diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..9e63f40 --- /dev/null +++ b/.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 diff --git a/scripts/model.csl b/models/model.csl similarity index 100% rename from scripts/model.csl rename to models/model.csl diff --git a/scripts/model.sm b/models/model.sm similarity index 100% rename from scripts/model.sm rename to models/model.sm diff --git a/scripts/__pycache__/depgraph.cpython-310.pyc b/scripts/__pycache__/depgraph.cpython-310.pyc deleted file mode 100644 index a3f146f..0000000 Binary files a/scripts/__pycache__/depgraph.cpython-310.pyc and /dev/null differ diff --git a/scripts/__pycache__/depgraph.cpython-39.pyc b/scripts/__pycache__/depgraph.cpython-39.pyc deleted file mode 100644 index 3300b8a..0000000 Binary files a/scripts/__pycache__/depgraph.cpython-39.pyc and /dev/null differ diff --git a/scripts/__pycache__/prefix_parser.cpython-310.pyc b/scripts/__pycache__/prefix_parser.cpython-310.pyc deleted file mode 100644 index 7b951b1..0000000 Binary files a/scripts/__pycache__/prefix_parser.cpython-310.pyc and /dev/null differ diff --git a/scripts/__pycache__/prefix_parser.cpython-39.pyc b/scripts/__pycache__/prefix_parser.cpython-39.pyc deleted file mode 100644 index a9777f0..0000000 Binary files a/scripts/__pycache__/prefix_parser.cpython-39.pyc and /dev/null differ diff --git a/scripts/__pycache__/reactions_v5.cpython-310.pyc b/scripts/__pycache__/reactions_v5.cpython-310.pyc deleted file mode 100644 index b9e14bf..0000000 Binary files a/scripts/__pycache__/reactions_v5.cpython-310.pyc and /dev/null differ diff --git a/scripts/__pycache__/reactions_v5.cpython-39.pyc b/scripts/__pycache__/reactions_v5.cpython-39.pyc deleted file mode 100644 index ce16b96..0000000 Binary files a/scripts/__pycache__/reactions_v5.cpython-39.pyc and /dev/null differ diff --git a/scripts/admin.sh b/scripts/admin.sh index 6db42fc..0eb3cf8 100755 --- a/scripts/admin.sh +++ b/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 diff --git a/scripts/admin150k.sh b/scripts/admin150k.sh deleted file mode 100755 index fa848ea..0000000 --- a/scripts/admin150k.sh +++ /dev/null @@ -1,14 +0,0 @@ -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_150000time.txt python3 main.py 150000 loose &> ../results/ragtimer/2reaction_150000.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_150000time.txt python3 main.py 150000 loose &> ../results/ragtimer/6reaction_150000.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_150000time.txt python3 main.py 150000 &> ../results/ragtimer/8reaction_150000.txt diff --git a/scripts/admin250k.sh b/scripts/admin250k.sh deleted file mode 100755 index 2b6fda9..0000000 --- a/scripts/admin250k.sh +++ /dev/null @@ -1,14 +0,0 @@ -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_250000time.txt python3 main.py 250000 loose &> ../results/ragtimer/2reaction_250000.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_250000time.txt python3 main.py 250000 loose &> ../results/ragtimer/6reaction_250000.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_250000time.txt python3 main.py 250000 &> ../results/ragtimer/8reaction_250000.txt diff --git a/scripts/admin500k.sh b/scripts/admin500k.sh deleted file mode 100755 index c8be07c..0000000 --- a/scripts/admin500k.sh +++ /dev/null @@ -1,14 +0,0 @@ -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_500000time.txt python3 main.py 500000 loose &> ../results/ragtimer/2reaction_500000.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_500000time.txt python3 main.py 500000 loose &> ../results/ragtimer/6reaction_500000.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_500000time.txt python3 main.py 500000 &> ../results/ragtimer/8reaction_500000.txt diff --git a/scripts/main.py b/scripts/main.py index 5bf7f22..590bde5 100644 --- a/scripts/main.py +++ b/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*"="} + """) diff --git a/scripts/2reaction_100runs_out.txt b/scripts/textfiles/2reaction_100runs_out.txt similarity index 100% rename from scripts/2reaction_100runs_out.txt rename to scripts/textfiles/2reaction_100runs_out.txt diff --git a/scripts/6reaction_output.txt b/scripts/textfiles/6reaction_output.txt similarity index 100% rename from scripts/6reaction_output.txt rename to scripts/textfiles/6reaction_output.txt diff --git a/scripts/checkoutput.txt b/scripts/textfiles/checkoutput.txt similarity index 100% rename from scripts/checkoutput.txt rename to scripts/textfiles/checkoutput.txt diff --git a/scripts/lazy_paths.txt b/scripts/textfiles/lazy_paths.txt similarity index 100% rename from scripts/lazy_paths.txt rename to scripts/textfiles/lazy_paths.txt diff --git a/scripts/nolines.txt b/scripts/textfiles/nolines.txt similarity index 100% rename from scripts/nolines.txt rename to scripts/textfiles/nolines.txt diff --git a/scripts/prefix_result.txt b/scripts/textfiles/prefix_result.txt similarity index 100% rename from scripts/prefix_result.txt rename to scripts/textfiles/prefix_result.txt diff --git a/scripts/prefix_test.txt b/scripts/textfiles/prefix_test.txt similarity index 100% rename from scripts/prefix_test.txt rename to scripts/textfiles/prefix_test.txt diff --git a/scripts/prefix_time.txt b/scripts/textfiles/prefix_time.txt similarity index 100% rename from scripts/prefix_time.txt rename to scripts/textfiles/prefix_time.txt diff --git a/scripts/quick_result.txt b/scripts/textfiles/quick_result.txt similarity index 100% rename from scripts/quick_result.txt rename to scripts/textfiles/quick_result.txt diff --git a/scripts/quick_result_time.txt b/scripts/textfiles/quick_result_time.txt similarity index 100% rename from scripts/quick_result_time.txt rename to scripts/textfiles/quick_result_time.txt diff --git a/scripts/reaction_list.txt b/scripts/textfiles/reaction_list.txt similarity index 100% rename from scripts/reaction_list.txt rename to scripts/textfiles/reaction_list.txt diff --git a/scripts/subtract_test.txt b/scripts/textfiles/subtract_test.txt similarity index 100% rename from scripts/subtract_test.txt rename to scripts/textfiles/subtract_test.txt diff --git a/scripts/test.txt b/scripts/textfiles/test.txt similarity index 100% rename from scripts/test.txt rename to scripts/textfiles/test.txt diff --git a/scripts/test_print_all_lines.txt b/scripts/textfiles/test_print_all_lines.txt similarity index 100% rename from scripts/test_print_all_lines.txt rename to scripts/textfiles/test_print_all_lines.txt diff --git a/scripts/test_v2.txt b/scripts/textfiles/test_v2.txt similarity index 100% rename from scripts/test_v2.txt rename to scripts/textfiles/test_v2.txt diff --git a/scripts/testprint.txt b/scripts/textfiles/testprint.txt similarity index 100% rename from scripts/testprint.txt rename to scripts/textfiles/testprint.txt diff --git a/scripts/trace_list.txt b/scripts/textfiles/trace_list.txt similarity index 100% rename from scripts/trace_list.txt rename to scripts/textfiles/trace_list.txt