Switch to GNU autotools

.gitignore

-boxmox/boxmox/README.aux
-boxmox/boxmox/README.log
-boxmox/boxmox/README.toc
-boxmox/boxmox/README.pdf
-boxmox/boxmox/compiled_mechs
-boxmox/bin/kpp
-boxmox/src/*.o
-boxmox/src/lex.yy.c
-boxmox/src/y.tab.c
-boxmox/src/y.tab.h
-**.DS_Store
\ No newline at end of file
+bin/
+share
+build
+
+doc/boxmox_README.pdf
+
+**.DS_Store
+
+# http://www.gnu.org/software/automake
+
+Makefile.in
+/ar-lib
+/mdate-sh
+/py-compile
+/test-driver
+/ylwrap
+.deps/
+.dirstamp
+
+# http://www.gnu.org/software/autoconf
+
+autom4te.cache
+/autoscan.log
+/autoscan-*.log
+/aclocal.m4
+/compile
+/config.cache
+/config.guess
+/config.h.in
+/config.log
+/config.status
+/config.sub
+/configure
+/configure.scan
+/depcomp
+/install-sh
+/missing
+/stamp-h1
+
+# https://www.gnu.org/software/libtool/
+
+/ltmain.sh
+
+# http://www.gnu.org/software/texinfo
+
+/texinfo.tex
+
+# http://www.gnu.org/software/m4/
+
+m4/libtool.m4
+m4/ltoptions.m4
+m4/ltsugar.m4
+m4/ltversion.m4
+m4/lt~obsolete.m4
+
+# Generated Makefile
+# (meta build system like autotools,
+# can automatically generate from config.status script
+# (which is called by configure script))
+Makefile
\ No newline at end of file

Makefile.am

@@ -29,17 +29,10 @@
 #
 #######################################################################################
 
-SUBDIRS = src
-dist_doc_DATA = README.md
-
-boxmox_clean:
-	@rm -f boxmox/README.pdf boxmox/README.aux boxmox/README.log boxmox/README.toc
-
-boxmox_doc:
-	@echo "Tex'ing BOXMOX readme (boxmox/README.pdf, if pdflatex is available)"
-	-cd boxmox; pdflatex README.tex
-	-cd boxmox; pdflatex README.tex
-	
-boxmox: boxmox_doc
-	@echo "Setting the execute bit for user commands"
-	@chmod +x boxmox/bin/*
+SUBDIRS = src doc
+dist_doc_DATA = README.md doc/kpp_UserManual.pdf doc/boxmox_README.pdf
+dist_bin_SCRIPTS = scripts/list_BOXMOX_mechanisms \
+				   scripts/new_BOXMOX_experiment \
+				   scripts/new_BOXMOX_experiment_from_example \
+				   scripts/prepare_BOXMOX_mechanism \
+				   scripts/validate_BOXMOX_installation

configure.ac

 dnl run `autoreconf -i` to generate a configure script. 
 dnl Then run ./configure to generate a Makefile.
 dnl Finally run make to generate the project.
+m4_include([latex_autoconf_macros/ac_prog_pdflatex.m4])
 
 AC_INIT([boxmox], [1.8], [christoph.knote@med.uni-augsburg.de])
 dnl we use the build type foreign here instead of gnu because I do not have a NEWS file and similar, yet.
@@ -8,8 +9,10 @@ AM_INIT_AUTOMAKE([-Wall foreign])
 AC_PROG_CC
 AC_PROG_LEX(noyywrap)
 AC_PROG_YACC
+AC_PROG_PDFLATEX
 AC_CONFIG_FILES([
     Makefile
     src/Makefile
+    doc/Makefile
 ])
 AC_OUTPUT

doc/Makefile.am

+doc_DATA = boxmox_README.pdf
+
+boxmox_README.pdf : boxmox_README.tex
+	@pdflatex@ $<
+	@pdflatex@ $<
+	rm -f *.log *.out *.toc *.aux
+
+dist_doc_DATA = boxmox_README.tex boxmox_README.pdf
\ No newline at end of file

doc/boxmox_README.tex

@@ -343,7 +343,7 @@ values.
 A typical \emph{BOXMOX.nml} file looks like this:
 
 \begin{alltt}
-\input{examples/BOXMOX.nml}
+\input{../case_studies/BOXMOX.nml}
 \end{alltt}
 
 

latex_autoconf_macros/LICENSE

+		    GNU GENERAL PUBLIC LICENSE
+		       Version 2, June 1991
+
+ Copyright (C) 1989, 1991 Free Software Foundation, Inc.
+                       59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
+ Everyone is permitted to copy and distribute verbatim copies
+ of this license document, but changing it is not allowed.
+
+			    Preamble
+
+  The licenses for most software are designed to take away your
+freedom to share and change it.  By contrast, the GNU General Public
+License is intended to guarantee your freedom to share and change free
+software--to make sure the software is free for all its users.  This
+General Public License applies to most of the Free Software
+Foundation's software and to any other program whose authors commit to
+using it.  (Some other Free Software Foundation software is covered by
+the GNU Library General Public License instead.)  You can apply it to
+your programs, too.
+
+  When we speak of free software, we are referring to freedom, not
+price.  Our General Public Licenses are designed to make sure that you
+have the freedom to distribute copies of free software (and charge for
+this service if you wish), that you receive source code or can get it
+if you want it, that you can change the software or use pieces of it
+in new free programs; and that you know you can do these things.
+
+  To protect your rights, we need to make restrictions that forbid
+anyone to deny you these rights or to ask you to surrender the rights.
+These restrictions translate to certain responsibilities for you if you
+distribute copies of the software, or if you modify it.
+
+  For example, if you distribute copies of such a program, whether
+gratis or for a fee, you must give the recipients all the rights that
+you have.  You must make sure that they, too, receive or can get the
+source code.  And you must show them these terms so they know their
+rights.
+
+  We protect your rights with two steps: (1) copyright the software, and
+(2) offer you this license which gives you legal permission to copy,
+distribute and/or modify the software.
+
+  Also, for each author's protection and ours, we want to make certain
+that everyone understands that there is no warranty for this free
+software.  If the software is modified by someone else and passed on, we
+want its recipients to know that what they have is not the original, so
+that any problems introduced by others will not reflect on the original
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+
+  Finally, any free program is threatened constantly by software
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+
+  The precise terms and conditions for copying, distribution and
+modification follow.
+
+		    GNU GENERAL PUBLIC LICENSE
+   TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION
+
+  0. This License applies to any program or other work which contains
+a notice placed by the copyright holder saying it may be distributed
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+Activities other than copying, distribution and modification are not
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+  1. You may copy and distribute verbatim copies of the Program's
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+You may charge a fee for the physical act of transferring a copy, and
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+  2. You may modify your copy or copies of the Program or any portion
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+    c) If the modified program normally reads commands interactively
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+exercise the right to control the distribution of derivative or
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+In addition, mere aggregation of another work not based on the Program
+with the Program (or with a work based on the Program) on a volume of
+a storage or distribution medium does not bring the other work under
+the scope of this License.
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+  3. You may copy and distribute the Program (or a work based on it,
+under Section 2) in object code or executable form under the terms of
+Sections 1 and 2 above provided that you also do one of the following:
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+    an offer, in accord with Subsection b above.)
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+The source code for a work means the preferred form of the work for
+making modifications to it.  For an executable work, complete source
+code means all the source code for all modules it contains, plus any
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+operating system on which the executable runs, unless that component
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+If distribution of executable or object code is made by offering
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+
+  4. You may not copy, modify, sublicense, or distribute the Program
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+otherwise to copy, modify, sublicense or distribute the Program is
+void, and will automatically terminate your rights under this License.
+However, parties who have received copies, or rights, from you under
+this License will not have their licenses terminated so long as such
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+
+  5. You are not required to accept this License, since you have not
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+distribute the Program or its derivative works.  These actions are
+prohibited by law if you do not accept this License.  Therefore, by
+modifying or distributing the Program (or any work based on the
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+  6. Each time you redistribute the Program (or any work based on the
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+this License.
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+  7. If, as a consequence of a court judgment or allegation of patent
+infringement or for any other reason (not limited to patent issues),
+conditions are imposed on you (whether by court order, agreement or
+otherwise) that contradict the conditions of this License, they do not
+excuse you from the conditions of this License.  If you cannot
+distribute so as to satisfy simultaneously your obligations under this
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+may not distribute the Program at all.  For example, if a patent
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+refrain entirely from distribution of the Program.
+
+If any portion of this section is held invalid or unenforceable under
+any particular circumstance, the balance of the section is intended to
+apply and the section as a whole is intended to apply in other
+circumstances.
+
+It is not the purpose of this section to induce you to infringe any
+patents or other property right claims or to contest validity of any
+such claims; this section has the sole purpose of protecting the
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+This section is intended to make thoroughly clear what is believed to
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+
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+later version", you have the option of following the terms and conditions
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+Software Foundation.  If the Program does not specify a version number of
+this License, you may choose any version ever published by the Free Software
+Foundation.
+
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+of promoting the sharing and reuse of software generally.
+
+			    NO WARRANTY
+
+  11. BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY
+FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW.  EXCEPT WHEN
+OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES
+PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED
+OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
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+PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING,
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+
+  12. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
+WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR
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+INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING
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+TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY
+YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER
+PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE
+POSSIBILITY OF SUCH DAMAGES.
+
+		     END OF TERMS AND CONDITIONS
+
+	    How to Apply These Terms to Your New Programs
+
+  If you develop a new program, and you want it to be of the greatest
+possible use to the public, the best way to achieve this is to make it
+free software which everyone can redistribute and change under these terms.
+
+  To do so, attach the following notices to the program.  It is safest
+to attach them to the start of each source file to most effectively
+convey the exclusion of warranty; and each file should have at least
+the "copyright" line and a pointer to where the full notice is found.
+
+    <one line to give the program's name and a brief idea of what it does.>
+    Copyright (C) <year>  <name of author>
+
+    This program is free software; you can redistribute it and/or modify
+    it under the terms of the GNU General Public License as published by
+    the Free Software Foundation; either version 2 of the License, or
+    (at your option) any later version.
+
+    This program is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+
+    You should have received a copy of the GNU General Public License
+    along with this program; if not, write to the Free Software
+    Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
+
+
+Also add information on how to contact you by electronic and paper mail.
+
+If the program is interactive, make it output a short notice like this
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+
+    Gnomovision version 69, Copyright (C) year name of author
+    Gnomovision comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
+    This is free software, and you are welcome to redistribute it
+    under certain conditions; type `show c' for details.
+
+The hypothetical commands `show w' and `show c' should show the appropriate
+parts of the General Public License.  Of course, the commands you use may
+be called something other than `show w' and `show c'; they could even be
+mouse-clicks or menu items--whatever suits your program.
+
+You should also get your employer (if you work as a programmer) or your
+school, if any, to sign a "copyright disclaimer" for the program, if
+necessary.  Here is a sample; alter the names:
+
+  Yoyodyne, Inc., hereby disclaims all copyright interest in the program
+  `Gnomovision' (which makes passes at compilers) written by James Hacker.
+
+  <signature of Ty Coon>, 1 April 1989
+  Ty Coon, President of Vice
+
+This General Public License does not permit incorporating your program into
+proprietary programs.  If your program is a subroutine library, you may
+consider it more useful to permit linking proprietary applications with the
+library.  If this is what you want to do, use the GNU Library General
+Public License instead of this License.

latex_autoconf_macros/README

+These macros for Autoconf test if latex and/or some others applications are installed
+
+To use this macro, just do the following :
+
+    add m4_include([latex.m4]) to the configure.in file
+
+    use autoconf -I<path to folder of latex.m4>
+
+or 
+    aclocal -I <path to folder that contains these macro>
+    autoconf
+    
+Then, you can use the following macro :
+
+AC_LATEX_CLASS_ARTICLE
+-> set $article to yes if class article exists
+
+AC_LATEX_CLASS_BOOK
+-> set $book to yes if class book exists
+
+AC_LATEX_CLASS_REPORT
+-> set $report to yes if class report exists
+
+AC_LATEX_CLASS(<class>,<var>)
+or
+AC_LATEX_CLASS(<class>,<var>,<action if yes>)
+or
+AC_LATEX_CLASS(<class>,<var>,<action if yes>,<action if no>)
+-> set $<var> to yes if <class> exists
+
+AC_LATEX_CLASSES ([<class1, class2, ...>],<var>)
+-> set $<var> to the first class that exists
+
+AC_LATEX_PACKAGE_AMSMATH
+-> set $amsmath to the right way to include amsmath
+
+AC_LATEX_PACKAGE_FONTENC
+-> set $fontenc to OT1 or T1
+
+AC_LATEX_PACKAGE_INPUT(<package>,<class>,<var>)
+-> set $<var> to yes if <package> can be \input within <class>
+
+AC_LATEX_PACKAGE_OPT(<package>,<class>,<var>,<opt>)
+-> set $<var> to yes if <package> with <opt> works within <class>
+
+AC_LATEX_PACKAGE(<package>,<class>,<var>)
+or
+AC_LATEX_PACKAGE(<package>,<class>,<var>,<action if yes>)
+or
+AC_LATEX_PACKAGE(<package>,<class>,<var>,<action if yes>,<action if no>)
+-> set $<var> to yes if <package> can be use within <class>
+
+AC_LATEX_PACKAGES([<package1>,<package2>,...],<class>,<var>)
+-> set $<var> to the first package that works with <class>
+
+AC_PROG_DVIPDF
+-> test if dvipdf exists and set $dvipdf
+
+AC_PROG_DVIPS
+-> test if dvips exists and set $dvips
+
+AC_PROG_FIG2DEV
+-> test if fig2dev exists and set $fig2dev
+
+AC_PROG_GNUPLOT
+-> test if gnuplot exists and set $gnuplot
+
+AC_PROG_GUNZIP
+-> test if gunzip exists and set $gunzip
+
+AC_PROG_GZIP
+-> test if gzip exists and set $gzip
+
+AC_PROG_LATEX
+-> test if latex exists and set $latex
+
+AC_PROG_MF
+-> test if mf exists and set $mf
+
+AC_PROG_PDFLATEX
+-> test if pdflatex exists and set $pdflatex
+
+AC_PROG_PS2PDF
+-> test if ps2pdf exists and set $ps2pdf
+
+AC_PROG_BIBTEX
+-> test if bibtex exists and set $bibtex
+
+AC_PROG_LATEX2HTML
+-> test if latex2html exists and set $latex2html
+
+AC_PROG_LATEX2MAN
+-> test if latex2man exists and set $latex2man
+
+AC_PROG_MAKEINDEX
+-> test if makeindex exists and set $makeindex
+
+AC_PROG_JPEG2PS
+-> test if jpeg2ps exists and set $jpeg2ps
+
+AC_LATEX_DVIPS_T (<paper>,<var>,[on|off])
+-> test if option -t <paper> in dvips works and set var to yes or no. if last parameter is on, use -t landscape and -t <paper>
+
+AC_LATEX_DVIPS_T_A4 
+-> test if option -t a4 in dvips works and set dvips_t_a4 to yes or no
+
+AC_LATEX_DVIPS_T_LETTER
+-> test if option -t letter in dvips works and set dvips_t_letter to yes or no
+
+AC_LATEX_DVIPS_T_A4_LANDSCAPE
+-> test if option -t a4 -t landscape in dvips works and set dvips_t_a4_landscape to yes or no
+
+AC_LATEX_DVIPS_T_LETTER_LANDSCAPE
+-> test if option -t letter -t landscape in dvips works and set dvips_t_letter_landscape to yes or no
+
+AC_LATEX_DVIPS_O_STDOUT
+-> test if option -t- in dvips works and set dvips_o_stdout to yes or no
+
+AC_PROG_MKTEXPK
+-> test if mktexpk exists and set $mktexpk
+
+AC_PROG_TEXHASH
+-> test if texhash exists and set $texhash
+
+AC_PROG_KPSEWHICH
+-> test if kpsewhich exists and set $kpsewhich
+
+AC_TEXMF_PATH
+-> test for a local texmf path where to install class and package
+
+AC_PROG_PNGTOPNM
+-> test if pngtopnm exists and set $pngtopnm
+
+AC_PROG_PNMTOPS
+-> test if pnmtops exists and set $pnmtops
+
+AC_PROG_JPEGTOPNM
+-> test if jpegtopnm exists and set $jpegtopnm
+
+AC_PROG_LATEX2PNG
+-> test if latex2png exists and set $latex2png
+
+AC_PROG_LATEX2RTF
+-> test if latex2rtf exists and set $latex2rtf
+
+AC_PROG_PSBOOK
+-> test if psbook exists and set $psbook
+
+AC_PROG_PSNUP
+-> test if psnup exists and set $psnup
+
+AC_PROG_PSSELECT
+-> test if psselect exists and set $psselect
+
+AC_PROG_PSRESIZE
+-> test if psresize exists and set $psresize
+
+AC_PROG_DVIBOOK
+-> test if dvibook exists and set $dvibook
+
+History :
+2004-08-14 : Version 1.3 of these macros
+2004-07-24 : Changing .dvips folder to be destroy at end
+2004-07-14 : Changing AC_LATEX_CLASS and AC_LATEX_PACKAGE to add feature
+             to support if and else operation
+             Adding AC_PROG_PNGTOPNM
+             Adding AC_PROG_PNMTOPS
+             Adding AC_PROG_JPEGTOPNM
+             Adding AC_PROG_LATEX2PNG
+             Adding AC_PROG_LATEX2RTF
+             Adding AC_PROG_PSBOOK
+             Adding AC_PROG_PSNUP
+             Adding AC_PROG_PSSELECT
+             Adding AC_PROG_PSRESIZE
+             Adding AC_PROG_DVIBOOK
+2004-06-18 : Adding AC_PROG_TEXHASH
+             Adding AC_PROG_KPSEWHICH
+             Adding AC_TEXMF_PATH
+2004-04-21 : Adding AC_LATEX_DVIPS_T_LETTER
+             Adding AC_LATEX_DVIPS_T_A4_LANDSCAPE
+             Adding AC_LATEX_DVIPS_T_LETTER_LANDSCAPE
+             Adding AC_LATEX_DVIPS_O_STDOUT
+             Adding AC_PROG_MKTEXPK
+             Bugs correction and adding some comments
+2004-04-20 : Adding AC_PROG_BIBTEX
+             Adding AC_PROG_LATEX2HTML
+             Adding AC_PROG_LATEX2MAN
+             Adding AC_PROG_MAKEINDEX
+             Adding AC_PROG_JPEG2PS
+             Adding AC_LATEX_DVIPS_T
+             Adding AC_LATEX_DVIPS_T_A4
+2004-04-19 : Version 1
\ No newline at end of file

latex_autoconf_macros/_ac_latex_test.m4

+#
+#   Copyright (C) 2004  Boretti Mathieu
+#
+#   This program is free software; you can redistribute it and/or modify
+#   it under the terms of the GNU General Public License as published by
+#   the Free Software Foundation; either version 2 of the License, or
+#   (at your option) any later version.
+#
+#   This program is distributed in the hope that it will be useful,
+#   but WITHOUT ANY WARRANTY; without even the implied warranty of
+#   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+#   GNU General Public License for more details.
+#
+#   You should have received a copy of the GNU General Public License
+#   along with this program; if not, write to the Free Software
+#   Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
+#
+#
+# Internal macro to test a latex file
+#
+
+AC_DEFUN([_AC_LATEX_TEST],[
+AC_REQUIRE([AC_PROG_LATEX])
+rm -rf .tmps_latex 
+mkdir .tmps_latex 
+cd .tmps_latex 
+ifelse($#,2,[
+$2="no"; export $2;
+cat > testconf.tex << \EOF
+$1
+EOF
+],$#,3,[
+echo "\\documentclass{$3}" > testconf.tex
+cat >> testconf.tex << \EOF
+$1
+EOF
+],$#,4,[
+echo "\\documentclass{$3}" > testconf.tex
+echo "\\usepackage{$4}" > testconf.tex
+cat >> testconf.tex << \EOF
+$1
+])
+cat testconf.tex | $latex 2>&1 1>/dev/null && $2=yes; export $2;
+cd .. 
+rm -rf .tmps_latex 
+])

latex_autoconf_macros/ac_latex_class.m4

+#
+#   Copyright (C) 2004  Boretti Mathieu
+#
+#   This program is free software; you can redistribute it and/or modify
+#   it under the terms of the GNU General Public License as published by
+#   the Free Software Foundation; either version 2 of the License, or
+#   (at your option) any later version.
+#
+#   This program is distributed in the hope that it will be useful,
+#   but WITHOUT ANY WARRANTY; without even the implied warranty of
+#   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+#   GNU General Public License for more details.
+#
+#   You should have received a copy of the GNU General Public License
+#   along with this program; if not, write to the Free Software
+#   Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
+#
+#
+# AC_LATEX_CLASS(<class>,<variable>)
+#
+# Test the presences of class and set $<variable> 
+# to yes or no
+#
+#
+dnl @synopsis AC_LATEX_CLASSE(<class1>,<var>)
+dnl
+dnl Test if class1 exists
+dnl and set $var to the right value
+dnl
+dnl  AC_LATEX_CLASSES([book],book)
+dnl  should set $book="yes"
+dnl
+dnl  AC_LATEX_CLASSES(allo,book)
+dnl  should set $book="no"
+dnl
+dnl @version 1.3
+dnl @author Mathieu Boretti boretti@eig.unige.ch
+dnl
+AC_DEFUN([AC_LATEX_CLASS],[
+AC_CACHE_CHECK([for class $1],[ac_cv_latex_class_]translit($1,[-],[_]),[
+_AC_LATEX_TEST([
+\begin{document}
+\end{document}
+],[ac_cv_latex_class_]translit($1,[-],[_]),$1)
+])
+$2=$[ac_cv_latex_class_]translit($1,[-],[_]) ; export $2;
+AC_SUBST($2)
+ifelse($#,2,[],$#,3,[
+    if test "[$]$2" = "yes" ;
+    then
+        $3
+    fi
+],$#,4,[
+    ifelse($3,[],[
+        if test "[$]$2" = "no" ;
+        then
+            $4
+        fi
+    ],[
+        if test "[$]$2" = "yes" ;
+        then
+            $3
+        else
+            $4
+        fi
+    ])
+])
+
+])
\ No newline at end of file

latex_autoconf_macros/ac_latex_class_article.m4

+#
+#   Copyright (C) 2004  Boretti Mathieu
+#
+#   This program is free software; you can redistribute it and/or modify
+#   it under the terms of the GNU General Public License as published by
+#   the Free Software Foundation; either version 2 of the License, or
+#   (at your option) any later version.
+#
+#   This program is distributed in the hope that it will be useful,
+#   but WITHOUT ANY WARRANTY; without even the implied warranty of
+#   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+#   GNU General Public License for more details.
+#
+#   You should have received a copy of the GNU General Public License
+#   along with this program; if not, write to the Free Software
+#   Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
+#
+#
+# AC_LATEX_CLASS_ARTICLE
+#
+# Test the presences class article and
+# set article to yes if exists, 
+# else Error
+#
+#
+dnl @synopsis AC_LATEX_CLASS_ARTICLE
+dnl
+dnl same as AC_LATEX_CLASS(article,article)
+dnl
+dnl @version 1.3
+dnl @author Mathieu Boretti boretti@eig.unige.ch
+dnl
+AC_DEFUN([AC_LATEX_CLASS_ARTICLE],[
+AC_LATEX_CLASS(article,article,[],[AC_MSG_ERROR([Unable to find the article class])])
+])
\ No newline at end of file

latex_autoconf_macros/ac_latex_class_book.m4

+#
+#   Copyright (C) 2004  Boretti Mathieu
+#
+#   This program is free software; you can redistribute it and/or modify
+#   it under the terms of the GNU General Public License as published by
+#   the Free Software Foundation; either version 2 of the License, or
+#   (at your option) any later version.
+#
+#   This program is distributed in the hope that it will be useful,
+#   but WITHOUT ANY WARRANTY; without even the implied warranty of
+#   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+#   GNU General Public License for more details.
+#
+#   You should have received a copy of the GNU General Public License
+#   along with this program; if not, write to the Free Software
+#   Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
+#
+#
+# AC_LATEX_CLASS_BOOK
+#
+# Test the presences class book and
+# set book to yes if exists, 
+# else Error
+#
+#
+dnl @synopsis AC_LATEX_CLASS_BOOK
+dnl
+dnl same as AC_LATEX_CLASS(book,book)
+dnl
+dnl @version 1.3
+dnl @author Mathieu Boretti boretti@eig.unige.ch
+dnl
+AC_DEFUN([AC_LATEX_CLASS_BOOK],[
+AC_LATEX_CLASS(book,book,[],[AC_MSG_ERROR([Unable to find the book class])])
+])
\ No newline at end of file

latex_autoconf_macros/ac_latex_class_report.m4

+#
+#   Copyright (C) 2004  Boretti Mathieu
+#
+#   This program is free software; you can redistribute it and/or modify
+#   it under the terms of the GNU General Public License as published by
+#   the Free Software Foundation; either version 2 of the License, or
+#   (at your option) any later version.
+#
+#   This program is distributed in the hope that it will be useful,
+#   but WITHOUT ANY WARRANTY; without even the implied warranty of
+#   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+#   GNU General Public License for more details.
+#
+#   You should have received a copy of the GNU General Public License
+#   along with this program; if not, write to the Free Software
+#   Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
+#
+#
+# AC_LATEX_CLASS_REPORT
+#
+# Test the presences class report and
+# set report to yes if exists, 
+# else Error
+#
+#
+dnl @synopsis AC_LATEX_CLASS_REPORT
+dnl
+dnl same as AC_LATEX_CLASS(report,report)
+dnl
+dnl @version 1.3
+dnl @author Mathieu Boretti boretti@eig.unige.ch
+dnl
+AC_DEFUN([AC_LATEX_CLASS_REPORT],[
+AC_LATEX_CLASS(report,report,[],[AC_MSG_ERROR([Unable to find the report class])])
+])
\ No newline at end of file

latex_autoconf_macros/ac_latex_classes.m4

+#
+#   Copyright (C) 2004  Boretti Mathieu
+#
+#   This program is free software; you can redistribute it and/or modify
+#   it under the terms of the GNU General Public License as published by
+#   the Free Software Foundation; either version 2 of the License, or
+#   (at your option) any later version.
+#
+#   This program is distributed in the hope that it will be useful,
+#   but WITHOUT ANY WARRANTY; without even the implied warranty of
+#   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+#   GNU General Public License for more details.
+#
+#   You should have received a copy of the GNU General Public License
+#   along with this program; if not, write to the Free Software
+#   Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
+#
+#
+# AC_LATEX_CLASSES([<class1>,<class2>,...,<classn>],<variable>)
+#
+# Test the presences of class1 or class2 or ...
+# and set $<variable> to the right value or no if not found
+#
+dnl @synopsis AC_LATEX_CLASSES([<class1>,<class2>,...],<var>)
+dnl
+dnl Test if class1 exists and if not class2 and so
+dnl and set $var to the right value
+dnl
+dnl  AC_LATEX_CLASSES([allo,book,bnjour],book)
+dnl  should set $book="book"
+dnl
+dnl @version 1.3
+dnl @author Mathieu Boretti boretti@eig.unige.ch
+dnl
+define(_AC_LATEX_CLASSES_INTERNE,[
+	ifelse($#,1,[],$#,2,[
+		AC_LATEX_CLASS($2,$1)
+	],[
+		AC_LATEX_CLASS($2,$1)
+		if test "$$1" = "yes";
+		then
+			$1=$2 ; export $1 ;
+		else
+			_AC_LATEX_CLASSES_INTERNE($1,m4_shift(m4_shift($@)))
+		fi;
+	])
+])
+
+AC_DEFUN([AC_LATEX_CLASSES],[
+	_AC_LATEX_CLASSES_INTERNE($2,$1)
+	AC_SUBST($2)
+])

latex_autoconf_macros/ac_latex_dvips_o_stdout.m4

+#
+#   Copyright (C) 2004  Boretti Mathieu
+#
+#   This program is free software; you can redistribute it and/or modify
+#   it under the terms of the GNU General Public License as published by
+#   the Free Software Foundation; either version 2 of the License, or
+#   (at your option) any later version.
+#
+#   This program is distributed in the hope that it will be useful,
+#   but WITHOUT ANY WARRANTY; without even the implied warranty of
+#   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+#   GNU General Public License for more details.
+#
+#   You should have received a copy of the GNU General Public License
+#   along with this program; if not, write to the Free Software
+#   Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
+#
+#
+# AC_LATEX_DVIPS_O_STDOUT
+#
+# Test dvips with option -o- and set $dvips_o_stdout to the right value
+#
+#
+dnl @synopsis AC_LATEX_DVIPS_O_STDOUT
+dnl
+dnl test if dvips -o- works. If so, set $dvips_o_stdout to yes else to no
+dnl
+dnl @version 1.3
+dnl @author Mathieu Boretti boretti@eig.unige.ch
+dnl
+AC_DEFUN([AC_LATEX_DVIPS_O_STDOUT],[
+AC_REQUIRE([AC_LATEX_CLASS_BOOK])
+AC_CACHE_CHECK([for option -o- in dvips],ac_cv_dvips_o_stdout,[
+rm -rf .dvips
+mkdir .dvips
+cd .dvips
+cat > test.tex << EOF
+\documentclass{book}
+\begin{document}
+Test
+\end{document}
+EOF
+$latex test.tex 1>/dev/null 2>&1
+ac_cv_dvips_o_stdout="no"; export ac_cv_dvips_o_stdout;
+$dvips -o- test.dvi   1>/dev/null 2>&1 && ac_cv_dvips_o_stdout="yes"; export ac_cv_dvips_o_stdout 
+cd ..
+rm -rf .dvips
+])
+DVIPS_O_STDOUT=$ac_cv_dvips_o_stdout; export DVIPS_O_STDOUT;
+if test $DVIPS_O_STDOUT = "no" ;
+then
+    AC_MSG_ERROR(Unable to find the option -o- in dvips)
+fi
+AC_SUBST(DVIPS_O_STDOUT)
+])

latex_autoconf_macros/ac_latex_dvips_t.m4

+#
+#   Copyright (C) 2004  Boretti Mathieu
+#
+#   This program is free software; you can redistribute it and/or modify
+#   it under the terms of the GNU General Public License as published by
+#   the Free Software Foundation; either version 2 of the License, or
+#   (at your option) any later version.
+#
+#   This program is distributed in the hope that it will be useful,
+#   but WITHOUT ANY WARRANTY; without even the implied warranty of
+#   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+#   GNU General Public License for more details.
+#
+#   You should have received a copy of the GNU General Public License
+#   along with this program; if not, write to the Free Software
+#   Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
+#
+#
+# AC_LATEX_DVIPS_T(<paper>,<var>,[<on|off>])
+#
+# Test dvips with option -o ... -T <paper> et set $<var> to the right value
+#
+#
+dnl @synopsis AC_LATEX_DVIPS_T(<paper>,<var>) or AC_LATEX_DVIPS_T(<paper>,<var>,on|off)
+dnl
+dnl This macro test if dvips -o ... -t <paper> works. When using the on option, test
+dnl if dvips -o ... -t <paper> -t landscape works.
+dnl if it works, set $var to yes, else $var="no"
+dnl
+dnl @version 1.3
+dnl @author Mathieu Boretti boretti@eig.unige.ch
+dnl
+AC_DEFUN([AC_LATEX_DVIPS_T],[
+AC_REQUIRE([AC_LATEX_CLASS_BOOK])
+if test "$3" = "on" ;
+then
+_ac_latex_dvips_local=" -t landscape" ; export _ac_latex_dvips_local ;
+else
+_ac_latex_dvips_local=" " ; export _ac_latex_dvips_local ;
+fi
+AC_CACHE_CHECK([for option -t $1 $_ac_latex_dvips_local with dvips],[ac_cv_dvips_t_]translit($1,[-],[_])[_]translit($3,[-],[_]),[
+rm -rf .dvips
+mkdir .dvips
+cd .dvips
+cat > test.tex << EOF
+\documentclass{book}
+\begin{document}
+Test
+\end{document}
+EOF
+$latex test.tex 1>/dev/null 2>&1
+[ac_cv_dvips_t_]translit($1,[-],[_])[_]translit($3,[-],[_])="yes"; export [ac_cv_dvips_t_]translit($1,[-],[_])[_]translit($3,[-],[_]);
+$dvips -o test.ps test.dvi -t $1 $_ac_latex_dvips_local 2>&1 1>/dev/null | (grep "dvips: no match for papersize" 1>/dev/null 2>&1 && [ac_cv_dvips_t_]translit($1,[-],[_])[_]translit($3,[-],[_])="no"; export [ac_cv_dvips_t_]translit($1,[-],[_])[_]translit($3,[-],[_]))
+cd ..
+rm -rf .dvips
+])
+$2=$[ac_cv_dvips_t_]translit($1,[-],[_])[_]translit($3,[-],[_]); export $2;
+AC_SUBST($2)
+])

latex_autoconf_macros/ac_latex_dvips_t_a4.m4

+#
+#   Copyright (C) 2004  Boretti Mathieu
+#
+#   This program is free software; you can redistribute it and/or modify
+#   it under the terms of the GNU General Public License as published by
+#   the Free Software Foundation; either version 2 of the License, or
+#   (at your option) any later version.
+#
+#   This program is distributed in the hope that it will be useful,
+#   but WITHOUT ANY WARRANTY; without even the implied warranty of
+#   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+#   GNU General Public License for more details.
+#
+#   You should have received a copy of the GNU General Public License
+#   along with this program; if not, write to the Free Software
+#   Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
+#
+#
+# AC_LATEX_DVIPS_T_A4
+#
+# Test dvips -t a4 and set dvips_t_a4
+#
+#
+dnl @synopsis AC_LATEX_DVIPS_T_A4
+dnl
+dnl same as AC_LATEX_DVIPS_T(a4,dvips_t_a4)
+dnl
+dnl @version 1.3
+dnl @author Mathieu Boretti boretti@eig.unige.ch
+dnl
+AC_DEFUN([AC_LATEX_DVIPS_T_A4],[
+AC_LATEX_DVIPS_T(a4,dvips_t_a4)
+if test $dvips_t_a4 = "no";
+then
+    AC_MSG_ERROR([Unable to find the -t a4 option in dvips])
+fi
+])
\ No newline at end of file

latex_autoconf_macros/ac_latex_dvips_t_a4_landscape.m4

+#
+#   Copyright (C) 2004  Boretti Mathieu
+#
+#   This program is free software; you can redistribute it and/or modify
+#   it under the terms of the GNU General Public License as published by
+#   the Free Software Foundation; either version 2 of the License, or
+#   (at your option) any later version.
+#
+#   This program is distributed in the hope that it will be useful,
+#   but WITHOUT ANY WARRANTY; without even the implied warranty of
+#   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+#   GNU General Public License for more details.
+#
+#   You should have received a copy of the GNU General Public License
+#   along with this program; if not, write to the Free Software
+#   Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
+#
+#
+# AC_LATEX_DVIPS_T_A4_LANDSCAPE
+#
+# Test dvips -t a4 -t landscape and set dvips_t_a4_landscape
+#
+#
+dnl @synopsis AC_LATEX_DVIPS_T_A4_LANDSCAPE
+dnl
+dnl same as AC_LATEX_DVIPS_T(a4,dvips_t_a4_landscape,on)
+dnl
+dnl @version 1.3
+dnl @author Mathieu Boretti boretti@eig.unige.ch
+dnl
+AC_DEFUN([AC_LATEX_DVIPS_T_A4_LANDSCAPE],[
+AC_REQUIRE([AC_LATEX_DVIPS_T_A4])
+AC_LATEX_DVIPS_T(a4,dvips_t_a4_landscape,on)
+if test $dvips_t_a4_landscape = "no";
+then
+    AC_MSG_ERROR([Unable to find the -t a4 -t landscape option in dvips])
+fi
+])

latex_autoconf_macros/ac_latex_dvips_t_letter.m4

+#
+#   Copyright (C) 2004  Boretti Mathieu
+#
+#   This program is free software; you can redistribute it and/or modify
+#   it under the terms of the GNU General Public License as published by
+#   the Free Software Foundation; either version 2 of the License, or
+#   (at your option) any later version.
+#
+#   This program is distributed in the hope that it will be useful,
+#   but WITHOUT ANY WARRANTY; without even the implied warranty of
+#   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+#   GNU General Public License for more details.
+#
+#   You should have received a copy of the GNU General Public License
+#   along with this program; if not, write to the Free Software
+#   Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
+#
+#
+# AC_LATEX_DVIPS_T_LETTER
+#
+# Test dvips -t letter and set dvips_t_letter
+#
+#
+dnl @synopsis AC_LATEX_DVIPS_T_LETTER
+dnl
+dnl same as AC_LATEX_DVIPS_T(letter,dvips_t_letter)
+dnl
+dnl @version 1.3
+dnl @author Mathieu Boretti boretti@eig.unige.ch
+dnl
+
+AC_DEFUN([AC_LATEX_DVIPS_T_LETTER],[
+AC_LATEX_DVIPS_T(letter,dvips_t_letter)
+if test $dvips_t_letter = "no";
+then
+    AC_MSG_ERROR([Unable to find the -t letter option in dvips])
+fi
+])
\ No newline at end of file

latex_autoconf_macros/ac_latex_dvips_t_letter_landscape.m4

+#
+#   Copyright (C) 2004  Boretti Mathieu
+#
+#   This program is free software; you can redistribute it and/or modify
+#   it under the terms of the GNU General Public License as published by
+#   the Free Software Foundation; either version 2 of the License, or
+#   (at your option) any later version.
+#
+#   This program is distributed in the hope that it will be useful,
+#   but WITHOUT ANY WARRANTY; without even the implied warranty of
+#   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+#   GNU General Public License for more details.
+#
+#   You should have received a copy of the GNU General Public License
+#   along with this program; if not, write to the Free Software
+#   Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
+#
+#
+# AC_LATEX_DVIPS_T_LETTER_LANDSCAPE
+#
+# Test dvips -t letter -t landscape and set dvips_t_letter_landscape
+#
+#
+dnl @synopsis AC_LATEX_DVIPS_T_LETTER_LANDSCAPE
+dnl
+dnl same as AC_LATEX_DVIPS_T(letter,dvips_t_letter_landscape,on)
+dnl
+dnl @version 1.3
+dnl @author Mathieu Boretti boretti@eig.unige.ch
+dnl
+AC_DEFUN([AC_LATEX_DVIPS_T_LETTER_LANDSCAPE],[
+AC_REQUIRE([AC_LATEX_DVIPS_T_LETTER])
+AC_LATEX_DVIPS_T(letter,dvips_t_letter_landscape,on)
+if test $dvips_t_letter_landscape = "no";
+then
+    AC_MSG_ERROR([Unable to find the -t letter -t landscape option in dvips])
+fi
+])
\ No newline at end of file

latex_autoconf_macros/ac_latex_package.m4

+#
+#   Copyright (C) 2004  Boretti Mathieu
+#
+#   This program is free software; you can redistribute it and/or modify
+#   it under the terms of the GNU General Public License as published by
+#   the Free Software Foundation; either version 2 of the License, or
+#   (at your option) any later version.
+#
+#   This program is distributed in the hope that it will be useful,
+#   but WITHOUT ANY WARRANTY; without even the implied warranty of
+#   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+#   GNU General Public License for more details.
+#
+#   You should have received a copy of the GNU General Public License
+#   along with this program; if not, write to the Free Software
+#   Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
+#
+#
+# AC_LATEX_PACKAGE([<packagen>],<class>,<variable>)
+#
+# Test the presences of package and set $<variable> 
+# to yes or no
+#
+#
+dnl @synopsis AC_LATEX_PACKAGE(<package>,<class>,<variable>)
+dnl
+dnl This macro test if package in <class> exists
+dnl and set <variable> to the right value
+dnl
+dnl  AC_LATEX_PACKAGE(varioref,book,vbook)
+dnl  should set $vbook="yes"
+dnl
+dnl  AC_LATEX_PACKAGE(xyz,book,vbook)
+dnl  should set $vbook="no"
+dnl
+dnl @version 1.3
+dnl @author Mathieu Boretti boretti@eig.unige.ch
+dnl
+
+AC_DEFUN([AC_LATEX_PACKAGE],[
+if test "$[ac_cv_latex_class_]translit($2,[-],[_])" = "" ;
+then
+	AC_LATEX_CLASS($2,boretti_classesansparametre)
+	export boretti_classesansparametre;
+else
+	boretti_classesansparametre=$[ac_cv_latex_class_]translit($2,[-],[_]) ;
+	export boretti_classesansparemetre;
+fi;
+if test $boretti_classesansparametre = "no" ;
+then
+    AC_MSG_ERROR([Unable to find $2 class])
+fi
+AC_CACHE_CHECK([for $1 in class $2],[ac_cv_latex_]translit($1,[-],[_])[_]translit($2,[-],[_]),[
+_AC_LATEX_TEST([
+\documentclass{$2}
+\usepackage{$1}
+\begin{document}
+\end{document}
+],[ac_cv_latex_]translit($1,[-],[_])[_]translit($2,[-],[_]))
+])
+$3=$[ac_cv_latex_]translit($1,[-],[_])[_]translit($2,[-],[_]); export $3;
+AC_SUBST($3)
+ifelse($#,3,[],$#,4,[
+    if test "[$]$3" = "yes" ;
+    then
+        $4
+    fi
+],$#,5,[
+    ifelse($4,[],[
+        if test "[$]$3" = "no" ;
+        then
+            $5
+        fi
+    ],[
+        if test "[$]$3" = "yes" ;
+        then
+            $4
+        else
+            $5
+        fi
+    ])
+])
+])