Add Codecov coverage using gcovr

Uses QMC_COMPLEX=1 and deterministic tests
Enable Codecov configuration
Install gcovr in docker container

.github/workflows/ci-github-actions.yaml

@@ -53,13 +53,19 @@ jobs:
       matrix:
         jobname: [
           clang-openmpi-ubsan, # undefined behavior sanitizer
+          coverage, # run code coverage and upload to codecov
         ]
         include:
 
         - jobname: clang-openmpi-ubsan
           container: 
             image: williamfgc/qmcpack-ci:ubuntu20-openmpi
             options: -u 1001
+
+        - jobname: coverage
+          container: 
+            image: williamfgc/qmcpack-ci:ubuntu20-openmpi
+            options: -u 1001
 
     steps:
     - name: Checkout Action
@@ -73,3 +79,16 @@ jobs:
 
     - name: Test
       run: tests/test_automation/github-actions/ci/run_step.sh test
+
+    - name: Coverage
+      if: contains(matrix.jobname, 'coverage')
+      run: tests/test_automation/github-actions/ci/run_step.sh coverage
+
+    - name: Upload Coverage
+      if: contains(matrix.jobname, 'coverage')
+      uses: codecov/codecov-action@v1
+      with:
+        file:  ../qmcpack-build/coverage.xml
+        flags: QMC_COMPLEX-deterministic # optional
+        name: codecov-QMCPACK # optional
+        fail_ci_if_error: true # optional (default = false)

codecov.yaml

@@ -0,0 +1,13 @@
+# Configuration file for codecov reporting code coverage
+
+# Disable codecov comments in every PR
+comment: off
+
+# Ignore testing directory itself
+ignore:
+  - "tests"
+
+# Fixes report prefix paths from CI dynamic coverage action
+# from https://docs.codecov.io/docs/fixing-paths
+fixes:
+  - "/__w/::"

tests/test_automation/github-actions/ci/run_step.sh

@@ -39,6 +39,12 @@ case "$1" in
                       -DCMAKE_BUILD_TYPE=RelWithDebInfo -DENABLE_SANITIZER=msan \
                       ${GITHUB_WORKSPACE}
       ;;
+      *"coverage"*)
+        echo 'Configure for code coverage with gcc and gcovr'
+        cmake -GNinja -DMPI_C_COMPILER=mpicc -DMPI_CXX_COMPILER=mpicxx \
+                      -DCMAKE_BUILD_TYPE=Debug -DENABLE_GCOV=TRUE -DQMC_COMPLEX=1 \
+                      ${GITHUB_WORKSPACE}
+      ;;
       # Configure with default compilers
       *)
         echo 'Configure for default system compilers and options'
@@ -59,7 +65,7 @@ case "$1" in
     cd ${GITHUB_WORKSPACE}/../qmcpack-build
 
     # Enable oversubscription in OpenMPI
-    if [[ "${GH_JOBNAME}" =~ (openmpi) ]]
+    if [[ "${GH_JOBNAME}" =~ (openmpi|coverage) ]]
     then
       echo "Enabling OpenMPI oversubscription"
       export OMPI_MCA_rmaps_base_oversubscribe=1
@@ -76,7 +82,18 @@ case "$1" in
     # Run only deterministic tests (reasonable for CI)
     ctest -L deterministic
     ;;
-
+
+  # Generate coverage reports
+  coverage)
+    cd ${GITHUB_WORKSPACE}/../qmcpack-build
+    sudo apt-get install gcovr -y
+    # filter unreachable branches with gcovr
+    # see https://gcovr.com/en/stable/faq.html#why-does-c-code-have-so-many-uncovered-branches
+    gcovr --exclude-unreachable-branches --exclude-throw-branches --root=${GITHUB_WORKSPACE}/.. --xml-pretty -o coverage.xml
+    du -hs coverage.xml
+    cat coverage.xml
+    ;;
+
   # Install the library (not triggered at the moment)
   install)
     cd ${GITHUB_WORKSPACE}/../qmcpack-build