Add coverage reports to channelflow (epfl-ecps#8)

* Added coverage computation to unit and integration tests

The code is compiled passing '--coverage -g' during the 'Unit and
integration tests' stage. Once tests are run data is processed using
lcov and printed to stdout, if tests succeeded.

* Tests done for coverage are built in debug mode with -Og

* Added summary badges to the README file.

- Build status
- Total coverage
- License

.codecov.yml

@@ -0,0 +1,4 @@
+coverage:
+  ignore:
+  - tests/
+  - bundled/

.travis.yml

@@ -34,8 +34,8 @@ jobs:
             - ubuntu-toolchain-r-test
             - sourceline: 'ppa:likemartinma/devel'
           packages:
+            - lcov
             - ccache
-            - g++-8
             - openmpi-bin
             - libopenmpi-dev
             - libhdf5-dev
@@ -45,8 +45,8 @@ jobs:
             - libeigen3-dev
       env:
         - CMAKE_PREFIX_PATH=/usr/lib/x86_64-linux-gnu
-        - OMPI_CC=gcc-8
-        - OMPI_CXX=g++-8
+        - OMPI_CC=gcc
+        - OMPI_CXX=g++
         - CPLUS_INCLUDE_PATH=/usr/lib/openmpi/include
       script: ./share/qa/unit_and_integration_test.sh
 
@@ -171,5 +171,8 @@ jobs:
 install:
   - ccache -M 2G
 
+after_success:
+  - if [[ -f "${TRAVIS_BUILD_DIR}/cmake-build-release/Testing/Temporary/LastTest.log" ]] ; then ./share/qa/compute_coverage.sh ; fi
+
 after_failure:
   - if [[ -f "${TRAVIS_BUILD_DIR}/cmake-build-release/Testing/Temporary/LastTest.log" ]] ; then cat "${TRAVIS_BUILD_DIR}/cmake-build-release/Testing/Temporary/LastTest.log" ; fi

README.md

@@ -1,3 +1,7 @@
+[![Build Status](https://travis-ci.com/epfl-ecps/channelflow.svg?branch=master)](https://travis-ci.com/epfl-ecps/channelflow)
+[![codecov](https://codecov.io/gh/epfl-ecps/channelflow/branch/master/graph/badge.svg)](https://codecov.io/gh/epfl-ecps/channelflow)
+[![License: GPL v2](https://img.shields.io/badge/License-GPL%20v2-blue.svg)](https://www.gnu.org/licenses/old-licenses/gpl-2.0.en.html)
+
 # Channelflow Project
 
 Channelflow is a software system for numerical analysis of the incompressible fluid flow in

share/qa/compute_coverage.sh

@@ -0,0 +1,17 @@
+#!/bin/bash -e
+
+if [[ "${OMPI_CC}" == "gcc" ]]
+then
+    # Go to the build directory and compute coverage
+    cd ${TRAVIS_BUILD_DIR}/cmake-build-release
+    lcov --version
+    echo $PWD
+    lcov --rc lcov_branch_coverage=1 --directory . --capture --output-file coverage.info
+    lcov --rc lcov_branch_coverage=1 --remove coverage.info '/*tests/*' --output-file coverage.info
+    lcov --rc lcov_branch_coverage=1 --remove coverage.info '/*/bundled/*' --output-file coverage.info
+    lcov --rc lcov_branch_coverage=1 --remove coverage.info '/usr/*' --output-file coverage.info
+    lcov --rc lcov_branch_coverage=1 --list coverage.info
+
+    # Upload to codecov website
+    bash <(curl -s https://codecov.io/bash) || echo "Codecov did not collect coverage reports"
+fi

share/qa/unit_and_integration_test.sh

@@ -7,9 +7,17 @@
 ccache -V
 ccache -z
 
-# Parallel build in Release mode
 mkdir ${TRAVIS_BUILD_DIR}/cmake-build-release && cd ${TRAVIS_BUILD_DIR}/cmake-build-release
-CC="ccache mpicc" CXX="ccache mpicxx" cmake -DCMAKE_BUILD_TYPE:STRING=Release -DWITH_HDF5CXX:BOOL=ON -DWITH_PYTHON:BOOL=OFF -DBUILD_SHARED_LIBS:BOOL=ON -DWITH_NSOLVER:BOOL=ON -DWITH_NETCDF:STRING=Serial ${TRAVIS_BUILD_DIR}
+# Tests done for coverage are built in debug mode, to hit assertions.
+# We use -Og not to slow down excessively the executables and tests
+if [[ "${OMPI_CC}" == "gcc" ]]
+then
+    # Parallel build in Release mode
+    CXXFLAGS="--coverage -ggdb3 -Og" CC="ccache mpicc" CXX="ccache mpicxx" cmake -DCMAKE_EXPORT_COMPILE_COMMANDS:BOOL=ON -DCMAKE_BUILD_TYPE:STRING=Debug -DWITH_HDF5CXX:BOOL=ON -DWITH_PYTHON:BOOL=OFF -DBUILD_SHARED_LIBS:BOOL=ON -DWITH_NSOLVER:BOOL=ON -DWITH_NETCDF:STRING=Serial ${TRAVIS_BUILD_DIR}
+else
+    # Parallel build in Release mode
+    CC="ccache mpicc" CXX="ccache mpicxx" cmake -DCMAKE_EXPORT_COMPILE_COMMANDS:BOOL=ON -DCMAKE_BUILD_TYPE:STRING=Release -DWITH_HDF5CXX:BOOL=ON -DWITH_PYTHON:BOOL=OFF -DBUILD_SHARED_LIBS:BOOL=ON -DWITH_NSOLVER:BOOL=ON -DWITH_NETCDF:STRING=Serial ${TRAVIS_BUILD_DIR}
+fi
 make -j 4
 
 # Print ccache statistics