First working build based on autotools

.gitignore

@@ -58,15 +58,68 @@ xcuserdata
 DerivedData
 *.xcuserstate
 
+# -- Automake files (http://www.gnu.org/software/automake)
+
+Makefile
+Makefile.in
+.dirstamp
+/ar-lib
+/mdate-sh
+/py-compile
+/test-driver
+/ylwrap
+
+# --- Autoconf files (http://www.gnu.org/software/autoconf)
+
+config.h
+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
+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*
 config.sh
-**/exe
+exe
 vgcore* 
 *.o
 *.dSYM
 *.swp
 *.swo
+*.gcno
+*.lo
 
 test/*.txt
 test/ut*/run_single_unittest.sh

AUTHORS

@@ -0,0 +1,10 @@
+This neural network library was originally created in 2017-2018 by Francesco Calcavecchia,
+while working in a postdoctoral position for the Dynamic of Condensed Matter group,
+led by Prof. Dr. Thomas D. Kühne at Paderborn University (Germany).
+In early 2018, Jan Kessler (from the same research group) began contributing and became
+the main developer and administrator in mid 2018.
+
+Here we maintain a list of people who significantly contributed to the project, by any means:
+
+    Jan Kessler (Ithanil)
+    Francesco Calcavecchia (francesco086)

Makefile.am

@@ -0,0 +1,5 @@
+AUTOMAKE_OPTIONS = foreign
+ACLOCAL_AMFLAGS = -I m4
+
+SUBDIRS = bin
+#SUBDIRS = bin test benchmark examples doc

benchmark/Makefile.am

@@ -0,0 +1 @@
+SUBDIRS = common bench_actfs_derivs bench_actfs_ffprop

benchmark/bench_actfs_derivs/Makefile.am

@@ -0,0 +1,2 @@
+bin_PROGRAMS = exe    
+exe_SOURCES = ../common/Timer.cpp ../common/FFNNBenchmarks.cpp main.cpp

benchmark/bench_actfs_ffprop/Makefile.am

@@ -0,0 +1,2 @@
+bin_PROGRAMS = exe    
+exe_SOURCES = ../common/Timer.cpp ../common/FFNNBenchmarks.cpp main.cpp

configure.ac

@@ -0,0 +1,91 @@
+#                                               -*- Autoconf -*-
+# Process this file with autoconf to produce a configure script.
+
+AC_PREREQ([2.69])
+AC_INIT([DCM-FFNN], [0.3], [[email protected]])
+: ${CXXFLAGS=""}
+#AC_CONFIG_SRCDIR([include/InputUnit.hpp])
+AC_CONFIG_HEADERS([config.h])
+AC_CONFIG_MACRO_DIRS([m4])
+LT_INIT
+
+# Checks for programs.
+AC_PROG_CXX
+AC_PROG_CPP
+AC_PROG_LN_S
+
+# Checks for libraries.
+
+# Checks for header files.
+
+AC_CHECK_HEADERS([gsl/gsl_vector.h gsl/gsl_matrix.h gsl/gsl_blas.h gsl/gsl_multifit_nlinear.h])
+
+# Checks for typedefs, structures, and compiler characteristics.
+AC_CHECK_HEADER_STDBOOL
+AC_C_INLINE
+AC_TYPE_SIZE_T
+
+# Checks for library functions.
+AC_CHECK_FUNCS([pow sqrt])
+
+# Add debug support
+AC_ARG_ENABLE(debug,
+  AS_HELP_STRING(
+    [--enable-debug],
+    [enable debugging, default: no]),
+    [case "${enableval}" in
+      yes) debug=true ;;
+      no)  debug=false ;;
+      *)   AC_MSG_ERROR([bad value ${enableval} for --enable-debug]) ;;
+    esac],
+    [debug=false])
+AM_CONDITIONAL(DEBUG, test x"$debug" = x"true")
+AM_COND_IF(DEBUG,
+    AC_DEFINE(DEBUG, 1, [Define to 0 if this is a release build]),
+    AC_DEFINE(DEBUG, 0, [Define to 1 or higher if this is a debug build]))
+
+
+# Add debug support
+AC_ARG_ENABLE(coverage,
+  AS_HELP_STRING(
+    [--enable-coverage],
+    [enable coverage, default: no]),
+    [case "${enableval}" in
+      yes) coverage=true ;;
+      no)  coverage=false ;;
+      *)   AC_MSG_ERROR([bad value ${enableval} for --enable-coverage]) ;;
+    esac],
+    [debug=false])
+AM_CONDITIONAL(COVERAGE, test x"$coverage" = x"true")
+AM_COND_IF(COVERAGE,
+    AC_DEFINE(COVERAGE, 1, [Define to 0 if you don't need code coverage statistics.]),
+    AC_DEFINE(COVERAGE, 0, [Define to 1 or higher if you want to generate code coverage statistics.]))
+
+AC_CONFIG_FILES([Makefile
+                 benchmark/Makefile
+                 benchmark/bench_actfs_derivs/Makefile
+                 benchmark/bench_actfs_ffprop/Makefile
+                 bin/Makefile
+                 doc/Makefile
+                 examples/Makefile
+                 examples/ex1/Makefile
+                 examples/ex2/Makefile
+                 examples/ex3/Makefile
+                 examples/ex4/Makefile
+                 examples/ex5/Makefile
+                 examples/ex6/Makefile
+                 examples/ex7/Makefile
+                 examples/ex8/Makefile
+                 examples/ex9/Makefile
+                 test/Makefile
+                 test/ut1/Makefile
+                 test/ut2/Makefile
+                 test/ut3/Makefile
+                 test/ut4/Makefile
+                 test/ut5/Makefile
+                 test/ut6/Makefile
+                 test/ut7/Makefile
+                 test/ut8/Makefile
+                 test/ut9/Makefile])
+AM_INIT_AUTOMAKE([subdir-objects])
+AC_OUTPUT

doc/Makefile.am

@@ -0,0 +1 @@
+SUBDIRS = doxygen

examples/Makefile.am

@@ -0,0 +1 @@
+SUBDIRS = ex1 ex2 ex3 ex4 ex5 ex6 ex7 ex8 ex9

examples/ex1/Makefile.am

@@ -0,0 +1,2 @@
+bin_PROGRAMS = exe    
+exe_SOURCES = main.cpp

examples/ex2/Makefile.am

@@ -0,0 +1,2 @@
+bin_PROGRAMS = exe    
+exe_SOURCES = main.cpp

examples/ex3/Makefile.am

@@ -0,0 +1,2 @@
+bin_PROGRAMS = exe    
+exe_SOURCES = main.cpp

examples/ex4/Makefile.am

@@ -0,0 +1,2 @@
+bin_PROGRAMS = exe    
+exe_SOURCES = main.cpp

examples/ex5/Makefile.am

@@ -0,0 +1,2 @@
+bin_PROGRAMS = exe    
+exe_SOURCES = main.cpp

examples/ex6/Makefile.am

@@ -0,0 +1,2 @@
+bin_PROGRAMS = exe    
+exe_SOURCES = main.cpp

examples/ex7/Makefile.am

@@ -0,0 +1,2 @@
+bin_PROGRAMS = exe    
+exe_SOURCES = main.cpp

examples/ex8/Makefile.am

@@ -0,0 +1,2 @@
+bin_PROGRAMS = exe    
+exe_SOURCES = main.cpp

examples/ex9/Makefile.am

@@ -0,0 +1,2 @@
+bin_PROGRAMS = exe    
+exe_SOURCES = main.cpp

script/update_file_lists.sh

@@ -0,0 +1,15 @@
+#!/bin/bash
+
+cd include
+rm *.hpp # remove old links
+ln -sf ../src/*/*.hpp ./ # make new links to all header files in src
+cd ..
+
+cd bin
+echo "libffnn_la_HEADERS = \\" > headers.am
+find ../src/ -name *.hpp | tr '\n' ' ' >> headers.am
+
+echo "libffnn_la_SOURCES = \\" > sources.am
+find ../src/ -name *.cpp | tr '\n' ' ' >> sources.am
+
+cd ..

test/Makefile.am

@@ -0,0 +1,4 @@
+bin_PROGRAMS = exe
+exe_SOURCES = main.cpp
+
+SUBDIRS = ut1 ut2 ut3 ut4 ut5 ut6 ut7 ut8 ut9

test/ut1/Makefile.am

@@ -0,0 +1,2 @@
+bin_PROGRAMS = exe    
+exe_SOURCES = main.cpp

test/ut2/Makefile.am

@@ -0,0 +1,2 @@
+bin_PROGRAMS = exe    
+exe_SOURCES = main.cpp

test/ut3/Makefile.am

@@ -0,0 +1,2 @@
+bin_PROGRAMS = exe    
+exe_SOURCES = main.cpp

test/ut4/Makefile.am

@@ -0,0 +1,2 @@
+bin_PROGRAMS = exe    
+exe_SOURCES = main.cpp

test/ut5/Makefile.am

@@ -0,0 +1,2 @@
+bin_PROGRAMS = exe    
+exe_SOURCES = main.cpp

test/ut6/Makefile.am

@@ -0,0 +1,2 @@
+bin_PROGRAMS = exe    
+exe_SOURCES = main.cpp

test/ut7/Makefile.am

@@ -0,0 +1,2 @@
+bin_PROGRAMS = exe    
+exe_SOURCES = main.cpp

test/ut8/Makefile.am

@@ -0,0 +1,2 @@
+bin_PROGRAMS = exe    
+exe_SOURCES = main.cpp

test/ut9/Makefile.am

@@ -0,0 +1,2 @@
+bin_PROGRAMS = exe    
+exe_SOURCES = main.cpp