Some clean-up stuff

.gitignore

@@ -0,0 +1,21 @@
+# Files created by OS
+.DS_Store
+desktop.ini
+.directory
+
+# Things visual studio code creates
+.vscode
+
+# Some editors create a yourfile.name~ file as a backup file
+.py~
+.ivy~
+.sm~
+.prism~
+.csl~
+.xml~
+.bak
+
+# Python distribution files
+.Python
+__pycache__/
+.pyc

scripts/admin.sh

@@ -1,14 +1,35 @@
-cp ../models/SingleSpecies/2reaction.ragtimer ../model.ragtimer
-cp ../models/SingleSpecies/model.sm ../model.sm
-cp ../models/SingleSpecies/model.csl ../model.csl
-/usr/bin/time -o ../results/ragtimer/2reaction_50000time.txt python3 main.py 50000 loose &> ../results/ragtimer/2reaction_50000.txt
-
-cp ../models/KuwaharaEnzyme/6reaction.ragtimer ../model.ragtimer
-cp ../models/KuwaharaEnzyme/model.sm ../model.sm
-cp ../models/KuwaharaEnzyme/model.csl ../model.csl
-/usr/bin/time -o ../results/ragtimer/6reaction_50000time.txt python3 main.py 50000 loose &> ../results/ragtimer/6reaction_50000.txt
-
-cp ../models/DonovanYeastPolarization/8reaction_input_adding.txt ../model.ragtimer
-cp ../models/DonovanYeastPolarization/model.sm ../model.sm
-cp ../models/DonovanYeastPolarization/model.csl ../model.csl
-/usr/bin/time -o ../results/ragtimer/8reaction_50000time.txt python3 main.py 50000 &> ../results/ragtimer/8reaction_50000.txt
+#!/bin/sh
+
+# Rather than having four shell scripts with basically the same thing in them, you could just pass
+# in the model size via a parameter
+
+set -e
+
+ragrun() {
+	export MODEL_SIZE=$1
+	echo "Running Ragtimer for model size ${MODEL_SIZE}.."
+
+	echo -n "Testing on the Single-species models..."
+	cp ../models/SingleSpecies/2reaction.ragtimer ../model.ragtimer
+	cp ../models/SingleSpecies/model.sm ../model.sm
+	cp ../models/SingleSpecies/model.csl ../model.csl
+	/usr/bin/time -o "../results/ragtimer/2reaction_${MODEL_SIZE}time.txt" python3 main.py $MODEL_SIZE loose &> "../results/ragtimer/2reaction_${MODEL_SIZE}.txt"
+	echo "done."
+
+	echo -n "Testing on the Kuwahara Enzyme models..."
+	cp ../models/KuwaharaEnzyme/6reaction.ragtimer ../model.ragtimer
+	cp ../models/KuwaharaEnzyme/model.sm ../model.sm
+	cp ../models/KuwaharaEnzyme/model.csl ../model.csl
+	/usr/bin/time -o "../results/ragtimer/6reaction_${MODEL_SIZE}time.txt" python3 main.py ${MODEL_SIZE} loose &> "../results/ragtimer/6reaction_${MODEL_SIZE}.txt"
+	echo "done."
+
+	echo -n "Testing on Donovan Yeast Polarization models..."
+	cp ../models/DonovanYeastPolarization/8reaction_input_adding.txt ../model.ragtimer
+	cp ../models/DonovanYeastPolarization/model.sm ../model.sm
+	cp ../models/DonovanYeastPolarization/model.csl ../model.csl
+	/usr/bin/time -o "../results/ragtimer/8reaction_${MODEL_SIZE}time.txt" python3 main.py ${MODEL_SIZE} &> "../results/ragtimer/8reaction_${MODEL_SIZE}.txt"
+	echo "done."
+
+}
+
+ragrun $1

scripts/main.py

@@ -11,12 +11,12 @@
 
     PRINTING = False
 
-    print()
-    print(80*"=")
-    print("Expect to see a message claiming an error: assertion failure.")
-    print("This message indicates correct functionality.")
-    print(80*"=")
-    print()
+    print(f"""
+{80*"="}
+Expect to see a message claiming an error: assertion failure.
+This message indicates correct functionality.
+{80*"="}
+""")
 
     i = sys.argv[1]
     each = False
@@ -29,7 +29,7 @@
         loose = True
 
     reactions1 = depgraph.makeDepGraph(reactions_v5.Options.infile, printing=PRINTING)
-    
+
     # with open("trace_list.txt", "w") as t:
     #     t.write("")
 
@@ -38,10 +38,10 @@
     for r in reactions1:
         # print(r)
         if (r.tier == 0):
-            depgraph.printPrefixes("trace_list.txt", "", r, paths)
-            
+            depgraph.printPrefixes("textfiles/trace_list.txt", "", r, paths)
+
                 # NEED TO HANDLE CASE WHERE THEY MAKE EQUIV. TRACES???
-            
+
             # extraEnabled = 0
             # for dr in range(len(r.dependCount)):
             #     if r.dependCount[dr] > 0:
@@ -52,13 +52,13 @@
             # # print(paths)
             # # input("newpaths")
 
-    with open("trace_list.txt", "w") as trace_list:
+    with open("textfiles/trace_list.txt", "w") as trace_list:
         for path in paths:
             trace_list.write("_PREFIX_\t" + path + "\n")
 
     # print(paths)
     # quit()
-    
+
     o = subprocess.check_output(["make", "test"],universal_newlines=True)
     prefix = prefix_parser.parsePrefix(o)
 
@@ -82,7 +82,7 @@
                         if s2 not in enabledReacts:
                             enabledReacts.append(s2)
                         # print("enabledReacts",enabledReacts)
-                # invalid trace at line 1 at 0 with transition r6 
+                # invalid trace at line 1 at 0 with transition r6
                 pathnumber = int(lines[line].split(" trace at line ")[1].split(" ")[0]) - 1
                 # print(pathnumber)
                 rempath = paths[pathnumber]
@@ -100,14 +100,14 @@
                 break
         # print("new1", paths)
 
-        with open("trace_list.txt", "w") as trace_list:
+        with open("textfiles/trace_list.txt", "w") as trace_list:
             for path in paths:
                 # print("PREFIX PATH: ", paths)
                 trace_list.write("_PREFIX_\t" + path + "\n")
 
         o = subprocess.check_output(["make", "test"],universal_newlines=True)
         prefix = prefix_parser.parsePrefix(o)
-                            
+
 
                 # reactionname = line.split("with transition ")[1].strip()
                 # for r in reactions1:
@@ -124,7 +124,7 @@
         #     prefix = prefix_parser.parsePrefix(o)
         # input("===")
 
-                    
+
         # print(prefix)
 
     j = len(prefix.values)
@@ -138,9 +138,9 @@
     prob = float(0.0)
 
     for a in range(len(paths)):
-        print(50*"-")
-        print(paths[a])
-        print(50*"-")
+        print(f"""{50*"-"}
+{paths[a]}
+{50*"-"}""")
         reactions_v5.randTest(iters, reactions1, prefix, a, loose=loose, printing=PRINTING)
 
         # os.system("make test")
@@ -150,11 +150,8 @@
             if "Total" in line:
                 prob += float(line.split(": ")[1])
 
-    print()
-    print(80*"=")
-    print("Total Sum of Unique Path Probabilities:", prob)
-    print(80*"=")
-    print()
-    print()
-    print()
-    print()
+    print(f"""
+{80*"="}
+Total Sum of Unique Path Probabilities: {prob}
+{80*"="}
+    """)