[WIP] Automatically run calibration setup during CES calibration

[Copilot]

• Add setupLocalCalibration() helper function to scripts/start/run.R (top-level, testable)
• Call setupLocalCalibration(cfg$remind_folder) in the calibrate branch before the iteration loop
• Add tests in tests/testthat/test_01-run.R
• Update tutorials/12_Calibrating_CES_Parameters.md to mention automatic setup

Original prompt

Goal

Automatically run the equivalent of make set-local-calibration when REMIND is executing a CES calibration run.

Repo

• Repository: remindmodel/remind

Current behavior

• CES calibration runs are handled in scripts/start/run.R under the branch cfg$gms$CES_parameters == "calibrate".
• Setting up local calibration collection currently requires a manual step: make set-local-calibration, which runs ./scripts/utils/set-local-calibration.sh to create calibration_results/, initialize a local git repo, install hooks, and create calibration_results/.Rprofile_calibration_results.
• scripts/utils/set-local-calibration.sh currently fails if calibration_results/ already exists.

Desired behavior

• Only when cfg$gms$CES_parameters == "calibrate":
  • If calibration_results/ already exists: do nothing.
  • If calibration_results/ does not exist: automatically run the equivalent of make set-local-calibration (i.e., execute ./scripts/utils/set-local-calibration.sh).
• The setup should occur early enough in the calibration run that subsequent workflow is ready for collecting calibration outputs.

Implementation details

1. Update scripts/start/run.R:
   • In the else if (cfg$gms$CES_parameters == "calibrate") branch, before starting iterations, check for presence of calibration_results directory.
   • If missing, invoke ./scripts/utils/set-local-calibration.sh.
   • Handle non-zero exit codes by stopping with a clear error message.
   • Ensure this is only executed for CES calibration runs; do not affect CES_parameters == "load" or other modes.
2. Add/adjust tests if the repository has test coverage for start scripts:
   • Prefer a unit/integration test in tests/testthat that verifies the call is attempted when the directory is absent, and skipped when present.
   • If running the real shell script is too heavy for tests, mock the system call (e.g., via withr::with_envvar + wrapper function, or refactor into a small helper to allow mocking).
3. Update documentation (optional but preferred):
   • Update tutorials/12_Calibrating_CES_Parameters.md to mention that local calibration setup is now automatic when running CES calibration, while make set-local-calibration remains available as a manual command.

Acceptance criteria

• Running a CES calibration with no calibration_results/ directory automatically creates it and sets up the local git/hook structure (same effect as make set-local-calibration).
• Running a CES calibration when calibration_results/ already exists does not attempt to re-run setup and does not fail.
• Non-calibration runs are unchanged.
• CI/tests (if present) pass.

Notes

• The Makefile target is:
  • set-local-calibration: @./scripts/utils/set-local-calibration.sh
• The setup script currently appends to .gitignore and initializes a git repo within calibration_results/; this is acceptable behavior per user confirmation.

This pull request was created from Copilot chat.

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