Address GitHub Actions warnings re: node.js 16

[khaeru]

GitHub Actions has started warning about deprecation of Node.js 16, for instance here:

Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/checkout@v3, actions/setup-python@v4, ts-graphviz/setup-graphviz@v1.2.0, r-lib/actions/setup-r@v2, actions/cache@v3. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.

This PR updates 'first-party' actions as suggested:

• actions/checkout v3 → v4
• actions/setup-python v4 → v5

Per third-party actions:

• codecov/codecov-action: v4 is available with Node.js 20: https://github.com/codecov/codecov-action/releases
• pre-commit/action: ~pending pre-commit/action#188~ it seems this action is actually abandoned and won't receive updates. One alternate approach is to inline the few steps; see e.g. transport-data/tools#14.
• r-lib/actions/setup-r: r-lib/actions#792.
• ts-graphviz/setup-graphviz: pending ts-graphviz/setup-graphviz#558

Other housekeeping:

• Replace black with ruff format for code style (iiasa/message_ix#772).
• Tweak the "publish" CI workflow:
  • Remove the trigger for pushes to main (analogous to #515).
  • Add concurrency: setting to prevent 2 conflicting jobs being started on a release (one triggered by the release event, one by the tag creation event).

How to review

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

PR checklist

• [x] Continuous integration checks all ✅
• [x] ~Add or expand tests;~ coverage checks both ✅
• ~Add, expand, or update documentation.~ N/A, CI changes only
• ~Update release notes.~

[codecov[bot]]

Codecov Report

All modified and coverable lines are covered by tests :white_check_mark:

Comparison is base (8a2aa91) 98.9% compared to head (8679d00) 98.9%.

Additional details and impacted files

```diff @@ Coverage Diff @@ ## main #517 +/- ## ======================================= - Coverage 98.9% 98.9% -0.1% ======================================= Files 44 44 Lines 4795 4795 ======================================= - Hits 4744 4743 -1 - Misses 51 52 +1 ``` | [Files](https://app.codecov.io/gh/iiasa/ixmp/pull/517?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=iiasa) | Coverage Δ | | |---|---|---| | [ixmp/tests/test\_model.py](https://app.codecov.io/gh/iiasa/ixmp/pull/517?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=iiasa#diff-aXhtcC90ZXN0cy90ZXN0X21vZGVsLnB5) | `100.0% <ø> (ø)` | | ... and [1 file with indirect coverage changes](https://app.codecov.io/gh/iiasa/ixmp/pull/517/indirect-changes?src=pr&el=tree-more&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=iiasa)

[khaeru]

Yes, we'll need to make similar changes for each repo in the stack. Please let me know if you'd like me to handle certain of those.