Automake changes, can compile files in src and doc

Makefile.am

@@ -0,0 +1,5 @@
+SUBDIRS = src doc
+include aminclude.am
+EXTRA_DIST = Doxyfile trees/*tax* old_Makefile bootstrap example/eg* doc/manual.pdf
+#DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
+distdir = $(PACKAGE)-$(VERSION)

README

@@ -0,0 +1 @@
+README.md

bootstrap

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+#!/bin/bash
+
+
+aclocal
+autoconf
+automake -a
+./configure
+

configure.ac

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+#AC_INIT([hybrid_sim],esyscmd([sh -c "date \"+%Y%m%d\" | tr -d '\n'"]),[joe.zhu@pg.canterbury.ac.nz])
+AC_INIT([hybrid_sim],[beta],[joe.zhu@pg.canterbury.ac.nz])
+dnl AC_CONFIG_SRCDIR([simu.c])
+#AC_CONFIG_SRCDIR([main.cpp])
+#AC_CONFIG_HEADER([config.h])
+
+AM_INIT_AUTOMAKE
+AC_PROG_INSTALL
+AC_PREREQ
+AC_CANONICAL_HOST
+
+# Checks for programs.
+#AC_PROG_CC
+AC_PROG_CXX
+AC_PROG_RANLIB
+
+# Checks for libraries.
+#AC_CHECK_LIB([m], [log])
+
+# Checks for header files.
+AC_HEADER_STDC
+#AC_CHECK_HEADERS([float.h stdlib.h string.h unistd.h])
+AC_LANG(C++) 
+AC_CHECK_HEADERS([iostream string sstream fstream vector iomanip valarray math.h stdio.h ctime])
+
+# Checks for typedefs, structures, and compiler characteristics.
+AC_C_CONST
+AC_C_INLINE
+AC_TYPE_SIZE_T
+
+# Checks for library functions.
+AC_FUNC_MALLOC
+AC_FUNC_REALLOC
+
+AC_CHECK_FUNCS([floor])
+AC_CHECK_FUNCS([pow])
+AC_HEADER_STDBOOL
+
+DX_INIT_DOXYGEN(hybrid_sim, Doxyfile, html/)
+DX_HTML_FEATURE(ON)
+DX_CHM_FEATURE(OFF)
+DX_CHI_FEATURE(OFF)
+DX_MAN_FEATURE(OFF)
+DX_RTF_FEATURE(OFF)
+DX_XML_FEATURE(OFF)
+DX_PDF_FEATURE(OFF)
+DX_PS_FEATURE(OFF)
+
+
+# Check for presence of pdfLaTeX
+AC_CHECK_PROG(PDFLATEX, pdflatex, pdflatex)
+AC_CHECK_PROG(BIBTEX, bibtex,bibtex)
+if test -z "$PDFLATEX"; then
+  AC_MSG_WARN([Unable to create PDF version of the user manual.])
+fi
+
+AM_CONDITIONAL([HAVE_PDFLATEX], test -n "$PDFLATEX")
+
+AC_CONFIG_FILES([Makefile src/Makefile doc/Makefile])
+AC_OUTPUT
+

doc/Makefile.am

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+#docfiles = manual.tex 
+if HAVE_PDFLATEX
+doc_DATA = manual.pdf
+MANNAME = manual
+MANTEXSRC = $(MANNAME).tex
+MANAUX = $(MANNAME).aux
+MANPDF = $(MANNAME).pdf
+DOCDIR=$(abs_top_builddir)/doc
+CLEANFILES = $(MANPDF) $(MANNAME).log $(MANNAME).idx $(MANNAME).out \
+ $(MANNAME).toc $(MANAUX)
+
+$(MANPDF): $(srcdir)/$(MANTEXSRC)
+	$(PDFLATEX) $(MANTEXSRC)
+	$(BIBTEX) $(MANAUX)
+	$(PDFLATEX) $(MANTEXSRC)
+	$(PDFLATEX) $(MANTEXSRC)
+endif
+#dist_doc_DATA = $(docfiles)
+
+EXTRA_DIST = manual.pdf 
+
+#SUBDIRS =

doc/manual.tex

@@ -0,0 +1,6 @@
+\documentclass{article}
+\title{scrm manual}
+\maketitle
+\begin{document}
+
+\end{document}

src/Makefile.am

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+bin_PROGRAMS = scrm
+PROG = SCRM
+scrm_SOURCES = forest.cc forest.h forest-debug.cc \
+model.cc model.h \
+node.cc node.h \
+node_container.cc node_container.h \
+time_interval.cc time_interval.h \ 
+tree_point.cc tree_point.h
+scrm.cc 
+
+
+include_HEADERS = forest.h model.h node.h node_container.h time_interval.h tree_point.h
+
+