Merge branch 'develop' into feature/factorize-chkbdrytria

.github/workflows/long-tests.yml

@@ -26,3 +26,5 @@ jobs:
       cmake_build_type: RelWithAssert
       add_cmake_cfg_args: -D LONG_TESTS=ON
       branch_name:  ${{github.event.inputs.branch}}
+      code_coverage: true
+    secrets: inherit

.github/workflows/main-job.yml

@@ -17,6 +17,12 @@ on:
         required: false
         type: string
 
+      code_coverage:
+        description: 'Code coverage'
+        required: false
+        default: true
+        type: boolean
+
 # job
 jobs:
   ci:
@@ -141,6 +147,24 @@ jobs:
                 int: int64_t
 
     steps:
+      - name: Set cmake_build_type and export coverage flags
+        run: |
+          if ${{ matrix.os == 'ubuntu-20.04' && inputs.code_coverage == true }}; then
+            # if code coverage is enabled, linux build is runned in Debug mode
+
+            if [[ ${{ inputs.cmake_build_type }} != Debug ]]; then
+              echo "WARNING: build type is forced to debug mode on ubuntu to allow coverage."
+            fi
+
+            echo "BUILD_TYPE=Debug" >> "$GITHUB_ENV"
+            echo "C_FLG_PROF=-fprofile-arcs -ftest-coverage" >> "$GITHUB_ENV"
+
+          else
+            echo "BUILD_TYPE=${{ inputs.cmake_build_type }}" >> "$GITHUB_ENV"
+          fi
+
+        shell: bash
+
       - name: Print options and set environment variables
         run: |
           echo "${{ github.event.inputs.name }}:
@@ -149,7 +173,7 @@ jobs:
             Scotch:  ${{ matrix.scotch }},
             VTK:     ${{ matrix.vtk }},
             int:     ${{ matrix.int }},
-            Build:   ${{ inputs.cmake_build_type }}"
+            Build:   ${{ env.BUILD_TYPE }}"
 
           # gfortran compiler and scotch makefile depends on the os
           if [ "$RUNNER_OS" == "macOS" ]; then
@@ -170,9 +194,14 @@ jobs:
       - name: Set environment variables for output comparison
         if: "! contains(github.event.head_commit.message, '[skip output comparison]')"
         run: |
-          echo "C_FLG=\"-DCMAKE_C_FLAGS=-DMMG_COMPARABLE_OUTPUT\"" >> "$GITHUB_ENV"
+          echo "C_FLG=-DMMG_COMPARABLE_OUTPUT" >> "$GITHUB_ENV"
           echo "MMG_ERROR_RULE=\"COMMAND_ERROR_IS_FATAL ANY\"" >> "$GITHUB_ENV"
 
+      - name: Assign CMAKE_C_FLAGS if needed
+        if: ${{ env.C_FLG || env.C_FLG_PROF }}
+        run: |
+          echo "CMAKE_C_FLG=-DCMAKE_C_FLAGS=\"${{ env.C_FLG }} ${{ env.C_FLG_PROF }}\"" >> "$GITHUB_ENV"
+
       - name: Install VTK
         # Download vtk only if used
         if: matrix.vtk == 'on'
@@ -195,7 +224,7 @@ jobs:
           cd src
           cp ${{ env.SCOTCH_MAKE }} Makefile.inc
           make scotch -j ${{ env.NJOBS }}
-          make install scotch -j ${{ env.NJOBS }}
+          make prefix=../../scotch-install install -j ${{ env.NJOBS }}
 
       - name: Install LibCommons
         # LinearElasticity don't build with MSVC
@@ -220,29 +249,30 @@ jobs:
           make install
 
       # checkout the provided branch name if workflow is manually run
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         if: inputs.branch_name
         with:
           ref: ${{github.event.inputs.branch}}
           path: mmg
 
       # checkout the event branch for automatic workflows
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         if: inputs.branch_name == ''
         with:
           path: mmg
 
       - name: Test compilation with shared libs linkage
         run: |
           cmake -Smmg -Bbuild_shared \
-          ${{ env.C_FLG }} \
+          ${{ env.CMAKE_C_FLG }} \
           ${{ env.FORT_FLG }} \
             -DCI_CONTEXT=ON \
             -DBUILD_TESTING=ON \
-            -DCMAKE_BUILD_TYPE=${{ inputs.cmake_build_type }} \
+            -DUSE_POINTMAP=${{ matrix.pointmap }} \
+            -DCMAKE_BUILD_TYPE=${{ env.BUILD_TYPE }} \
             -DMMG_PATTERN=${{ matrix.pattern }} \
             -DUSE_SCOTCH=${{ matrix.scotch }} \
-            -DSCOTCH_DIR=scotch \
+            -DSCOTCH_DIR=scotch-install \
             -DUSE_VTK=${{ matrix.vtk }} \
             -DMMG5_INT=${{ matrix.int }} \
             -DBUILD_SHARED_LIBS=ON \
@@ -251,42 +281,44 @@ jobs:
             -DTEST_LIBMMG2D=ON \
             -DTEST_LIBMMG3D=ON \
             ${{ inputs.add_cmake_cfg_args }}
-            cmake --build build_shared --config ${{ inputs.cmake_build_type }} -j ${{ env.NJOBS }}
+            cmake --build build_shared --config ${{ env.BUILD_TYPE }} -j ${{ env.NJOBS }}
         shell: bash
 
       - name: Test compilation without library linkage
         run: |
           cmake -Smmg -Bbuild_nolibs \
-          ${{ env.C_FLG }} \
+          ${{ env.CMAKE_C_FLG }} \
           ${{ env.FORT_FLG }} \
             -DCI_CONTEXT=ON \
             -DBUILD_TESTING=ON \
-            -DCMAKE_BUILD_TYPE=${{ inputs.cmake_build_type }} \
+            -DUSE_POINTMAP=${{ matrix.pointmap }} \
+            -DCMAKE_BUILD_TYPE=${{ env.BUILD_TYPE }} \
             -DMMG_PATTERN=${{ matrix.pattern }} \
             -DUSE_SCOTCH=${{ matrix.scotch }} \
-            -DSCOTCH_DIR=scotch \
+            -DSCOTCH_DIR=scotch-install \
             -DUSE_VTK=${{ matrix.vtk }} \
             -DMMG5_INT=${{ matrix.int }} \
             -DLIBMMG_STATIC=OFF \
             -DLIBMMGS_STATIC=OFF \
             -DLIBMMG2D_STATIC=OFF \
             -DLIBMMG3D_STATIC=OFF \
             ${{ inputs.add_cmake_cfg_args }}
-            cmake --build build_nolibs --config ${{ inputs.cmake_build_type }} -j ${{ env.NJOBS }}
+            cmake --build build_nolibs --config ${{ env.BUILD_TYPE }} -j ${{ env.NJOBS }}
         shell: bash
 
       - name: Configure Mmg with static libs (default behaviour)
         run: |
           cmake -Smmg -Bbuild \
-          ${{ env.C_FLG }} \
+          ${{ env.CMAKE_C_FLG }} \
           ${{ env.FORT_FLG }} \
             -DCMAKE_INSTALL_PREFIX=mmg-install \
             -DCI_CONTEXT=ON \
             -DBUILD_TESTING=ON \
-            -DCMAKE_BUILD_TYPE=${{ inputs.cmake_build_type }} \
+            -DUSE_POINTMAP=${{ matrix.pointmap }} \
+            -DCMAKE_BUILD_TYPE=${{ env.BUILD_TYPE }} \
             -DMMG_PATTERN=${{ matrix.pattern }} \
             -DUSE_SCOTCH=${{ matrix.scotch }} \
-            -DSCOTCH_DIR=scotch \
+            -DSCOTCH_DIR=scotch-install \
             -DUSE_VTK=${{ matrix.vtk }} \
             -DMMG5_INT=${{ matrix.int }} \
             -DTEST_LIBMMG=ON \
@@ -298,15 +330,15 @@ jobs:
 
       - name: Build Mmg
         run: |
-          cmake --build build --config ${{ inputs.cmake_build_type }} -j ${{ env.NJOBS }}
+          cmake --build build --config ${{ env.BUILD_TYPE }} -j ${{ env.NJOBS }}
       - name: Install Mmg
         run: |
-          cmake --build build --target install --config ${{ inputs.cmake_build_type }} -j ${{ env.NJOBS }}
+          cmake --build build --target install --config ${{ env.BUILD_TYPE }} -j ${{ env.NJOBS }}
 
       - name: Archive production artifacts
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
-          name: Mmg-bin
+          name: Mmg-bin-${{ matrix.os }}-${{ matrix.pattern }}-${{ matrix.pointmap }}-${{ matrix.scotch }}-${{ matrix.vtk }}-${{ matrix.int }}
           path: |
             build/bin
 
@@ -315,25 +347,35 @@ jobs:
         if: matrix.vtk == 'off' && matrix.int == 'int32_t'
         run: |
           cd build
-          ctest --timeout 7200 -VV -C ${{ inputs.cmake_build_type }} -j ${{ env.NJOBS }}
+          ctest --timeout 7200 -VV -C ${{ env.BUILD_TYPE }} -j ${{ env.NJOBS }}
 
       - name: Test Mmg with in64_t integers
         # Run long tests only on ubuntu with pattern off, scotch on, vtk on and int64_t integers
         if: matrix.os == 'ubuntu-20.04' && matrix.pattern == 'off' && matrix.scotch == 'on' && matrix.vtk == 'on' && matrix.int == 'int64_t'
         run: |
           cd build
-          ctest --timeout 7200 -VV -C ${{ inputs.cmake_build_type }} -j ${{ env.NJOBS }}
+          ctest --timeout 7200 -VV -C ${{ env.BUILD_TYPE }} -j ${{ env.NJOBS }}
 
       - name: Test non native I/Os of Mmg
         if: matrix.vtk == 'on'
         run: |
           cd build
-          ctest -R "msh|vtk" -VV -C ${{ inputs.cmake_build_type }} -j ${{ env.NJOBS }}
-
-      # - name: Archive production artifacts for tests
-      #  if: success() || failure()
-      #  uses: actions/upload-artifact@v2
-      #  with:
-      #    name: Mmg-tests
-      #    path: |
-      #      build/TEST_OUTPUTS
+          ctest -R "msh|vtk" -VV -C ${{ env.BUILD_TYPE }} -j ${{ env.NJOBS }}
+
+      - name: Archive production artifacts for tests
+        if: success() || failure()
+        uses: actions/upload-artifact@v4
+        with:
+          name: Mmg-tests-${{ matrix.os }}-${{ matrix.pattern }}-${{ matrix.pointmap }}-${{ matrix.scotch }}-${{ matrix.vtk }}-${{ matrix.int }}
+          path: |
+            build/TEST_OUTPUTS
+
+      - name: Upload coverage to Codecov
+        if: matrix.os == 'ubuntu-20.04' && inputs.code_coverage == true
+        uses: codecov/codecov-action@v4
+        with:
+          fail_ci_if_error: true
+          root_dir: .
+          verbose: true
+        env:
+          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

codecov.yml

@@ -0,0 +1,3 @@
+fixes:
+   - "mmg/mmg::"
+