Examples and clean-ups (#1)

- Attempt at implementing an example for DRS
- Complete reactions set
- New automaton
- Formula
- Fixed automaton scaling
- Proc index in the formula
- Benchmark generators
- Scripts to reproduce experiments for reaction mining

experiments/drs_cell_signal/run.sh

@@ -0,0 +1,97 @@
+#!/usr/bin/env bash
+
+x_values="2 3 4"
+y_values="`seq 2 20`"
+z_values="`seq 2 20`"
+aut_values="a b"
+
+reactics="$1"
+reactics_opts="-z -x -vv -B -c"
+
+input_generator="../../examples/bdd/generators/gen_drs.py"
+
+benchname="sig"
+formname="f0"
+
+outdir="results_${benchname}"
+
+if [[ -z "$1" ]]
+then
+    echo "Usage: $0 <path to reactics>"
+    exit 1
+fi
+
+if [[ ! -x "$reactics" ]]
+then
+    echo "Provided path to ReactICS not executable"
+fi
+
+if [[ ! -d "$outdir" ]]
+then
+    echo "Creating output directory: $outdir"
+    mkdir -p $outdir
+fi
+
+#ulimit -t 3600
+#ulimit -v 2097152
+ulimit -t 3600
+#ulimit -v 1000000
+
+for a in $aut_values
+do
+    for z in $z_values
+    do
+        for y in $y_values
+        do
+            for x in $x_values
+            do
+
+                if [[ $y -lt $z ]]
+                then
+                    # Skip undesired values
+                    continue
+                fi
+
+                if [[ $y -ne $z ]]
+                then
+                    # More aggressive skipping
+                    continue
+                fi
+
+                bench_identifier="${benchname}_F${formname}_A${a}"
+
+                filename_base="${outdir}/${benchname}_F${formname}__x${x}_y${y}_z${z}_A${a}" 
+                outfile="${filename_base}.out"
+                infile="${filename_base}.drs"
+
+                stopfile="DONE_${bench_identifier}"
+
+                if [[ -e "$stopfile" ]]
+                then
+                    echo "Time limit -- SKIPPING"
+                    continue
+                fi
+
+                $input_generator $x $y $z $a > ${infile}
+
+                $reactics $reactics_opts $formname $infile |& tee ${outfile}
+                exitcode=$?
+                echo "ReactICS exit code: $exitcode"
+
+                result="$(tail -1 $outfile | grep -E '.*;.*;.*;.*'| sed "s/STAT/$n /")" 
+                if [ "$result" = "" ]
+                then
+                    echo "TIME LIMIT; marking as finished"
+                    #touch $stopfile
+                else
+                    echo "$x ; $y ; $z ; $a ; $exitcode $result" >> $outdir/summary_${bench_identifier}.txt
+                    echo "$x $y $z $a $(echo $result | sed 's/;/ /g')" >> $outdir/${bench_identifier}.dat
+                    echo $result
+                fi
+
+            done
+        done
+    done
+done
+
+# EOF