Remove external sources from coverage (#484)

* Filter external directory from coverage
* And split this tasks from the main workflow file

Author: Nicolas Cornu

.github/workflows/coreneuron-ci.yml

@@ -161,28 +161,3 @@ jobs:
 #           BRANCH: gh-pages # The branch the action should deploy to.
 #           FOLDER: ${{runner.workspace}}/nrn/build/docs # The folder the action should deploy.
 #           CLEAN: false # Automatically remove deleted files from the deploy branch
-  coverage:
-    runs-on: ubuntu-16.04
-    name: "Coverage Test"
-    steps:
-      - name: Install packages
-        run: |
-          sudo apt-get install doxygen bison flex libboost-all-dev libopenmpi-dev openmpi-bin python3-dev python3-pip lcov
-        shell: bash
-      - uses: actions/checkout@v2
-        with:
-          fetch-depth: 2
-      - name: Build and Test for Coverage
-        id: build-test
-        shell: bash
-        working-directory: ${{runner.workspace}}/CoreNeuron
-        run:  |
-          mkdir build && cd build
-          cmake .. -DCORENRN_ENABLE_MPI=ON -DCMAKE_C_FLAGS="-coverage -O0" -DCMAKE_CXX_FLAGS="-coverage -O0";
-          make
-          (cd ..;  lcov --capture  --initial --directory . --no-external --output-file build/coverage-base.info)
-          make test
-          (cd ..; lcov --capture  --directory . --no-external --output-file build/coverage-run.info)
-          lcov --add-tracefile coverage-base.info --add-tracefile coverage-run.info --output-file coverage-combined.info
-          genhtml coverage-combined.info --output-directory coverage --demangle-cpp --ignore-errors source
-          bash <(curl -s https://codecov.io/bash)

.github/workflows/coverage.yml

@@ -0,0 +1,46 @@
+name: Coverage
+
+on:
+  push:
+    branches:
+      - master
+      - live-debug*
+      - release/**
+  pull_request:
+    branches:
+      - master
+      - release/**
+
+env:
+  BUILD_TYPE: Release
+  DEFAULT_PY_VERSION: 3.8
+
+jobs:
+  coverage:
+    runs-on: ubuntu-16.04
+    name: "Coverage Test"
+    steps:
+      - name: Install packages
+        run: |
+          sudo apt-get install doxygen bison flex libboost-all-dev libopenmpi-dev openmpi-bin python3-dev python3-pip lcov
+        shell: bash
+      - uses: actions/checkout@v2
+        with:
+          fetch-depth: 2
+      - name: Build and Test for Coverage
+        id: build-test
+        shell: bash
+        working-directory: ${{runner.workspace}}/CoreNeuron
+        run:  |
+          mkdir build && cd build
+          cmake .. -DCORENRN_ENABLE_MPI=ON -DCMAKE_C_FLAGS="-coverage -O0" -DCMAKE_CXX_FLAGS="-coverage -O0";
+          make -j2
+          (cd ..;  lcov --capture  --initial --directory . --no-external --output-file build/coverage-base.info)
+          make test
+          (cd ..; lcov --capture  --directory . --no-external --output-file build/coverage-run.info)
+          lcov --add-tracefile coverage-base.info --add-tracefile coverage-run.info --output-file coverage-combined.info
+          lcov --remove coverage-combined.info --output-file coverage.info "*/external/*"
+          lcov --list coverage.info
+      - name: Upload to codecov.io
+        run: bash <(curl -s https://codecov.io/bash) -f build/coverage.info
+