Refactor

.fprettify

@@ -0,0 +1,10 @@
+indent = 4
+line-length = 88
+whitespace-comma = true
+whitespace-assignment = true
+whitespace-decl = true
+whitespace-relational = true
+whitespace-logical = true
+whitespace-plusminus = true
+whitespace-print = true
+whitespace-intrinsics = true

.github/workflows/main.yml

@@ -2,30 +2,92 @@ name: CI
 
 on:
   push:
-    branches: [ master ]
+    branches: [ main ]
   pull_request:
-    branches: [ master ]
-
+    types: [opened, synchronize, reopened, ready_for_review]
   workflow_dispatch:
 
 jobs:
-  build:
+  test:
+    name: Run Tests
+    runs-on: ubuntu-latest
+    if: github.event_name == 'push' || github.event_name == 'pull_request'
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Install dependencies
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y \
+            gfortran \
+            cmake \
+            ninja-build \
+            libnetcdf-dev \
+            libnetcdff-dev \
+            liblapack-dev \
+            libblas-dev \
+            python3-pip \
+            python3-numpy \
+            python3-scipy \
+            python3-matplotlib \
+            python3-netcdf4 \
+            openmpi-bin \
+            libopenmpi-dev \
+            libgsl-dev \
+            libfftw3-dev
+          pip3 install --user scikit-build-core git+https://github.com/jameskermode/f90wrap simsopt
+
+      - name: Build SIMPLE
+        run: |
+          make clean
+          make
+          pip3 install -e . --no-build-isolation
+
+      - name: Run Fast Tests
+        run: make test-fast
+
+      - name: Run Slow Tests
+        run: make test
+
+      - name: Run Regression Tests
+        if: github.event_name == 'push' || (github.event_name == 'pull_request' && github.event.pull_request.draft == false)
+        run: make test-regression
+
+      - name: Upload test results
+        if: always()
+        uses: actions/upload-artifact@v4
+        with:
+          name: test-results
+          path: |
+            build/Testing/
+
+  build-docs:
+    name: Build Documentation
     runs-on: ubuntu-latest
 
     container:
       image: texlive/texlive:latest
 
     steps:
-      - uses: actions/checkout@v2
-      - name: Build
+      - uses: actions/checkout@v4
+
+      - name: Install LyX
+        run: |
+          echo "LyX installation"
+          apt-get update
+          apt-get install -y lyx
+
+      - name: Build LaTeX documents
         run: |
-         cd DOC
-         latexmk -pdf canonical_and_boozer_flux_coords_via_VMEC.tex
-         lyx --export pdf2 neo-orb.lyx
-      - name: Upload doc artifacts
-        uses: actions/upload-artifact@v2
+          cd DOC
+          latexmk -pdf canonical_and_boozer_flux_coords_via_VMEC.tex
+          lyx --export pdf2 neo-orb.lyx
+
+      - name: Upload documentation artifacts
+        uses: actions/upload-artifact@v4
         with:
-          name: doc
+          name: documentation
           path: |
             DOC/canonical_and_boozer_flux_coords_via_VMEC.pdf
-            DOC/neo-orb.pdf
+            DOC/neo-orb.pdf

.pre-commit-config.yaml

@@ -0,0 +1,30 @@
+# See https://pre-commit.com for more information
+# See https://pre-commit.com/hooks.html for more hooks
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v5.0.0
+    hooks:
+      - id: trailing-whitespace
+        args: [--markdown-linebreak-ext=md]
+      - id: end-of-file-fixer
+      - id: check-yaml
+      - id: check-added-large-files
+        args: ['--maxkb=1000']
+      - id: check-merge-conflict
+      - id: check-case-conflict
+      - id: check-executables-have-shebangs
+      - id: check-shebang-scripts-are-executable
+      - id: check-toml
+      - id: detect-private-key
+      - id: mixed-line-ending
+
+  - repo: local
+    hooks:
+      - id: run-fast-tests
+        name: Run Fast Tests
+        entry: make test-fast
+        language: system
+        pass_filenames: false
+        always_run: true
+        verbose: true
+        stages: [pre-commit]

.vscode/settings.json

@@ -0,0 +1,19 @@
+{
+    "fortran.formatting.formatter": "fprettify",
+    "fortran.formatting.fprettifyArgs": [
+        "-i 4",
+        "--enable-decl",
+        "--whitespace-comma",
+        "--whitespace-assignment",
+        "--whitespace-decl",
+        "--whitespace-relational",
+        "--whitespace-logical",
+        "--whitespace-print",
+        "--whitespace-intrinsics",
+        "--case",
+        "1",
+        "1",
+        "1",
+        "1"
+    ],
+}

CLAUDE.md

@@ -20,9 +20,13 @@ This file provides guidance to Claude Code (claude.ai/code) when working with co
 - **Reconfigure**: `make reconfigure` - Forces CMake reconfiguration
 
 ### Testing
-- **Run tests**: `make test` - Executes ctest in build directory
+- **Run tests**: `make test` - Runs all tests including slow ones (excludes regression tests)
+- **Fast tests only**: `make test-fast` - Excludes slow and regression tests
+- **All tests**: `make test-regression` - Includes all tests including regression tests
 - **Python tests**: Located in `test/python/` directory
 - **Golden record testing**: Use `examples/golden_record.py` to compare against reference behavior
+- **Verbose output**: Now default for all test targets. Use `VERBOSE=0` to disable
+- **Single test**: `make test TEST=test_name` - Run specific test by name
 - Note: Test system is currently under development
 
 ### Build Configuration
@@ -32,7 +36,7 @@ This file provides guidance to Claude Code (claude.ai/code) when working with co
 
 ### Dependencies
 - Required: NetCDF, LAPACK/BLAS, libneo, GVEC (minimal)
-- Compilers: GNU Fortran or Intel Fortran
+- Compiler: GNU Fortran (gfortran)
 - Optional: OpenMP (enabled by default)
 
 ### GVEC Integration

CMakeLists.txt

@@ -9,17 +9,7 @@ set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} ${CMAKE_SOURCE_DIR}/cmake)
 project (SIMPLE)
 enable_language(C Fortran)
 
-# Fetch GVEC as a minimal library (before setting SIMPLE-specific flags)
-include(FetchContent)
-
-FetchContent_Declare(
-  gvec
-  GIT_REPOSITORY https://gitlab.mpcdf.mpg.de/calbert/gvec.git
-  GIT_TAG        develop
-)
-
-set(GVEC_FOR_SIMPLE TRUE CACHE BOOL "Build minimal GVEC for SIMPLE")
-FetchContent_MakeAvailable(gvec)
+add_compile_options(-g -fbacktrace)
 
 include(Util)
 
@@ -38,6 +28,22 @@ endif()
 option(ENABLE_PYTHON_INTERFACE "Enables the Python-Wrapper." ON)
 option(SIMPLE_TESTING "Enable testing." ON)
 option(ENABLE_OPENMP "Enable OpenMP compiler flags." ON)
+option(ENABLE_GVEC "Enable GVEC field support (experimental)" OFF)
+
+# Conditionally fetch GVEC if enabled
+if(ENABLE_GVEC)
+    message(STATUS "GVEC support enabled - fetching GVEC library")
+    include(FetchContent)
+    FetchContent_Declare(
+      gvec
+      GIT_REPOSITORY https://gitlab.mpcdf.mpg.de/calbert/gvec.git
+      GIT_TAG        develop
+    )
+    set(GVEC_FOR_SIMPLE TRUE CACHE BOOL "Build minimal GVEC for SIMPLE")
+    FetchContent_MakeAvailable(gvec)
+else()
+    message(STATUS "GVEC support disabled")
+endif()
 
 set(CMAKE_MACOSX_RPATH 1)
 
@@ -78,54 +84,37 @@ endif()
 message(STATUS "CMake build type: " ${CMAKE_BUILD_TYPE})
 
 include_directories ($ENV{NETCDFF_INCLUDE} ${NFINC})
-link_directories ($ENV{NETCDF_LIB} $ENV{NETCDFF_LIB} ${NFLIBS} $ENV{HOME}/.local/lib)
-
-set(CMAKE_INTERPROCEDURAL_OPTIMIZATION TRUE)
+link_directories ($ENV{NETCDF_LIB} $ENV{NETCDFF_LIB} ${NFLIBS})
 
 # Set SIMPLE-specific compiler flags after GVEC to avoid affecting it
-if (CMAKE_Fortran_COMPILER_ID MATCHES Intel)
-	add_compile_options(-mkl -qopenmp -warn all,nounused)
-	link_libraries("-mkl -qopenmp")
-	if (CMAKE_BUILD_TYPE MATCHES Debug)
-		add_compile_options(-O0 -g -traceback)
-	elseif (CMAKE_BUILD_TYPE MATCHES Profile)
-		add_compile_options(-O2 -g -shared-intel -debug inline-debug-info
-			-D TBB_USE_THREADING_TOOLS -qopenmp-link dynamic -parallel-source-info=2)
-	elseif (CMAKE_BUILD_TYPE MATCHES Release)
-		add_compile_options(-O3 -g -traceback)
-	elseif (CMAKE_BUILD_TYPE MATCHES Fast)
-		add_compile_options(-O3 -march=native -mtune=native)
-	endif()
-else()
-	add_compile_options(-Wall -Wextra -Wimplicit-interface -Wno-external-argument-mismatch -fPIC -fmax-errors=5)
-	add_compile_options(-Wno-unused-dummy-argument)
-	add_compile_options(-ffree-line-length-132)
-	# If not apple
-	if (NOT APPLE)
-		add_link_options(-Wl,-z,noexecstack)
-	endif()
-	if (ENABLE_OPENMP)
-		add_compile_options(-fopenmp)
-		add_link_options(-fopenmp)
-	endif()
-	if (CMAKE_BUILD_TYPE MATCHES Debug)
-		add_compile_options(-C)
-		add_compile_options(-O0 -g -ggdb
-			-ffpe-trap=invalid,zero,overflow -fbounds-check -fcheck=all,no-array-temps
-			-finit-real=nan -fno-omit-frame-pointer -fno-inline)
-			add_compile_options(-fbacktrace)
-	elseif (CMAKE_BUILD_TYPE MATCHES Profile)
-		add_compile_options(-O2 -p -g -shared-libgcc)
-	elseif (CMAKE_BUILD_TYPE MATCHES Release)
-		add_compile_options(-O3 -g)
-		add_compile_options(-fbacktrace)
-	elseif (CMAKE_BUILD_TYPE MATCHES Fast)
-		add_compile_options(-O3 -ffast-math -ffp-contract=fast -funroll-loops -mtune=native)
-		if(${CMAKE_HOST_SYSTEM_PROCESSOR} STREQUAL "arm64")
-				add_compile_options(-march=native)
-		else()
-		add_compile_options(-march=haswell)
-		endif()
+# GNU Fortran compiler flags
+add_compile_options(-Wall -Wextra -Wimplicit-interface -Wno-external-argument-mismatch -fPIC -fmax-errors=5)
+add_compile_options(-Wno-unused-dummy-argument)
+add_compile_options(-ffree-line-length-132)
+add_compile_options(-g -fbacktrace)
+# If not apple
+if (NOT APPLE)
+	add_link_options(-Wl,-z,noexecstack)
+endif()
+if (ENABLE_OPENMP)
+	add_compile_options(-fopenmp)
+	add_link_options(-fopenmp)
+endif()
+if (CMAKE_BUILD_TYPE MATCHES Debug)
+	add_compile_options(-C)
+	add_compile_options(-O0 -ggdb
+		-ffpe-trap=invalid,zero,overflow -fbounds-check -fcheck=all,no-array-temps
+		-finit-real=nan -fno-omit-frame-pointer -fno-inline)
+elseif (CMAKE_BUILD_TYPE MATCHES Profile)
+	add_compile_options(-O2 -p -shared-libgcc)
+elseif (CMAKE_BUILD_TYPE MATCHES Release)
+	add_compile_options(-O3)
+elseif (CMAKE_BUILD_TYPE MATCHES Fast)
+	add_compile_options(-O3 -ffast-math -ffp-contract=fast -funroll-loops -mtune=native)
+	if(${CMAKE_HOST_SYSTEM_PROCESSOR} STREQUAL "arm64")
+			add_compile_options(-march=native)
+	else()
+	add_compile_options(-march=haswell)
 	endif()
 endif()
 

Makefile

@@ -2,7 +2,10 @@ CONFIG ?= Release
 BUILD_DIR := build
 BUILD_NINJA := $(BUILD_DIR)/build.ninja
 
-.PHONY: all configure reconfigure build test install clean
+# Common ctest command with optional verbose and test name filtering
+CTEST_CMD = cd $(BUILD_DIR) && ctest --test-dir test --output-on-failure $(if $(filter 1,$(VERBOSE)),-V) $(if $(TEST),-R $(TEST))
+
+.PHONY: all configure reconfigure build test test-fast test-slow test-regression test-all install clean
 all: build
 
 $(BUILD_NINJA):
@@ -16,16 +19,29 @@ reconfigure:
 build: configure
 	cmake --build $(BUILD_DIR) --config $(CONFIG)
 
-# Run tests with optional verbose output and single test selection
-# Usage: make test [VERBOSE=1] [TEST=test_name] [INCLUDE_SLOW=1]
-# Example: make test VERBOSE=1 TEST=test_gvec
-# By default, tests labeled "slow" are excluded. To include them: make test INCLUDE_SLOW=1
+# Test targets
+# Usage: make [test-target] [TEST=test_name] [VERBOSE=1]
+# Example: make test TEST=test_gvec VERBOSE=1
+
+# Run all tests except regression tests (default)
 test: build
-	cd $(BUILD_DIR) && ctest --test-dir test --output-on-failure $(if $(VERBOSE),-V) $(if $(TEST),-R $(TEST)) $(if $(INCLUDE_SLOW),,-LE "slow")
+	$(CTEST_CMD) -LE "regression"
+
+# Run only fast tests (exclude slow and regression tests)
+test-fast: build
+	$(CTEST_CMD) -LE "slow|regression"
+
+# Run only slow tests
+test-slow: build
+	$(CTEST_CMD) -L "slow" -LE "regression"
+
+# Run only regression tests
+test-regression: build
+	$(CTEST_CMD) -L "regression"
 
-# Run all tests including slow ones
+# Run all tests including regression tests
 test-all: build
-	cd $(BUILD_DIR) && ctest --test-dir test --output-on-failure $(if $(VERBOSE),-V) $(if $(TEST),-R $(TEST))
+	$(CTEST_CMD)
 
 doc: configure
 	cmake --build --preset default --target doc

README.md

@@ -23,9 +23,14 @@ Required libraries:
 * NetCDF
 * LAPACK/BLAS
 
-Supported compilers:
-* GNU Fortan
-* Intel Fortran
+Required compiler:
+* GNU Fortran (gfortran)
+
+For Python wrappers, do
+```bash
+pip install git+https://github.com/jameskermode/f90wrap
+pip install -e . --no-build-isolation
+```
 
 ## Usage