.
• This is a refactoring of components with existing test coverage.
• Instructions for manual testing are as follows:
  1. [add testing steps and prerequisites here if you didn't write automated tests covering all your changes]

License

• I agree to license these and all my past contributions to the core galaxy codebase under the MIT license.

[mr-c]

• h5py 3.11.0 fails to build under Python 3.13. 3.12 milestone

https://pypi.org/project/h5py/3.12.1/ :-)
https://docs.h5py.org/en/stable/whatsnew/3.12.html#new-features

h5py now has pre-built packages for Python 3.13.

[nsoranzo]

Just 2 dependencies left, then lib2to3 should hopefully be the only remaining issue.
@mvdbeek What's your thinking about lib2to3? Should we try to add it to future, or just get rid of it from our code base, or something else?

[mvdbeek]

I would try to keep that functionality if it all possible ? Having this proven track record of being able to re-run old jobs feels like something pretty important.

[nsoranzo]

Only mercurial is left 🎉

I would try to keep that functionality if it all possible ? Having this proven track record of being able to re-run old jobs feels like something pretty important.

@mvdbeek This should now be handled by the workaround I've added in the commit "Use fissix to replace lib2to3 under Python >=3.13". Let me know if that looks good to you.

[nsoranzo]

This is now out of draft, although it would make sense to merge #19075 first (which should be ready in a couple of days).

[jdavcs]

Everything looks good. Integration test failure unrelated.