Code coverage reporting for C++ code (#94)

* Making modifications to CMakeLists and the github action in order to record and upload code coverage numbers.

* Slightly different incantation, --no-build-isolation assumes all build back end is pre-installed.

* Need to install `lcov` on the ubuntu image.

* Attempting to combine coverage reports into one file to address "invalid token" error.

* Making a few attempts, just committing this as a checkpoint.

* Taking a more straightforward approach, and just looking at env var.

* Attempting to fix the upload error by changing the final output file name.

.github/workflows/testing-and-coverage.yml

@@ -13,6 +13,8 @@ jobs:
   build:
 
     runs-on: ubuntu-latest
+    env:
+      INCLUDE_COVERAGE: TRUE
     strategy:
       matrix:
         python-version: ['3.9', '3.10', '3.11', '3.12']
@@ -21,20 +23,32 @@ jobs:
     - uses: actions/checkout@v4
       with:
         submodules: recursive
+
     - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
+
     - name: Install dependencies
       run: |
         sudo apt-get update
+        sudo apt-get install -yy lcov
         python -m pip install --upgrade pip
-        pip install -e .[dev]
+        python -m pip install .[dev]
         if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+
     - name: Run unit tests with pytest
       run: |
-        python -m pytest -s tests --cov=lephare --cov-report=xml
+        python -m pytest -s tests --cov=lephare --cov-report=lcov
+
+    - name: Collect C++ coverage
+      run: |
+        lcov --output-file coverage.cpp --capture --directory build
+        lcov --output-file coverage.cpp --extract coverage.cpp $PWD/src/"*"
+        cat coverage.lcov coverage.cpp > coverage.txt
+
     - name: Upload coverage report to codecov
       uses: codecov/codecov-action@v4
       with:
+        files: coverage.txt
         token: ${{ secrets.CODECOV_TOKEN }}

CMakeLists.txt

@@ -64,6 +64,14 @@ else()
     add_compile_options("-mno-vzeroupper" "-mavx2" "-floop-unroll-and-jam" )
 endif()
 
+# only set these flags if in `INCLUDE_COVERAGE` env var is set (to any value)
+if(DEFINED ENV{INCLUDE_COVERAGE})
+  message(STATUS "Building with code coverage enabled.")
+  SET(GCC_COVERAGE_COMPILE_FLAGS "-g -O0 -coverage -fprofile-arcs -ftest-coverage")
+  SET(GCC_COVERAGE_LINK_FLAGS    "-coverage -lgcov")
+  SET( CMAKE_CXX_FLAGS  "${CMAKE_CXX_FLAGS} ${GCC_COVERAGE_COMPILE_FLAGS}" )
+  SET( CMAKE_EXE_LINKER_FLAGS  "${CMAKE_EXE_LINKER_FLAGS} ${GCC_COVERAGE_LINK_FLAGS}" )
+endif()
 
 add_library(lepharelib STATIC ${SOURCES})
 find_package(OpenMP)

setup.py

@@ -55,7 +55,7 @@ def build_extension(self, ext):
                 cmake_args += ["-A", "x64"]
             build_args += ["--", "/m"]
         else:
-            cmake_args += ["-DCMAKE_BUILD_TYPE=" + cfg]
+            cmake_args += ["-DCMAKE_BUILD_TYPE:STRING=" + cfg]
             build_args += ["--", "-j2"]
 
         env = os.environ.copy()