Update CI and code quality

[khaeru]

• Use astral-sh/setup-uv in "pytest" CI workflow, parallel to Update code quality configuration ixmp#555 and Clean up CI & miscellaneous updates for 3.10 message_ix#911.
• Update ruff version and format some files.
• Update mypy configuration as suggested at Using mypy via pre-commit python/mypy#13916, i.e. invoke mypy on all files, even those not modified in a particular commit.
  • Address many mypy errors in common code and in .model.transport.
  • Mark other code via pyproject.toml as excluded, for now.

How to review

@glatterf42:

• Note that the CI checks all pass.
• Read the diff for non-code files. (No need to review all the typing changes.)

All others: please ignore! Changes to type hints only.

PR checklist

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

[codecov]

Codecov Report

Attention: Patch coverage is 95.52239% with 6 lines in your changes missing coverage. Please review.

Project coverage is 76.7%. Comparing base (c782c30) to head (080d9a5).

Files with missing lines	Patch %	Lines
message_ix_models/model/transport/ldv.py	81.8%	2 Missing ⚠️
message_ix_models/model/transport/report.py	66.6%	1 Missing ⚠️
message_ix_models/model/transport/workflow.py	0.0%	1 Missing ⚠️
message_ix_models/model/water/report.py	0.0%	1 Missing ⚠️
message_ix_models/report/__init__.py	80.0%	1 Missing ⚠️

Additional details and impacted files

@@           Coverage Diff           @@
##            main    #281     +/-   ##
=======================================
- Coverage   77.6%   76.7%   -0.9%     
=======================================
  Files        211     211             
  Lines      16079   16108     +29     
=======================================
- Hits       12481   12363    -118     
- Misses      3598    3745    +147     

Files with missing lines	Coverage Δ
...l/material/material_demand/material_demand_calc.py	88.3% <ø> (ø)
message_ix_models/model/transport/base.py	97.9% <100.0%> (ø)
message_ix_models/model/transport/config.py	97.6% <100.0%> (ø)
message_ix_models/model/transport/files.py	98.6% <100.0%> (+<0.1%)	⬆️
message_ix_models/model/transport/ikarus.py	85.3% <100.0%> (+0.1%)	⬆️
message_ix_models/model/transport/non_ldv.py	98.1% <100.0%> (ø)
message_ix_models/model/transport/operator.py	86.8% <100.0%> (+0.1%)	⬆️
message_ix_models/model/transport/plot.py	75.8% <100.0%> (ø)
message_ix_models/model/transport/roadmap.py	56.0% <ø> (ø)
message_ix_models/model/transport/testing.py	100.0% <100.0%> (ø)
... and 36 more

... and 7 files with indirect coverage changes

[glatterf42]

Thanks, looks good to me. I love that we're type hinting more stuff :)