Add code coverage to CI (NanoComp#1651)

* Add code coverage to CI

* remove ignore from codecov.yml

* misssing brace

* specify source files and show coverage report in output

* remove badge

* fix path of coverage.xml to match git file structure

* show Codecov report in PR

.github/workflows/build-ci.yml

@@ -125,6 +125,10 @@ jobs:
     - name: Install Python dependencies
       run: pip install -r python/requirements.txt
 
+    - name: Install coverage
+      if: ${{ matrix.enable-mpi == false && matrix.python-version == 3.6 }}
+      run: pip install coverage==4.5.4
+
     - name: Install mpi4py
       if: ${{ matrix.enable-mpi && steps.cache.outputs.cache-hit != true }}
       run: pip install mpi4py
@@ -136,28 +140,59 @@ jobs:
         echo "MEEP_VERSION=${MEEP_VERSION}" >> $GITHUB_ENV
 
     - name: Run configure
+      if: ${{ !(matrix.enable-mpi == false && matrix.python-version == 3.6) }}
       run: |
         mkdir -p build &&
         pushd build &&
         ../configure --enable-maintainer-mode --prefix=${HOME}/local --with-libctl=${HOME}/local/share/libctl ${MPICONF} &&
         popd
 
+    - name: Run configure
+      if: ${{ matrix.enable-mpi == false && matrix.python-version == 3.6 }}
+      run: ./configure --enable-maintainer-mode --prefix=${HOME}/local --with-libctl=${HOME}/local/share/libctl ${MPICONF}
+
+    - name: Run make
+      if: ${{ matrix.enable-mpi == false && matrix.python-version == 3.6 }}
+      run: make ${MKCHECKFLAGS}
+
+    - name: Run make check
+      if: ${{ matrix.enable-mpi == false && matrix.python-version == 3.6 }}
+      run: |
+        pushd python/ &&
+        make ${MKCHECKFLAGS} check &&
+        popd
+
     - name: Run make distcheck
+      if: ${{ !(matrix.enable-mpi == false && matrix.python-version == 3.6) }}
       run: |
         pushd build &&
         make ${MKCHECKFLAGS} distcheck DISTCHECK_CONFIGURE_FLAGS="--with-libctl=${HOME}/local/share/libctl ${MPICONF}" &&
         popd
 
+    - name: Generate coverage report
+      if: ${{ matrix.enable-mpi == false && matrix.python-version == 3.6 }}
+      run: |
+        pushd python/ &&
+        coverage report -i &&
+        coverage xml -i &&
+        popd
+
+    - name: Upload coverage to Codecov
+      if: ${{ matrix.enable-mpi == false && matrix.python-version == 3.6 }}
+      uses: codecov/codecov-action@v1
+      with:
+        files: ${{ github.workspace }}/python/coverage.xml
+
     - name: Archive C++ test logs
+      if: ${{ failure() && !(matrix.enable-mpi == false && matrix.python-version == 3.6) }}
       uses: actions/upload-artifact@v2
-      if: failure()
       with:
         name: cpp-tests-mpi-${{ matrix.enable-mpi }}-log
         path: ${{ github.workspace }}/build/meep-${{ env.MEEP_VERSION }}/_build/sub/tests/test-suite.log
 
     - name: Archive Python test logs
+      if: ${{ failure() && !(matrix.enable-mpi == false && matrix.python-version == 3.6) }}
       uses: actions/upload-artifact@v2
-      if: failure()
       with:
         name: py${{ matrix.python-version }}-tests-mpi-${{ matrix.enable-mpi }}-log
         path: ${{ github.workspace }}/build/meep-${{ env.MEEP_VERSION }}/_build/sub/python/test-suite.log

codecov.yml

@@ -0,0 +1,14 @@
+coverage:
+  status:
+    project:
+      default:
+        informational: true
+    patch:
+      default:
+        informational: true
+
+comment:
+  layout: "reach, diff, files"
+
+fixes:
+  - "meep/::python/"

python/Makefile.am

@@ -88,7 +88,7 @@ TESTS =                                   \
     $(WVG_SRC_TEST)
 
 if WITH_COVERAGE
-  PY_LOG_COMPILER = coverage run -a --omit=$(top_srcdir)/python/tests/*,${HOME}/virtualenv/*,$(top_srcdir)/python/examples/*
+  PY_LOG_COMPILER = coverage run -a --source=$(top_srcdir)/python/meep --omit=$(top_srcdir)/python/tests/*,$(top_srcdir)/python/examples/*,$(top_srcdir)/python/meep/materials.py
 else
   PY_LOG_COMPILER = $(RUNCODE) $(PYTHON)
 endif