Coverage

.travis.yml

@@ -1,17 +1,42 @@
-branches:
-  only:
-    - master
+# branches:
+#   only:
+#     - master
 jobs:
   include:
-    - language: nix
+    - name: getCoverage
+      language: nix
       install:
+        - nix-env -i lcov
+      script:
+        # - nix-build .
+        - nix-shell --pure --run ./scripts/mkCoverage.sh
+        - bash <(curl -s https://codecov.io/bash) -f shellBuild/coverage.info.cleaned || echo "Codecov did not collect coverage reports"
+      cache:
+        directories:
+          - $HOME/nix.store
+          - /nix/
+      before_install:
+        - sudo mkdir -p /etc/nix
+        - echo "substituters = https://cache.nixos.org/ file://$HOME/nix.store" | sudo tee -a /etc/nix/nix.conf > /dev/null
+        - echo 'require-sigs = false' | sudo tee -a /etc/nix/nix.conf > /dev/null
+      before_cache:
+        - mkdir -p $HOME/nix.store
+        - nix copy --to file://$HOME/nix.store -f default.nix buildInputs
+    - name: runCachix
+      if: branch = master
+      language: nix
+      install:
+        - nix-env -i lcov
         - "nix-env -iA cachix -f https://cachix.org/api/v1/install"
       script:
         - cachix use dseams
-        - cachix push dseams --watch-store&
+        - then cachix push dseams --watch-store&
         - nix-build .
         - sleep 30s # wait for the cachix push to complete
-    - language: python
+      cache: nix
+    - name: docBuilder
+      if: branch = master
+      language: python
       python: "3.6"
       before_install:
         - cp scripts/ci/texlive.profile $HOME/texlive.profile

CMakeLists.txt

@@ -233,6 +233,8 @@ add_subdirectory(src)
 # # Install runtime data
 # install(DIRECTORY ${PROJECT_SOURCE_DIR}/data DESTINATION ${INSTALL_DATA} COMPONENT runtime)
 
+set(CMAKE_CXX_FLAGS "-g -O0 -fprofile-arcs -ftest-coverage")
+set(CMAKE_C_FLAGS "-g -O0 -fprofile-arcs -ftest-coverage")
 #
 # Dependency Management
 #

README.md

@@ -4,6 +4,7 @@
 
 [![Build Status](https://travis-ci.org/d-SEAMS/seams-core.svg?branch=master)](https://travis-ci.org/d-SEAMS/seams-core)
 [![built with nix](https://builtwithnix.org/badge.svg)](https://builtwithnix.org)
+[![codecov](https://codecov.io/gh/d-SEAMS/seams-core/branch/master/graph/badge.svg)](https://codecov.io/gh/d-SEAMS/seams-core)
 
 - Check our build status [here](https://travis-ci.org/d-SEAMS/seams-core).
 - The docs themselves are [here](https://docs.dseams.info) and development is

cmake/CodeCoverage.cmake

@@ -0,0 +1,204 @@
+# Copyright (c) 2012 - 2015, Lars Bilke
+# All rights reserved.
+#
+# Redistribution and use in source and binary forms, with or without modification,
+# are permitted provided that the following conditions are met:
+#
+# 1. Redistributions of source code must retain the above copyright notice, this
+#    list of conditions and the following disclaimer.
+#
+# 2. Redistributions in binary form must reproduce the above copyright notice,
+#    this list of conditions and the following disclaimer in the documentation
+#    and/or other materials provided with the distribution.
+#
+# 3. Neither the name of the copyright holder nor the names of its contributors
+#    may be used to endorse or promote products derived from this software without
+#    specific prior written permission.
+#
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+# ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+# WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR
+# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON
+# ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+#
+#
+#
+# 2012-01-31, Lars Bilke
+# - Enable Code Coverage
+#
+# 2013-09-17, Joakim Söderberg
+# - Added support for Clang.
+# - Some additional usage instructions.
+#
+# USAGE:
+
+# 0. (Mac only) If you use Xcode 5.1 make sure to patch geninfo as described here:
+#      http://stackoverflow.com/a/22404544/80480
+#
+# 1. Copy this file into your cmake modules path.
+#
+# 2. Add the following line to your CMakeLists.txt:
+#      INCLUDE(CodeCoverage)
+#
+# 3. Set compiler flags to turn off optimization and enable coverage:
+#    SET(CMAKE_CXX_FLAGS "-g -O0 -fprofile-arcs -ftest-coverage")
+#	 SET(CMAKE_C_FLAGS "-g -O0 -fprofile-arcs -ftest-coverage")
+#
+# 3. Use the function SETUP_TARGET_FOR_COVERAGE to create a custom make target
+#    which runs your test executable and produces a lcov code coverage report:
+#    Example:
+#	 SETUP_TARGET_FOR_COVERAGE(
+#				my_coverage_target  # Name for custom target.
+#				test_driver         # Name of the test driver executable that runs the tests.
+#									# NOTE! This should always have a ZERO as exit code
+#									# otherwise the coverage generation will not complete.
+#				coverage            # Name of output directory.
+#				)
+#
+#    If you need to exclude additional directories from the report, specify them
+#    using the LCOV_REMOVE_EXTRA variable before calling SETUP_TARGET_FOR_COVERAGE.
+#    For example:
+#
+#    set(LCOV_REMOVE_EXTRA "'thirdparty/*'")
+#
+# 4. Build a Debug build:
+#	 cmake -DCMAKE_BUILD_TYPE=Debug ..
+#	 make
+#	 make my_coverage_target
+#
+#
+
+# Check prereqs
+FIND_PROGRAM( GCOV_PATH gcov )
+FIND_PROGRAM( LCOV_PATH lcov )
+FIND_PROGRAM( GENHTML_PATH genhtml )
+FIND_PROGRAM( GCOVR_PATH gcovr PATHS ${CMAKE_SOURCE_DIR}/tests)
+
+# IF(NOT GCOV_PATH)
+# 	MESSAGE(FATAL_ERROR "gcov not found! Aborting...")
+# ENDIF() # NOT GCOV_PATH
+
+IF("${CMAKE_CXX_COMPILER_ID}" MATCHES "(Apple)?[Cc]lang")
+	IF("${CMAKE_CXX_COMPILER_VERSION}" VERSION_LESS 3)
+		MESSAGE(FATAL_ERROR "Clang version must be 3.0.0 or greater! Aborting...")
+	ENDIF()
+ELSEIF(NOT CMAKE_COMPILER_IS_GNUCXX)
+	MESSAGE(FATAL_ERROR "Compiler is not GNU gcc! Aborting...")
+ENDIF() # CHECK VALID COMPILER
+
+SET(CMAKE_CXX_FLAGS_COVERAGE
+    "-g -O0 --coverage -fprofile-arcs -ftest-coverage"
+    CACHE STRING "Flags used by the C++ compiler during coverage builds."
+    FORCE )
+SET(CMAKE_C_FLAGS_COVERAGE
+    "-g -O0 --coverage -fprofile-arcs -ftest-coverage"
+    CACHE STRING "Flags used by the C compiler during coverage builds."
+    FORCE )
+SET(CMAKE_EXE_LINKER_FLAGS_COVERAGE
+    ""
+    CACHE STRING "Flags used for linking binaries during coverage builds."
+    FORCE )
+SET(CMAKE_SHARED_LINKER_FLAGS_COVERAGE
+    ""
+    CACHE STRING "Flags used by the shared libraries linker during coverage builds."
+    FORCE )
+MARK_AS_ADVANCED(
+    CMAKE_CXX_FLAGS_COVERAGE
+    CMAKE_C_FLAGS_COVERAGE
+    CMAKE_EXE_LINKER_FLAGS_COVERAGE
+    CMAKE_SHARED_LINKER_FLAGS_COVERAGE )
+
+IF ( NOT (CMAKE_BUILD_TYPE STREQUAL "Debug" OR CMAKE_BUILD_TYPE STREQUAL "Coverage"))
+  MESSAGE( WARNING "Code coverage results with an optimized (non-Debug) build may be misleading" )
+ENDIF() # NOT CMAKE_BUILD_TYPE STREQUAL "Debug"
+
+
+# Param _targetname     The name of new the custom make target
+# Param _testrunner     The name of the target which runs the tests.
+#						MUST return ZERO always, even on errors.
+#						If not, no coverage report will be created!
+# Param _outputname     lcov output is generated as _outputname.info
+#                       HTML report is generated in _outputname/index.html
+# Optional fourth parameter is passed as arguments to _testrunner
+#   Pass them in list form, e.g.: "-j;2" for -j 2
+FUNCTION(SETUP_TARGET_FOR_COVERAGE _targetname _testrunner _outputname)
+
+	# IF(NOT LCOV_PATH)
+	# 	MESSAGE(FATAL_ERROR "lcov not found! Aborting...")
+	# ENDIF() # NOT LCOV_PATH
+
+	# IF(NOT GENHTML_PATH)
+	# 	MESSAGE(FATAL_ERROR "genhtml not found! Aborting...")
+	# ENDIF() # NOT GENHTML_PATH
+
+	SET(coverage_info "${CMAKE_BINARY_DIR}/${_outputname}.info")
+	SET(coverage_cleaned "${coverage_info}.cleaned")
+
+	SEPARATE_ARGUMENTS(test_command UNIX_COMMAND "${_testrunner}")
+
+	# Setup target
+	ADD_CUSTOM_TARGET(${_targetname}
+
+		# Cleanup lcov
+		lcov --directory . --zerocounters
+
+		# Run tests
+		COMMAND ${test_command} ${ARGV3}
+
+		# Capturing lcov counters and generating report
+		COMMAND lcov --directory . --capture --output-file ${coverage_info}
+		COMMAND lcov --remove ${coverage_info} 'tests/*' '**/tests/*' '**/boost/*' '/nix/*' '/usr/*' ${LCOV_REMOVE_EXTRA} --output-file ${coverage_cleaned}
+		COMMAND genhtml -o ${_outputname} ${coverage_cleaned}
+		# COMMAND ${CMAKE_COMMAND} -E remove ${coverage_info} ${coverage_cleaned}
+
+		WORKING_DIRECTORY ${CMAKE_BINARY_DIR}
+		COMMENT "Resetting code coverage counters to zero.\nProcessing code coverage counters and generating report."
+	)
+
+	# Show info where to find the report
+	ADD_CUSTOM_COMMAND(TARGET ${_targetname} POST_BUILD
+		COMMAND ;
+		COMMENT "Open ./${_outputname}/index.html in your browser to view the coverage report."
+	)
+
+ENDFUNCTION() # SETUP_TARGET_FOR_COVERAGE
+
+# Param _targetname     The name of new the custom make target
+# Param _testrunner     The name of the target which runs the tests
+# Param _outputname     cobertura output is generated as _outputname.xml
+# Optional fourth parameter is passed as arguments to _testrunner
+#   Pass them in list form, e.g.: "-j;2" for -j 2
+FUNCTION(SETUP_TARGET_FOR_COVERAGE_COBERTURA _targetname _testrunner _outputname)
+
+	IF(NOT PYTHON_EXECUTABLE)
+		MESSAGE(FATAL_ERROR "Python not found! Aborting...")
+	ENDIF() # NOT PYTHON_EXECUTABLE
+
+	IF(NOT GCOVR_PATH)
+		MESSAGE(FATAL_ERROR "gcovr not found! Aborting...")
+	ENDIF() # NOT GCOVR_PATH
+
+	ADD_CUSTOM_TARGET(${_targetname}
+
+		# Run tests
+		${_testrunner} ${ARGV3}
+
+		# Running gcovr
+		COMMAND ${GCOVR_PATH} -x -r ${CMAKE_SOURCE_DIR} -e '${CMAKE_SOURCE_DIR}/tests/'  -o ${_outputname}.xml
+		WORKING_DIRECTORY ${CMAKE_BINARY_DIR}
+		COMMENT "Running gcovr to produce Cobertura code coverage report."
+	)
+
+	# Show info where to find the report
+	ADD_CUSTOM_COMMAND(TARGET ${_targetname} POST_BUILD
+		COMMAND ;
+		COMMENT "Cobertura code coverage report saved in ${_outputname}.xml."
+	)
+
+ENDFUNCTION() # SETUP_TARGET_FOR_COVERAGE_COBERTURA
+

nix/nixpkgs/default.src.json

@@ -2,6 +2,6 @@
   "owner": "NixOS",
   "repo": "nixpkgs-channels",
   "branch": "nixos-unstable",
-  "rev": "ae002fe44e96b868c62581e8066d559ca2179e01",
-  "sha256": "1bawyz3ksw2sihv6vsgbvhdm4kn63xrrj5bavg6mz5mxml9rji89"
+  "rev": "8130f3c1c2bb0e533b5e150c39911d6e61dcecc2",
+  "sha256": "154nrhmm3dk5kmga2w5f7a2l6j79dvizrg4wzbrcwlbvdvapdgkb"
 }

nix/yodaStruct.nix

@@ -10,6 +10,7 @@
 , liblapack
 , blas
 , lib
+, lcov
 , boost
 , gsl
 , rang

scripts/mkCoverage.sh

@@ -0,0 +1,13 @@
+#!/usr/bin/env bash
+
+topLevel=$(git rev-parse --show-toplevel)
+cd $topLevel
+if [[ "$PWD" =~ seams-core ]]; then
+	rm -rf shellBuild
+	mkdir shellBuild
+	cd shellBuild
+	# cmake .. -DCMAKE_CXX_FLAGS="-pg -fsanitize=address " -DCMAKE_EXE_LINKER_FLAGS=-pg -DCMAKE_SHARED_LINKER_FLAGS=-pg
+	cmake .. -DCMAKE_BUILD_TYPE=Debug
+	# cmake .. -DCMAKE_BUILD_TYPE=Release
+	make testCoverage -j4
+fi

shell.nix

@@ -16,6 +16,7 @@ pkgs.mkShell {
   buildInputs = with pkgs; [
     gdb
     git
+    lcov
     lua
     luaPackages.luafilesystem
   ]

tests/CMakeLists.txt

@@ -11,6 +11,7 @@ add_executable(yodaStruct_test
                ${PROJECT_SOURCE_DIR}/src/mol_sys.cpp
 )
 
+#
 # Standard cmake stuff
 # include(FindBLAS)
 # include(FindLAPACK)
@@ -47,3 +48,15 @@ include_directories(
   )
 # Run unit tests
 add_test(NAME yodaStruct-unit-tests COMMAND $<TARGET_FILE:yodaStruct_test>)
+
+# Coverage
+include(CodeCoverage)
+ setup_target_for_coverage(
+   testCoverage  # Name for custom target.
+    yodaStruct_test         # Name of the test driver executable that runs the tests.
+    # NOTE! This should always have a ZERO as exit code
+    # otherwise the coverage generation will not complete.
+    coverage            # Name of output directory.
+    )
+# target_compile_options(yodaStruct_test PRIVATE -g -O0 -fprofile-arcs -ftest-coverage)
+# target_link_options(yodaStruct_test PRIVATE -lgcov --coverage)