Use pre-commit to invoke ruff, mypy

[khaeru]

This PR streamlines the use of code quality tools:

• Add .pre-commit-config.yaml, configuration for pre-commit to:
  • Invoke mypy.
  • Invoke black.
  • Invoke ruff.
• Replace isort and flake8 configuration with equivalent ruff configuration.
• Remove .github/workflow/lint.yaml with a "Code quality" job within .github/workflow/pytest.yaml that invokes pre-commit/action.

The advantages are:

• pre-commit runs both on developers' machines and in the GitHub Actions runners, using the same configuration.
• We no longer need to maintain iiasa/actions/.github/workflows/lint.yaml (common re-usable workflow) and .github/workflows/lint.yaml (invoking the former), and the interaction between the two.
• The replacement "Code quality" job is significantly shorter and simpler; it also runs faster.
• Ruff is significantly faster than flake8+isort, thus better when run via a developer's editor/IDE.

Some disadvantages:

• The mypy configuration is a little complex:
  • In order to allow use of local development versions/editable installs for type hints, I had to write a custom "local" hook that checks an environment variable and uses a local environment.
  • We cannot (see Support updating additional_dependencies in autoupdate pre-commit/pre-commit#1351) automatically update the packages in the virtual environment that pre-commits creates for running mypy, so we have to force this in order to get early warning of upstream typing changes. This PR adds a workflow step to do this.
• The pre-commit maintainer seems to be very brusque, so it might be hard to get help if we need it. However, our use case is simple and should remain so.

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 release notes. N/A

[codecov]

Codecov Report

Merging #742 (f9afa5f) into main (31d9c58) will decrease coverage by 0.1%.
The diff coverage is 100.0%.

@@           Coverage Diff           @@
##            main    #742     +/-   ##
=======================================
- Coverage   94.3%   94.3%   -0.1%     
=======================================
  Files         43      43             
  Lines       3475    3474      -1     
=======================================
- Hits        3280    3279      -1     
  Misses       195     195             

Files	Coverage Δ
message_ix/reporting/__init__.py	100.0% <ø> (ø)
message_ix/testing/__init__.py	99.6% <100.0%> (ø)