Confirm support for Python 3.13 and drop 3.8

[khaeru]

• Check/confirm that message-ix-models is compatible with the new version. This includes:
  • Confirm support for Python 3.13 and drop 3.8 ixmp#544
  • Update Python support for 3.13 message_ix#881
  • Add an explicit CI job for ixmp/message-ix 3.9.0.
  • Bump GAMS version in CI from 29.1.0 to 43.4.1.
• Drop support for Python 3.8, which reached end-of-life (no more updates, even security updates) "approximately [during, before, or after] October 2024" per PEP 569.
  • Remove any code marked as for Python 3.8 compatibility only. Depending on these changes, part or all of the functionality may remain usable with Python 3.8 if users have extreme need.
  • Make any general clean-ups or improvements possible with features available from Python 3.9.
    • Type hint using generics, e.g. list[str] instead of from typing import List/List[str].
    • Use from collections.abc import Sequence et al instead of deprecated from typing import Sequence.

How to review

• Read the diff and note that the CI checks all pass.

PR checklist

• Continuous integration checks all ✅
• Add or expand tests; coverage checks both ✅
• Add, expand, or update documentation. N/A
• Update doc/whatsnew.

[codecov]

Codecov Report

Attention: Patch coverage is 97.24138% with 4 lines in your changes missing coverage. Please review.

Project coverage is 75.6%. Comparing base (012b501) to head (0c40618).
Report is 13 commits behind head on main.

Files with missing lines	Patch %	Lines
...ge_ix_models/util/compat/message_data/utilities.py	0.0%	2 Missing ⚠️
message_ix_models/project/navigate/__init__.py	85.7%	1 Missing ⚠️
message_ix_models/util/click.py	75.0%	1 Missing ⚠️

Additional details and impacted files

@@           Coverage Diff           @@
##            main    #250     +/-   ##
=======================================
- Coverage   76.5%   75.6%   -1.0%     
=======================================
  Files        203     203             
  Lines      15578   15600     +22     
=======================================
- Hits       11927   11801    -126     
- Misses      3651    3799    +148     

Files with missing lines	Coverage Δ
message_ix_models/model/build.py	100.0% <100.0%> (ø)
message_ix_models/model/disutility.py	100.0% <100.0%> (ø)
message_ix_models/model/emissions.py	98.0% <100.0%> (ø)
message_ix_models/model/macro.py	100.0% <100.0%> (ø)
message_ix_models/model/material/build.py	67.8% <100.0%> (+0.2%)	⬆️
message_ix_models/model/material/data_aluminum.py	90.5% <100.0%> (ø)
message_ix_models/model/material/data_methanol.py	92.0% <100.0%> (ø)
message_ix_models/model/material/data_petro.py	78.7% <100.0%> (-0.2%)	⬇️
message_ix_models/model/material/data_steel.py	87.0% <100.0%> (ø)
message_ix_models/model/material/data_util.py	33.3% <100.0%> (+0.1%)	⬆️
... and 43 more

... and 4 files with indirect coverage changes

---- 🚨 Try these New Features:

• Flaky Tests Detection - Detect and resolve failed and flaky tests

[glatterf42]

Thanks, this is looking great :)
I hope it also explains all CI failures today, as in: GAMS was bumped here, requiring a different license, but the nightly tests and test-snapshot still wanted to use the older version requiring the older license, and failed. In that case, I'd just ask to please also adapt the snapshot-workflow file to use the newer GAMS version :)

[khaeru]

adapt the snapshot-workflow file to use the newer GAMS version

Ah good catch—will do.