Explicit Coverage Step for C++ sources as codecov/codecov-action@v3 n…

…ot handling it well (#280)

* Explicit Coverage Step for C++ sources as codecov/codecov-action@v3 is not handling it well
* Coverage for run_spark_hdfs.py

.github/workflows/basic.yml

@@ -155,8 +155,18 @@ jobs:
         python -m pip install --upgrade pip
         python -m pip install jsondiff
         source $SPARK_ENV
-        python tests/run_spark_hdfs.py $GENOMICSDB_BUILD_DIR $CMAKE_INSTALL_PREFIX local hdfs://localhost:9000/ client $GENOMICSDB_RELEASE_VERSION $GITHUB_WORKSPACE/tests Coverage
+        python tests/run_spark_hdfs.py $GENOMICSDB_BUILD_DIR $CMAKE_INSTALL_PREFIX local hdfs://localhost:9000/ client $GENOMICSDB_RELEASE_VERSION $GITHUB_WORKSPACE/tests "" Coverage
         $GITHUB_WORKSPACE/.github/scripts/test_hdfs_htslib_support.sh
 
+    - name: Coverage
+      shell: bash
+      working-directory: ${{env.GENOMICSDB_BUILD_DIR}}
+      run: |
+        lcov --directory . --capture --output-file coverage.info
+        lcov --remove coverage.info '/opt*' '/usr*' '*/dependencies/*' '*/src/test*' '*.pb.h' '*.pb.cc' '*/protobuf-install/*' '*/awssdk-install/*' '*/gcssdk-install/*' 'v1/*' '/Library/*' -o coverage.info
+
     - name: Upload Coverage to CodeCov
       uses: codecov/codecov-action@v3
+      with:
+        files: build/coverage.info, build/target/jacoco-reports/jacoco-ut/jacoco.xml, build/target/jacoco-reports/jacoco-ci/jacoco-ci.xml
+        verbose: true

scripts/prereqs/system/install_macos_prereqs.sh

@@ -32,6 +32,7 @@ brew list mpich &>/dev/null || brew install mpich
 brew list ossp-uuid &>/dev/null || brew install ossp-uuid
 brew list libcsv &>/dev/null || brew install libcsv
 brew list automake &> /dev/null || brew install automake
+brew list lcov &> /dev/null || brew install lcov
 brew list openssl@1.1 &> /dev/null || brew install openssl@1.1
 brew list zstd &> /dev/null || brew install zstd
 echo "export OPENSSL_ROOT_DIR=$(brew --prefix openssl@1.1)" >> $PREREQS_ENV