Add CodeCov checks (#1)

* add CodeCoverage.cmake

* add codecoverage option to cmake file

* add docker file for code coverage

* reorganize the docker folder

* fix bugs in the cmake files

* update docker image with no shell script

* update the CI workflow to add the Codecov checks

* reduce the iteration number for the Codecov checks

---------

Co-authored-by: Jian Sun <sunjian@ucar.edu>

.github/workflows/CPU_Beltrami_build_run.yml

@@ -1,22 +1,44 @@
 name: Samurai CPU test with Beltrami
 
-on:
-  workflow_dispatch:
-    branches: [ "main" ]
-  push:
-    branches: [ "main" ]
-  pull_request:
-    branches: [ "main" ]
+on: [pull_request, workflow_dispatch]
 
 jobs:
+  docker-build-and-test:
+    name: Build and Test - ${{ matrix.dockerfile }}
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest]
+        dockerfile:
+          - Dockerfile
+          - Dockerfile.coverage 
+    steps:
+    - name: Checkout code from a pull request or push
+      uses: actions/checkout@v3
 
-  build_run:
+    - name: Delete huge unnecessary tools folder
+      run: rm -rf /opt/hostedtoolcache
 
-    runs-on: ubuntu-latest
+    - name: Build Docker image
+      run: docker build -f docker/${{ matrix.dockerfile }} -t samurai .
 
-    steps:
-    - uses: actions/checkout@v3
-    - name: Build the Docker image
-      run: docker build . --file Dockerfile --tag samurai_build_run:latest
     - name: Running the Docker image for Beltrami case
-      run: docker run samurai_build_run:latest
+      # only run this if we are not running codecoverage tests
+      if: matrix.dockerfile != 'Dockerfile.coverage'
+      run: docker run --name test-container -t samurai
+
+    - name: Run coverage tests in container
+      if: matrix.dockerfile == 'Dockerfile.coverage'
+      run: docker run --name test-container -t samurai make coverage
+
+    - name: Copy coverage from container
+      if: matrix.dockerfile == 'Dockerfile.coverage'
+      run: docker cp test-container:/app/samurai/build/coverage.info .
+
+    - name: Upload coverage reports to Codecov
+      if: matrix.dockerfile == 'Dockerfile.coverage'
+      uses: codecov/codecov-action@v4.0.1
+      with:
+        token: ${{ secrets.CODECOV_TOKEN }}
+        files: coverage.info

CMakeLists.txt

@@ -103,7 +103,18 @@ message("netCDF_INSTALL_PREFIX: ${netCDF_INSTALL_PREFIX}")
 message("HDF5_INSTALL_PREFIX: ${HDF5_INSTALL_PREFIX}")
 message("HDF5_C_INCLUDE_DIR: ${HDF5_C_INCLUDE_DIR}")
 
-# recurse into src directory for the build
+# Enable CodeCoverage analysis
+option(ENABLE_COVERAGE "Enable code coverage output" OFF)
+if(ENABLE_COVERAGE)
+  include(CodeCoverage)
+  append_coverage_compiler_flags()
+  setup_target_for_coverage_lcov(
+      NAME coverage
+      EXECUTABLE "./release/bin/samurai"
+      EXECUTABLE_ARGS -params /app/samurai/ncar_scripts/TDRP/beltrami.tdrp
+      BASE_DIRECTORY "${PROJECT_SOURCE_DIR}/src")
+endif()
 
-add_subdirectory(src)  
+# recurse into src directory for the build
 
+add_subdirectory(src)