Merge pull request #36 from DCM-UPB/polish

unmerged changes + polish

.gitignore

@@ -1,4 +1,4 @@
-# -- Mac OS files (from github's Global/OSX.gitignore) --
+<# -- Mac OS files (from github's Global/OSX.gitignore) --
 .DS_Store
 .AppleDouble
 .LSOverride
@@ -58,85 +58,13 @@ xcuserdata
 DerivedData
 *.xcuserstate
 
-# -- Automake files (http://www.gnu.org/software/automake)
-
-Makefile
-Makefile.in
-.libs
-.dirstamp
-test-suite.log
-/ar-lib
-/mdate-sh
-/py-compile
-/test-driver
-/ylwrap
-
-# --- Autoconf files (http://www.gnu.org/software/autoconf)
-
-aminclude_static.am
-config.h
-config.h.in
-config.h.in~
-config.log
-config.status
-.deps
-autom4te.cache
-/autoscan.log
-/autoscan-*.log
-/aclocal.m4
-/compile
-/config.guess
-/config.h.in
-/config.sub
-/configure
-/configure.scan
-/depcomp
-/install-sh
-/missing
-/stamp-h1
-
-# --- Files added by autoreconf -i
-
-/ltmain.sh
-libtool
-COPYING
-INSTALL
-
-# --- Texinfo files (http://www.gnu.org/software/texinfo)
-
-/texinfo.tex
-
-# --- M4 files (http://www.gnu.org/software/m4)
-
-m4/libtool.m4
-m4/ltoptions.m4
-m4/ltsugar.m4
-m4/ltversion.m4
-m4/lt~obsolete.m4
-
 # -- project specific ignores --
+lib*
+build
 config.sh
-exe
-exe.prof*
-vgcore* 
-*.o
-*.dSYM
-*.swp
-*.swo
-*.gcno
-*.lo
-*.la
-*.gcda
-*.log
-*.trs
+vgcore*
 
-test/*.txt
-test/ut*/*.txt
-
-benchmark/*/benchmark_*.out
-
-examples/*/*.txt
-examples/*/*/*.txt
+benchmark/*/*.out
 
 doc/*.aux
 doc/*.dvi
@@ -149,8 +77,6 @@ doc/*.fdb_latexmk
 doc/*.fls
 doc/*.ilg
 doc/*.ind
-doc/*.lb
 doc/auto
+
 doc/doxygen/*/*
-!doc/doxygen/doxygen.conf
-!doc/doxygen/doxygen.html

.travis.yml

@@ -1,73 +1,93 @@
-sudo: required
-dist: trusty
+dist: xenial
 language: c++
 services:
 - docker
 
+addons:
+  apt:
+    packages:
+    - valgrind
+    - libgsl-dev
+
+  homebrew:
+    packages:
+    - valgrind
+    - gsl
+
 matrix:
   include:
-  #- os: linux
-  #  env:
-  #    - MATRIX_EVAL="wget ftp://ftp.gnu.org/gnu/gsl/gsl-2.3.tar.gz && tar -xvf gsl-2.3.tar.gz && cd gsl-2.3 && ./configure && make -j2 && sudo make install && cd ../ && export LDFLAGS=-L/usr/local/lib && export CPPFLAGS=-I/usr/local/include"
-  #    - USE_DOCKER="FALSE"
-  #    - USE_GCOV="FALSE"
-
   - os: linux // arch linux docker
     env:
+    - MYCXX="g++"
     - USE_DOCKER="TRUE"
-    - USE_OPENMP="FALSE"
     - USE_GCOV="FALSE"
-
-  - os: linux // with enabled openmp
-    env:
-    - USE_DOCKER="TRUE"
     - USE_OPENMP="TRUE"
-    - USE_GCOV="FALSE"
 
   - os: osx
-    osx_image: xcode8
+    osx_image: xcode10.1
     env:
-    - MATRIX_EVAL="brew update && brew install gsl valgrind"
     - MYCXX="g++"
     - USE_DOCKER="FALSE"
-    - USE_GCOV="FALSE"
+    - USE_GCOV="TRUE"
+    - USE_OPENMP="FALSE"
 
   - os: osx
-    osx_image: xcode8
+    osx_image: xcode10.1
     env:
-    - MATRIX_EVAL="brew update && brew install gsl valgrind"
     - MYCXX="clang++"
     - USE_DOCKER="FALSE"
-    - USE_GCOV="TRUE"
+    - USE_GCOV="FALSE"
+    - USE_OPENMP="FALSE"
 
 before_install:
 - |
   if [[ "$USE_DOCKER" == "TRUE" ]]; then
   docker pull nnvmc/base;
-  local configopt="--enable-debug"
-  if [[ "$USE_OPENMP" == "TRUE" ]]; then configopt="${configopt} --enable-openmp"; fi;
-  if [[ "$USE_GCOV" == "TRUE" ]]; then configopt="${configopt} --enable-coverage"; fi;
-  docker run -it -v $(pwd):/root/repo nnvmc/base /bin/bash -c "cd /root/repo && ./autogen.sh && ./configure ${configopt}";
   else
-  eval "${MATRIX_EVAL}" && ${MYCXX} -v;
-  ./autogen.sh
-  local configopt="--enable-debug"
-  if [[ "$USE_GCOV" == "TRUE" ]]; then pip install cpp-coveralls; configopt="${configopt} --enable-coverage"; fi;
-  ./configure CXX=${MYCXX} ${configopt};
+  ${MYCXX} -v;
   fi;
+  echo "CXX_COMPILER=${MYCXX}" >> config.sh;
+  echo "CXX_FLAGS=\"-O0 -g -Wall -Wno-unused-function ${configopt}\"" >> config.sh;
+  if [[ "$USE_GCOV" == "TRUE" ]]; then
+  echo "USE_COVERAGE=1" >> config.sh;
+  else
+  echo "USE_COVERAGE=0" >> config.sh;
+  fi;
+  if [[ "$USE_OPENMP" == "TRUE" ]]; then
+  echo "USE_OPENMP=1" >> config.sh;
+  else
+  echo "USE_OPENMP=0" >> config.sh;
+  fi;
+  echo "GSL_ROOT=" >> config.sh;
 
 script:
 - |
   if [[ "$USE_DOCKER" == "TRUE" ]]; then
-  docker run -it -v $(pwd):/root/repo nnvmc/base /bin/bash -c "cd /root/repo && make check" || exit 1;
-  if [[ "$USE_GCOV" == "TRUE" ]]; then
-  docker run -e TRAVIS=$TRAVIS -e TRAVIS_JOB_ID=$TRAVIS_JOB_ID -it -v $(pwd):/root/repo nnvmc/base /bin/bash -c "pip install cpp-coveralls && cd /root/repo && coveralls -b lib -e test -e benchmark -e include -e lib -e examples -e script -i src --gcov-options '\-lp'";
+  docker run -it -v $(pwd):/root/repo nnvmc/base /bin/bash -c "cd /root/repo && ./build.sh" || exit 1;
+  else
+  ./build.sh || exit 1;
   fi;
+
+- |
+  if [[ "$USE_DOCKER" == "TRUE" ]]; then
+  if [[ "$USE_OPENMP" == "TRUE" ]]; then
+  docker run -it -v $(pwd):/root/repo nnvmc/base /bin/bash -c "cd /root/repo/build && make test";
+  elif [[ "$USE_GCOV" == "TRUE" ]]; then
+  docker run -it -v $(pwd):/root/repo nnvmc/base /bin/bash -c "cd /root/repo/build && make test";
+  docker run -e TRAVIS=$TRAVIS -e TRAVIS_JOB_ID=$TRAVIS_JOB_ID -it -v $(pwd):/root/repo nnvmc/base /bin/bash -c "pip install cpp-coveralls && cd /root/repo/build && coveralls --verbose -b ./ -r ../ -i include -i src -x .cpp -x .hpp --gcov-options '\-lp'";
   else
-  make check || exit 1;
-  if [[ "$USE_GCOV" == "TRUE" ]]; then coveralls -b lib -e test -e benchmark -e include -e lib -e examples -e script -i src --gcov-options '\-lp' ; fi;
+  docker run -it -v $(pwd):/root/repo nnvmc/base /bin/bash -c "cd /root/repo/test && ./run.sh";
+  fi;
+  else
+  if [[ "$USE_OPENMP" == "TRUE" ]]; then
+  cd build && make test && cd ..;
+  elif [[ "$USE_GCOV" == "TRUE" ]]; then
+  cd build && make test;
+  sudo pip install cpp-coveralls && coveralls --verbose -b ./ -r ../ -i include -i src -x .cpp -x .hpp --gcov-options '\-lp' && cd .. ;
+  else
+  cd test && ./run.sh && cd .. ;
+  fi;
   fi;
-- cat test/test-suite.log test/exe.log test/ut*/exe.log
 
 notifications:
   email:

CMakeLists.txt

@@ -0,0 +1,41 @@
+cmake_minimum_required (VERSION 3.5)
+include(FindPackageHandleStandardArgs)
+
+project (ffnn LANGUAGES CXX VERSION 0.0.1)
+
+set(CMAKE_CXX_STANDARD 11)
+set(CMAKE_CXX_STANDARD_REQUIRED ON)
+set(CMAKE_POSITION_INDEPENDENT_CODE ON)
+set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${USER_CXX_FLAGS}")
+
+if (USE_COVERAGE)
+  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fprofile-arcs -ftest-coverage")
+endif()
+
+# find packages
+message(STATUS "Configured GSL_ROOT_DIR: ${GSL_ROOT_DIR}")
+
+if (USE_OPENMP)
+  find_package(OpenMP)
+  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OpenMP_CXX_FLAGS} -DOPENMP")
+  message(STATUS "OPENMP_LIBRARY_PATHS: ${OpenMP_CXX_LIBRARY}")
+  message(STATUS "OPENMP_LIBRARIES: ${OpenMP_CXX_LIBRARIES}")
+endif()
+
+find_package(GSL)
+message(STATUS "GSL_INCLUDE_DIRS: ${GSL_INCLUDE_DIRS}")
+message(STATUS "GSL_LIBRARIES: ${GSL_LIBRARIES}")
+
+message(STATUS "Configured CMAKE_CXX_COMPILER: ${CMAKE_CXX_COMPILER}")
+message(STATUS "Configured CMAKE_CXX_FLAGS: ${CMAKE_CXX_FLAGS}")
+
+# set header / library paths
+include_directories(include/ "${GSL_INCLUDE_DIRS}") # headers
+
+enable_testing()
+
+# continue with subdirectories
+add_subdirectory(src) 
+add_subdirectory(test)
+add_subdirectory(benchmark)
+add_subdirectory(examples)