changes for windows test

Author: tstohn

test/test_c.sh

@@ -1,28 +1,25 @@
-#!/bin/bash
+#!/usr/bin/env bash
+set -euo pipefail
 
 # Configuration
 EXE="./bin/loco"
-# This is the output file name loco usually generates (adjust if loco adds suffixes)
 OUT_FILE="bin/test_c_laplacian.tsv"
 TOTAL_RUNS=5
 REQUIRED_PASSES=4
 PASS_COUNT=0
 
-# The command to run
 CMD="$EXE -i ./test/simulatedData3.tsv -o bin -p test_c -c -n 20 -s 100 -x 0.5 -t 50 -q 2 -m 2 -a 0.01"
 
 check_output() {
-    # If the file doesn't even exist, fail immediately
-    if [ ! -f "$1" ]; then return 1; fi
-
-    # awk logic:
-    # NR > 1 && NR <= 6: Check only the first 5 data rows
-    # $3 < 0.05 and $5 < 0.05: Verify p-values
-    # $6 == "A,B,C,D,E": Verify the clique column
-    # $1 ~ /^[ABCDE]_[ABCDE]$/: Verify ProteinPair only contains A,B,C,D,E
+    if [ ! -f "$1" ]; then
+        return 1
+    fi
+
     awk -F'\t' '
     NR > 1 && NR <= 6 {
-        if ($3 >= 0.01 || $5 >= 0.01) exit 1 
+        gsub(/\r/, "", $0)
+
+        if ($3 >= 0.01 || $5 >= 0.01) exit 1
         if ($6 != "A,B,C,D,E") exit 1
         if ($1 !~ /^[ABCDE]_[ABCDE]$/) exit 1
     }
@@ -31,25 +28,29 @@ check_output() {
 
 echo "Starting $TOTAL_RUNS iterations of Loco..."
 
-for i in $(seq 1 $TOTAL_RUNS); do
+# ✅ POSIX-safe loop (NO seq!)
+i=1
+while [ "$i" -le "$TOTAL_RUNS" ]; do
     echo -n "Run $i: Executing... "
-    
-    # Execute the loco command (silencing stdout to keep logs clean)
-    $CMD > /dev/null 2>&1
-    
+
+    # run silently
+    $CMD > /dev/null 2>&1 || true
+
     if check_output "$OUT_FILE"; then
-        ((PASS_COUNT++))
+        PASS_COUNT=$((PASS_COUNT + 1))
         echo "VALID"
     else
-        echo "INVALID (Criteria not met or file missing)"
+        echo "INVALID"
     fi
+
+    i=$((i + 1))
 done
 
 echo "---------------------------------------"
 echo "Results: $PASS_COUNT / $TOTAL_RUNS passed."
 
 if [ "$PASS_COUNT" -ge "$REQUIRED_PASSES" ]; then
-    echo "OVERALL SUCCESS: Quality threshold ($REQUIRED_PASSES/$TOTAL_RUNS) met."
+    echo "OVERALL SUCCESS: Quality threshold met."
     exit 0
 else
     echo "OVERALL FAILURE: Logic check failed."