From 91cf1239de568ab227362c2fa85cdf905085efd7 Mon Sep 17 00:00:00 2001
From: William F Godoy <williamfgc@yahoo.com>
Date: Tue, 30 Mar 2021 15:31:00 -0400
Subject: [PATCH] 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      | 19 +++++++++++++++++
 codecov.yaml                                  | 13 ++++++++++++
 .../github-actions/ci/run_step.sh             | 21 +++++++++++++++++--
 3 files changed, 51 insertions(+), 2 deletions(-)
 create mode 100644 codecov.yaml

diff --git a/.github/workflows/ci-github-actions.yaml b/.github/workflows/ci-github-actions.yaml
index 835511a80c..ef7837ce7d 100644
--- a/.github/workflows/ci-github-actions.yaml
+++ b/.github/workflows/ci-github-actions.yaml
@@ -53,6 +53,7 @@ jobs:
       matrix:
         jobname: [
           clang-openmpi-ubsan, # undefined behavior sanitizer
+          coverage, # run code coverage and upload to codecov
         ]
         include:
 
@@ -60,6 +61,11 @@ jobs:
           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)
diff --git a/codecov.yaml b/codecov.yaml
new file mode 100644
index 0000000000..5f5f1563be
--- /dev/null
+++ b/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/::"
diff --git a/tests/test_automation/github-actions/ci/run_step.sh b/tests/test_automation/github-actions/ci/run_step.sh
index 22d595557c..bb2bf64c3f 100755
--- a/tests/test_automation/github-actions/ci/run_step.sh
+++ b/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