Replace dense matrix spline implementation with efficient sparse matrix approach

.github/workflows/test-on-pr.yml

@@ -1,16 +1,24 @@
 name: Run Test
 
 on:
-  pull_request:
+  push:
     branches:
       - main
-  push:
+      - master
+  pull_request:
+    types: [opened, synchronize, reopened, ready_for_review]
     branches:
-      - '**'
+      - main
+      - master
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
 
 jobs:
   run-golden-record:
     runs-on: ubuntu-24.04
+    if: github.event_name == 'push' || (github.event_name == 'pull_request' && github.event.pull_request.draft == false)
 
     env:
       CC: gcc
@@ -24,18 +32,38 @@ jobs:
 
       - name: Set up Python 3
         run: |
-          sudo apt-get update -y
-          sudo apt-get install -y -q --no-install-recommends python3-dev
           python -m pip install --upgrade pip
           pip install numpy
 
-      - name: Install required packages
+      - name: Cache apt packages
+        uses: awalsh128/cache-apt-pkgs-action@v1
+        with:
+          packages: git cmake make ninja-build gcc g++ gfortran jq libopenblas-dev liblapack-dev libsuitesparse-dev libfftw3-dev libgsl-dev libhdf5-dev libnetcdf-dev libnetcdff-dev python3-dev libevent-dev libnuma-dev libhwloc-dev libnl-3-dev libnl-route-3-dev libltdl-dev openmpi-bin openmpi-common libopenmpi-dev
+          version: 1.0
+          execute_install_scripts: true
+
+      - name: Ensure BLAS and MPI are properly configured
         run: |
-          sudo apt update
-          sudo apt install git cmake make ninja-build gcc g++ gfortran jq
-          sudo apt install openmpi-bin openmpi-common libopenmpi-dev
-          sudo apt install libopenblas-dev libsuitesparse-dev
-          sudo apt install libfftw3-dev libgsl-dev libhdf5-dev libnetcdf-dev libnetcdff-dev
+          # Fallback installation to ensure pkg-config files are present
+          sudo apt-get update
+          sudo apt-get install -y --reinstall libopenblas-dev pkg-config
+          sudo apt-get install -y --reinstall openmpi-bin openmpi-common libopenmpi-dev
+
+          # Verify BLAS can be found
+          pkg-config --exists openblas && echo "OpenBLAS pkg-config found" || echo "Warning: OpenBLAS pkg-config not found"
+
+          # Verify MPI can be found
+          pkg-config --exists ompi && echo "OpenMPI pkg-config found" || echo "Warning: OpenMPI pkg-config not found"
+          which mpifort && echo "mpifort found at: $(which mpifort)" || echo "Warning: mpifort not found"
+
+          # Set environment variables to help CMake
+          echo "BLA_VENDOR=OpenBLAS" >> $GITHUB_ENV
+          echo "MPI_HOME=/usr" >> $GITHUB_ENV
+
+      - name: Set up Python 3
+        run: |
+          python -m pip install --upgrade pip
+          pip install numpy
 
       - name: Clone test data
         id: data
@@ -63,6 +91,7 @@ jobs:
           cd python
           pip install -e .
 
+
       - name: Build NEO-2 (current version)
         id: build
         run: |

.github/workflows/unit-tests-coverage.yml

@@ -0,0 +1,123 @@
+name: Unit Tests with Coverage
+
+on:
+  push:
+    branches:
+      - main
+      - master
+  pull_request:
+    types: [opened, synchronize, reopened, ready_for_review]
+    branches:
+      - main
+      - master
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  unit-tests-coverage:
+    runs-on: ubuntu-24.04
+    if: github.event_name == 'push' || (github.event_name == 'pull_request' && github.event.pull_request.draft == false)
+
+    env:
+      CC: gcc
+      CXX: g++
+      FC: gfortran
+      MPI_HOME: /usr
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+
+      - name: Cache apt packages
+        uses: awalsh128/cache-apt-pkgs-action@v1
+        with:
+          packages: git cmake make ninja-build gcc g++ gfortran jq lcov libopenblas-dev liblapack-dev libsuitesparse-dev libfftw3-dev libgsl-dev libhdf5-dev libnetcdf-dev libnetcdff-dev python3-dev libevent-dev libnuma-dev libhwloc-dev libnl-3-dev libnl-route-3-dev libltdl-dev openmpi-bin openmpi-common libopenmpi-dev
+          version: 1.0
+          execute_install_scripts: true
+
+      - name: Ensure BLAS and MPI are properly configured
+        run: |
+          # Fallback installation to ensure pkg-config files are present
+          sudo apt-get update
+          sudo apt-get install -y --reinstall libopenblas-dev pkg-config
+          sudo apt-get install -y --reinstall openmpi-bin openmpi-common libopenmpi-dev
+
+          # Verify BLAS can be found
+          pkg-config --exists openblas && echo "OpenBLAS pkg-config found" || echo "Warning: OpenBLAS pkg-config not found"
+
+          # Verify MPI can be found
+          pkg-config --exists ompi && echo "OpenMPI pkg-config found" || echo "Warning: OpenMPI pkg-config not found"
+          which mpifort && echo "mpifort found at: $(which mpifort)" || echo "Warning: mpifort not found"
+
+          # Set environment variables to help CMake
+          echo "BLA_VENDOR=OpenBLAS" >> $GITHUB_ENV
+          echo "MPI_HOME=/usr" >> $GITHUB_ENV
+
+      - name: Set up Python 3
+        run: |
+          python -m pip install --upgrade pip
+          pip install numpy lcov-cobertura
+
+
+
+      - name: Build NEO-2 with coverage flags
+        run: |
+          cmake --preset default -DCMAKE_BUILD_TYPE=Coverage
+          cmake --build --preset default
+
+      - name: Run unit tests with coverage
+        run: |
+          make test
+
+      - name: Generate coverage report
+        run: |
+          # Capture coverage data
+          cd build && lcov --capture --directory . --output-file coverage.info \
+            --rc branch_coverage=1 \
+            --rc geninfo_unexecuted_blocks=1 \
+            --ignore-errors inconsistent,mismatch,empty,unused
+
+          # Filter coverage data to include only source code
+          lcov --remove coverage.info \
+            '*/build/*' \
+            '*/TEST/*' \
+            '*/libneo/*' \
+            '*/thirdparty/*' \
+            '*/DOC/*' \
+            '*/MULTI-SPEC-TOOLS/*' \
+            '*/tools/*' \
+            '/usr/*' \
+            '/tmp/*' \
+            --output-file coverage_filtered.info \
+            --rc branch_coverage=1 \
+            --ignore-errors unused,empty
+
+          # Generate XML for Codecov
+          lcov_cobertura coverage_filtered.info -o coverage.xml
+
+          # Show coverage summary
+          echo "=== Coverage Summary ===" >> $GITHUB_STEP_SUMMARY
+          lcov --summary coverage_filtered.info >> $GITHUB_STEP_SUMMARY || echo "No coverage data found" >> $GITHUB_STEP_SUMMARY
+
+      - name: Upload coverage to Codecov
+        uses: codecov/codecov-action@v4
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          file: ./build/coverage.xml
+          flags: unittests
+          name: unit-tests-coverage
+          fail_ci_if_error: false
+          verbose: true
+
+      - name: Upload coverage artifacts
+        if: always()
+        uses: actions/upload-artifact@v4
+        with:
+          name: coverage-reports
+          path: |
+            build/coverage.info
+            build/coverage_filtered.info
+            build/coverage.xml
+          retention-days: 7

.gitignore

@@ -66,3 +66,16 @@ DOC/latex/*
 build/cmake_install.cmake
 
 .DS_Store
+
+# Ignore coverage files and reports
+*.gcov
+*.gcda
+*.gcno
+coverage.info
+coverage_filtered.info
+coverage.xml
+
+# Ignore test output directories  
+TEST/Testing/
+*/TEST/Testing/
+*/*/TEST/Testing/

CLAUDE.md

@@ -72,4 +72,7 @@ Install with: `cd python && pip install -e .`
 - Maintain separation between QL and PAR implementations
 - Output data in HDF5 format for efficiency
 - Keep MPI code isolated to PAR variant
-- Test changes with golden record tests before submitting PRs
+- Test changes with golden record tests before submitting PRs
+
+## Build Tips
+- You don't have to run make clean usually. Only as a last resort when build fails repeatedly.

CMakeLists.txt

@@ -4,6 +4,7 @@ set(CMAKE_DISABLE_IN_SOURCE_BUILD ON)
 project(NEO-2)
 set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} ${PROJECT_SOURCE_DIR}/cmake)
 enable_language(C Fortran)
+enable_testing()
 
 if(EXISTS ${CMAKE_BINARY_DIR}/BuildConfig.cmake.in)
   include (${CMAKE_BINARY_DIR}/BuildConfig.cmake.in)
@@ -46,12 +47,23 @@ if(CMAKE_Fortran_COMPILER_ID MATCHES "GNU")
   )
   string(REPLACE ";" "" MY_DEBUG_FLAG  ${MY_DEBUG_FLAG_LIST})
   set(CMAKE_Fortran_FLAGS_DEBUG "${MY_DEBUG_FLAG}")
+
+  # Coverage build type - optimized with coverage instrumentation
+  set(CMAKE_Fortran_FLAGS_COVERAGE "-O1 -g --coverage -fbacktrace -fopenmp")
+  set(CMAKE_C_FLAGS_COVERAGE "-O1 -g --coverage -fopenmp")
+  set(CMAKE_CXX_FLAGS_COVERAGE "-O1 -g --coverage -fopenmp")
+  set(CMAKE_EXE_LINKER_FLAGS_COVERAGE "--coverage -fopenmp")
+  set(CMAKE_SHARED_LINKER_FLAGS_COVERAGE "--coverage -fopenmp")
 elseif(CMAKE_Fortran_COMPILER_ID MATCHES "Intel")
   set(CMAKE_Fortran_FLAGS_DEBUG "-cpp -mkl -g -warn all -stand f08 ")
+  # Intel coverage flags (if needed)
+  set(CMAKE_Fortran_FLAGS_COVERAGE "-O1 -g -prof-gen=srcpos")
+  set(CMAKE_C_FLAGS_COVERAGE "-O1 -g -prof-gen=srcpos")
+  set(CMAKE_CXX_FLAGS_COVERAGE "-O1 -g -prof-gen=srcpos")
 endif()
 
-set (CMAKE_Fortran_FLAGS_COVERAGE "--coverage")
-set (CMAKE_Fortran_FLAGS_TEST "-O2 --coverage")
+# Mark Coverage as a valid build type
+set(CMAKE_CONFIGURATION_TYPES "Debug;Release;Coverage" CACHE STRING "" FORCE)
 
 ### Upstream dependencies
 find_package(MPI REQUIRED)
@@ -104,6 +116,7 @@ add_subdirectory(NEO-2-PAR)
 add_subdirectory(NEO-2-QL)
 add_subdirectory(MULTI-SPEC-TOOLS)
 add_subdirectory(tools/create_surfaces)
+add_subdirectory(TEST)
 
 ### Optional target for docs
 find_package(LATEX)

COMMON/CMakeLists.txt

@@ -1,5 +1,4 @@
 project(NEO-2-COMMON)
-enable_testing()
 
 ### FGSL user-defined interface
 set(FGSL_USERINTERFACE_SOURCE_FILES
@@ -68,6 +67,7 @@ set(COMMON_FILES
   sparse_mod.f90
   sparsevec_mod.f90
   spline_cof.f90
+  splinecof3_direct_sparse.f90
   spline_int.f90
   spline_mod.f90
   test_function.f90