add code coverage analysis using codecov.io

.github/actions/codecov/action.yml

@@ -0,0 +1,21 @@
+name: 'Upload Coverage Report'
+description: 'Generates and uploads code coverage to Codecov'
+
+inputs:
+  codecov_token:
+    description: 'Codecov upload token'
+    required: true
+
+runs:
+  using: "composite"
+  steps:
+    - name: Generate coverage report
+      run: docker run -v shared-data:/build -v $(pwd):/codecov -t partmc-test bash -c "lcov --capture --directory /build --output-file /codecov/coverage.info --no-external"
+      shell: bash
+
+    - name: Upload coverage report to codecov.io
+      uses: codecov/codecov-action@v5.5.0
+      with:
+        token: ${{ inputs.codecov_token }}
+        fail_ci_if_error: true
+

.github/workflows/camp.yml

@@ -12,4 +12,8 @@ jobs:
     - name: Build the testing docker image
       run: docker build -f Dockerfile.camp -t partmc-test .
     - name: Run the tests in the docker container
-      run: docker run -t partmc-test bash -c 'cd /build; make test'
+      run: docker run -v shared-data:/build -t partmc-test bash -c 'cd /build; make test'
+    - name: Generate and upload coverage report
+      uses: ./.github/actions/codecov
+      with:
+        codecov_token: ${{ secrets.CODECOV_TOKEN }}

.github/workflows/cloud_parcel.yml

@@ -10,6 +10,10 @@ jobs:
     steps:
     - uses: actions/checkout@v1
     - name: Build the testing docker image
-      run: docker build -f Dockerfile.cloud_parcel -t partmc-cloud-parcel .
+      run: docker build -f Dockerfile.cloud_parcel -t partmc-test .
     - name: Run the tests in the docker container
-      run: docker run -t partmc-cloud-parcel bash -c 'cd /build; make test'
+      run: docker run -v shared-data:/build  -t partmc-test bash -c 'cd /build; make test'
+    - name: Generate and upload coverage report
+      uses: ./.github/actions/codecov
+      with:
+        codecov_token: ${{ secrets.CODECOV_TOKEN }}

.github/workflows/main.yml

@@ -12,4 +12,8 @@ jobs:
     - name: Build the testing docker image
       run: docker build -t partmc-test .
     - name: Run the tests in the docker container
-      run: docker run -t partmc-test bash -c 'cd /build; make test'
+      run: docker run -v shared-data:/build -t partmc-test bash -c 'cd /build; make test'
+    - name: Generate and upload coverage report
+      uses: ./.github/actions/codecov
+      with:
+        codecov_token: ${{ secrets.CODECOV_TOKEN }}

.github/workflows/mpi.yml

@@ -12,4 +12,8 @@ jobs:
     - name: Build the testing docker image
       run: docker build -f Dockerfile.mpi -t partmc-test . 
     - name: Run the tests in the docker container
-      run: docker run -t partmc-test bash -c 'cd /build; CTEST_OUTPUT_ON_FAILURE=1 OMPI_MCA_rmaps_base_oversubscribe=false make test'
+      run: docker run -v shared-data:/build -t partmc-test bash -c 'cd /build; CTEST_OUTPUT_ON_FAILURE=1 OMPI_MCA_rmaps_base_oversubscribe=false make test'
+    - name: Generate and upload coverage report
+      uses: ./.github/actions/codecov
+      with:
+        codecov_token: ${{ secrets.CODECOV_TOKEN }}

.github/workflows/tchem.yml

@@ -12,4 +12,8 @@ jobs:
     - name: Build the testing docker image
       run: docker build -f Dockerfile.tchem -t partmc-test .
     - name: Run the tests in the docker container
-      run: docker run -t partmc-test bash -c 'export CTEST_PARALLEL_LEVEL=4; cd /build; make test'
+      run: docker run -v shared-data:/build -t partmc-test bash -c 'export CTEST_PARALLEL_LEVEL=4; cd /build; make test'
+    - name: Generate and upload coverage report
+      uses: ./.github/actions/codecov
+      with:
+        codecov_token: ${{ secrets.CODECOV_TOKEN }}

Dockerfile

@@ -9,6 +9,7 @@ RUN dnf -y update \
         netcdf-fortran-devel \
         gsl-devel \
         cmake \
+        lcov \
     && dnf clean all
 
 # NOTE: Modify .dockerignore to whitelist files/directories to copy.
@@ -17,8 +18,8 @@ COPY . /partmc/
 RUN mkdir /build \
     && cd /build \
     && cmake -D CMAKE_BUILD_TYPE=release \
-             -D CMAKE_C_FLAGS_RELEASE="-O2 -g -Werror -Wall -Wextra" \
-             -D CMAKE_Fortran_FLAGS_RELEASE="-O2 -g -Werror -fimplicit-none -Wall -Wextra -Wconversion -Wunderflow -Wimplicit-interface -Wno-compare-reals -Wno-unused -Wno-unused-parameter -Wno-unused-dummy-argument -fbounds-check" \
+             -D CMAKE_C_FLAGS_RELEASE="-O2 -g -Werror -Wall -Wextra --coverage" \
+             -D CMAKE_Fortran_FLAGS_RELEASE="-O2 -g -Werror -fimplicit-none -Wall -Wextra -Wconversion -Wunderflow -Wimplicit-interface -Wno-compare-reals -Wno-unused -Wno-unused-parameter -Wno-unused-dummy-argument -fbounds-check --coverage" \
              -D ENABLE_GSL:BOOL=TRUE \
              /partmc \
     && make

Dockerfile.camp

@@ -12,6 +12,7 @@ RUN dnf -y update \
         openblas-devel \
         gsl-devel \
         cmake \
+        lcov \
     && dnf clean all
 
 # Build the SuiteSparse libraries for sparse matrix support
@@ -76,8 +77,8 @@ RUN mkdir /build \
     && cmake -D CMAKE_BUILD_TYPE=release \
              -D CMAKE_C_FLAGS_DEBUG="-g" \
              -D CMAKE_Fortran_FLAGS_DEBUG="-g" \
-             -D CMAKE_C_FLAGS_RELEASE="-O2 -g -Werror -Wall -Wextra" \
-             -D CMAKE_Fortran_FLAGS_RELEASE="-O2 -g -Werror -fimplicit-none -Wall -Wextra -Wconversion -Wunderflow -Wimplicit-interface -Wno-compare-reals -Wno-unused -Wno-unused-parameter -Wno-unused-dummy-argument -fbounds-check" \
+             -D CMAKE_C_FLAGS_RELEASE="-O2 -g -Werror -Wall -Wextra --coverage" \
+             -D CMAKE_Fortran_FLAGS_RELEASE="-O2 -g -Werror -fimplicit-none -Wall -Wextra -Wconversion -Wunderflow -Wimplicit-interface -Wno-compare-reals -Wno-unused -Wno-unused-parameter -Wno-unused-dummy-argument -fbounds-check --coverage" \
              -D ENABLE_GSL:BOOL=TRUE \
              -D ENABLE_CAMP:BOOL=TRUE \
              /partmc \

Dockerfile.cloud_parcel

@@ -8,6 +8,7 @@ RUN dnf -y update \
         sundials-devel \
         gsl-devel \
         cmake \
+        lcov \
     && dnf clean all
 
 # NOTE: Modify .dockerignore to whitelist files/directories to copy.
@@ -16,8 +17,8 @@ COPY . /partmc/
 RUN mkdir /build \
     && cd /build \
     && cmake -D CMAKE_BUILD_TYPE=release \
-             -D CMAKE_C_FLAGS_RELEASE="-O2 -g -Werror -Wall -Wextra" \
-             -D CMAKE_Fortran_FLAGS_RELEASE="-O2 -g -Werror -fimplicit-none -Wall -Wextra -Wconversion -Wunderflow -Wimplicit-interface -Wno-compare-reals -Wno-unused -Wno-unused-parameter -Wno-unused-dummy-argument -fbounds-check" \
+             -D CMAKE_C_FLAGS_RELEASE="-O2 -g -Werror -Wall -Wextra --coverage" \
+             -D CMAKE_Fortran_FLAGS_RELEASE="-O2 -g -Werror -fimplicit-none -Wall -Wextra -Wconversion -Wunderflow -Wimplicit-interface -Wno-compare-reals -Wno-unused -Wno-unused-parameter -Wno-unused-dummy-argument -fbounds-check --coverage" \
              -D ENABLE_GSL:BOOL=TRUE \
              -D ENABLE_SUNDIALS:BOOL=TRUE \
              /partmc \

Dockerfile.mpi

@@ -9,6 +9,7 @@ RUN dnf -y update \
         gsl-devel \
         openmpi-devel \
         cmake \
+        lcov \
     && dnf clean all
 
 # NOTE: Modify .dockerignore to whitelist files/directories to copy.
@@ -24,8 +25,8 @@ ENV CC=mpicc
 RUN mkdir /build \
     && cd /build \
     && cmake -D CMAKE_BUILD_TYPE=release \
-             -D CMAKE_C_FLAGS_RELEASE="-O2 -g -Werror -Wall -Wextra" \
-             -D CMAKE_Fortran_FLAGS_RELEASE="-O2 -g -Werror -fimplicit-none -Wall -Wextra -Wconversion -Wunderflow -Wimplicit-interface -Wno-compare-reals -Wno-unused -Wno-unused-parameter -Wno-unused-dummy-argument -fbounds-check" \
+             -D CMAKE_C_FLAGS_RELEASE="-O2 -g -Werror -Wall -Wextra --coverage" \
+             -D CMAKE_Fortran_FLAGS_RELEASE="-O2 -g -Werror -fimplicit-none -Wall -Wextra -Wconversion -Wunderflow -Wimplicit-interface -Wno-compare-reals -Wno-unused -Wno-unused-parameter -Wno-unused-dummy-argument -fbounds-check --coverage" \
              -D ENABLE_GSL:BOOL=TRUE \
              -D ENABLE_MPI:BOOL=TRUE \
              /partmc \

Dockerfile.tchem

@@ -165,8 +165,8 @@ RUN cd /build \
     && cmake -DCMAKE_BUILD_TYPE=release \
              -DCMAKE_C_COMPILER=gcc \
              -DCMAKE_Fortran_COMPILER=gfortran \ 
-             -DCMAKE_C_FLAGS_RELEASE="-O2 -g -Werror -Wall -Wextra" \
-             -DCMAKE_Fortran_FLAGS_RELEASE="-O2 -g -Werror -fimplicit-none -Wall -Wextra -Wconversion -Wunderflow -Wimplicit-interface -Wno-compare-reals -Wno-unused -Wno-unused-parameter -Wno-unused-dummy-argument -fbounds-check" \
+             -DCMAKE_C_FLAGS_RELEASE="-O2 -g -Werror -Wall -Wextra --coverage" \
+             -DCMAKE_Fortran_FLAGS_RELEASE="-O2 -g -Werror -fimplicit-none -Wall -Wextra -Wconversion -Wunderflow -Wimplicit-interface -Wno-compare-reals -Wno-unused -Wno-unused-parameter -Wno-unused-dummy-argument -fbounds-check --coverage" \
              -D ENABLE_GSL:BOOL=TRUE \
              -D ENABLE_TCHEM:BOOL=TRUE  \
              -D ENABLE_SUNDIALS:BOOL=TRUE \