document bug and pipeline

install.sh

@@ -115,7 +115,7 @@ then
   if hash glucose 2>/dev/null
   then
     pathglucose="$(which glucose)"
-    rm $pathglucose
+    rm -i $pathglucose
   fi
   glucose_url=http://www.labri.fr/perso/lsimon/downloads/softwares/glucose-syrup-4.1.tgz
   glucose_archive=${glucose_url##*/}
@@ -131,6 +131,7 @@ then
 fi
 
 ### MiniMaxSat
+# FIX ME binary for linux
 if ! hash minimaxsat1.0 2>/dev/null
 then
   curl -fsSLO https://github.com/izquierdo/tesis_postgrado/raw/master/src/MiniMaxSat/minimaxsat1.0

sepi_graphs.pl

@@ -9,6 +9,7 @@
 % Only for separate compilation/linting
 :- use_module(doc).
 :- use_module(biocham).
+:- use_module(library(pcre)).
 
 :- doc('This section describes commands to detect model reduction
 	relationships between reaction models based solely on the
@@ -159,7 +160,7 @@ read_lines(end_of_file, _, "") :- !.
 read_lines(Codes, _, Solution) :-
 	atom_codes(Solution, Codes),
 	re_match("v .*", Solution).
-read_lines(_, Out, Solution) :- % debug Codes
+read_lines(_, Out, Solution) :- % debug read_lines(Codes, Out, Solution)
 	% atom_codes(Line, Codes), % debug
 	% debug(bottom, "Line is: ~w", [Line]),
 	read_line_to_codes(Out, Line2),
@@ -391,6 +392,7 @@ search_sepi(G1, G2, Stream, Merge, Bottom) :-
 	debug(bottom, "Done writing clauses", []).
 
 /*  write_header  */
+/*  FIX ME header becomes false when adding clauses for all reductions and for bottom minimisation*/
 /*  write_header(+G1, +G2, +Stream) -> write the input file's header 
 	for the SAT solver (in a simplified version of the DIMACS format).
 	+G1: graph 1 [NbVertexe, NbSpecie, EdgesList, Id]