Fix versioning

Makefile.am_BLUEPRINT

@@ -45,7 +45,19 @@ install-data-local:
 uninstall-local:
 	rmdir $(DESTDIR)$(pkgdatadir)/compiled_mechs 2>/dev/null || :
 
-all-local:
+dist-hook:
+	chmod u+w $(distdir)/boxmox/wrapper
+	@sed 's/__BOXMOX_VERSION__/'$(VERSION)'/g' $(distdir)/boxmox/wrapper > tmp; mv tmp $(distdir)/boxmox/wrapper
+	chmod u+w $(distdir)/drv/boxmox.f90
+	@sed 's/__BOXMOX_VERSION__/'$(VERSION)'/g' $(distdir)/drv/boxmox.f90 > tmp; mv tmp $(distdir)/drv/boxmox.f90
+	chmod u+w $(distdir)/drv/boxmox_adjoint.f90
+	@sed 's/__BOXMOX_VERSION__/'$(VERSION)'/g' $(distdir)/drv/boxmox_adjoint.f90 > tmp; mv tmp $(distdir)/drv/boxmox_adjoint.f90
+	chmod u+w $(distdir)/scripts/new_BOXMOX_experiment
+	@sed 's/__BOXMOX_VERSION__/'$(VERSION)'/g' $(distdir)/scripts/new_BOXMOX_experiment > tmp; mv tmp $(distdir)/scripts/new_BOXMOX_experiment
+	chmod u+w $(distdir)/scripts/new_BOXMOX_experiment_from_example
+	@sed 's/__BOXMOX_VERSION__/'$(VERSION)'/g' $(distdir)/scripts/new_BOXMOX_experiment_from_example > tmp; mv tmp $(distdir)/scripts/new_BOXMOX_experiment_from_example
+
+install-data-hook:
 	@echo " "
 	@echo " --- YOU ARE GOOD TO GO ---"
 	@echo " "

boxmox/UserManual.tex

@@ -15,11 +15,11 @@
 \ \\[8cm]
 
 {\LARGE BOXMOX extensions to KPP} \\[1cm]
-Christoph Knote (christoph.knote@lmu.de)\\
-Meteorological Institute, LMU Munich, Germany
+Christoph Knote (christoph.knote@med.uni-augsburg.de)\\
+Model-Based Environmental Exposure Science, Faculty of Medicine, University of Augsburg, Germany
 \\[1cm]
-Version 1.8a\\
-09/2019
+Version 1.8\\
+03/2022
 
 % version   name  comment
 % 0.9       CK    initial release
@@ -34,6 +34,7 @@ Version 1.8a\\
 % 1.7       CK    revamped mixing process options, included simple aerosol as
 %                 surface density area and radius
 % 1.8a      CK    implemented NOx fixing
+% 1.8       CK    move to GNU autotools for distribution
 \end{center}
 
 \thispagestyle{empty}
@@ -46,11 +47,20 @@ Version 1.8a\\
 
 \section*{Version history}
 
-\subsection*{1.8a}
+\subsection*{1.8}
 \textit{not released yet}
 
 New features
 
+\begin{itemize}
+  \item Move to GNU autotools for distribution
+\end{itemize}
+
+\subsection*{1.8a}
+\textit{not released}
+
+New features
+
 \begin{itemize}
   \item Implemented NO$_x$ fixing method for steady state calculations
 \end{itemize}
@@ -200,49 +210,22 @@ doi:10.5194/acp-6-187-2006, 2006.
 \emph{BOXMOX is a Linux program, we assume you are working on a reasonably
 recent Linux distribution.}
 
-You should have received or downloaded the \emph{install\_BOXMOX.bash} shell
-script. The script is written in {\tt bash}, a shell that is installed on most
-*nix machines, but might not be your default. Do not worry. Open the script in
-your favorite text editor and adapt the user section to your machine. You need
-to set
+Requirements for installing and running BOXMOX:
 
 \begin{itemize}
-  \item absolute path to the location you want BOXMOX to be
   \item C compiler (usually {\tt gcc} or {\tt cc})
-  \item C compile flags (if any)
-  \item absolute path to the FLEX binary (test with {\tt which flex})
-  \item absolute path to the FLEX library (libfl.a, try {\tt type -a libfl.a})
+  \item Fortran compiler ({\tt gfortran} is assumed)
+  \item flex (test with {\tt which flex})
+  \item flex library (libfl.a, try {\tt type -a libfl.a})
+  \item yacc or bison
 \end{itemize}
 
-Save the file. Now execute it:
+BOXMOX installation is then straightforward:
 
 \begin{verbatim}
-me@mymachine> bash install_BOXMOX.bash
-
-BOXMOX extension to KPP (1.7)
-
-Output directory: /glade/u/home/knote/testy
-C compiler:       gcc
-C compiler flags: -O
-FLEX binary:      /usr/bin/flex
-FLEX library:     /usr/lib64/libfl.a
-
-Downloading BOXMOX
-Downloading KPP
-Unpacking KPP
-Patching KPP
-Compiling KPP
-Tex'ing BOXMOX readme (boxmox/README.pdf)
-
- --- YOU ARE GOOD TO GO ---
-
-Remember to set the following env. variables and
-add them to your .bashrc. to remember them permanently:
-
-export KPP_HOME=/glade/u/home/knote/boxmox
-export PATH=$KPP_HOME/bin:$PATH
-
-me@mymachine>
+./configure --prefix=<absolue path to where BOXMOX should be installed>
+make
+make install
 \end{verbatim}
 
 Once you see the message ``YOU ARE GOOD TO GO'', everything should have worked
@@ -288,7 +271,7 @@ me@mymachine>
 
 This creates a box model executable for the chosen mechanism (in this case,
 MOZART-4) which you can now use for your experiments. The executables can be
-found in \emph{\$KPP\_HOME/boxmox/compiled\_mechs/\mech}.
+found in \emph{\$KPP\_HOME/compiled\_mechs/\mech}.
 
 \subsubsection{{\tt new\_BOXMOX\_experiment}}
 

build_dist.sh

 #!/bin/sh
 buildDir=$1
 
+echo
+echo " ---  pruning existing build dir ---"
+echo
+
+if [ ! -z "$buildDir" ]
+then
+  rm -rf $buildDir
+fi
+
 echo
 echo " ---  prep Makefile.am ---"
 echo
 
-# fancy shit: no wildcards in automake, add all files to be distributed with BOXMOX/KPP explicitly
+# (1) fancy shit: no wildcards in automake, add all files to be distributed with BOXMOX/KPP explicitly
 cp Makefile.am_BLUEPRINT Makefile.am
 
 # list all files in these subdirectories

configure.ac

@@ -6,19 +6,23 @@ 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.
 AM_INIT_AUTOMAKE([-Wall foreign tar-pax])
 AC_PROG_CC
-if test x$CC = "x" ; then
+if test "x$CC" = "x" ; then
     AC_MSG_ERROR([C compiler is required to build KPP.])
 fi
 AC_PROG_LEX(noyywrap)
-if test x$LEX = "x" ; then
+if test "x$LEX" = "x" ; then
     AC_MSG_ERROR([flex is required to build KPP.])
 fi
 AC_PROG_YACC
-if test x$YACC = "x" ; then
+if test "x$YACC" = "x" ; then
     AC_MSG_ERROR([bison or yacc is required to build KPP.])
 fi
+AC_PROG_SED
+if test "x$SED" = "x" ; then
+    AC_MSG_ERROR([sed is required to build BOXMOX.])
+fi
 AC_PROG_FC
-if test x$FC = "x" ; then
+if test "x$FC" = "x" ; then
     AC_MSG_ERROR([Fortran compiler is required to build BOXMOX mechanisms.])
 fi
 AC_PROG_MKDIR_P

scripts/list_BOXMOX_mechanisms

@@ -29,7 +29,7 @@ validate_BOXMOX_installation || { echo "Validating BOXMOX installation failed";
 BOXMOX_MECH_PATH=${KPP_HOME}/compiled_mechs
 
 if [ ! -z $(ls -A ${BOXMOX_MECH_PATH}) ]; then
-  for mech in $(find ${BOXMOX_MECH_PATH}/*)
+  for mech in $(ls -1 -d ${BOXMOX_MECH_PATH}/*)
   do
     mechList+=($(basename $mech))
   done
@@ -37,7 +37,7 @@ fi
 
 if $all
 then
-  for mech in $(find ${KPP_HOME}/models/*.eqn)
+  for mech in $(ls -1 ${KPP_HOME}/models/*.eqn)
   do
     mechi=$(basename $mech)
     mechList+=(${mechi/.eqn/})