Added BVH accelerated point localization and updated localization API

.gitattributes

@@ -0,0 +1,3 @@
+# SWIG output regenerated from client.i; collapsed in GitHub diffs
+src/pcms/fortranapi/client_wrap.c linguist-generated
+src/pcms/fortranapi/pcms.f90 linguist-generated

.github/workflows/clang-tidy.yml

@@ -105,7 +105,7 @@ jobs:
       with:
         repo-name: 'meshFields-openmpi'
         repo-path: 'SCOREC/meshFields'
-        repo-ref: 'b1482bbba288df210784b2345eae08e34faabdc4'
+        repo-ref: 'b9984520c20f73955a3b4e25e4907780b91d430f'
         cache: true
         options: '-DCMAKE_CXX_COMPILER=`which mpicxx`
                   -DCMAKE_C_COMPILER=`which mpicc`
@@ -165,7 +165,7 @@ jobs:
       with:
         repo-name: 'redev-openmpi'
         repo-path: 'SCOREC/redev'
-        repo-ref: 'ac09848a5f9b89493e8b679c9080b9efe5538376'
+        repo-ref: '1e4c876f786b420f060695ba2c1079447e975b69'
         cache: true
         options: '-DCMAKE_CXX_COMPILER=`which mpicxx`
                   -DMPIEXEC_EXECUTABLE=`which mpirun`

.github/workflows/cmake-test.yml

@@ -16,6 +16,15 @@ jobs:
     runs-on: ubuntu-latest
     timeout-minutes: 30
 
+    env:
+      # Builds that depend on Kokkos must not share a cache entry across
+      # shared/static or Serial/OpenMP configurations.
+      DEP_CACHE_SUFFIX: ${{ matrix.python_api == 'ON' && '-shared' || '' }}${{ matrix.openmp == 'ON' && '-openmp' || '' }}
+      # Use more than one thread so threading bugs can show up.
+      OMP_NUM_THREADS: ${{ matrix.openmp == 'ON' && '2' || '1' }}
+      OMP_PROC_BIND: 'false'
+      KOKKOS_ENABLE_OPENMP: ${{ matrix.openmp == 'ON' && 'ON' || 'OFF' }}
+
     defaults:
       run:
         shell: bash
@@ -29,6 +38,7 @@ jobs:
         python_api: [OFF, ON]
         meshfields: [ON]
         petsc: [ON]
+        openmp: [OFF]
         include:
           - build_type: Release
             memory_test: OFF
@@ -44,6 +54,15 @@ jobs:
             python_api: OFF
             meshfields: ON
             petsc: OFF
+          # Kokkos OpenMP backend (all other entries use Serial)
+          - build_type: Release
+            memory_test: OFF
+            compiler: g++
+            language: 'cpp'
+            python_api: ON
+            meshfields: ON
+            petsc: ON
+            openmp: ON
         exclude:
           - build_type: Release
             memory_test: ON
@@ -67,7 +86,7 @@ jobs:
       if: matrix.python_api == 'ON'
       run: |
         sudo apt-get install -yq python3 python3-pip python3-dev python3-pybind11 pybind11-dev
-        pip3 install numpy
+        pip3 install numpy pytest
 
     - uses: actions/checkout@v4
 
@@ -86,11 +105,11 @@ jobs:
         repo-path: 'kokkos/kokkos'
         repo-ref: '4.6.01'
         cache: true
-        cache-suffix: ${{ matrix.python_api == 'ON' && '-shared' || '' }}
+        cache-suffix: ${{ env.DEP_CACHE_SUFFIX }}
         options: '-DCMAKE_CXX_STANDARD=20
                   -DBUILD_SHARED_LIBS=${{ matrix.python_api }}
                   -DKokkos_ENABLE_SERIAL=ON
-                  -DKokkos_ENABLE_OPENMP=OFF
+                  -DKokkos_ENABLE_OPENMP=${{ env.KOKKOS_ENABLE_OPENMP }}
                   -DKokkos_ENABLE_CUDA=OFF
                   -DKokkos_ENABLE_CUDA_LAMBDA=OFF
                   -DKokkos_ENABLE_CUDA_CONSTEXPR=OFF'
@@ -102,7 +121,7 @@ jobs:
         repo-path: 'kokkos/kokkos-kernels'
         repo-ref: '4.6.01'
         cache: true
-        cache-suffix: ${{ matrix.python_api == 'ON' && '-shared' || '' }}
+        cache-suffix: ${{ env.DEP_CACHE_SUFFIX }}
         options: '-DCMAKE_CXX_STANDARD=20
                   -DBUILD_SHARED_LIBS=${{ matrix.python_api }}
                   -DKokkos_DIR=${{ runner.temp }}/build-kokkos/install/lib/cmake/Kokkos'
@@ -114,7 +133,7 @@ jobs:
         repo-path: 'SCOREC/omega_h'
         repo-ref: '2b2e778472f48a85a5ff5e70083e3a415e58be72'
         cache: true
-        cache-suffix: ${{ matrix.python_api == 'ON' && '-shared' || '' }}
+        cache-suffix: ${{ env.DEP_CACHE_SUFFIX }}
         options: '-DCMAKE_CXX_COMPILER=`which mpicxx`
                   -DCMAKE_C_COMPILER=`which mpicc`
                   -DCMAKE_BUILD_TYPE="RelWithDebInfo"
@@ -132,9 +151,9 @@ jobs:
       with:
         repo-name: 'meshFields'
         repo-path: 'SCOREC/meshFields'
-        repo-ref: 'b1482bbba288df210784b2345eae08e34faabdc4'
+        repo-ref: 'b9984520c20f73955a3b4e25e4907780b91d430f'
         cache: true
-        cache-suffix: ${{ matrix.python_api == 'ON' && '-shared' || '' }}
+        cache-suffix: ${{ env.DEP_CACHE_SUFFIX }}
         options: '-DCMAKE_CXX_COMPILER=`which mpicxx`
                   -DCMAKE_C_COMPILER=`which mpicc`
                   -DBUILD_SHARED_LIBS=${{ matrix.python_api }}
@@ -165,7 +184,7 @@ jobs:
       with:
         repo-name: 'redev'
         repo-path: 'SCOREC/redev'
-        repo-ref: 'ac09848a5f9b89493e8b679c9080b9efe5538376'
+        repo-ref: '1e4c876f786b420f060695ba2c1079447e975b69'
         cache: true
         cache-suffix: ${{ matrix.python_api == 'ON' && '-shared' || '' }}
         options: '-DCMAKE_CXX_COMPILER=`which mpicxx`
@@ -203,7 +222,7 @@ jobs:
       uses: actions/cache@v3
       with:
         path: ${{ runner.temp }}/petsc
-        key: build-petsc-${{ steps.clone-petsc.outputs.petsc-commit-hash }}-${{ matrix.python_api }}
+        key: build-petsc-${{ steps.clone-petsc.outputs.petsc-commit-hash }}-${{ matrix.python_api }}${{ matrix.openmp == 'ON' && '-openmp' || '' }}
 
     - name: build petsc
       if: matrix.petsc == 'ON' && steps.cache-petsc.outputs.cache-hit != 'true'
@@ -214,6 +233,7 @@ jobs:
           --with-kokkos-dir="${{ runner.temp }}/build-kokkos/install/" \
           --with-kokkos-kernels-dir="${{ runner.temp }}/build-kokkos-kernels/install/" \
           --with-cuda=0 \
+          --with-openmp=${{ matrix.openmp == 'ON' && '1' || '0' }} \
           --with-shared-libraries=${{ matrix.python_api == 'ON' && '1' || '0' }} \
           --download-fblaslapack
         make all check
@@ -288,12 +308,25 @@ jobs:
       run: |
         export PYTHONPATH=${{ runner.temp }}/build-pcms/install/lib/python3.12/site-packages:$PYTHONPATH
         export PYTHONPATH=${{ runner.temp }}/build-omega_h/install/lib/python/dist-packages:$PYTHONPATH
-        cd ${{ github.workspace }}/src/pcms/pythonapi
-        python3 test_file_io.py
-        python3 test_omega_h_field.py
-        python3 test_uniform_grid_field.py
-        python3 test_field_copy.py
-        python3 test_mls_interpolation.py
+        cd ${{ github.workspace }}
+        pytest -v --tb=short -p no:cacheprovider
+
+    # The docs need the compiled pcms module for the Python API, so they are
+    # built in one Python-enabled configuration.
+    - name: Build documentation
+      if: matrix.python_api == 'ON' && matrix.openmp != 'ON'
+      run: |
+        sudo apt-get install -yq doxygen
+        pip3 install -r docs/requirements.txt
+        export PYTHONPATH=${{ runner.temp }}/build-pcms/install/lib/python3.12/site-packages:$PYTHONPATH
+        export PYTHONPATH=${{ runner.temp }}/build-omega_h/install/lib/python/dist-packages:$PYTHONPATH
+        sphinx-build -b html docs docs/_build/html
+
+    - name: Upload documentation
+      if: matrix.python_api == 'ON' && matrix.openmp != 'ON'
+      uses: actions/upload-pages-artifact@v3
+      with:
+        path: docs/_build/html
 
     - name: Test PCMS Installation
       if: matrix.python_api == 'OFF'
@@ -316,3 +349,14 @@ jobs:
           ${{ matrix.petsc == 'ON' && format('-DPETSC_LINK_STATIC=ON -DPETSC_DIR={0}/petsc -DPETSC_ARCH=ubuntu-kokkos', runner.temp) || '' }} \
           --debug-output
         cmake --build ${{github.workspace}}/examples/external-usage-example/build
+
+  deploy-docs:
+    needs: test-build
+    if: github.event_name == 'push' && github.ref == 'refs/heads/develop'
+    runs-on: ubuntu-latest
+    permissions:
+      pages: write
+      id-token: write
+    steps:
+    - name: Deploy to GitHub Pages
+      uses: actions/deploy-pages@v4