Some misc changes to the artefact scripts

artefact/bulk_bench.sh

@@ -6,19 +6,20 @@ TOOL=$3
 
 # The tested limit was 2^26kB 67_108_864kB ~ 67GB
 if [[ -z "${MEMORY_LIMIT}" ]]; then
-  echo "Please set env. variable MEMORY_LIMIT appropriate for your system (number, in kB)."
+  >&2 echo " !!! Please set env. variable MEMORY_LIMIT appropriate for your system (number, in kB)."
   exit 1
 fi
 
 ulimit -v $MEMORY_LIMIT
 
 for MODEL in `ls $MODEL_DIR | grep "\.bnet"`
 do
+    >&2 echo "$TOOL $MODEL_DIR/$MODEL"
     timeout $TIMEOUT ./env/bin/python3 $TOOL $MODEL_DIR/$MODEL
     ret=$?
     # 124 is the return code for timeout.
     if [ $ret -eq 124 ]; then
-            echo -e "$MODEL_DIR/$MODEL\tTIMEOUT"
+            echo -e "$MODEL\  tTIMEOUT"
     fi
     # Properly exit the loop if Ctrl+C is pressed.
     trap 'exit 2' SIGINT

artefact/bulk_bench_attr.sh

@@ -4,6 +4,6 @@ set -x
 
 mkdir -p ./results/attr/
 
-echo "model elapsed attractors" > ./results/attr/bbm_aeon.tsv
+echo -e "model\telapsed\tattractors" > ./results/attr/bbm_aeon.tsv
 ./bulk_bench.sh ./models/bbm-bnet-inputs-random-128 1h ./bench/attr-aeon.py >> ./results/attr/bbm_aeon.tsv
 trap 'exit 2' SIGINT

artefact/env_check.sh

@@ -5,20 +5,29 @@ PYTHON=./env/bin/python3
 
 # Check that necessary system dependencies are present.
 
+echo " > Checking 'clingo'"
 clingo --version > /dev/null
 ret=$?
 if [ $ret -ne 0 ]; then
     echo "Missing 'clingo'. Maybe run 'apt install gringo'?"
     exit 1
 fi
 
-$PYTHON bench/aeon-attractors.py 1 1 ./models/bbm/005.bnet
+echo " > Checking 'mole'"
+mole &> /dev/null
+ret=$?
+if [ $ret -ne 1 ]; then
+    echo "Missing 'mole'. Forgot to add ./dependencies/mole-140428 to PATH?"
+    exit 1
+fi
+
+echo " > Checking 'AEON.py'"
+$PYTHON ./bench/attr-aeon.py ./models/bbm-bnet-inputs-random-128/005.bnet > /dev/null
 ret=$?
 if [ $ret -ne 0 ]; then
-    echo "Error running tsconj. Installation failed?"
+    echo "Error running AEON. Installation failed?"
     exit 1
 fi
 
-echo 
 echo
 echo " >> Everything seems to be in order."

artefact/env_setup.sh

@@ -11,7 +11,7 @@ PIP=./env/bin/pip3
 
 # Install fixed versions of relevant dependencies 
 # to aid reproducibility.
-$PIP install -r ./dependencies/requirements.txt
+$PIP install -r ./requirements.txt
 
 # Install AEON
 $PIP install biodivine_aeon==0.2.0a4