From 4b8f4c454ee46494c51c5006a159cfdc447ac48c Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Fri, 17 Apr 2026 02:17:27 +0000
Subject: [PATCH 1/4] Add .github/copilot-instructions.md for cloud agent
 onboarding

Agent-Logs-Url: https://github.com/hansec/OpenFUSIONToolkit/sessions/f08beca4-8f0b-4c06-a98a-0459a987893d

Co-authored-by: hansec <821577+hansec@users.noreply.github.com>
---
 .github/copilot-instructions.md | 208 ++++++++++++++++++++++++++++++++
 1 file changed, 208 insertions(+)
 create mode 100644 .github/copilot-instructions.md

diff --git a/.github/copilot-instructions.md b/.github/copilot-instructions.md
new file mode 100644
index 00000000..1ef07570
--- /dev/null
+++ b/.github/copilot-instructions.md
@@ -0,0 +1,208 @@
+# Copilot Instructions for OpenFUSIONToolkit
+
+## Project Overview
+
+The Open FUSION Toolkit (OFT) is a scientific computing suite for plasma and fusion research. It provides finite element methods on unstructured 2D/3D meshes for MHD equilibrium, stability, and time-dependent simulations.
+
+The codebase is a hybrid Fortran/C/C++/Python project:
+- **Core computational code**: Fortran 90 (`.F90` files) with C/C++ bridge files
+- **Python interface**: `ctypes`-based wrappers calling into compiled Fortran shared libraries
+- **Build system**: CMake (requires ≥ 3.27), orchestrated by `src/utilities/build_libs.py`
+
+### Component Tools
+
+| Tool | Purpose | Key Fortran Source | Python Module |
+|---|---|---|---|
+| **TokaMaker** | Axisymmetric Grad-Shafranov MHD equilibria | `src/physics/grad_shaf*.F90` | `OpenFUSIONToolkit.TokaMaker` |
+| **ThinCurr** | Thin-wall eddy current modeling | `src/physics/thin_wall*.F90` | `OpenFUSIONToolkit.ThinCurr` |
+| **Marklin** | 3D force-free ideal MHD equilibria | `src/physics/taylor.F90` | `OpenFUSIONToolkit.Marklin` |
+| **MUG** | Time-dependent extended MHD | `src/physics/xmhd*.F90` | *(Fortran executables only)* |
+
+## Repository Layout
+
+```
+src/
+├── base/           # Core runtime (I/O, XML, sorting, stitching)
+├── grid/           # Mesh types, readers (Cubit, Gmsh, native, T3D), multigrid
+├── fem/            # Finite element basis functions and operators (H1, Hcurl, Lagrange)
+├── lin_alg/        # Linear algebra (native solvers, PETSc, ARPACK, SuperLU, UMFPACK)
+├── physics/        # Physics modules (Grad-Shafranov, thin-wall, Taylor, xMHD, tracing)
+├── bin/            # Standalone Fortran executables
+├── python/
+│   ├── OpenFUSIONToolkit/         # Python package (ctypes wrappers)
+│   │   ├── TokaMaker/            # TokaMaker Python API
+│   │   ├── ThinCurr/             # ThinCurr Python API
+│   │   └── Marklin/              # Marklin Python API
+│   └── wrappers/                 # Fortran-side C-interop wrapper subroutines
+├── ext_libs/       # Bundled 3rd-party sources (triangle, minpack, bvls, dlsode)
+├── tests/          # Regression tests (pytest-driven, Fortran + Python)
+├── examples/       # Jupyter notebook examples per tool
+├── utilities/      # Build scripts, code generators, helper tools
+├── docs/           # Doxygen documentation sources
+├── cmake/          # CMake find-modules for external dependencies
+├── include/        # C/Fortran header files
+└── CMakeLists.txt  # Top-level CMake configuration
+```
+
+## Build System
+
+OFT uses a two-stage build process:
+
+### Stage 1: Build external libraries
+
+```bash
+mkdir builds && cd builds
+source ../setup_env.sh  # activates Python venv
+python ../src/utilities/build_libs.py \
+  --nthread=4 --oblas_dynamic_arch \
+  --build_umfpack=1 --build_superlu=1 \
+  --build_arpack=1 --oft_build_tests=1
+```
+
+This downloads and compiles dependencies (OpenBLAS, HDF5, METIS, etc.) and generates `config_cmake.sh` — a shell script containing the full CMake invocation with all paths.
+
+### Stage 2: Configure, build, and install OFT
+
+```bash
+# Still in builds/
+bash config_cmake.sh        # runs cmake, creates builds/build_release/
+cd build_release
+make                         # compile
+make install                 # install to builds/install_release/
+```
+
+### Key CMake options (set via build_libs.py flags)
+
+- `OFT_BUILD_TESTS` — build test executables (enable with `--oft_build_tests=1`)
+- `OFT_BUILD_PYTHON` — build Python wrappers (default ON)
+- `OFT_USE_MPI` — enable MPI parallelism (set by `--build_mpich=1` or `--build_openmpi=1`)
+- `OFT_BUILD_DOCS` — build Doxygen documentation
+- `OFT_BUILD_EXAMPLES` — build example programs
+
+### Important Environment Notes
+
+- The project uses a Python virtual environment at `oft_venv/`. **Always** `source setup_env.sh` before running builds or tests.
+- The `copilot-setup-steps.yml` workflow mirrors the Ubuntu 24.04 GCC 14 + OpenMP CI configuration and pre-builds external libraries in a cached `builds/` directory. After this workflow runs, the agent environment has:
+  - Compilers: `gcc-14`, `g++-14`, `gfortran-14`
+  - Python venv with: `pytest`, `numpy`, `scipy`, `h5py`, `triangle`, `matplotlib`, `xarray`
+  - Pre-built external libraries in `builds/`
+  - OFT compiled and installed in `builds/install_release/`
+
+## Testing
+
+Tests use **pytest** and are organized under `src/tests/` in subdirectories matching the source layout: `base/`, `grid/`, `lin_alg/`, `fem/`, `physics/`.
+
+### Test structure
+
+Each test subdirectory has:
+- `test_*.py` — pytest test files
+- `test_*.F90` — corresponding Fortran test programs (compiled during build)
+- Various data files (`.h5`, `.g`, `.inp`, etc.)
+
+### Running tests
+
+From `builds/build_release/`:
+
+```bash
+source ../../setup_env.sh
+make test                    # runs: pytest -m "not slow" base grid lin_alg fem physics
+make test_full               # runs all tests including slow ones
+make test_examples           # runs example notebook tests
+```
+
+Or run individual test files:
+
+```bash
+cd builds/build_release/tests
+../../run_test.sh physics/test_TokaMaker.py -k "test_name"
+```
+
+### Test conventions
+
+- Tests marked `@pytest.mark.slow` are excluded from default CI runs
+- Tests marked `@pytest.mark.mpi` require MPI (`OFT_HAVE_MPI=1`)
+- Tests marked `@pytest.mark.coverage` are for code coverage runs
+- `oft_testing.py` provides `run_OFT()` helper for running Fortran executables with timeout
+- Physics Python tests (TokaMaker, ThinCurr) use `multiprocessing.Process` to isolate OFT runtime (only one `OFT_env` instance per process)
+- Test timeout is multiplied by 4× when `OFT_DEBUG_TEST=1`
+
+## Linting
+
+### Python linting
+
+Python code is linted with **ruff**. Configuration is in `src/python/pyproject.toml`:
+
+```bash
+cd src/python && ruff check
+```
+
+Rules: Pyflakes (`F`) + pycodestyle (`E`) with ignores for `E722`, `F403`, `F405`. Target: Python 3.7.
+
+### Fortran stack checking
+
+A custom lint checks Fortran debug stack entries:
+
+```bash
+cd src && python utilities/generate_stack.py -l
+```
+
+This validates that all `SUBROUTINE`/`FUNCTION` entries have matching debug stack annotations. Run from the `src/` directory.
+
+## CI Workflows
+
+| Workflow | File | Trigger | Purpose |
+|---|---|---|---|
+| **CI Build** | `ci_build.yaml` | push to main, PRs | Full matrix build (GCC, Intel, macOS) × (OpenMP, MPICH, OpenMPI) |
+| **Lint** | `lint.yaml` | push to main, PRs | ruff check + Fortran stack check |
+| **Coverage** | `cov_build.yaml` | push to main | Build with `--coverage`, upload to Codecov |
+| **CD Nightly** | `cd_nightly.yaml` | schedule | Nightly package builds |
+| **Copilot Setup** | `copilot-setup-steps.yml` | manual/PR | Agent environment setup |
+
+### CI configuration used in copilot-setup-steps
+
+- **OS**: Ubuntu 24.04
+- **Compilers**: `gcc-14` / `g++-14` / `gfortran-14`
+- **Parallel**: OpenMP only (no MPI)
+- **Libraries**: OpenBLAS, UMFPACK, SuperLU, ARPACK, HDF5, METIS
+
+## Coding Conventions
+
+### Fortran
+
+- Free-form Fortran 90+ (`.F90` extension, preprocessed)
+- SPDX license header: `! SPDX-License-Identifier: LGPL-3.0-only`
+- Doxygen-style comments with `!>` and `!!` markers
+- Module names typically prefixed with `oft_` (e.g., `oft_gs`, `oft_la_base`)
+- Line length: unlimited (`-ffree-line-length-none`), but keep reasonable
+- New functions/subroutines must have Doxygen documentation
+
+### Python
+
+- SPDX license header comment block at top of each file
+- Doxygen-style docstrings with `@param`, `@result`, `@authors`, `@date`
+- Target Python 3.7+ (for OMFIT compatibility)
+- Use `ctypes` for Fortran interop; wrapper patterns in `_interface.py` files
+- All Python wrappers live under `src/python/OpenFUSIONToolkit/`
+
+### Pull Requests
+
+- PRs for a specific tool should be titled: `ToolName: description` (e.g., `TokaMaker: Fix boundary condition`)
+- Keep changes focused on a single feature; secondary changes should be minimal
+- Comment on whether APIs or input files change
+- Run regression tests before submitting
+
+## Common Pitfalls
+
+1. **Single OFT_env instance**: The Python `OFT_env` class enforces a singleton. Tests use `multiprocessing.Process` to work around this. Never create two `OFT_env` instances in the same process.
+
+2. **Source setup_env.sh**: Always source this before any build/test commands. It activates the Python venv. In CI, this file is generated during prerequisites setup.
+
+3. **Build from `builds/` directory**: The `build_libs.py` script must run from the `builds/` directory. It creates `config_cmake.sh` there. CMake then creates `build_release/` and `install_release/` inside `builds/`.
+
+4. **Tests run from build tree**: Tests must be run from `builds/build_release/tests/` (or via `make test` from `builds/build_release/`), not from the source tree, because compiled Fortran test executables are in the build tree.
+
+5. **ext_libs/ is bundled third-party code**: Do not modify files in `src/ext_libs/`. These are upstream sources (triangle, minpack, bvls, dlsode).
+
+6. **Fortran/Python interop**: The Python package calls compiled Fortran via `ctypes`. The Fortran-side wrappers are in `src/python/wrappers/` and use `ISO_C_BINDING`. Changes to Fortran function signatures require corresponding updates to both `wrappers/*_f.F90` and `python/OpenFUSIONToolkit/*/_interface.py`.
+
+7. **CMake template files**: Some files use `@VARIABLE@` CMake substitution (e.g., `__init__.py`, `pyproject.toml.in`, `run_test.sh.in`). Edit the `.in` template, not the generated file.

From decfd9dbbb58b2225740173e7ccb945b19193ff6 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Sun, 19 Apr 2026 03:14:43 +0000
Subject: [PATCH 2/4] Remove triangle Python package from copilot-setup-steps
 and update instructions

Agent-Logs-Url: https://github.com/hansec/OpenFUSIONToolkit/sessions/aee6c3b1-2da4-4c48-a08b-9527e7444d09

Co-authored-by: hansec <821577+hansec@users.noreply.github.com>
---
 .github/copilot-instructions.md           | 2 +-
 .github/workflows/copilot-setup-steps.yml | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/copilot-instructions.md b/.github/copilot-instructions.md
index 1ef07570..11ddaa3c 100644
--- a/.github/copilot-instructions.md
+++ b/.github/copilot-instructions.md
@@ -84,7 +84,7 @@ make install                 # install to builds/install_release/
 - The project uses a Python virtual environment at `oft_venv/`. **Always** `source setup_env.sh` before running builds or tests.
 - The `copilot-setup-steps.yml` workflow mirrors the Ubuntu 24.04 GCC 14 + OpenMP CI configuration and pre-builds external libraries in a cached `builds/` directory. After this workflow runs, the agent environment has:
   - Compilers: `gcc-14`, `g++-14`, `gfortran-14`
-  - Python venv with: `pytest`, `numpy`, `scipy`, `h5py`, `triangle`, `matplotlib`, `xarray`
+  - Python venv with: `pytest`, `numpy`, `scipy`, `h5py`, `matplotlib`, `xarray`
   - Pre-built external libraries in `builds/`
   - OFT compiled and installed in `builds/install_release/`
 
diff --git a/.github/workflows/copilot-setup-steps.yml b/.github/workflows/copilot-setup-steps.yml
index 9a4b29a2..fd1bae4a 100644
--- a/.github/workflows/copilot-setup-steps.yml
+++ b/.github/workflows/copilot-setup-steps.yml
@@ -34,7 +34,7 @@ jobs:
         python3 -m venv ${{ github.workspace }}/oft_venv
         echo "source ${{ github.workspace }}/oft_venv/bin/activate" > ${{ github.workspace }}/setup_env.sh
         source ${{ github.workspace }}/setup_env.sh
-        python -m pip install pytest numpy scipy h5py triangle matplotlib xarray
+        python -m pip install pytest numpy scipy h5py matplotlib xarray
 
     - name: Check compilers
       run: |

From e6282068f8580428a9deac28f9fa26dea60c0ca1 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Sun, 19 Apr 2026 17:45:52 +0000
Subject: [PATCH 3/4] Update copilot-setup-steps: rename step and update
 build_libs.py flags

Agent-Logs-Url: https://github.com/hansec/OpenFUSIONToolkit/sessions/7927ae3e-309f-4315-92b4-16b51c8abbbe

Co-authored-by: hansec <821577+hansec@users.noreply.github.com>
---
 .github/workflows/copilot-setup-steps.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/copilot-setup-steps.yml b/.github/workflows/copilot-setup-steps.yml
index fd1bae4a..742c1e72 100644
--- a/.github/workflows/copilot-setup-steps.yml
+++ b/.github/workflows/copilot-setup-steps.yml
@@ -55,14 +55,14 @@ jobs:
       if: ${{ steps.cache-ext-libs.outputs.cache-hit != 'true' }}
       run: mkdir builds
 
-    - name: Build external libraries (OpenMP)
+    - name: Build external libraries
       if: ${{ steps.cache-ext-libs.outputs.cache-hit != 'true' }}
       shell: bash
       timeout-minutes: 30
       working-directory: builds
       run: |
         source ${{ github.workspace }}/setup_env.sh
-        python ../src/utilities/build_libs.py --oblas_dynamic_arch --build_umfpack=1 --build_superlu=1 --no_dl_progress --nthread=4 --build_arpack=1 --oft_build_tests=1
+        python ../src/utilities/build_libs.py --build_umfpack=1 --build_superlu=1 --no_dl_progress --nthread=4 --build_arpack=1 --oft_build_tests=1 --build_mpich=1
 
     - name: Upload library failure log
       uses: actions/upload-artifact@v4

From f75d3bab26e7806d7cbdde937e6f88dc9208547e Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Tue, 21 Apr 2026 20:05:58 +0000
Subject: [PATCH 4/4] Update copilot-instructions.md: align build flags and add
 --collect-only example

Agent-Logs-Url: https://github.com/hansec/OpenFUSIONToolkit/sessions/271b180f-f526-455c-b78e-e5c08b62c8dc

Co-authored-by: hansec <821577+hansec@users.noreply.github.com>
---
 .github/copilot-instructions.md | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/copilot-instructions.md b/.github/copilot-instructions.md
index 11ddaa3c..573cbaca 100644
--- a/.github/copilot-instructions.md
+++ b/.github/copilot-instructions.md
@@ -54,9 +54,8 @@ OFT uses a two-stage build process:
 mkdir builds && cd builds
 source ../setup_env.sh  # activates Python venv
 python ../src/utilities/build_libs.py \
-  --nthread=4 --oblas_dynamic_arch \
-  --build_umfpack=1 --build_superlu=1 \
-  --build_arpack=1 --oft_build_tests=1
+  --nthread=4 --build_umfpack=1 --build_superlu=1 \
+  --build_arpack=1 --oft_build_tests=1 --build_mpich=1
 ```
 
 This downloads and compiles dependencies (OpenBLAS, HDF5, METIS, etc.) and generates `config_cmake.sh` — a shell script containing the full CMake invocation with all paths.
@@ -115,6 +114,7 @@ Or run individual test files:
 ```bash
 cd builds/build_release/tests
 ../../run_test.sh physics/test_TokaMaker.py -k "test_name"
+../../run_test.sh physics/test_TokaMaker.py --collect-only
 ```
 
 ### Test conventions