Merge branch 'SimVascular:main' into precomputed-velocities-SimVascul…

…ar#202
zasexton · Mar 28, 2024 · b71169c · b71169c
2 parents bd0fa14 + 6dd920b
commit b71169c
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Showing 20 changed files with 132 additions and 98 deletions.
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
diff --git a/.github/workflows/test_macos12.yml b/.github/workflows/test_macos12.yml
@@ -0,0 +1,33 @@
+name: macOS 12
+on: [push, pull_request]
+jobs:
+  test:
+    runs-on: macos-12
+    steps:
+      - uses: actions/checkout@v3
+      - name: Install MacOS dependencies
+        run: |
+          brew reinstall -v gcc
+          brew install -v cmake vtk openblas lapack mesa open-mpi qt
+          brew install lcov
+          sudo ln -s /usr/local/opt/qt5/mkspecs /usr/local/mkspecs
+          sudo ln -s /usr/local/opt/qt5/plugins /usr/local/plugins
+      - name: Build svFSIplus
+        run: |
+          mkdir build
+          cd build
+          cmake -DENABLE_COVERAGE=ON -DENABLE_ARRAY_INDEX_CHECKING=ON -DENABLE_UNIT_TEST=ON ..
+          make -j2
+      - name: Install test dependencies
+        run: |
+          conda create -n svfsiplus python=3.9
+          conda run -n svfsiplus pip install pytest pytest-cov pytest-mock numpy meshio pandas
+      - name: Run integration tests
+        run: |
+          git lfs pull
+          cd tests
+          conda run -n svfsiplus pytest -rPv --durations=0
+      - name: Run unit tests
+        run: |
+          cd build/svFSI-build/Source/svFSI
+          ctest --verbose
diff --git a/.github/workflows/test_ubuntu20.yml b/.github/workflows/test_ubuntu20.yml
@@ -0,0 +1,25 @@
+name: Ubuntu 20.04
+on: [push, pull_request]
+jobs:
+  test:
+    runs-on: ubuntu-20.04
+    container: msalvad/ubuntu20_vtk9:v1
+    steps:
+      - uses: actions/checkout@v3
+      - name: Build svFSIplus
+        run: |
+          mkdir build
+          cd build
+          cmake -DENABLE_COVERAGE=ON -DENABLE_ARRAY_INDEX_CHECKING=ON -DENABLE_UNIT_TEST=ON ..
+          make -j2
+          cd ..
+      - name: Run integration tests
+        run: |
+          git config --global --add safe.directory /__w/svFSIplus/svFSIplus
+          git lfs pull
+          cd tests
+          conda run -n svfsiplus pytest -rPv --durations=0
+      - name: Run unit tests
+        run: |
+          cd build/svFSI-build/Source/svFSI
+          ctest --verbose
diff --git a/.github/workflows/test_ubuntu22.yml b/.github/workflows/test_ubuntu22.yml
@@ -0,0 +1,38 @@
+name: Ubuntu 22.04
+on: [push, pull_request]
+jobs:
+  test:
+    runs-on: ubuntu-22.04
+    container: msalvad/ubuntu22_vtk9:v1
+    steps:
+      - uses: actions/checkout@v3
+      - name: Build svFSIplus
+        run: |
+          mkdir build
+          cd build
+          cmake -DENABLE_COVERAGE=ON -DENABLE_ARRAY_INDEX_CHECKING=ON -DENABLE_UNIT_TEST=ON ..
+          make -j2
+          cd ..
+      - name: Run integration tests
+        run: |
+          git config --global --add safe.directory /__w/svFSIplus/svFSIplus
+          git lfs pull
+          cd tests
+          conda run -n svfsiplus pytest -rPv --durations=0
+      - name: Run unit tests
+        run: |
+          cd build/svFSI-build/Source/svFSI
+          ctest --verbose
+      - name: Generate code coverage
+        run: |
+          cd build/svFSI-build
+          make coverage
+      - name: Save coverage report
+        uses: actions/upload-artifact@v3
+        with:
+          name: coverage_report
+          path: build/svFSI-build/coverage
+      - name: Upload coverage reports to Codecov
+        uses: codecov/codecov-action@v3
+        env:
+          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
diff --git a/tests/cases/cep/cable_TTP_1d/result_001.vtu b/tests/cases/cep/cable_TTP_1d/result_001.vtu
diff --git a/tests/cases/cep/cable_TTP_1d/svFSI.xml b/tests/cases/cep/cable_TTP_1d/svFSI.xml
@@ -31,8 +31,8 @@
 <Add_equation type="CEP" > 
    <Coupled> true </Coupled>
    <Min_iterations> 1 </Min_iterations>  
-   <Max_iterations> 5 </Max_iterations> 
-   <Tolerance> 1e-6 </Tolerance> 
+   <Max_iterations> 2 </Max_iterations> 
+   <Tolerance> 1e-12 </Tolerance> 
 
    <Domain id="1" >
      <Electrophysiology_model> TTP </Electrophysiology_model> 
@@ -58,7 +58,7 @@
 
    <LS type="GMRES" >
       <Max_iterations> 100 </Max_iterations> 
-      <Tolerance> 1e-6 </Tolerance>
+      <Tolerance> 1e-12 </Tolerance>
       <Krylov_space_dimension> 50 </Krylov_space_dimension>
    </LS>
 

diff --git a/tests/cases/cep/niederer_benchmark_ECGs_quadrature/result_BICG_CN_epicardium_BO_001.vtu b/tests/cases/cep/niederer_benchmark_ECGs_quadrature/result_BICG_CN_epicardium_BO_001.vtu
diff --git a/tests/cases/cep/niederer_benchmark_ECGs_quadrature/result_CG_RK4_myocardium_BO_001.vtu b/tests/cases/cep/niederer_benchmark_ECGs_quadrature/result_CG_RK4_myocardium_BO_001.vtu
diff --git a/tests/cases/cep/niederer_benchmark_ECGs_quadrature/result_GMRES_FE_epicardium_TTP_001.vtu b/tests/cases/cep/niederer_benchmark_ECGs_quadrature/result_GMRES_FE_epicardium_TTP_001.vtu
diff --git a/tests/cases/cep/niederer_benchmark_ECGs_quadrature/result_GMRES_FE_pfib_AP_001.vtu b/tests/cases/cep/niederer_benchmark_ECGs_quadrature/result_GMRES_FE_pfib_AP_001.vtu
diff --git a/tests/cases/cep/niederer_benchmark_ECGs_quadrature/svFSI_BICG_CN_epicardium_BO.xml b/tests/cases/cep/niederer_benchmark_ECGs_quadrature/svFSI_BICG_CN_epicardium_BO.xml
@@ -68,7 +68,7 @@
    <Coupled> true </Coupled>
    <Min_iterations> 1 </Min_iterations>  
    <Max_iterations> 1 </Max_iterations> 
-   <Tolerance> 1e-6 </Tolerance> 
+   <Tolerance> 1e-12 </Tolerance> 
 
    <Domain id="1" >
        <Electrophysiology_model> BO </Electrophysiology_model>
@@ -105,7 +105,7 @@
 
    <LS type="BICG" >
       <Max_iterations> 100 </Max_iterations>
-      <Tolerance> 1e-6 </Tolerance>
+      <Tolerance> 1e-12 </Tolerance>
    </LS>
 
   <ECGLeads>

diff --git a/tests/cases/cep/niederer_benchmark_ECGs_quadrature/svFSI_CG_RK4_myocardium_BO.xml b/tests/cases/cep/niederer_benchmark_ECGs_quadrature/svFSI_CG_RK4_myocardium_BO.xml
@@ -68,7 +68,7 @@
    <Coupled> true </Coupled>
    <Min_iterations> 1 </Min_iterations>  
    <Max_iterations> 1 </Max_iterations> 
-   <Tolerance> 1e-6 </Tolerance> 
+   <Tolerance> 1e-12 </Tolerance> 
 
    <Domain id="1" >
        <Electrophysiology_model> BO </Electrophysiology_model>
@@ -105,7 +105,7 @@
 
    <LS type="CG" >
       <Preconditioner> svfsi </Preconditioner> 
-      <Tolerance> 1e-6 </Tolerance>
+      <Tolerance> 1e-12 </Tolerance>
    </LS>
 
   <ECGLeads>

diff --git a/tests/cases/cep/niederer_benchmark_ECGs_quadrature/svFSI_GMRES_FE_epicardium_TTP.xml b/tests/cases/cep/niederer_benchmark_ECGs_quadrature/svFSI_GMRES_FE_epicardium_TTP.xml
@@ -68,7 +68,7 @@
    <Coupled> true </Coupled>
    <Min_iterations> 1 </Min_iterations>  
    <Max_iterations> 1 </Max_iterations> 
-   <Tolerance> 1e-6 </Tolerance> 
+   <Tolerance> 1e-12 </Tolerance> 
 
    <Domain id="1" >
        <Electrophysiology_model> TTP </Electrophysiology_model>
@@ -117,7 +117,7 @@
 
    <LS type="GMRES" >
       <Max_iterations> 100 </Max_iterations>
-      <Tolerance> 1e-6 </Tolerance>
+      <Tolerance> 1e-12 </Tolerance>
       <Krylov_space_dimension> 50 </Krylov_space_dimension>
    </LS>
 

diff --git a/tests/cases/cep/niederer_benchmark_ECGs_quadrature/svFSI_GMRES_FE_pfib_AP.xml b/tests/cases/cep/niederer_benchmark_ECGs_quadrature/svFSI_GMRES_FE_pfib_AP.xml
@@ -68,7 +68,7 @@
    <Coupled> true </Coupled>
    <Min_iterations> 1 </Min_iterations>  
    <Max_iterations> 1 </Max_iterations> 
-   <Tolerance> 1e-6 </Tolerance> 
+   <Tolerance> 1e-12 </Tolerance> 
 
    <Domain id="1" >
        <Electrophysiology_model> AP </Electrophysiology_model>
@@ -105,7 +105,7 @@
 
    <LS type="GMRES" >
       <Max_iterations> 100 </Max_iterations>
-      <Tolerance> 1e-6 </Tolerance>
+      <Tolerance> 1e-12 </Tolerance>
       <Krylov_space_dimension> 50 </Krylov_space_dimension>
    </LS>
 

diff --git a/tests/cases/cep/purkinje/result_001.vtu b/tests/cases/cep/purkinje/result_001.vtu
diff --git a/tests/cases/cep/purkinje/svFSI.xml b/tests/cases/cep/purkinje/svFSI.xml
@@ -39,8 +39,8 @@
 <Add_equation type="CEP" > 
    <Coupled> true </Coupled>
    <Min_iterations> 1 </Min_iterations>  
-   <Max_iterations> 3 </Max_iterations> 
-   <Tolerance> 1e-6 </Tolerance> 
+   <Max_iterations> 2 </Max_iterations> 
+   <Tolerance> 1e-12 </Tolerance> 
 
   <Domain id="1" >
      <Electrophysiology_model> TTP </Electrophysiology_model>
@@ -68,7 +68,7 @@
 
    <LS type="GMRES" >
       <Max_iterations> 100 </Max_iterations>
-      <Tolerance> 1e-6 </Tolerance>
+      <Tolerance> 1e-12 </Tolerance>
       <Krylov_space_dimension> 50 </Krylov_space_dimension>
    </LS>
 

diff --git a/tests/cases/cep/spiral_BO_2d/result_001.vtu b/tests/cases/cep/spiral_BO_2d/result_001.vtu
diff --git a/tests/cases/cep/spiral_BO_2d/svFSI.xml b/tests/cases/cep/spiral_BO_2d/svFSI.xml
@@ -49,8 +49,8 @@
 <Add_equation type="CEP" > 
    <Coupled> true </Coupled>
    <Min_iterations> 1 </Min_iterations>  
-   <Max_iterations> 5 </Max_iterations> 
-   <Tolerance> 1e-4 </Tolerance> 
+   <Max_iterations> 2 </Max_iterations> 
+   <Tolerance> 1e-12 </Tolerance> 
 
   <Domain id="1" >
      <Electrophysiology_model> BO </Electrophysiology_model>
@@ -88,7 +88,7 @@
 
    <LS type="CG" >
       <Preconditioner> rcs </Preconditioner> 
-      <Tolerance> 1e-6 </Tolerance>
+      <Tolerance> 1e-12 </Tolerance>
    </LS>
 
 </Add_equation>

diff --git a/tests/cases/cep/square_AP_2d/result_001.vtu b/tests/cases/cep/square_AP_2d/result_001.vtu
diff --git a/tests/cases/cep/square_AP_2d/svFSI.xml b/tests/cases/cep/square_AP_2d/svFSI.xml
@@ -49,8 +49,8 @@
 <Add_equation type="CEP" > 
    <Coupled> true </Coupled>
    <Min_iterations> 1 </Min_iterations>  
-   <Max_iterations> 4 </Max_iterations> 
-   <Tolerance> 1e-4 </Tolerance> 
+   <Max_iterations> 2 </Max_iterations> 
+   <Tolerance> 1e-12 </Tolerance> 
 
   <Domain id="1" >
      <Electrophysiology_model> AP </Electrophysiology_model>
@@ -75,7 +75,7 @@
 
    <LS type="CG" >
       <Preconditioner> fsils </Preconditioner> 
-      <Tolerance> 1e-6 </Tolerance>
+      <Tolerance> 1e-12 </Tolerance>
    </LS>
 
 </Add_equation>