Coverage (SimVascular#42)

* add coverage

* fix indent

* install lcov

* fix install

* fix paths

* upgrade python

* change directories

* remove --ignore-errors inconsistent

* remove --ignore-errors unmapped

* double quotes

* double asterik

* exclude usr

* too much exclude

* explucde instead of remove

* change back " to '

* build twice

* use tempdir

* remove unused helper functions

* test mean output

* test io derivative

* test io mean derivative

* add mean variable (doesn't run yet)

* add missing assert

* split test files

* delete overlap

* add variable derivative

* add tests

* format and simplify

.github/workflows/codechecks.yml

@@ -5,7 +5,7 @@ jobs:
  clang-format:
  runs-on: ubuntu-latest
  steps:
- - uses: actions/checkout@v2
+ - uses: actions/checkout@v3
  - name: Install dependencies
  run: |
  sudo apt install clang-format

.github/workflows/documentation.yml

@@ -7,7 +7,7 @@ jobs:
  documentation:
  runs-on: ubuntu-latest
  steps:
- - uses: actions/checkout@v2
+ - uses: actions/checkout@v3
  - name: Make build directory
  run: mkdir docs/build
  - name: Build doxygen documentation

.github/workflows/test.yml

@@ -10,18 +10,18 @@ jobs:
  os: [ubuntu-20.04, ubuntu-22.04, macos-11, macos-12]
  fail-fast: false
  steps:
- - uses: actions/checkout@v2
+ - uses: actions/checkout@v3
  - name: Install ubuntu dependencies
- if: ${{ matrix.os == 'ubuntu-*' }}
- run: sudo apt update && sudo apt install build-essential cmake
+ if: startsWith(matrix.os, 'ubuntu')
+ run: sudo apt update && sudo apt install build-essential cmake lcov
  - name: Install svZeroDPlus
  run: |
- conda create -n zerod python=3.9
+ conda create -n zerod python=3.11.4
  conda run -n zerod pip install -e ".[dev]"
  - name: Test the build
  run: |
  cd tests
- conda run -n zerod pytest
+ conda run -n zerod pytest -v --durations=0
  - name: Build using CMake
  run: |
  mkdir Release
@@ -38,4 +38,20 @@ jobs:
  cd test_01
  ./svZeroD_interface_test01 ../../../../Release ../../test_01/svzerod_3Dcoupling.json
  cd ../test_02
- ./svZeroD_interface_test02 ../../../../Release ../../test_02/svzerod_tuned.json
+ ./svZeroD_interface_test02 ../../../../Release ../../test_02/svzerod_tuned.json
+ - name: Generate code coverage
+ if: startsWith(matrix.os, 'ubuntu-22.04')
+ run: |
+ cd Release
+ cmake -DENABLE_COVERAGE=ON ..
+ cmake --build .
+ cd ../tests
+ conda run -n zerod pytest -v --durations=0 --coverage
+ cd ../Release
+ make coverage
+ - name: Save coverage report
+ if: startsWith(matrix.os, 'ubuntu-22.04')
+ uses: actions/upload-artifact@v3
+ with:
+ name: coverage_report
+ path: Release/coverage

CMakeLists.txt

@@ -4,6 +4,28 @@ set(CMAKE_CXX_STANDARD_REQUIRED True)
 project(svZeroDSolver)
 include(FetchContent)
 
+# -----------------------------------------------------------------------------
+# Enable code coverage
+# -----------------------------------------------------------------------------
+set(ENABLE_COVERAGE OFF CACHE BOOL "Enable code coverage")
+# coverage
+if(ENABLE_COVERAGE)
+ # set compiler flags
+ set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -O0 -coverage -g")
+
+ # find required tools
+ find_program(LCOV lcov REQUIRED)
+ find_program(GENHTML genhtml REQUIRED)
+
+ # add coverage target
+ add_custom_target(coverage
+ # gather data
+ COMMAND ${LCOV} --directory . --capture --output-file coverage.info --ignore-errors gcov --exclude '/usr/include/*' --exclude '/usr/lib/*' --exclude '*/_deps/*'
+ # generate report
+ COMMAND ${GENHTML} --demangle-cpp -o coverage coverage.info
+ WORKING_DIRECTORY ${CMAKE_BINARY_DIR})
+endif()
+
 # -----------------------------------------------------------------------------
 # Fetch Eigen
 # -----------------------------------------------------------------------------

src/interface/interface.h

@@ -3,7 +3,6 @@
 #include "algebra/sparsesystem.hpp"
 #include "algebra/state.hpp"
 #include "helpers/debug.hpp"
-#include "helpers/endswith.hpp"
 #include "io/configreader.hpp"
 #include "io/csvwriter.hpp"
 #include "model/model.hpp"

src/io/configreader.hpp

@@ -40,7 +40,6 @@
 #include <string>
 
 #include "../helpers/debug.hpp"
-#include "../helpers/startswith.hpp"
 #include "../model/model.hpp"
 
 namespace IO {

src/io/csvwriter.hpp

@@ -39,7 +39,6 @@
 #include <vector>
 
 #include "../algebra/state.hpp"
-#include "../helpers/startswith.hpp"
 #include "../model/model.hpp"
 
 namespace IO {

src/optimize/calibrate.hpp

@@ -40,7 +40,6 @@
 #include <nlohmann/json.hpp>
 
 #include "helpers/debug.hpp"
-#include "helpers/endswith.hpp"
 #include "levenbergmarquardtoptimizer.hpp"
 #include "model/model.hpp"
 

src/solve/solver.hpp

@@ -35,7 +35,6 @@
 #include "algebra/integrator.hpp"
 #include "algebra/state.hpp"
 #include "helpers/debug.hpp"
-#include "helpers/endswith.hpp"
 #include "io/configreader.hpp"
 #include "io/csvwriter.hpp"
 #include "model/model.hpp"