ci: split workflow stages and add macOS arm64

[zandivx]

This should be revisited after #128 is merged as this simplifies the build process.

[qodo-code-review]

Review Summary by Qodo

Split CI workflow into stages and add macOS arm64 support

✨ Enhancement

Walkthroughs

Description

• Split monolithic CI workflow into three separate jobs: pre-commit, build, and test
• Added macOS arm64 (macos-14) support with platform-specific dependency installation
• Implemented build artifact caching and upload/download for cross-job artifact sharing
• Replaced CMake commands with Makefile targets for simplified build and test execution

Diagram

flowchart LR
  A["Pre-commit<br/>ubuntu-latest"] --> B["Build<br/>ubuntu-latest &<br/>macos-14"]
  B --> C["Test<br/>ubuntu-latest &<br/>macos-14"]
  B -- "Upload artifacts" --> D["Artifact Storage"]
  D -- "Download artifacts" --> C

Loading

File Changes

1. .github/workflows/ci.yml ⚙️ Configuration changes +155/-12

Refactor workflow into stages with macOS arm64 support

• Refactored single build-and-test job into three separate jobs: pre-commit, build, and test
• Added macOS arm64 (macos-14) platform support with matrix strategy for both build and test jobs
• Introduced platform-specific dependency installation for Ubuntu and macOS with conditional steps
• Replaced CMake configuration and build commands with make all and make test targets
• Added build artifact upload/download mechanism to share artifacts between build and test jobs
• Enhanced cache key to include runner.arch for better platform-specific caching
• Removed doxygen from Ubuntu dependencies list

.github/workflows/ci.yml

---

[qodo-code-review]

Code Review by Qodo

🐞 Bugs (1) 📘 Rule violations (1) 📎 Requirement gaps (0) 🎨 UX Issues (0)

1. CI missing doxygen dependency 🐞 Bug ≡ Correctness

Description

The workflow removed installation of doxygen, but CMake configuration unconditionally fails with a
fatal error when Doxygen is not present, so make all in the build job will fail and block the
entire pipeline. This also affects the new macOS arm64 job because Homebrew dependencies do not
include doxygen.

Code

.github/workflows/ci.yml[32]

-            doxygen \

Evidence

The CI workflow no longer installs Doxygen on Ubuntu and never installs it on macOS. The build uses
make all, which runs a CMake configure; the top-level project always adds the KiLCA subdirectory,
and KiLCA’s CMakeLists aborts configuration with FATAL_ERROR when Doxygen is missing—making CI
failure deterministic.

.github/workflows/ci.yml[56-103]
.github/workflows/ci.yml[172-194]
CMakeLists.txt[102-109]
KiLCA/CMakeLists.txt[309-319]

Agent prompt

The issue below was found during a code review. Follow the provided context and guidance below and implement a solution

## Issue description
CI no longer installs `doxygen`, but the CMake configure step fails with a fatal error when Doxygen is missing, causing `make all` (and thus CI) to fail.

## Issue Context
`KiLCA/CMakeLists.txt` calls `find_package(Doxygen)` and then `message(FATAL_ERROR ...)` when not found, and the root `CMakeLists.txt` always includes `add_subdirectory(KiLCA)`.

## Fix Focus Areas
- .github/workflows/ci.yml[56-103]
- .github/workflows/ci.yml[172-194]

### Suggested change
- Ubuntu: add `doxygen` back to the `apt-get install` package list.
- macOS: add `doxygen` to the `brew install` package list.

(Alternative long-term fix: change `KiLCA/CMakeLists.txt` to make Doxygen optional unless building the `doc` target.)

ⓘ Copy this prompt and use it to remediate the issue with your preferred AI generation tools

---

2. ci.yml 2-space indentation 📘 Rule violation ⚙ Maintainability

Description

The updated GitHub Actions workflow uses 2-space indentation (e.g., before pre-commit:), but the
project style requires 4-space indentation. This can create inconsistent formatting and violates the
repo’s indentation policy for modified files.

Code

.github/workflows/ci.yml[R10-12]

+  pre-commit:
+    name: Pre-commit
    runs-on: ubuntu-latest

Evidence

PR Compliance ID 3 requires 4-space indentation (no tabs). In .github/workflows/ci.yml, the added
job keys are indented with 2 spaces (e.g.,   pre-commit:), which does not meet the 4-space
indentation requirement.

AGENTS.md
.github/workflows/ci.yml[10-12]
AGENTS.md[138-146]

Agent prompt

The issue below was found during a code review. Follow the provided context and guidance below and implement a solution

## Issue description
The GitHub Actions workflow `.github/workflows/ci.yml` uses 2-space indentation, but the repository policy requires 4-space indentation for modified files.

## Issue Context
The project coding-style documentation specifies `Indentation: 4 spaces (no tabs)` and the PR compliance checklist enforces this formatting rule.

## Fix Focus Areas
- .github/workflows/ci.yml[10-204]

ⓘ Copy this prompt and use it to remediate the issue with your preferred AI generation tools

---

ⓘ The new review experience is currently in Beta. Learn more

[qodo-code-review]

CI Feedback 🧐

A test triggered by this PR failed. Here is an AI-generated analysis of the failure:

Action: Pre-commit

Failed stage: Run pre-commit hooks [❌]

Failed test name: ""

Failure summary: The action failed because pre-commit hooks reported errors and auto-formatting changes that were not committed: - check-executables-have-shebangs failed: python/susc_functions/f2py_Ifuncs.sh is marked executable but has no (or an invalid) shebang (lines 212-218). - check-shebang-scripts-are-executable failed: KiLCA/flre/tensor/math2f90.pl has a shebang but is not marked executable (lines 221-227). - isort failed because it modified files that were not committed: python/KIMpy/init.py and python/KIMpy/electromagnetic_solver.py (lines 236-240). - black failed due to formatting differences (and likely would modify files), as shown by diffs in python/KIMpy/electromagnetic_solver.py and test/ql-balance/golden_record/ensure_golden.py (lines 241+). These hook failures caused the job to exit with code 1 (line 401).

Relevant error logs: 1: ##[group]Runner Image Provisioner 2: Hosted Compute Agent ... 197: [INFO] Initializing environment for https://github.com/pycqa/isort. 198: [INFO] Initializing environment for https://github.com/psf/black-pre-commit-mirror. 199: [INFO] Installing environment for https://github.com/pre-commit/pre-commit-hooks. 200: [INFO] Once installed this environment will be reused. 201: [INFO] This may take a few minutes... 202: [INFO] Installing environment for https://github.com/Lucas-C/pre-commit-hooks. 203: [INFO] Once installed this environment will be reused. 204: [INFO] This may take a few minutes... 205: [INFO] Installing environment for https://github.com/pycqa/isort. 206: [INFO] Once installed this environment will be reused. 207: [INFO] This may take a few minutes... 208: [INFO] Installing environment for https://github.com/psf/black-pre-commit-mirror. 209: [INFO] Once installed this environment will be reused. 210: [INFO] This may take a few minutes... 211: check for case conflicts.................................................Passed 212: check that executables have shebangs.....................................Failed 213: - hook id: check-executables-have-shebangs 214: - exit code: 1 215: python/susc_functions/f2py_Ifuncs.sh: marked executable but has no (or invalid) shebang! 216: If it isn't supposed to be executable, try: `chmod -x python/susc_functions/f2py_Ifuncs.sh` 217: If on Windows, you may also need to: `git add --chmod=-x python/susc_functions/f2py_Ifuncs.sh` 218: If it is supposed to be executable, double-check its shebang. 219: check illegal windows names..........................(no files to check)Skipped 220: check for merge conflicts................................................Passed 221: check that scripts with shebangs are executable..........................Failed 222: - hook id: check-shebang-scripts-are-executable 223: - exit code: 1 224: KiLCA/flre/tensor/math2f90.pl: has a shebang but is not marked executable! 225: If it is supposed to be executable, try: `chmod +x KiLCA/flre/tensor/math2f90.pl` 226: If on Windows, you may also need to: `git add --chmod=+x KiLCA/flre/tensor/math2f90.pl` 227: If it is not supposed to be executable, double-check its shebang is wanted. 228: check for broken symlinks............................(no files to check)Skipped 229: check toml...............................................................Passed 230: check yaml...............................................................Passed 231: detect private key.......................................................Passed 232: fix end of files.........................................................Passed 233: mixed line ending........................................................Passed 234: trim trailing whitespace.................................................Passed 235: Tabs remover.............................................................Passed 236: isort....................................................................Failed 237: - hook id: isort 238: - files were modified by this hook 239: Fixing /home/runner/work/KAMEL/KAMEL/python/KIMpy/__init__.py 240: Fixing /home/runner/work/KAMEL/KAMEL/python/KIMpy/electromagnetic_solver.py 241: black....................................................................Failed 242: - hook id: black ... 293: # B0 on xl grid from geometry (avoids HDF5 grid mismatch for backs/B0) 294: - self._b0_xl = np.abs(self.btor) * np.sqrt(1.0 + (self.xl / (self._q_xl * self.R0))**2) 295: + self._b0_xl = np.abs(self.btor) * np.sqrt(1.0 + (self.xl / (self._q_xl * self.R0)) ** 2) 296: # Aligned potential for BCs 297: self.phi_aligned = 1j * self._e0r_xl / (self._kp_xl * self._b0_xl) 298: @@ -104,14 +104,10 @@ class KIMElectromagneticSolver: 299: crossings = [] 300: for i in range(len(q_abs) - 1): 301: if (q_abs[i] - q_res) * (q_abs[i + 1] - q_res) < 0: 302: - r_cross = r[i] + (q_res - q_abs[i]) * (r[i + 1] - r[i]) / ( 303: - q_abs[i + 1] - q_abs[i] 304: - ) 305: + r_cross = r[i] + (q_res - q_abs[i]) * (r[i + 1] - r[i]) / (q_abs[i + 1] - q_abs[i]) 306: crossings.append(r_cross) 307: if not crossings: 308: - raise ValueError( 309: - f"No resonant surface found for m={self.m_mode}, n={self.n_mode}" 310: - ) 311: + raise ValueError(f"No resonant surface found for m={self.m_mode}, n={self.n_mode}") 312: return crossings[-1] ... 386: a_mat[:, 0] = 0.0 387: a_mat[:, -1] = 0.0 388: diff --git a/test/ql-balance/golden_record/ensure_golden.py b/test/ql-balance/golden_record/ensure_golden.py 389: index 2a6f3b8..ed6469f 100755 390: --- a/test/ql-balance/golden_record/ensure_golden.py 391: +++ b/test/ql-balance/golden_record/ensure_golden.py 392: @@ -108,9 +108,7 @@ def setup_runfolder() -> Path: 393: shutil.rmtree(RUNFOLDER_DIR) 394: RUNFOLDER_DIR.mkdir(parents=True) 395: - main_nml_template = str( 396: - MAIN_REF_DIR / "QL-Balance" / "namelists" / "balance_conf.nml" 397: - ) 398: + main_nml_template = str(MAIN_REF_DIR / "QL-Balance" / "namelists" / "balance_conf.nml") 399: setup_runfolder_external(str(RUNFOLDER_DIR), nml_template=main_nml_template) 400: return RUNFOLDER_DIR 401: ##[error]Process completed with exit code 1. 402: Post job cleanup.

[zandivx]

!build