some small change

Author: mahi045

README.md

@@ -7,7 +7,7 @@ The tool counts the number of minimal trap spaces and fixed points of a Boolean
 
 ### Clone the repo
 ```
-git clone --recurse-submodules git@github.com:meelgroup/bn-counting.git
+git clone --recurse-submodules https://github.com/meelgroup/bn-counting.git
 ```
 
 ### Dependencies
@@ -31,11 +31,11 @@ chmod +x build.sh
 ```
 
 
-## Run ApproxASP
+## Run
 First cd to script: `cd script`
 
 
-### Running first task
+### Running first task: C-MTS-1 and C-FIX-1
 `Input`: 
 - `Boolean Network`: a Boolean network (.bnet file)
 
@@ -51,7 +51,7 @@ python3 run_fixed_point.py -t 1 -bn t1_244.bnet
 ```
 it should print the count in line: `C-FIX-1:`
 
-### Running second task
+### Running second task: C-MTS-2 and C-FIX-2
 `Input`: 
 - `Boolean network`: a Boolean network (.bnet file)
 - `phenotype`: a phenotype, we specify it in a file. You can see example in file `phen_244.txt`
@@ -68,7 +68,7 @@ python3 run_fixed_point.py -t 2 -bn t1_244.bnet -phen phen_244.txt
 ```
 it should print the count in line: `C-FIX-2:`
 
-### Running third task
+### Running third task: C-MTS-3 and C-FIX-3
 `Input`: 
 - `Boolean network`: a Boolean network (.bnet file)
 - `phenotype`: a phenotype, we specify it in a file. You can see example in file `phen_244.txt`
@@ -87,7 +87,7 @@ python3 run_fixed_point.py -t 3 -bn t1_244.bnet -phen phen_244.txt -pert pert_24
 it should print the count in line: `C-FIX-3:`
 
 ## Preprocessing BNs
-We used [tsconj](https://github.com/daemontus/tsconj) and [fASP](https://github.com/giang-trinh/fASP) to process BNs to ASP program, for minimal trap space and fixed points, respectively. The original implementation is modified for our usage. 
+We used [tsconj](https://github.com/daemontus/tsconj) and [fASP](https://github.com/giang-trinh/fASP) to encode BNs to ASP program, for minimal trap space and fixed points, respectively. The original implementation is modified for our usage. 
 
 
 ## Benchmark:

build.sh

@@ -7,7 +7,7 @@ echo "Building ApproxASP..."
 cd "$ROOT_DIR/ApproxASP"
 mkdir -p build && cd build
 cmake -DCLINGO_BUILD_SHARED=ON ..
-make -j12
+make -j$(nproc)
 cp approxasp "$ROOT_DIR/script"
 
 echo "Done. Copied binaries to:"

script/helper.py

@@ -3,7 +3,7 @@
 
 
 def run(cmd, timeout, ttl = 3, silent = False):
-    proc = sp.Popen([cmd], stdout=sp.PIPE, stderr=sp.PIPE, shell=True)
+    proc = sp.Popen([cmd], stdout=sp.PIPE, stderr=sp.PIPE, check=True, text=True)
     # print(cmd)
     try:
         (out, err) = proc.communicate(timeout = int(timeout * 1.1) + 1)

script/run_fixed_point.py

@@ -13,7 +13,6 @@
 # First, prepare ASP programs for all "normal" networks without any special requirements.
 
 
-file_path = "t1_244.bnet"
 
 def preprocess_bn(bn_path):
     # preprocess BN