Miscellaneous improvements for 2024-W10

[khaeru]

• Update the SSPUpdate class to pull data from the SSP 2024 "release 3.0" data files, and to handle both the earlier and current structures.
  • Improve ExoDataSource with raise_on_extra_kw() utility method, automatic copy of source keyword arguments.
• Expose .util.nodes_ex_world() for use as a reporting (genno) operator.
• Raise DeprecationWarning from .util.sdmx.eval_anno(); remove internal usage of this deprecated method.
• Close message_data ModuleNotFoundError when using mix-models #37.
• Improve logging.
  • Use multi-threaded logging for better performance; logging to stdout and file is on a separate thread.
  • Add automatic file logging. Log versions of packages to file when using .workflow.make_click_command().
  • Add mix-models last-log CLI command to retrieve the location of the latest log file.
• Improve performance in .disutility.data_conversion().
• Use platformdirs.user_cache_path() in more places; remove cache-path handling code.
• Add .util.datetime_now_with_tz().
• Add .util.show_versions().
• .util.private_data_path() now returns an alternate, local data path if message_data is not installed.

Housekeeping/CI:

• Bump versions of GitHub Actions.
• Add dependabot config for GitHub Actions.
• Bump ruff, mypy versions; update ruff config locations.
• Apply ruff v0.3.2 to all code.
• Reduce max-complexity 13 → 11.

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.
• Update doc/whatsnew.

[codecov]

Codecov Report

Attention: Patch coverage is 92.61364% with 26 lines in your changes are missing coverage. Please review.

Project coverage is 75.6%. Comparing base (583d3e9) to head (3b7bb24).
Report is 1 commits behind head on main.

Additional details and impacted files

@@           Coverage Diff           @@
##            main    #156     +/-   ##
=======================================
+ Coverage   75.4%   75.6%   +0.1%     
=======================================
  Files         93      93             
  Lines       6211    6372    +161     
=======================================
+ Hits        4684    4818    +134     
- Misses      1527    1554     +27     

Files	Coverage Δ
message_ix_models/__init__.py	100.0% <100.0%> (ø)
message_ix_models/model/__init__.py	100.0% <ø> (ø)
message_ix_models/model/bare.py	100.0% <100.0%> (ø)
message_ix_models/model/disutility.py	100.0% <100.0%> (ø)
message_ix_models/model/macro.py	100.0% <ø> (ø)
message_ix_models/model/snapshot.py	100.0% <ø> (ø)
message_ix_models/model/structure.py	100.0% <100.0%> (ø)
...ssage_ix_models/model/water/data/infrastructure.py	4.0% <ø> (ø)
message_ix_models/project/ssp/__init__.py	94.7% <ø> (-0.2%)	⬇️
message_ix_models/project/ssp/structure.py	100.0% <ø> (ø)
... and 40 more

[khaeru]

@glatterf42 FYI I ran into some dependency trouble here:

1. For upstream.version <= v3.6.0 in the pytest workflow, we require pandas < 2.0.
2. message_ix_models.tools.iea.web imports dask.dataframe.
3. In recent versions of dask ≥ 2024.3.0, dask[dataframe] must be explicitly installed to bring in dask-expr and import dask.dataframe.
4. dask-expr (any version) requires pandas > 2, which conflicts with (1).

This is the same root cause we ran into with iiasa/ixmp#522. Here I (think I have) resolved it by capping the dask version in upstream.extra-deps in the workflow.

[glatterf42]

LGTM :)