From 578eb82010510075e1d35e666224836bf0e5fbd9 Mon Sep 17 00:00:00 2001
From: Hashara <kumarasinghe.k.a.s.h@gmail.com>
Date: Wed, 2 Jul 2025 11:51:56 +1000
Subject: [PATCH 01/16] add memory extract to the linux and mac

---
 .github/workflows/ci.yaml    | 36 +++++++++++++
 test_scripts/test_iqtree.ps1 | 82 +++++++++++++++++++-----------
 test_scripts/test_iqtree.sh  | 98 +++++++++++++++++++++++-------------
 3 files changed, 151 insertions(+), 65 deletions(-)

diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
index 9095dd1f..4bf935f1 100644
--- a/.github/workflows/ci.yaml
+++ b/.github/workflows/ci.yaml
@@ -70,6 +70,14 @@ jobs:
         run: |
           chmod +x test_scripts/test_iqtree.sh
           ./test_scripts/test_iqtree.sh
+          
+      - name: Upload timing log
+        if: always()  # ensures it uploads even if previous steps fail
+        uses: actions/upload-artifact@v4
+        with:
+          name: time-log-linux-${{ matrix.gcc-version }}
+          path: time_log.tsv
+
 
       - name: Run verify_results.sh
         run: |
@@ -117,6 +125,13 @@ jobs:
           chmod +x test_scripts/test_iqtree.sh
           ./test_scripts/test_iqtree.sh
 
+      - name: Upload timing log
+        if: always()  # ensures it uploads even if previous steps fail
+        uses: actions/upload-artifact@v4
+        with:
+          name: time-log-Linux-AArch64
+          path: time_log.tsv
+
       - name: Run verify_results.sh
         run: |
           chmod +x test_scripts/verify_results.sh
@@ -202,6 +217,13 @@ jobs:
           chmod +x test_scripts/test_iqtree.sh
           ./test_scripts/test_iqtree.sh
 
+      - name: Upload timing log
+        if: always()  # ensures it uploads even if previous steps fail
+        uses: actions/upload-artifact@v4
+        with:
+          name: time-log-Mac-x86-64
+          path: time_log.tsv
+
       - name: Run verify_results.sh
         run: |
           chmod +x test_scripts/verify_results.sh
@@ -250,6 +272,13 @@ jobs:
           chmod +x test_scripts/test_iqtree.sh
           ./test_scripts/test_iqtree.sh
 
+      - name: Upload timing log
+        if: always()  # ensures it uploads even if previous steps fail
+        uses: actions/upload-artifact@v4
+        with:
+          name: time-log-Mac-Arm
+          path: time_log.tsv
+
       - name: Run verify_results.sh
         run: |
           chmod +x test_scripts/verify_results.sh
@@ -362,6 +391,13 @@ jobs:
         run: |
           ./test_scripts/test_iqtree.ps1
 
+      - name: Upload timing log
+        if: always()  # ensures it uploads even if previous steps fail
+        uses: actions/upload-artifact@v4
+        with:
+          name: time-log-Windows-x86-64
+          path: time_log.tsv
+
       - name: Run verify_results.ps1
         shell: pwsh
         run: |
diff --git a/test_scripts/test_iqtree.ps1 b/test_scripts/test_iqtree.ps1
index 593c484f..cbd8e42f 100755
--- a/test_scripts/test_iqtree.ps1
+++ b/test_scripts/test_iqtree.ps1
@@ -1,71 +1,93 @@
 $SEED=73073
 
+$LOGFILE = "time_log.tsv"
+"Command`tRealTime(s)`tPeakMemory(MB)" | Out-File -FilePath $LOGFILE -Encoding utf8
+
+function Measure-IQTree {
+    param (
+        [string]$CommandLine
+    )
+
+    Write-Host "`n===== RUNNING: $CommandLine ====="
+
+    $startTime = Get-Date
+
+    # Start the process
+    $process = Start-Process powershell -ArgumentList "-Command $CommandLine" -PassThru -Wait
+
+    $endTime = Get-Date
+    $elapsed = ($endTime - $startTime).TotalSeconds
+
+    # Get peak memory (approx, in MB)
+    $memMB = [math]::Round($process.PeakWorkingSet64 / 1MB, 2)
+
+    # Append to log
+    "$CommandLine`t$elapsed`t$memMB" | Out-File -FilePath $LOGFILE -Append -Encoding utf8
+}
+
+
 # ./build/iqtree3 -s test_scripts/test_data/small.fa -p test_scripts/test_data/small.nex -m "MFP+MERGE" -T 1 -seed $SEED
 
-./build/iqtree3 -s test_scripts/test_data/turtle.fa -B 1000 -T 1 -seed $SEED
+Measure-IQTree "./build/iqtree3 -s test_scripts/test_data/turtle.fa -B 1000 -T 1 -seed $SEED"
 
-./build/iqtree3 -s test_scripts/test_data/turtle.fa -p test_scripts/test_data/turtle.nex -B 1000 -T 1 -seed $SEED
+Measure-IQTree "./build/iqtree3 -s test_scripts/test_data/turtle.fa -p test_scripts/test_data/turtle.nex -B 1000 -T 1 -seed $SEED"
 
-./build/iqtree3 -s test_scripts/test_data/turtle.fa -p test_scripts/test_data/turtle.nex -B 1000 -T 1 -m MFP+MERGE -rcluster 10 --prefix test_scripts/test_data/turtle.merge -seed $SEED
+Measure-IQTree "./build/iqtree3 -s test_scripts/test_data/turtle.fa -p test_scripts/test_data/turtle.nex -B 1000 -T 1 -m MFP+MERGE -rcluster 10 --prefix test_scripts/test_data/turtle.merge -seed $SEED"
 
 Get-Content test_scripts/test_data/turtle.fa.treefile, test_scripts/test_data/turtle.nex.treefile |
     Set-Content test_scripts/test_data/turtle.trees
-./build/iqtree3 -s test_scripts/test_data/turtle.fa -p test_scripts/test_data/turtle.merge.best_scheme.nex -z test_scripts/test_data/turtle.trees -zb 10000 -au -n 0 --prefix test_scripts/test_data/turtle.test -seed $SEED -T 1
+Measure-IQTree "./build/iqtree3 -s test_scripts/test_data/turtle.fa -p test_scripts/test_data/turtle.merge.best_scheme.nex -z test_scripts/test_data/turtle.trees -zb 10000 -au -n 0 --prefix test_scripts/test_data/turtle.test -seed $SEED -T 1"
 
-./build/iqtree3 -s test_scripts/test_data/turtle.fa -m GTR+F+I+R3+T -te test_scripts/test_data/turtle.trees -T 1 --prefix test_scripts/test_data/turtle.mix -seed $SEED
+Measure-IQTree "./build/iqtree3 -s test_scripts/test_data/turtle.fa -m GTR+F+I+R3+T -te test_scripts/test_data/turtle.trees -T 1 --prefix test_scripts/test_data/turtle.mix -seed $SEED"
 
-./build/iqtree3 -s test_scripts/test_data/turtle.fa -p test_scripts/test_data/turtle.nex.best_scheme.nex -z test_scripts/test_data/turtle.trees -n 0 -wpl --prefix test_scripts/test_data/turtle.wpl -seed $SEED -T 1
+Measure-IQTree "./build/iqtree3 -s test_scripts/test_data/turtle.fa -p test_scripts/test_data/turtle.nex.best_scheme.nex -z test_scripts/test_data/turtle.trees -n 0 -wpl --prefix test_scripts/test_data/turtle.wpl -seed $SEED -T 1"
 
-./build/iqtree3 -s test_scripts/test_data/turtle.fa -S test_scripts/test_data/turtle.nex --prefix test_scripts/test_data/turtle.loci -T 1 -seed $SEED
+Measure-IQTree "./build/iqtree3 -s test_scripts/test_data/turtle.fa -S test_scripts/test_data/turtle.nex --prefix test_scripts/test_data/turtle.loci -T 1 -seed $SEED"
 
-./build/iqtree3 -t test_scripts/test_data/turtle.nex.treefile --gcf test_scripts/test_data/turtle.loci.treefile -s test_scripts/test_data/turtle.fa --scf 100 -seed $SEED -T 1
+Measure-IQTree "./build/iqtree3 -t test_scripts/test_data/turtle.nex.treefile --gcf test_scripts/test_data/turtle.loci.treefile -s test_scripts/test_data/turtle.fa --scf 100 -seed $SEED -T 1"
 
-./build/iqtree3 -t test_scripts/test_data/turtle.fa.treefile --gcf test_scripts/test_data/turtle.loci.treefile -s test_scripts/test_data/turtle.fa --scf 100 -seed $SEED -T 1
+Measure-IQTree "./build/iqtree3 -t test_scripts/test_data/turtle.fa.treefile --gcf test_scripts/test_data/turtle.loci.treefile -s test_scripts/test_data/turtle.fa --scf 100 -seed $SEED -T 1"
 
 # link-exchange-rates model
 
-./build/iqtree3 -s test_scripts/test_data/turtle.fa -m "MIX{GTR+FO,GTR+FO}" --link-exchange-rates --prefix test_scripts/test_data/turtle.mix.link -seed $SEED -T 1
+Measure-IQTree "./build/iqtree3 -s test_scripts/test_data/turtle.fa -m `"MIX{GTR+FO,GTR+FO}`" --link-exchange-rates --prefix test_scripts/test_data/turtle.mix.link -seed $SEED -T 1"
 
-./build/iqtree3 -s test_scripts/test_data/turtle.fa -m "MIX{GTR{1,1,1,1,1,1}+FO,GTR{1,1,1,1,1,1}+FO}" --link-exchange-rates --prefix test_scripts/test_data/turtle.mix.jc.link -seed $SEED -T 1
+Measure-IQTree "./build/iqtree3 -s test_scripts/test_data/turtle.fa -m `"MIX{GTR{1,1,1,1,1,1}+FO,GTR{1,1,1,1,1,1}+FO}`" --link-exchange-rates --prefix test_scripts/test_data/turtle.mix.jc.link -seed $SEED -T 1"
 
-./build/iqtree3 -s test_scripts/test_data/turtle.fa -p test_scripts/test_data/turtle.nex -g test_scripts/test_data/turtle.constr.tree --prefix test_scripts/test_data/turtle.nex.constr -T 1 -seed $SEED
+Measure-IQTree "./build/iqtree3 -s test_scripts/test_data/turtle.fa -p test_scripts/test_data/turtle.nex -g test_scripts/test_data/turtle.constr.tree --prefix test_scripts/test_data/turtle.nex.constr -T 1 -seed $SEED"
 
-./build/iqtree3 -s test_scripts/test_data/turtle.fa -p test_scripts/test_data/turtle.nex -g test_scripts/test_data/turtle.constr.tree2 -B 1000 -alrt 1000 --prefix test_scripts/test_data/turtle.nex.constr2 -T 1 -seed $SEED
+Measure-IQTree "./build/iqtree3 -s test_scripts/test_data/turtle.fa -p test_scripts/test_data/turtle.nex -g test_scripts/test_data/turtle.constr.tree2 -B 1000 -alrt 1000 --prefix test_scripts/test_data/turtle.nex.constr2 -T 1 -seed $SEED"
 
-./build/iqtree3 -s test_scripts/test_data/turtle.fa -m "MIX+MF" --prefix test_scripts/test_data/turtle.mixfinder -T 1 -seed $SEED
+Measure-IQTree "./build/iqtree3 -s test_scripts/test_data/turtle.fa -m "MIX+MF" --prefix test_scripts/test_data/turtle.mixfinder -T 1 -seed $SEED"
 
 ## amino acid test cases
 # the data set is a subset of the turtle data set
 echo "Running amino acid test cases..."
 
-./build/iqtree3  -s test_scripts/test_data/turtle_aa.fasta -B 1000 -T 1 -seed $SEED
+Measure-IQTree "./build/iqtree3  -s test_scripts/test_data/turtle_aa.fasta -B 1000 -T 1 -seed $SEED"
 
-./build/iqtree3  -s test_scripts/test_data/turtle_aa.fasta -p test_scripts/test_data/turtle_aa.nex -B 1000 -T 1 -seed $SEED
+Measure-IQTree "./build/iqtree3  -s test_scripts/test_data/turtle_aa.fasta -p test_scripts/test_data/turtle_aa.nex -B 1000 -T 1 -seed $SEED"
 
-./build/iqtree3  -s test_scripts/test_data/turtle_aa.fasta -p test_scripts/test_data/turtle_aa.nex -B 1000 -T 1 -m MFP+MERGE -rcluster 10 --prefix test_scripts/test_data/turtle_aa.merge -seed $SEED
+Measure-IQTree "./build/iqtree3  -s test_scripts/test_data/turtle_aa.fasta -p test_scripts/test_data/turtle_aa.nex -B 1000 -T 1 -m MFP+MERGE -rcluster 10 --prefix test_scripts/test_data/turtle_aa.merge -seed $SEED"
 
 Get-Content test_scripts/test_data/turtle_aa.fasta.treefile, test_scripts/test_data/turtle_aa.nex.treefile |
     Set-Content test_scripts/test_data/turtle_aa.trees
-./build/iqtree3  -s test_scripts/test_data/turtle_aa.fasta -p test_scripts/test_data/turtle_aa.merge.best_scheme.nex -z test_scripts/test_data/turtle_aa.trees -zb 10000 -au -n 0 --prefix test_scripts/test_data/turtle_aa.test -seed $SEED -T 1
+Measure-IQTree "./build/iqtree3  -s test_scripts/test_data/turtle_aa.fasta -p test_scripts/test_data/turtle_aa.merge.best_scheme.nex -z test_scripts/test_data/turtle_aa.trees -zb 10000 -au -n 0 --prefix test_scripts/test_data/turtle_aa.test -seed $SEED -T 1"
 
-./build/iqtree3  -s test_scripts/test_data/turtle_aa.fasta -m GTR+F+I+R3+T -te test_scripts/test_data/turtle_aa.trees -T 1 --prefix test_scripts/test_data/turtle_aa.mix -seed $SEED
+Measure-IQTree "./build/iqtree3  -s test_scripts/test_data/turtle_aa.fasta -m GTR+F+I+R3+T -te test_scripts/test_data/turtle_aa.trees -T 1 --prefix test_scripts/test_data/turtle_aa.mix -seed $SEED"
 
-./build/iqtree3  -s test_scripts/test_data/turtle_aa.fasta -p test_scripts/test_data/turtle_aa.nex.best_scheme.nex -z test_scripts/test_data/turtle_aa.trees -n 0 -wpl --prefix test_scripts/test_data/turtle_aa.wpl -seed $SEED -T 1
+Measure-IQTree "./build/iqtree3  -s test_scripts/test_data/turtle_aa.fasta -p test_scripts/test_data/turtle_aa.nex.best_scheme.nex -z test_scripts/test_data/turtle_aa.trees -n 0 -wpl --prefix test_scripts/test_data/turtle_aa.wpl -seed $SEED -T 1"
 
-./build/iqtree3  -s test_scripts/test_data/turtle_aa.fasta -S test_scripts/test_data/turtle_aa.nex --prefix test_scripts/test_data/turtle_aa.loci -T 1 -seed $SEED
+Measure-IQTree "./build/iqtree3  -s test_scripts/test_data/turtle_aa.fasta -S test_scripts/test_data/turtle_aa.nex --prefix test_scripts/test_data/turtle_aa.loci -T 1 -seed $SEED"
 
-./build/iqtree3  -t test_scripts/test_data/turtle_aa.nex.treefile --gcf test_scripts/test_data/turtle_aa.loci.treefile -s test_scripts/test_data/turtle_aa.fasta --scf 100 -seed $SEED -T 1
+Measure-IQTree "./build/iqtree3  -t test_scripts/test_data/turtle_aa.nex.treefile --gcf test_scripts/test_data/turtle_aa.loci.treefile -s test_scripts/test_data/turtle_aa.fasta --scf 100 -seed $SEED -T 1"
 
-./build/iqtree3  -t test_scripts/test_data/turtle_aa.fasta.treefile --gcf test_scripts/test_data/turtle_aa.loci.treefile -s test_scripts/test_data/turtle_aa.fasta --scf 100 -seed $SEED -T 1
+Measure-IQTree "./build/iqtree3  -t test_scripts/test_data/turtle_aa.fasta.treefile --gcf test_scripts/test_data/turtle_aa.loci.treefile -s test_scripts/test_data/turtle_aa.fasta --scf 100 -seed $SEED -T 1"
 
 # link-exchange-rates model
 
-./build/iqtree3  -s test_scripts/test_data/turtle_aa.fasta -m "MIX{LG+F,WAG+F}" --prefix test_scripts/test_data/turtle_aa.mix -seed $SEED -T 1
-
-#./build/iqtree3  -s test_scripts/test_data/turtle_aa.fasta -m "MIX{GTR{1,1,1,1,1,1}+FO,GTR{1,1,1,1,1,1}+FO}" --link-exchange-rates --prefix test_scripts/test_data/turtle_aa.mix.jc.link -seed $SEED -T 1
-
-./build/iqtree3  -s test_scripts/test_data/turtle_aa.fasta -p test_scripts/test_data/turtle_aa.nex -g test_scripts/test_data/turtle.constr.tree --prefix test_scripts/test_data/turtle_aa.nex.constr -T 1 -seed $SEED
+Measure-IQTree "./build/iqtree3  -s test_scripts/test_data/turtle_aa.fasta -m `"MIX{LG+F,WAG+F}`" --prefix test_scripts/test_data/turtle_aa.mix -seed $SEED -T 1"
 
-./build/iqtree3  -s test_scripts/test_data/turtle_aa.fasta -p test_scripts/test_data/turtle_aa.nex -g test_scripts/test_data/turtle.constr.tree2 -B 1000 -alrt 1000 --prefix test_scripts/test_data/turtle_aa.nex.constr2 -T 1 -seed $SEED
+Measure-IQTree "./build/iqtree3  -s test_scripts/test_data/turtle_aa.fasta -p test_scripts/test_data/turtle_aa.nex -g test_scripts/test_data/turtle.constr.tree --prefix test_scripts/test_data/turtle_aa.nex.constr -T 1 -seed $SEED"
 
-#./build/iqtree3  -s test_scripts/test_data/turtle_aa.fasta -m "MIX+MF" --prefix test_scripts/test_data/turtle_aa.mixfinder -T 1 -seed $SEED # mixture finder is not supported for amino acid data
+Measure-IQTree "./build/iqtree3  -s test_scripts/test_data/turtle_aa.fasta -p test_scripts/test_data/turtle_aa.nex -g test_scripts/test_data/turtle.constr.tree2 -B 1000 -alrt 1000 --prefix test_scripts/test_data/turtle_aa.nex.constr2 -T 1 -seed $SEED"
diff --git a/test_scripts/test_iqtree.sh b/test_scripts/test_iqtree.sh
index 61cc7a8a..8a5d2ddf 100755
--- a/test_scripts/test_iqtree.sh
+++ b/test_scripts/test_iqtree.sh
@@ -2,76 +2,104 @@
 
 SEED=73073
 
-#build/iqtree3 -s test_scripts/test_data/small.fa -p test_scripts/test_data/small.nex -m "MFP+MERGE" -T 1 -seed $SEED
+LOGFILE="time_log.tsv"
+WD=test_scripts/test_data
+BUILD_DIR="build"
+
+# Initialize TSV file with header
+echo -e "Command\tRealTime(s)\tPeakMemory(MB)" > "$LOGFILE"
+
+run_timed() {
+    local CMD="$*"
+    echo -e "\n================ RUNNING ================="
+    echo "$CMD"
+    echo "=========================================="
+
+    local OS=$(uname)
+    local REAL USER SYS PEAK_MEM MEM_MB
+
+    if [[ "$OS" == "Darwin" ]]; then
+        # macOS
+        /usr/bin/time -l "$@" 2> tmp_time.txt
+        REAL=$(grep "real" tmp_time.txt | awk '{print $1}')
+        USER=$(grep "user" tmp_time.txt | awk '{print $1}')
+        SYS=$(grep "sys" tmp_time.txt | awk '{print $1}')
+        PEAK_MEM=$(grep "peak memory footprint" tmp_time.txt | awk '{print $1}')
+        MEM_MB=$(awk "BEGIN {printf \"%.2f\", $PEAK_MEM / (1024 * 1024)}")
+    else
+        # Linux
+        /usr/bin/time -f "%e %U %S %M" "$@" 2> tmp_time.txt
+        read REAL USER SYS MEM_KB < tmp_time.txt
+        MEM_MB=$(awk "BEGIN {printf \"%.2f\", $MEM_KB / 1024}")
+    fi
+
+    # Append to log
+    echo -e "$CMD\t$REAL\t$MEM_MB" >> "$LOGFILE"
 
-build/iqtree3 -s test_scripts/test_data/turtle.fa -B 1000 -T 1 -seed $SEED
+    rm -f tmp_time.txt
+}
 
-build/iqtree3 -s test_scripts/test_data/turtle.fa -p test_scripts/test_data/turtle.nex -B 1000 -T 1 -seed $SEED
+run_timed ${BUILD_DIR}/iqtree3 -s ${WD}/turtle.fa -B 1000 -T 1 -seed $SEED
 
-build/iqtree3 -s test_scripts/test_data/turtle.fa -p test_scripts/test_data/turtle.nex -B 1000 -T 1 -m MFP+MERGE -rcluster 10 --prefix test_scripts/test_data/turtle.merge -seed $SEED
+run_timed ${BUILD_DIR}/iqtree3 -s ${WD}/turtle.fa -p ${WD}/turtle.nex -B 1000 -T 1 -seed $SEED
 
-cat test_scripts/test_data/turtle.fa.treefile test_scripts/test_data/turtle.nex.treefile > test_scripts/test_data/turtle.trees
-build/iqtree3 -s test_scripts/test_data/turtle.fa -p test_scripts/test_data/turtle.merge.best_scheme.nex -z test_scripts/test_data/turtle.trees -zb 10000 -au -n 0 --prefix test_scripts/test_data/turtle.test -seed $SEED -T 1
+run_timed ${BUILD_DIR}/iqtree3 -s ${WD}/turtle.fa -p ${WD}/turtle.nex -B 1000 -T 1 -m MFP+MERGE -rcluster 10 --prefix ${WD}/turtle.merge -seed $SEED
 
-build/iqtree3 -s test_scripts/test_data/turtle.fa -m GTR+F+I+R3+T -te test_scripts/test_data/turtle.trees -T 1 --prefix test_scripts/test_data/turtle.mix -seed $SEED
+cat ${WD}/turtle.fa.treefile ${WD}/turtle.nex.treefile > ${WD}/turtle.trees
+run_timed ${BUILD_DIR}/iqtree3 -s ${WD}/turtle.fa -p ${WD}/turtle.merge.best_scheme.nex -z ${WD}/turtle.trees -zb 10000 -au -n 0 --prefix ${WD}/turtle.test -seed $SEED -T 1
 
-build/iqtree3 -s test_scripts/test_data/turtle.fa -p test_scripts/test_data/turtle.nex.best_scheme.nex -z test_scripts/test_data/turtle.trees -n 0 -wpl --prefix test_scripts/test_data/turtle.wpl -seed $SEED -T 1
+run_timed ${BUILD_DIR}/iqtree3 -s ${WD}/turtle.fa -m GTR+F+I+R3+T -te ${WD}/turtle.trees -T 1 --prefix ${WD}/turtle.mix -seed $SEED
 
-build/iqtree3 -s test_scripts/test_data/turtle.fa -S test_scripts/test_data/turtle.nex --prefix test_scripts/test_data/turtle.loci -T 1 -seed $SEED
+run_timed ${BUILD_DIR}/iqtree3 -s ${WD}/turtle.fa -p ${WD}/turtle.nex.best_scheme.nex -z ${WD}/turtle.trees -n 0 -wpl --prefix ${WD}/turtle.wpl -seed $SEED -T 1
 
-build/iqtree3 -t test_scripts/test_data/turtle.nex.treefile --gcf test_scripts/test_data/turtle.loci.treefile -s test_scripts/test_data/turtle.fa --scf 100 -seed $SEED -T 1
+run_timed ${BUILD_DIR}/iqtree3 -s ${WD}/turtle.fa -S ${WD}/turtle.nex --prefix ${WD}/turtle.loci -T 1 -seed $SEED
 
-build/iqtree3 -t test_scripts/test_data/turtle.fa.treefile --gcf test_scripts/test_data/turtle.loci.treefile -s test_scripts/test_data/turtle.fa --scf 100 -seed $SEED -T 1
+run_timed ${BUILD_DIR}/iqtree3 -t ${WD}/turtle.nex.treefile --gcf ${WD}/turtle.loci.treefile -s ${WD}/turtle.fa --scf 100 -seed $SEED -T 1
+
+run_timed ${BUILD_DIR}/iqtree3 -t ${WD}/turtle.fa.treefile --gcf ${WD}/turtle.loci.treefile -s ${WD}/turtle.fa --scf 100 -seed $SEED -T 1
 
 # link-exchange-rates model
 
-build/iqtree3 -s test_scripts/test_data/turtle.fa -m "MIX{GTR+FO,GTR+FO}" --link-exchange-rates --prefix test_scripts/test_data/turtle.mix.link -seed $SEED -T 1
+run_timed ${BUILD_DIR}/iqtree3 -s ${WD}/turtle.fa -m "MIX{GTR+FO,GTR+FO}" --link-exchange-rates --prefix ${WD}/turtle.mix.link -seed $SEED -T 1
 
-build/iqtree3 -s test_scripts/test_data/turtle.fa -m "MIX{GTR{1,1,1,1,1,1}+FO,GTR{1,1,1,1,1,1}+FO}" --link-exchange-rates --prefix test_scripts/test_data/turtle.mix.jc.link -seed $SEED -T 1
+run_timed ${BUILD_DIR}/iqtree3 -s ${WD}/turtle.fa -m "MIX{GTR{1,1,1,1,1,1}+FO,GTR{1,1,1,1,1,1}+FO}" --link-exchange-rates --prefix ${WD}/turtle.mix.jc.link -seed $SEED -T 1
 
-build/iqtree3 -s test_scripts/test_data/turtle.fa -p test_scripts/test_data/turtle.nex -g test_scripts/test_data/turtle.constr.tree --prefix test_scripts/test_data/turtle.nex.constr -T 1 -seed $SEED
+run_timed ${BUILD_DIR}/iqtree3 -s ${WD}/turtle.fa -p ${WD}/turtle.nex -g ${WD}/turtle.constr.tree --prefix ${WD}/turtle.nex.constr -T 1 -seed $SEED
 
-build/iqtree3 -s test_scripts/test_data/turtle.fa -p test_scripts/test_data/turtle.nex -g test_scripts/test_data/turtle.constr.tree2 -B 1000 -alrt 1000 --prefix test_scripts/test_data/turtle.nex.constr2 -T 1 -seed $SEED
+run_timed ${BUILD_DIR}/iqtree3 -s ${WD}/turtle.fa -p ${WD}/turtle.nex -g ${WD}/turtle.constr.tree2 -B 1000 -alrt 1000 --prefix ${WD}/turtle.nex.constr2 -T 1 -seed $SEED
 
-build/iqtree3 -s test_scripts/test_data/turtle.fa -m "MIX+MF" --prefix test_scripts/test_data/turtle.mixfinder -T 1 -seed $SEED
+run_timed ${BUILD_DIR}/iqtree3 -s ${WD}/turtle.fa -m "MIX+MF" --prefix ${WD}/turtle.mixfinder -T 1 -seed $SEED
 
 
 ## amino acid test cases
 # the data set is a subset of the turtle data set
 echo "Running amino acid test cases..."
-WD=test_scripts/test_data
-BUILD_DIR="build"
 AA_FASTA=${WD}/turtle_aa.fasta
 AA_NEX=${WD}/turtle_aa.nex
 AA_prefix=${WD}/turtle_aa
 
-${BUILD_DIR}/iqtree3 -s $AA_FASTA -B 1000 -T 1 -seed $SEED
+run_timed ${BUILD_DIR}/iqtree3 -s $AA_FASTA -B 1000 -T 1 -seed $SEED
 
-${BUILD_DIR}/iqtree3 -s $AA_FASTA -p $AA_NEX -B 1000 -T 1 -seed $SEED
+run_timed ${BUILD_DIR}/iqtree3 -s $AA_FASTA -p $AA_NEX -B 1000 -T 1 -seed $SEED
 
-${BUILD_DIR}/iqtree3 -s $AA_FASTA -p $AA_NEX -B 1000 -T 1 -m MFP+MERGE -rcluster 10 --prefix ${WD}/turtle_aa.merge -seed $SEED
+run_timed ${BUILD_DIR}/iqtree3 -s $AA_FASTA -p $AA_NEX -B 1000 -T 1 -m MFP+MERGE -rcluster 10 --prefix ${WD}/turtle_aa.merge -seed $SEED
 
 cat $AA_FASTA.treefile $AA_NEX.treefile > ${WD}/turtle_aa.trees
-${BUILD_DIR}/iqtree3 -s $AA_FASTA -p ${WD}/turtle_aa.merge.best_scheme.nex -z ${WD}/turtle_aa.trees -zb 10000 -au -n 0 --prefix ${WD}/turtle_aa.test -seed $SEED -T 1
+run_timed ${BUILD_DIR}/iqtree3 -s $AA_FASTA -p ${WD}/turtle_aa.merge.best_scheme.nex -z ${WD}/turtle_aa.trees -zb 10000 -au -n 0 --prefix ${WD}/turtle_aa.test -seed $SEED -T 1
 
-${BUILD_DIR}/iqtree3 -s $AA_FASTA -m GTR+F+I+R3+T -te ${WD}/turtle_aa.trees -T 1 --prefix ${WD}/turtle_aa.mix -seed $SEED
+run_timed ${BUILD_DIR}/iqtree3 -s $AA_FASTA -m GTR+F+I+R3+T -te ${WD}/turtle_aa.trees -T 1 --prefix ${WD}/turtle_aa.mix -seed $SEED
 
-${BUILD_DIR}/iqtree3 -s $AA_FASTA -p $AA_NEX.best_scheme.nex -z ${WD}/turtle_aa.trees -n 0 -wpl --prefix ${WD}/turtle_aa.wpl -seed $SEED -T 1
+run_timed ${BUILD_DIR}/iqtree3 -s $AA_FASTA -p $AA_NEX.best_scheme.nex -z ${WD}/turtle_aa.trees -n 0 -wpl --prefix ${WD}/turtle_aa.wpl -seed $SEED -T 1
 
-${BUILD_DIR}/iqtree3 -s $AA_FASTA -S $AA_NEX --prefix ${WD}/turtle_aa.loci -T 1 -seed $SEED
+run_timed ${BUILD_DIR}/iqtree3 -s $AA_FASTA -S $AA_NEX --prefix ${WD}/turtle_aa.loci -T 1 -seed $SEED
 
-${BUILD_DIR}/iqtree3 -t $AA_NEX.treefile --gcf ${WD}/turtle_aa.loci.treefile -s $AA_FASTA --scf 100 -seed $SEED -T 1
-
-${BUILD_DIR}/iqtree3 -t $AA_FASTA.treefile --gcf ${WD}/turtle_aa.loci.treefile -s $AA_FASTA --scf 100 -seed $SEED -T 1
-
-# link-exchange-rates model
+run_timed ${BUILD_DIR}/iqtree3 -t $AA_NEX.treefile --gcf ${WD}/turtle_aa.loci.treefile -s $AA_FASTA --scf 100 -seed $SEED -T 1
 
-${BUILD_DIR}/iqtree3 -s $AA_FASTA -m "MIX{LG+F,WAG+F}" --prefix ${WD}/turtle_aa.mix -seed $SEED -T 1
+run_timed ${BUILD_DIR}/iqtree3 -t $AA_FASTA.treefile --gcf ${WD}/turtle_aa.loci.treefile -s $AA_FASTA --scf 100 -seed $SEED -T 1
 
-#${BUILD_DIR}/iqtree3 -s $AA_FASTA -m "MIX{GTR{1,1,1,1,1,1}+FO,GTR{1,1,1,1,1,1}+FO}" --link-exchange-rates --prefix ${WD}/turtle_aa.mix.jc.link -seed $SEED -T 1
+run_timed ${BUILD_DIR}/iqtree3 -s $AA_FASTA -m "MIX{LG+F,WAG+F}" --prefix ${WD}/turtle_aa.mix -seed $SEED -T 1
 
-${BUILD_DIR}/iqtree3 -s $AA_FASTA -p $AA_NEX -g ${WD}/turtle.constr.tree --prefix $AA_NEX.constr -T 1 -seed $SEED
+run_timed ${BUILD_DIR}/iqtree3 -s $AA_FASTA -p $AA_NEX -g ${WD}/turtle.constr.tree --prefix $AA_NEX.constr -T 1 -seed $SEED
 
-${BUILD_DIR}/iqtree3 -s $AA_FASTA -p $AA_NEX -g ${WD}/turtle.constr.tree2 -B 1000 -alrt 1000 --prefix $AA_NEX.constr2 -T 1 -seed $SEED
+run_timed ${BUILD_DIR}/iqtree3 -s $AA_FASTA -p $AA_NEX -g ${WD}/turtle.constr.tree2 -B 1000 -alrt 1000 --prefix $AA_NEX.constr2 -T 1 -seed $SEED
 
-#${BUILD_DIR}/iqtree3 -s $AA_FASTA -m "MIX+MF" --prefix ${WD}/turtle_aa.mixfinder -T 1 -seed $SEED # mixture finder is not supported for amino acid data

From 53473be8693491685baeeeb3a89034d6c7163192 Mon Sep 17 00:00:00 2001
From: Hashara <kumarasinghe.k.a.s.h@gmail.com>
Date: Wed, 2 Jul 2025 12:51:50 +1000
Subject: [PATCH 02/16] bug fix; modify ps1 for measure memory

---
 test_scripts/test_iqtree.ps1 | 31 +++++++++++++++++++++----------
 test_scripts/test_iqtree.sh  |  2 --
 2 files changed, 21 insertions(+), 12 deletions(-)

diff --git a/test_scripts/test_iqtree.ps1 b/test_scripts/test_iqtree.ps1
index cbd8e42f..22ed581a 100755
--- a/test_scripts/test_iqtree.ps1
+++ b/test_scripts/test_iqtree.ps1
@@ -12,20 +12,33 @@ function Measure-IQTree {
 
     $startTime = Get-Date
 
-    # Start the process
-    $process = Start-Process powershell -ArgumentList "-Command $CommandLine" -PassThru -Wait
+    # Start the command in a child PowerShell process
+    $proc = Start-Process -FilePath "powershell" -ArgumentList "-NoProfile", "-Command", $CommandLine -PassThru
+    $procId = $proc.Id
+    $peakMemory = 0
+
+    # Monitor the child process's memory usage
+    while (-not $proc.HasExited) {
+        Start-Sleep -Milliseconds 200
+        try {
+            $currentMem = (Get-Process -Id $procId -ErrorAction Stop).WorkingSet64 / 1MB
+            if ($currentMem -gt $peakMemory) {
+                $peakMemory = $currentMem
+            }
+        } catch {
+            break
+        }
+    }
 
     $endTime = Get-Date
-    $elapsed = ($endTime - $startTime).TotalSeconds
+    $elapsed = [math]::Round(($endTime - $startTime).TotalSeconds, 2)
 
-    # Get peak memory (approx, in MB)
-    $memMB = [math]::Round($process.PeakWorkingSet64 / 1MB, 2)
-
-    # Append to log
-    "$CommandLine`t$elapsed`t$memMB" | Out-File -FilePath $LOGFILE -Append -Encoding utf8
+    # Write timing and memory data to log
+    "$CommandLine`t$elapsed`t$([math]::Round($peakMemory, 2))" | Out-File -FilePath $LOGFILE -Append -Encoding utf8
 }
 
 
+
 # ./build/iqtree3 -s test_scripts/test_data/small.fa -p test_scripts/test_data/small.nex -m "MFP+MERGE" -T 1 -seed $SEED
 
 Measure-IQTree "./build/iqtree3 -s test_scripts/test_data/turtle.fa -B 1000 -T 1 -seed $SEED"
@@ -74,8 +87,6 @@ Get-Content test_scripts/test_data/turtle_aa.fasta.treefile, test_scripts/test_d
     Set-Content test_scripts/test_data/turtle_aa.trees
 Measure-IQTree "./build/iqtree3  -s test_scripts/test_data/turtle_aa.fasta -p test_scripts/test_data/turtle_aa.merge.best_scheme.nex -z test_scripts/test_data/turtle_aa.trees -zb 10000 -au -n 0 --prefix test_scripts/test_data/turtle_aa.test -seed $SEED -T 1"
 
-Measure-IQTree "./build/iqtree3  -s test_scripts/test_data/turtle_aa.fasta -m GTR+F+I+R3+T -te test_scripts/test_data/turtle_aa.trees -T 1 --prefix test_scripts/test_data/turtle_aa.mix -seed $SEED"
-
 Measure-IQTree "./build/iqtree3  -s test_scripts/test_data/turtle_aa.fasta -p test_scripts/test_data/turtle_aa.nex.best_scheme.nex -z test_scripts/test_data/turtle_aa.trees -n 0 -wpl --prefix test_scripts/test_data/turtle_aa.wpl -seed $SEED -T 1"
 
 Measure-IQTree "./build/iqtree3  -s test_scripts/test_data/turtle_aa.fasta -S test_scripts/test_data/turtle_aa.nex --prefix test_scripts/test_data/turtle_aa.loci -T 1 -seed $SEED"
diff --git a/test_scripts/test_iqtree.sh b/test_scripts/test_iqtree.sh
index 8a5d2ddf..157f4197 100755
--- a/test_scripts/test_iqtree.sh
+++ b/test_scripts/test_iqtree.sh
@@ -87,8 +87,6 @@ run_timed ${BUILD_DIR}/iqtree3 -s $AA_FASTA -p $AA_NEX -B 1000 -T 1 -m MFP+MERGE
 cat $AA_FASTA.treefile $AA_NEX.treefile > ${WD}/turtle_aa.trees
 run_timed ${BUILD_DIR}/iqtree3 -s $AA_FASTA -p ${WD}/turtle_aa.merge.best_scheme.nex -z ${WD}/turtle_aa.trees -zb 10000 -au -n 0 --prefix ${WD}/turtle_aa.test -seed $SEED -T 1
 
-run_timed ${BUILD_DIR}/iqtree3 -s $AA_FASTA -m GTR+F+I+R3+T -te ${WD}/turtle_aa.trees -T 1 --prefix ${WD}/turtle_aa.mix -seed $SEED
-
 run_timed ${BUILD_DIR}/iqtree3 -s $AA_FASTA -p $AA_NEX.best_scheme.nex -z ${WD}/turtle_aa.trees -n 0 -wpl --prefix ${WD}/turtle_aa.wpl -seed $SEED -T 1
 
 run_timed ${BUILD_DIR}/iqtree3 -s $AA_FASTA -S $AA_NEX --prefix ${WD}/turtle_aa.loci -T 1 -seed $SEED

From 7b5dc3002b5d9bfa0447ce585169196633f03e45 Mon Sep 17 00:00:00 2001
From: Hashara <kumarasinghe.k.a.s.h@gmail.com>
Date: Wed, 2 Jul 2025 15:46:10 +1000
Subject: [PATCH 03/16] add memory checking for linux

---
 .github/workflows/ci.yaml                  | 41 +++-------------------
 test_scripts/test_data/expected_memory.tsv | 26 ++++++++++++++
 test_scripts/verify_memory.sh              | 39 ++++++++++++++++++++
 3 files changed, 70 insertions(+), 36 deletions(-)
 create mode 100644 test_scripts/test_data/expected_memory.tsv
 create mode 100644 test_scripts/verify_memory.sh

diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
index 4bf935f1..742a4263 100644
--- a/.github/workflows/ci.yaml
+++ b/.github/workflows/ci.yaml
@@ -70,14 +70,6 @@ jobs:
         run: |
           chmod +x test_scripts/test_iqtree.sh
           ./test_scripts/test_iqtree.sh
-          
-      - name: Upload timing log
-        if: always()  # ensures it uploads even if previous steps fail
-        uses: actions/upload-artifact@v4
-        with:
-          name: time-log-linux-${{ matrix.gcc-version }}
-          path: time_log.tsv
-
 
       - name: Run verify_results.sh
         run: |
@@ -125,13 +117,6 @@ jobs:
           chmod +x test_scripts/test_iqtree.sh
           ./test_scripts/test_iqtree.sh
 
-      - name: Upload timing log
-        if: always()  # ensures it uploads even if previous steps fail
-        uses: actions/upload-artifact@v4
-        with:
-          name: time-log-Linux-AArch64
-          path: time_log.tsv
-
       - name: Run verify_results.sh
         run: |
           chmod +x test_scripts/verify_results.sh
@@ -142,6 +127,11 @@ jobs:
           chmod +x test_scripts/verify_runtime.sh
           ./test_scripts/verify_runtime.sh 6
 
+      - name: Run verify_memory.sh
+        run: |
+          chmod +x test_scripts/verify_memory.sh
+          ./test_scripts/verify_memory.sh 6
+
   compile-linux-universal:
     name: Linux Universal
     runs-on: ubuntu-latest
@@ -217,13 +207,6 @@ jobs:
           chmod +x test_scripts/test_iqtree.sh
           ./test_scripts/test_iqtree.sh
 
-      - name: Upload timing log
-        if: always()  # ensures it uploads even if previous steps fail
-        uses: actions/upload-artifact@v4
-        with:
-          name: time-log-Mac-x86-64
-          path: time_log.tsv
-
       - name: Run verify_results.sh
         run: |
           chmod +x test_scripts/verify_results.sh
@@ -272,13 +255,6 @@ jobs:
           chmod +x test_scripts/test_iqtree.sh
           ./test_scripts/test_iqtree.sh
 
-      - name: Upload timing log
-        if: always()  # ensures it uploads even if previous steps fail
-        uses: actions/upload-artifact@v4
-        with:
-          name: time-log-Mac-Arm
-          path: time_log.tsv
-
       - name: Run verify_results.sh
         run: |
           chmod +x test_scripts/verify_results.sh
@@ -391,13 +367,6 @@ jobs:
         run: |
           ./test_scripts/test_iqtree.ps1
 
-      - name: Upload timing log
-        if: always()  # ensures it uploads even if previous steps fail
-        uses: actions/upload-artifact@v4
-        with:
-          name: time-log-Windows-x86-64
-          path: time_log.tsv
-
       - name: Run verify_results.ps1
         shell: pwsh
         run: |
diff --git a/test_scripts/test_data/expected_memory.tsv b/test_scripts/test_data/expected_memory.tsv
new file mode 100644
index 00000000..a85c9851
--- /dev/null
+++ b/test_scripts/test_data/expected_memory.tsv
@@ -0,0 +1,26 @@
+Command	diff-threshold	Linux-gcc-9	Linux-gcc-12	Linux-aarch64	mac-os-x86-64	mac-os-arm64	windows-x86
+build/iqtree3 -s test_scripts/test_data/turtle.fa -B 1000 -T 1 -seed 73073	3	18.98	18.89	17.73	13.53	15.53	57.84
+build/iqtree3 -s test_scripts/test_data/turtle.fa -p test_scripts/test_data/turtle.nex -B 1000 -T 1 -seed 73073	3	19.04	19.05	17.79	13.18	13.97	58.07
+build/iqtree3 -s test_scripts/test_data/turtle.fa -p test_scripts/test_data/turtle.nex -B 1000 -T 1 -m MFP+MERGE -rcluster 10 --prefix test_scripts/test_data/turtle.merge -seed 73073	3	19.15	19.08	17.99	13.54	15.52	58.04
+build/iqtree3 -s test_scripts/test_data/turtle.fa -p test_scripts/test_data/turtle.merge.best_scheme.nex -z test_scripts/test_data/turtle.trees -zb 10000 -au -n 0 --prefix test_scripts/test_data/turtle.test -seed 73073 -T 1	3	27.80	27.77	26.76	22.50	23.45	58
+build/iqtree3 -s test_scripts/test_data/turtle.fa -m GTR+F+I+R3+T -te test_scripts/test_data/turtle.trees -T 1 --prefix test_scripts/test_data/turtle.mix -seed 73073	3	9.79	10.05	8.92	4.39	5.44	58.15
+build/iqtree3 -s test_scripts/test_data/turtle.fa -p test_scripts/test_data/turtle.nex.best_scheme.nex -z test_scripts/test_data/turtle.trees -n 0 -wpl --prefix test_scripts/test_data/turtle.wpl -seed 73073 -T 1	3	9.27	9.30	8.18	3.61	4.75	58.3
+build/iqtree3 -s test_scripts/test_data/turtle.fa -S test_scripts/test_data/turtle.nex --prefix test_scripts/test_data/turtle.loci -T 1 -seed 73073	3	10.43	10.55	8.79	5.66	6.59	58.02
+build/iqtree3 -t test_scripts/test_data/turtle.nex.treefile --gcf test_scripts/test_data/turtle.loci.treefile -s test_scripts/test_data/turtle.fa --scf 100 -seed 73073 -T 1	3	6.30	6.55	5.92	2.29	2.75	55.18
+build/iqtree3 -t test_scripts/test_data/turtle.fa.treefile --gcf test_scripts/test_data/turtle.loci.treefile -s test_scripts/test_data/turtle.fa --scf 100 -seed 73073 -T 1	3	6.30	6.55	5.92	2.27	3.00	38.01
+build/iqtree3 -s test_scripts/test_data/turtle.fa -m MIX{GTR+FO,GTR+FO} --link-exchange-rates --prefix test_scripts/test_data/turtle.mix.link -seed 73073 -T 1	3	9.17	9.05	7.92	3.47	4.80	55.19
+build/iqtree3 -s test_scripts/test_data/turtle.fa -m MIX{GTR{1,1,1,1,1,1}+FO,GTR{1,1,1,1,1,1}+FO} --link-exchange-rates --prefix test_scripts/test_data/turtle.mix.jc.link -seed 73073 -T 1	3	9.17	8.84	7.92	3.74	4.49	54.57
+build/iqtree3 -s test_scripts/test_data/turtle.fa -p test_scripts/test_data/turtle.nex -g test_scripts/test_data/turtle.constr.tree --prefix test_scripts/test_data/turtle.nex.constr -T 1 -seed 73073	3	10.57	10.45	8.80	5.86	6.78	58.03
+build/iqtree3 -s test_scripts/test_data/turtle.fa -p test_scripts/test_data/turtle.nex -g test_scripts/test_data/turtle.constr.tree2 -B 1000 -alrt 1000 --prefix test_scripts/test_data/turtle.nex.constr2 -T 1 -seed 73073	3	18.82	18.70	17.55	13.29	14.00	58.3
+build/iqtree3 -s test_scripts/test_data/turtle.fa -m MIX+MF --prefix test_scripts/test_data/turtle.mixfinder -T 1 -seed 73073	3	14.55	15.50	11.68	9.21	9.28	57.19
+build/iqtree3 -s test_scripts/test_data/turtle_aa.fasta -B 1000 -T 1 -seed 73073	3	25.57	25.66	24.47	21.26	12.72	58
+build/iqtree3 -s test_scripts/test_data/turtle_aa.fasta -p test_scripts/test_data/turtle_aa.nex -B 1000 -T 1 -seed 73073	3	76.22	67.05	26.73	23.80	16.39	58.03
+build/iqtree3 -s test_scripts/test_data/turtle_aa.fasta -p test_scripts/test_data/turtle_aa.nex -B 1000 -T 1 -m MFP+MERGE -rcluster 10 --prefix test_scripts/test_data/turtle_aa.merge -seed 73073	3	27.49	27.51	26.11	22.30	16.56	58.13
+build/iqtree3 -s test_scripts/test_data/turtle_aa.fasta -p test_scripts/test_data/turtle_aa.merge.best_scheme.nex -z test_scripts/test_data/turtle_aa.trees -zb 10000 -au -n 0 --prefix test_scripts/test_data/turtle_aa.test -seed 73073 -T 1	3	33.53	33.46	32.43	31.32	30.30	57.96
+build/iqtree3 -s test_scripts/test_data/turtle_aa.fasta -p test_scripts/test_data/turtle_aa.nex.best_scheme.nex -z test_scripts/test_data/turtle_aa.trees -n 0 -wpl --prefix test_scripts/test_data/turtle_aa.wpl -seed 73073 -T 1	3	18.26	18.32	16.95	14.17	12.81	58.07
+build/iqtree3 -s test_scripts/test_data/turtle_aa.fasta -S test_scripts/test_data/turtle_aa.nex --prefix test_scripts/test_data/turtle_aa.loci -T 1 -seed 73073	3	16.49	16.11	13.53	11.07	9.69	57.98
+build/iqtree3 -t test_scripts/test_data/turtle_aa.nex.treefile --gcf test_scripts/test_data/turtle_aa.loci.treefile -s test_scripts/test_data/turtle_aa.fasta --scf 100 -seed 73073 -T 1	3	6.30	6.55	5.92	2.38	3.06	54.57
+build/iqtree3 -t test_scripts/test_data/turtle_aa.fasta.treefile --gcf test_scripts/test_data/turtle_aa.loci.treefile -s test_scripts/test_data/turtle_aa.fasta --scf 100 -seed 73073 -T 1	3	6.29	6.55	5.93	2.29	3.09	55.05
+build/iqtree3 -s test_scripts/test_data/turtle_aa.fasta -m MIX{LG+F,WAG+F} --prefix test_scripts/test_data/turtle_aa.mix -seed 73073 -T 1	3	11.79	11.80	10.67	6.39	6.78	55.1
+build/iqtree3 -s test_scripts/test_data/turtle_aa.fasta -p test_scripts/test_data/turtle_aa.nex -g test_scripts/test_data/turtle.constr.tree --prefix test_scripts/test_data/turtle_aa.nex.constr -T 1 -seed 73073	3	43.78	22.79	18.28	18.67	10.61	58.11
+build/iqtree3 -s test_scripts/test_data/turtle_aa.fasta -p test_scripts/test_data/turtle_aa.nex -g test_scripts/test_data/turtle.constr.tree2 -B 1000 -alrt 1000 --prefix test_scripts/test_data/turtle_aa.nex.constr2 -T 1 -seed 73073	3	50.73	51.92	26.53	23.55	16.72	57.86
diff --git a/test_scripts/verify_memory.sh b/test_scripts/verify_memory.sh
new file mode 100644
index 00000000..eaa1d6ab
--- /dev/null
+++ b/test_scripts/verify_memory.sh
@@ -0,0 +1,39 @@
+#!/bin/bash
+expected_column="$1"
+
+WD="test_scripts/test_data"
+input_file="${WD}/expected_memory.tsv"
+reported_file="${WD}/time_log.tsv"
+selected_columns_file="${WD}/selected_columns.tsv"
+cut -f1,2,3,"$expected_column" "$input_file" > "${selected_columns_file}"
+final_file="${WD}/combined_with_reported.tsv"
+
+# assuming the reported file and expected file have the same order of commands
+cut -f"$expected_column" "$reported_file" > /tmp/reported_column.tsv
+paste "$selected_columns_file" /tmp/reported_column.txt > "$final_file"
+
+
+fail_count=0
+
+echo -e "Command\tExpected\tThreshold\tActual\tExceededBy"
+
+# Skip header
+tail -n +2 "$input_file" | while IFS=$'\t' read -r command threshold expected reported; do
+    # Compute allowed = expected + threshold
+    allowed=$(echo "$expected + $threshold" | bc -l)
+    # Check if reported > allowed
+    is_exceed=$(echo "$reported > $allowed" | bc -l)
+    if [ "$is_exceed" -eq 1 ]; then
+        diff=$(echo "$reported - $expected" | bc -l)
+        echo -e "$command\t$expected\t$threshold\t$reported\t$diff"
+        ((fail_count++))
+    fi
+done
+
+echo
+if [ "$fail_count" -eq 0 ]; then
+    echo "✅ All runtime checks passed."
+else
+    echo "❌ $fail_count checks failed."
+    exit 1
+fi

From ced25348ba5aa12f771bf245eba30dc766f0fd3a Mon Sep 17 00:00:00 2001
From: Hashara <kumarasinghe.k.a.s.h@gmail.com>
Date: Wed, 2 Jul 2025 16:07:25 +1000
Subject: [PATCH 04/16] bug fix: memory checking for linux

---
 test_scripts/verify_memory.sh | 25 ++++++++++++++-----------
 1 file changed, 14 insertions(+), 11 deletions(-)

diff --git a/test_scripts/verify_memory.sh b/test_scripts/verify_memory.sh
index eaa1d6ab..1bb95e79 100644
--- a/test_scripts/verify_memory.sh
+++ b/test_scripts/verify_memory.sh
@@ -3,14 +3,14 @@ expected_column="$1"
 
 WD="test_scripts/test_data"
 input_file="${WD}/expected_memory.tsv"
-reported_file="${WD}/time_log.tsv"
+reported_file="time_log.tsv"
 selected_columns_file="${WD}/selected_columns.tsv"
-cut -f1,2,3,"$expected_column" "$input_file" > "${selected_columns_file}"
+cut -f1,2,"$expected_column" "$input_file" > "${selected_columns_file}"
 final_file="${WD}/combined_with_reported.tsv"
 
 # assuming the reported file and expected file have the same order of commands
-cut -f"$expected_column" "$reported_file" > /tmp/reported_column.tsv
-paste "$selected_columns_file" /tmp/reported_column.txt > "$final_file"
+cut -f3 "$reported_file" > /tmp/reported_column.tsv
+paste "$selected_columns_file" /tmp/reported_column.tsv > "$final_file"
 
 
 fail_count=0
@@ -18,19 +18,22 @@ fail_count=0
 echo -e "Command\tExpected\tThreshold\tActual\tExceededBy"
 
 # Skip header
-tail -n +2 "$input_file" | while IFS=$'\t' read -r command threshold expected reported; do
-    # Compute allowed = expected + threshold
+while IFS=$'\t' read -r command threshold expected reported; do
     allowed=$(echo "$expected + $threshold" | bc -l)
-    # Check if reported > allowed
     is_exceed=$(echo "$reported > $allowed" | bc -l)
-    if [ "$is_exceed" -eq 1 ]; then
+
+    if [ "$is_exceed" = "1" ]; then
         diff=$(echo "$reported - $expected" | bc -l)
-        echo -e "$command\t$expected\t$threshold\t$reported\t$diff"
+        echo "❌ $command exceeded the allowed memory usage."
+        echo "Expected: $expected MB, Threshold: $threshold MB, Reported: $reported MB"
         ((fail_count++))
+    else
+        echo "✅ $command passed the memory check."
+        diff=$(echo "$reported - $expected" | bc -l)
+        echo -e "$command\t$expected\t$threshold\t$reported\t$diff"
     fi
-done
+done < <(tail -n +2 "$final_file")
 
-echo
 if [ "$fail_count" -eq 0 ]; then
     echo "✅ All runtime checks passed."
 else

From 8a2ac58dda48b19f9a52e1f5e41757a715db8c22 Mon Sep 17 00:00:00 2001
From: Hashara <kumarasinghe.k.a.s.h@gmail.com>
Date: Thu, 3 Jul 2025 11:20:55 +1000
Subject: [PATCH 05/16]  memory checking for linux and mac

---
 .github/workflows/ci.yaml | 15 +++++++++++++++
 1 file changed, 15 insertions(+)

diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
index 742a4263..152a70f7 100644
--- a/.github/workflows/ci.yaml
+++ b/.github/workflows/ci.yaml
@@ -81,6 +81,11 @@ jobs:
           chmod +x test_scripts/verify_runtime.sh
           ./test_scripts/verify_runtime.sh "${{ matrix.runtime-arg }}"
 
+      - name: Run verify_memory.sh
+        run: |
+          chmod +x test_scripts/verify_memory.sh
+          ./test_scripts/verify_memory.sh "${{ matrix.runtime-arg }}"
+
   build-linux-aarch64:
     name: Linux aarch64
     runs-on: ubuntu-22.04-arm
@@ -217,6 +222,11 @@ jobs:
           chmod +x test_scripts/verify_runtime.sh
           ./test_scripts/verify_runtime.sh 7
 
+      - name: Run verify_memory.sh
+        run: |
+          chmod +x test_scripts/verify_memory.sh
+          ./test_scripts/verify_memory.sh 7
+
   build-macos-arm:
     name: Mac OS ARM64
     runs-on: macos-14
@@ -265,6 +275,11 @@ jobs:
           chmod +x test_scripts/verify_runtime.sh
           ./test_scripts/verify_runtime.sh 8
 
+      - name: Run verify_memory.sh
+        run: |
+          chmod +x test_scripts/verify_memory.sh
+          ./test_scripts/verify_memory.sh 8
+
   compile-mac-universal:
     name: Mac OS Universal
     runs-on: macos-14

From c1c7f002b6d96c4a639af1ab166a6f8253b8f628 Mon Sep 17 00:00:00 2001
From: Hashara <kumarasinghe.k.a.s.h@gmail.com>
Date: Thu, 3 Jul 2025 13:15:42 +1000
Subject: [PATCH 06/16]  memory checking for windows

---
 .github/workflows/ci.yaml      |  4 ++
 test_scripts/verify_memory.ps1 | 68 ++++++++++++++++++++++++++++++++++
 test_scripts/verify_memory.sh  |  2 +-
 3 files changed, 73 insertions(+), 1 deletion(-)
 create mode 100644 test_scripts/verify_memory.ps1

diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
index 152a70f7..ffe32155 100644
--- a/.github/workflows/ci.yaml
+++ b/.github/workflows/ci.yaml
@@ -391,3 +391,7 @@ jobs:
         shell: pwsh
         run: |
           ./test_scripts/verify_runtime.ps1
+
+      - name: Run verify_memory.sh
+        run: |
+          ./test_scripts/verify_memory.ps1
\ No newline at end of file
diff --git a/test_scripts/verify_memory.ps1 b/test_scripts/verify_memory.ps1
new file mode 100644
index 00000000..c962394c
--- /dev/null
+++ b/test_scripts/verify_memory.ps1
@@ -0,0 +1,68 @@
+param (
+    [int]$ExpectedColumn  # 3 = ExpectedMemory or Runtime
+)
+
+$WD = "test_scripts/test_data"
+$expectedFile = Join-Path $WD "expected_memory.tsv"
+$reportedFile = "time_log.tsv"
+$selectedColumnsFile = Join-Path $WD "selected_columns.tsv"
+$reportedColumnFile = "$env:TEMP\reported_column.tsv"
+$finalFile = Join-Path $WD "combined_with_reported.tsv"
+
+# Read expected: Command, Threshold, ExpectedColumn
+$expectedLines = Get-Content $expectedFile | Select-Object -Skip 1
+$selectedColumns = foreach ($line in $expectedLines) {
+    $parts = $line -split "`t"
+    "$($parts[0])`t$($parts[1])`t$($parts[$ExpectedColumn - 1])"
+}
+$selectedColumns | Set-Content $selectedColumnsFile
+
+# Read reported column from time_log.tsv (column 3 = RealTime, 4 = Memory)
+$reportedLines = Get-Content $reportedFile | Select-Object -Skip 1
+$reportedColumn = foreach ($line in $reportedLines) {
+    $parts = $line -split "`t"
+    $parts[2]  # column 3 = memory (0-based index)
+}
+$reportedColumn | Set-Content $reportedColumnFile
+
+# Combine both files
+$combinedLines = @()
+for ($i = 0; $i -lt $selectedColumns.Count; $i++) {
+    $combinedLines += "$($selectedColumns[$i])`t$($reportedColumn[$i])"
+}
+$combinedLines | Set-Content $finalFile
+
+# Now compare
+Write-Host "`nCommand`tExpected`tThreshold`tActual`tExceededBy"
+$failCount = 0
+$finalLines = Get-Content $finalFile
+
+foreach ($line in $finalLines) {
+    $parts = $line -split "`t"
+    $command = $parts[0]
+    $threshold = [double]$parts[1]
+    $expected = [double]$parts[2]
+    $reported = [double]$parts[3]
+
+    $allowed = $expected + $threshold
+    $exceededBy = $reported - $expected
+
+    if ($reported -gt $allowed) {
+        Write-Host "❌ $command exceeded the allowed usage."
+        Write-Host "Expected: $expected MB, Threshold: $threshold MB, Reported: $reported MB"
+        $failCount++
+    } else {
+        Write-Host "✅ $command passed the check."
+        Write-Host "Expected: $expected MB, Threshold: $threshold MB, Reported: $reported MB"
+    }
+}
+
+Write-Host ""
+
+if ($failCount -eq 0) {
+    Write-Host "✅ All runtime/memory checks passed."
+    exit 0
+} else {
+    Write-Host "❌ $failCount checks failed."
+    exit 1
+}
diff --git a/test_scripts/verify_memory.sh b/test_scripts/verify_memory.sh
index 1bb95e79..f7c12cef 100644
--- a/test_scripts/verify_memory.sh
+++ b/test_scripts/verify_memory.sh
@@ -30,7 +30,7 @@ while IFS=$'\t' read -r command threshold expected reported; do
     else
         echo "✅ $command passed the memory check."
         diff=$(echo "$reported - $expected" | bc -l)
-        echo -e "$command\t$expected\t$threshold\t$reported\t$diff"
+        echo "Expected: $expected MB, Threshold: $threshold MB, Reported: $reported MB"
     fi
 done < <(tail -n +2 "$final_file")
 

From fd310c806a4ed895f5c9b06d9806f2aa9e90c64c Mon Sep 17 00:00:00 2001
From: Hashara <kumarasinghe.k.a.s.h@gmail.com>
Date: Thu, 3 Jul 2025 14:10:07 +1000
Subject: [PATCH 07/16] fix index in memory checking

---
 .github/workflows/ci.yaml                  | 10 ++++++----
 test_scripts/test_data/expected_memory.tsv |  2 +-
 test_scripts/verify_memory.ps1             |  2 +-
 3 files changed, 8 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
index ffe32155..8f3537d1 100644
--- a/.github/workflows/ci.yaml
+++ b/.github/workflows/ci.yaml
@@ -25,11 +25,13 @@ jobs:
             cmake-version: 3.14.7
             upload: true
             runtime-arg: 4
+            memory-arg: 3
           # Latest supported gcc and cmake versions
           - gcc-version: 12
             cmake-version: latest
             upload: false
             runtime-arg: 5
+            memory-arg: 4
 
     steps:
       - name: Checkout
@@ -84,7 +86,7 @@ jobs:
       - name: Run verify_memory.sh
         run: |
           chmod +x test_scripts/verify_memory.sh
-          ./test_scripts/verify_memory.sh "${{ matrix.runtime-arg }}"
+          ./test_scripts/verify_memory.sh "${{ matrix.memory-arg }}"
 
   build-linux-aarch64:
     name: Linux aarch64
@@ -135,7 +137,7 @@ jobs:
       - name: Run verify_memory.sh
         run: |
           chmod +x test_scripts/verify_memory.sh
-          ./test_scripts/verify_memory.sh 6
+          ./test_scripts/verify_memory.sh 5
 
   compile-linux-universal:
     name: Linux Universal
@@ -225,7 +227,7 @@ jobs:
       - name: Run verify_memory.sh
         run: |
           chmod +x test_scripts/verify_memory.sh
-          ./test_scripts/verify_memory.sh 7
+          ./test_scripts/verify_memory.sh 6
 
   build-macos-arm:
     name: Mac OS ARM64
@@ -278,7 +280,7 @@ jobs:
       - name: Run verify_memory.sh
         run: |
           chmod +x test_scripts/verify_memory.sh
-          ./test_scripts/verify_memory.sh 8
+          ./test_scripts/verify_memory.sh 7
 
   compile-mac-universal:
     name: Mac OS Universal
diff --git a/test_scripts/test_data/expected_memory.tsv b/test_scripts/test_data/expected_memory.tsv
index a85c9851..983ad54f 100644
--- a/test_scripts/test_data/expected_memory.tsv
+++ b/test_scripts/test_data/expected_memory.tsv
@@ -22,5 +22,5 @@ build/iqtree3 -s test_scripts/test_data/turtle_aa.fasta -S test_scripts/test_dat
 build/iqtree3 -t test_scripts/test_data/turtle_aa.nex.treefile --gcf test_scripts/test_data/turtle_aa.loci.treefile -s test_scripts/test_data/turtle_aa.fasta --scf 100 -seed 73073 -T 1	3	6.30	6.55	5.92	2.38	3.06	54.57
 build/iqtree3 -t test_scripts/test_data/turtle_aa.fasta.treefile --gcf test_scripts/test_data/turtle_aa.loci.treefile -s test_scripts/test_data/turtle_aa.fasta --scf 100 -seed 73073 -T 1	3	6.29	6.55	5.93	2.29	3.09	55.05
 build/iqtree3 -s test_scripts/test_data/turtle_aa.fasta -m MIX{LG+F,WAG+F} --prefix test_scripts/test_data/turtle_aa.mix -seed 73073 -T 1	3	11.79	11.80	10.67	6.39	6.78	55.1
-build/iqtree3 -s test_scripts/test_data/turtle_aa.fasta -p test_scripts/test_data/turtle_aa.nex -g test_scripts/test_data/turtle.constr.tree --prefix test_scripts/test_data/turtle_aa.nex.constr -T 1 -seed 73073	3	43.78	22.79	18.28	18.67	10.61	58.11
+build/iqtree3 -s test_scripts/test_data/turtle_aa.fasta -p test_scripts/test_data/turtle_aa.nex -g test_scripts/test_data/turtle.constr.tree --prefix test_scripts/test_data/turtle_aa.nex.constr -T 1 -seed 73073	3	43.78	27.91	18.28	18.67	10.61	58.11
 build/iqtree3 -s test_scripts/test_data/turtle_aa.fasta -p test_scripts/test_data/turtle_aa.nex -g test_scripts/test_data/turtle.constr.tree2 -B 1000 -alrt 1000 --prefix test_scripts/test_data/turtle_aa.nex.constr2 -T 1 -seed 73073	3	50.73	51.92	26.53	23.55	16.72	57.86
diff --git a/test_scripts/verify_memory.ps1 b/test_scripts/verify_memory.ps1
index c962394c..6e7ef551 100644
--- a/test_scripts/verify_memory.ps1
+++ b/test_scripts/verify_memory.ps1
@@ -1,5 +1,5 @@
 param (
-    [int]$ExpectedColumn  # 3 = ExpectedMemory or Runtime
+    [int]   $ExpectedColumn = 7
 )
 
 $WD = "test_scripts/test_data"

From 5c1c5b82dedadc7a5f4f387f5dfc21bdc6f9cfeb Mon Sep 17 00:00:00 2001
From: Hashara <kumarasinghe.k.a.s.h@gmail.com>
Date: Thu, 3 Jul 2025 15:20:53 +1000
Subject: [PATCH 08/16] fix index in memory checking, update values for failing
 checks

---
 test_scripts/test_data/expected_memory.tsv | 8 ++++----
 test_scripts/verify_memory.ps1             | 2 +-
 2 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/test_scripts/test_data/expected_memory.tsv b/test_scripts/test_data/expected_memory.tsv
index 983ad54f..592ffefa 100644
--- a/test_scripts/test_data/expected_memory.tsv
+++ b/test_scripts/test_data/expected_memory.tsv
@@ -13,14 +13,14 @@ build/iqtree3 -s test_scripts/test_data/turtle.fa -m MIX{GTR{1,1,1,1,1,1}+FO,GTR
 build/iqtree3 -s test_scripts/test_data/turtle.fa -p test_scripts/test_data/turtle.nex -g test_scripts/test_data/turtle.constr.tree --prefix test_scripts/test_data/turtle.nex.constr -T 1 -seed 73073	3	10.57	10.45	8.80	5.86	6.78	58.03
 build/iqtree3 -s test_scripts/test_data/turtle.fa -p test_scripts/test_data/turtle.nex -g test_scripts/test_data/turtle.constr.tree2 -B 1000 -alrt 1000 --prefix test_scripts/test_data/turtle.nex.constr2 -T 1 -seed 73073	3	18.82	18.70	17.55	13.29	14.00	58.3
 build/iqtree3 -s test_scripts/test_data/turtle.fa -m MIX+MF --prefix test_scripts/test_data/turtle.mixfinder -T 1 -seed 73073	3	14.55	15.50	11.68	9.21	9.28	57.19
-build/iqtree3 -s test_scripts/test_data/turtle_aa.fasta -B 1000 -T 1 -seed 73073	3	25.57	25.66	24.47	21.26	12.72	58
+build/iqtree3 -s test_scripts/test_data/turtle_aa.fasta -B 1000 -T 1 -seed 73073	3	25.57	25.66	24.47	21.26	15.77	58
 build/iqtree3 -s test_scripts/test_data/turtle_aa.fasta -p test_scripts/test_data/turtle_aa.nex -B 1000 -T 1 -seed 73073	3	76.22	67.05	26.73	23.80	16.39	58.03
-build/iqtree3 -s test_scripts/test_data/turtle_aa.fasta -p test_scripts/test_data/turtle_aa.nex -B 1000 -T 1 -m MFP+MERGE -rcluster 10 --prefix test_scripts/test_data/turtle_aa.merge -seed 73073	3	27.49	27.51	26.11	22.30	16.56	58.13
+build/iqtree3 -s test_scripts/test_data/turtle_aa.fasta -p test_scripts/test_data/turtle_aa.nex -B 1000 -T 1 -m MFP+MERGE -rcluster 10 --prefix test_scripts/test_data/turtle_aa.merge -seed 73073	3	35.97	27.51	26.11	22.30	16.56	58.13
 build/iqtree3 -s test_scripts/test_data/turtle_aa.fasta -p test_scripts/test_data/turtle_aa.merge.best_scheme.nex -z test_scripts/test_data/turtle_aa.trees -zb 10000 -au -n 0 --prefix test_scripts/test_data/turtle_aa.test -seed 73073 -T 1	3	33.53	33.46	32.43	31.32	30.30	57.96
 build/iqtree3 -s test_scripts/test_data/turtle_aa.fasta -p test_scripts/test_data/turtle_aa.nex.best_scheme.nex -z test_scripts/test_data/turtle_aa.trees -n 0 -wpl --prefix test_scripts/test_data/turtle_aa.wpl -seed 73073 -T 1	3	18.26	18.32	16.95	14.17	12.81	58.07
 build/iqtree3 -s test_scripts/test_data/turtle_aa.fasta -S test_scripts/test_data/turtle_aa.nex --prefix test_scripts/test_data/turtle_aa.loci -T 1 -seed 73073	3	16.49	16.11	13.53	11.07	9.69	57.98
 build/iqtree3 -t test_scripts/test_data/turtle_aa.nex.treefile --gcf test_scripts/test_data/turtle_aa.loci.treefile -s test_scripts/test_data/turtle_aa.fasta --scf 100 -seed 73073 -T 1	3	6.30	6.55	5.92	2.38	3.06	54.57
 build/iqtree3 -t test_scripts/test_data/turtle_aa.fasta.treefile --gcf test_scripts/test_data/turtle_aa.loci.treefile -s test_scripts/test_data/turtle_aa.fasta --scf 100 -seed 73073 -T 1	3	6.29	6.55	5.93	2.29	3.09	55.05
 build/iqtree3 -s test_scripts/test_data/turtle_aa.fasta -m MIX{LG+F,WAG+F} --prefix test_scripts/test_data/turtle_aa.mix -seed 73073 -T 1	3	11.79	11.80	10.67	6.39	6.78	55.1
-build/iqtree3 -s test_scripts/test_data/turtle_aa.fasta -p test_scripts/test_data/turtle_aa.nex -g test_scripts/test_data/turtle.constr.tree --prefix test_scripts/test_data/turtle_aa.nex.constr -T 1 -seed 73073	3	43.78	27.91	18.28	18.67	10.61	58.11
-build/iqtree3 -s test_scripts/test_data/turtle_aa.fasta -p test_scripts/test_data/turtle_aa.nex -g test_scripts/test_data/turtle.constr.tree2 -B 1000 -alrt 1000 --prefix test_scripts/test_data/turtle_aa.nex.constr2 -T 1 -seed 73073	3	50.73	51.92	26.53	23.55	16.72	57.86
+build/iqtree3 -s test_scripts/test_data/turtle_aa.fasta -p test_scripts/test_data/turtle_aa.nex -g test_scripts/test_data/turtle.constr.tree --prefix test_scripts/test_data/turtle_aa.nex.constr -T 1 -seed 73073	3	43.78	35.18	18.28	18.67	10.61	58.11
+build/iqtree3 -s test_scripts/test_data/turtle_aa.fasta -p test_scripts/test_data/turtle_aa.nex -g test_scripts/test_data/turtle.constr.tree2 -B 1000 -alrt 1000 --prefix test_scripts/test_data/turtle_aa.nex.constr2 -T 1 -seed 73073	3	50.73	59.30	26.53	23.55	16.72	57.86
diff --git a/test_scripts/verify_memory.ps1 b/test_scripts/verify_memory.ps1
index 6e7ef551..5d7e2f28 100644
--- a/test_scripts/verify_memory.ps1
+++ b/test_scripts/verify_memory.ps1
@@ -1,5 +1,5 @@
 param (
-    [int]   $ExpectedColumn = 7
+    [int]   $ExpectedColumn = 8
 )
 
 $WD = "test_scripts/test_data"

From c9c09f4af7245a4965d7bfac4594442f0b7cd066 Mon Sep 17 00:00:00 2001
From: Hashara <kumarasinghe.k.a.s.h@gmail.com>
Date: Thu, 3 Jul 2025 15:48:10 +1000
Subject: [PATCH 09/16] update values for failing checks

---
 test_scripts/test_data/expected_memory.tsv   | 50 ++++++++++----------
 test_scripts/test_data/expected_runtimes.tsv | 24 +++++-----
 test_scripts/test_iqtree.ps1                 | 20 ++++++--
 3 files changed, 53 insertions(+), 41 deletions(-)

diff --git a/test_scripts/test_data/expected_memory.tsv b/test_scripts/test_data/expected_memory.tsv
index 592ffefa..c4ac1eec 100644
--- a/test_scripts/test_data/expected_memory.tsv
+++ b/test_scripts/test_data/expected_memory.tsv
@@ -1,26 +1,26 @@
 Command	diff-threshold	Linux-gcc-9	Linux-gcc-12	Linux-aarch64	mac-os-x86-64	mac-os-arm64	windows-x86
-build/iqtree3 -s test_scripts/test_data/turtle.fa -B 1000 -T 1 -seed 73073	3	18.98	18.89	17.73	13.53	15.53	57.84
-build/iqtree3 -s test_scripts/test_data/turtle.fa -p test_scripts/test_data/turtle.nex -B 1000 -T 1 -seed 73073	3	19.04	19.05	17.79	13.18	13.97	58.07
-build/iqtree3 -s test_scripts/test_data/turtle.fa -p test_scripts/test_data/turtle.nex -B 1000 -T 1 -m MFP+MERGE -rcluster 10 --prefix test_scripts/test_data/turtle.merge -seed 73073	3	19.15	19.08	17.99	13.54	15.52	58.04
-build/iqtree3 -s test_scripts/test_data/turtle.fa -p test_scripts/test_data/turtle.merge.best_scheme.nex -z test_scripts/test_data/turtle.trees -zb 10000 -au -n 0 --prefix test_scripts/test_data/turtle.test -seed 73073 -T 1	3	27.80	27.77	26.76	22.50	23.45	58
-build/iqtree3 -s test_scripts/test_data/turtle.fa -m GTR+F+I+R3+T -te test_scripts/test_data/turtle.trees -T 1 --prefix test_scripts/test_data/turtle.mix -seed 73073	3	9.79	10.05	8.92	4.39	5.44	58.15
-build/iqtree3 -s test_scripts/test_data/turtle.fa -p test_scripts/test_data/turtle.nex.best_scheme.nex -z test_scripts/test_data/turtle.trees -n 0 -wpl --prefix test_scripts/test_data/turtle.wpl -seed 73073 -T 1	3	9.27	9.30	8.18	3.61	4.75	58.3
-build/iqtree3 -s test_scripts/test_data/turtle.fa -S test_scripts/test_data/turtle.nex --prefix test_scripts/test_data/turtle.loci -T 1 -seed 73073	3	10.43	10.55	8.79	5.66	6.59	58.02
-build/iqtree3 -t test_scripts/test_data/turtle.nex.treefile --gcf test_scripts/test_data/turtle.loci.treefile -s test_scripts/test_data/turtle.fa --scf 100 -seed 73073 -T 1	3	6.30	6.55	5.92	2.29	2.75	55.18
-build/iqtree3 -t test_scripts/test_data/turtle.fa.treefile --gcf test_scripts/test_data/turtle.loci.treefile -s test_scripts/test_data/turtle.fa --scf 100 -seed 73073 -T 1	3	6.30	6.55	5.92	2.27	3.00	38.01
-build/iqtree3 -s test_scripts/test_data/turtle.fa -m MIX{GTR+FO,GTR+FO} --link-exchange-rates --prefix test_scripts/test_data/turtle.mix.link -seed 73073 -T 1	3	9.17	9.05	7.92	3.47	4.80	55.19
-build/iqtree3 -s test_scripts/test_data/turtle.fa -m MIX{GTR{1,1,1,1,1,1}+FO,GTR{1,1,1,1,1,1}+FO} --link-exchange-rates --prefix test_scripts/test_data/turtle.mix.jc.link -seed 73073 -T 1	3	9.17	8.84	7.92	3.74	4.49	54.57
-build/iqtree3 -s test_scripts/test_data/turtle.fa -p test_scripts/test_data/turtle.nex -g test_scripts/test_data/turtle.constr.tree --prefix test_scripts/test_data/turtle.nex.constr -T 1 -seed 73073	3	10.57	10.45	8.80	5.86	6.78	58.03
-build/iqtree3 -s test_scripts/test_data/turtle.fa -p test_scripts/test_data/turtle.nex -g test_scripts/test_data/turtle.constr.tree2 -B 1000 -alrt 1000 --prefix test_scripts/test_data/turtle.nex.constr2 -T 1 -seed 73073	3	18.82	18.70	17.55	13.29	14.00	58.3
-build/iqtree3 -s test_scripts/test_data/turtle.fa -m MIX+MF --prefix test_scripts/test_data/turtle.mixfinder -T 1 -seed 73073	3	14.55	15.50	11.68	9.21	9.28	57.19
-build/iqtree3 -s test_scripts/test_data/turtle_aa.fasta -B 1000 -T 1 -seed 73073	3	25.57	25.66	24.47	21.26	15.77	58
-build/iqtree3 -s test_scripts/test_data/turtle_aa.fasta -p test_scripts/test_data/turtle_aa.nex -B 1000 -T 1 -seed 73073	3	76.22	67.05	26.73	23.80	16.39	58.03
-build/iqtree3 -s test_scripts/test_data/turtle_aa.fasta -p test_scripts/test_data/turtle_aa.nex -B 1000 -T 1 -m MFP+MERGE -rcluster 10 --prefix test_scripts/test_data/turtle_aa.merge -seed 73073	3	35.97	27.51	26.11	22.30	16.56	58.13
-build/iqtree3 -s test_scripts/test_data/turtle_aa.fasta -p test_scripts/test_data/turtle_aa.merge.best_scheme.nex -z test_scripts/test_data/turtle_aa.trees -zb 10000 -au -n 0 --prefix test_scripts/test_data/turtle_aa.test -seed 73073 -T 1	3	33.53	33.46	32.43	31.32	30.30	57.96
-build/iqtree3 -s test_scripts/test_data/turtle_aa.fasta -p test_scripts/test_data/turtle_aa.nex.best_scheme.nex -z test_scripts/test_data/turtle_aa.trees -n 0 -wpl --prefix test_scripts/test_data/turtle_aa.wpl -seed 73073 -T 1	3	18.26	18.32	16.95	14.17	12.81	58.07
-build/iqtree3 -s test_scripts/test_data/turtle_aa.fasta -S test_scripts/test_data/turtle_aa.nex --prefix test_scripts/test_data/turtle_aa.loci -T 1 -seed 73073	3	16.49	16.11	13.53	11.07	9.69	57.98
-build/iqtree3 -t test_scripts/test_data/turtle_aa.nex.treefile --gcf test_scripts/test_data/turtle_aa.loci.treefile -s test_scripts/test_data/turtle_aa.fasta --scf 100 -seed 73073 -T 1	3	6.30	6.55	5.92	2.38	3.06	54.57
-build/iqtree3 -t test_scripts/test_data/turtle_aa.fasta.treefile --gcf test_scripts/test_data/turtle_aa.loci.treefile -s test_scripts/test_data/turtle_aa.fasta --scf 100 -seed 73073 -T 1	3	6.29	6.55	5.93	2.29	3.09	55.05
-build/iqtree3 -s test_scripts/test_data/turtle_aa.fasta -m MIX{LG+F,WAG+F} --prefix test_scripts/test_data/turtle_aa.mix -seed 73073 -T 1	3	11.79	11.80	10.67	6.39	6.78	55.1
-build/iqtree3 -s test_scripts/test_data/turtle_aa.fasta -p test_scripts/test_data/turtle_aa.nex -g test_scripts/test_data/turtle.constr.tree --prefix test_scripts/test_data/turtle_aa.nex.constr -T 1 -seed 73073	3	43.78	35.18	18.28	18.67	10.61	58.11
-build/iqtree3 -s test_scripts/test_data/turtle_aa.fasta -p test_scripts/test_data/turtle_aa.nex -g test_scripts/test_data/turtle.constr.tree2 -B 1000 -alrt 1000 --prefix test_scripts/test_data/turtle_aa.nex.constr2 -T 1 -seed 73073	3	50.73	59.30	26.53	23.55	16.72	57.86
+build/iqtree3 -s test_scripts/test_data/turtle.fa -B 1000 -T 1 -seed 73073	3	18.98	18.89	17.73	13.53	15.53	20.09
+build/iqtree3 -s test_scripts/test_data/turtle.fa -p test_scripts/test_data/turtle.nex -B 1000 -T 1 -seed 73073	3	19.04	19.05	17.79	13.18	13.97	20.16
+build/iqtree3 -s test_scripts/test_data/turtle.fa -p test_scripts/test_data/turtle.nex -B 1000 -T 1 -m MFP+MERGE -rcluster 10 --prefix test_scripts/test_data/turtle.merge -seed 73073	3	19.15	19.08	17.99	13.54	15.52	17.65
+build/iqtree3 -s test_scripts/test_data/turtle.fa -p test_scripts/test_data/turtle.merge.best_scheme.nex -z test_scripts/test_data/turtle.trees -zb 10000 -au -n 0 --prefix test_scripts/test_data/turtle.test -seed 73073 -T 1	3	27.80	27.77	26.76	22.50	23.45	28.15
+build/iqtree3 -s test_scripts/test_data/turtle.fa -m GTR+F+I+R3+T -te test_scripts/test_data/turtle.trees -T 1 --prefix test_scripts/test_data/turtle.mix -seed 73073	3	9.79	10.05	8.92	4.39	5.44	9.45
+build/iqtree3 -s test_scripts/test_data/turtle.fa -p test_scripts/test_data/turtle.nex.best_scheme.nex -z test_scripts/test_data/turtle.trees -n 0 -wpl --prefix test_scripts/test_data/turtle.wpl -seed 73073 -T 1	3	9.27	9.30	8.18	3.61	4.75	9.43
+build/iqtree3 -s test_scripts/test_data/turtle.fa -S test_scripts/test_data/turtle.nex --prefix test_scripts/test_data/turtle.loci -T 1 -seed 73073	3	10.43	10.55	8.79	5.66	6.59	10.3
+build/iqtree3 -t test_scripts/test_data/turtle.nex.treefile --gcf test_scripts/test_data/turtle.loci.treefile -s test_scripts/test_data/turtle.fa --scf 100 -seed 73073 -T 1	3	6.30	6.55	5.92	2.29	2.75	6.57
+build/iqtree3 -t test_scripts/test_data/turtle.fa.treefile --gcf test_scripts/test_data/turtle.loci.treefile -s test_scripts/test_data/turtle.fa --scf 100 -seed 73073 -T 1	3	6.30	6.55	5.92	2.27	3.00	6.59
+build/iqtree3 -s test_scripts/test_data/turtle.fa -m MIX{GTR+FO,GTR+FO} --link-exchange-rates --prefix test_scripts/test_data/turtle.mix.link -seed 73073 -T 1	3	9.17	9.05	7.92	3.47	4.80	9.2
+build/iqtree3 -s test_scripts/test_data/turtle.fa -m MIX{GTR{1,1,1,1,1,1}+FO,GTR{1,1,1,1,1,1}+FO} --link-exchange-rates --prefix test_scripts/test_data/turtle.mix.jc.link -seed 73073 -T 1	3	9.17	8.84	7.92	3.74	4.49	9.36
+build/iqtree3 -s test_scripts/test_data/turtle.fa -p test_scripts/test_data/turtle.nex -g test_scripts/test_data/turtle.constr.tree --prefix test_scripts/test_data/turtle.nex.constr -T 1 -seed 73073	3	10.57	10.45	8.80	5.86	6.78	10.43
+build/iqtree3 -s test_scripts/test_data/turtle.fa -p test_scripts/test_data/turtle.nex -g test_scripts/test_data/turtle.constr.tree2 -B 1000 -alrt 1000 --prefix test_scripts/test_data/turtle.nex.constr2 -T 1 -seed 73073	3	18.82	18.70	17.55	13.29	14.00	19.74
+build/iqtree3 -s test_scripts/test_data/turtle.fa -m MIX+MF --prefix test_scripts/test_data/turtle.mixfinder -T 1 -seed 73073	3	14.55	15.50	11.68	9.21	9.28	20.19
+build/iqtree3 -s test_scripts/test_data/turtle_aa.fasta -B 1000 -T 1 -seed 73073	3	25.57	25.66	24.47	21.26	15.77	22.72
+build/iqtree3 -s test_scripts/test_data/turtle_aa.fasta -p test_scripts/test_data/turtle_aa.nex -B 1000 -T 1 -seed 73073	3	76.22	67.05	26.73	23.80	16.39	24.45
+build/iqtree3 -s test_scripts/test_data/turtle_aa.fasta -p test_scripts/test_data/turtle_aa.nex -B 1000 -T 1 -m MFP+MERGE -rcluster 10 --prefix test_scripts/test_data/turtle_aa.merge -seed 73073	3	41.34	31.46	26.11	22.30	16.56	25.05
+build/iqtree3 -s test_scripts/test_data/turtle_aa.fasta -p test_scripts/test_data/turtle_aa.merge.best_scheme.nex -z test_scripts/test_data/turtle_aa.trees -zb 10000 -au -n 0 --prefix test_scripts/test_data/turtle_aa.test -seed 73073 -T 1	3	33.53	33.46	32.43	31.32	30.30	33.82
+build/iqtree3 -s test_scripts/test_data/turtle_aa.fasta -p test_scripts/test_data/turtle_aa.nex.best_scheme.nex -z test_scripts/test_data/turtle_aa.trees -n 0 -wpl --prefix test_scripts/test_data/turtle_aa.wpl -seed 73073 -T 1	3	18.26	18.32	16.95	14.17	12.81	14.99
+build/iqtree3 -s test_scripts/test_data/turtle_aa.fasta -S test_scripts/test_data/turtle_aa.nex --prefix test_scripts/test_data/turtle_aa.loci -T 1 -seed 73073	3	16.49	16.11	13.53	11.07	9.69	14.96
+build/iqtree3 -t test_scripts/test_data/turtle_aa.nex.treefile --gcf test_scripts/test_data/turtle_aa.loci.treefile -s test_scripts/test_data/turtle_aa.fasta --scf 100 -seed 73073 -T 1	3	6.30	6.55	5.92	2.38	3.06	6.74
+build/iqtree3 -t test_scripts/test_data/turtle_aa.fasta.treefile --gcf test_scripts/test_data/turtle_aa.loci.treefile -s test_scripts/test_data/turtle_aa.fasta --scf 100 -seed 73073 -T 1	3	6.29	6.55	5.93	2.29	3.09	6.64
+build/iqtree3 -s test_scripts/test_data/turtle_aa.fasta -m MIX{LG+F,WAG+F} --prefix test_scripts/test_data/turtle_aa.mix -seed 73073 -T 1	3	11.79	11.80	10.67	6.39	6.78	11.94
+build/iqtree3 -s test_scripts/test_data/turtle_aa.fasta -p test_scripts/test_data/turtle_aa.nex -g test_scripts/test_data/turtle.constr.tree --prefix test_scripts/test_data/turtle_aa.nex.constr -T 1 -seed 73073	3	59.79	60.66	18.28	18.67	10.61	16.95
+build/iqtree3 -s test_scripts/test_data/turtle_aa.fasta -p test_scripts/test_data/turtle_aa.nex -g test_scripts/test_data/turtle.constr.tree2 -B 1000 -alrt 1000 --prefix test_scripts/test_data/turtle_aa.nex.constr2 -T 1 -seed 73073	3	50.73	70.88	26.53	23.55	16.72	26.39
diff --git a/test_scripts/test_data/expected_runtimes.tsv b/test_scripts/test_data/expected_runtimes.tsv
index 527e905c..a025d890 100644
--- a/test_scripts/test_data/expected_runtimes.tsv
+++ b/test_scripts/test_data/expected_runtimes.tsv
@@ -2,21 +2,21 @@
 turtle.fa.iqtree	Total CPU time used	2	3.128169	3.299343	4.909145	4.93771	3.595236	3.21875
 turtle.loci.iqtree	Total CPU time used	2	3.376	3.6	4.561	5.737	2.786	3.359
 turtle.merge.iqtree	Total CPU time used	2	3.22134	3.336272	4.881305	4.074864	3.063053	3.34375
-turtle.mix.iqtree	Total CPU time used	1	2.288	2.437	3.653	2.043	2.607	2.391
-turtle.mix.jc.link.iqtree	Total CPU time used	1	0.678048	0.716485	1.05925	0.79052	0.798578	0.8125
-turtle.mix.link.iqtree	Total CPU time used	1	0.765474	0.829717	1.19517	0.856055	0.868658	0.90625
-turtle.mixfinder.iqtree	Total CPU time used	3	9.34105	9.95267	14.5544	9.57637	8.78048	8.40625
+turtle.mix.iqtree	Total CPU time used	1	2.288	2.437	3.653	4.416	2.607	2.391
+turtle.mix.jc.link.iqtree	Total CPU time used	1	0.678048	0.716485	1.05925	1.97384	0.798578	0.8125
+turtle.mix.link.iqtree	Total CPU time used	1	0.765474	0.829717	1.19517	2.31644	0.868658	0.90625
+turtle.mixfinder.iqtree	Total CPU time used	3	9.34105	9.95267	14.5544	13.1422	8.78048	8.40625
 turtle.nex.constr.iqtree	Total CPU time used	3	2.74033	2.88714	3.45122	4.30755	2.83421	2.85938
 turtle.nex.constr2.iqtree	Total CPU time used	3	3.172122	3.296328	3.914713	4.247386	3.261848	3.484375
 turtle.nex.iqtree	Total CPU time used	3	3.139167	3.257494	4.000374	4.824423	3.217744	3.578125
 turtle.test.iqtree	Total CPU time used	1	0.235	0.242	0.349	0.192	0.225	0.234
 turtle.wpl.iqtree	Total CPU time used	1	0.037859	0.036415	0.043837	0.041274	0.030318	0.015625
-turtle_aa.fasta.iqtree	Total CPU time used	12	61.60878	61.761949	100.241028	44.144877	44.523198	34.46875
-turtle_aa.loci.iqtree	Total CPU time used	12	55.21	56.31	89.16	32.3	45.828247	31.66
-turtle_aa.merge.iqtree	Total CPU time used	12	65.057715	65.34153	106.422985	48.539932	47.526024	36.890625
-turtle_aa.nex.constr.iqtree	Total CPU time used	12	60.3527	60.7689	98.7859	47.122	38.9924	34.4219
-turtle_aa.nex.constr2.iqtree	Total CPU time used	12	82.473306	82.646098	135.013106	54.514873	58.861398	47.40625
-turtle_aa.nex.iqtree	Total CPU time used	12	70.691887	71.079425	115.466386	54.95159	52.16108	40.890625
-turtle_aa.test.iqtree	Total CPU time used	1	1.69	1.81	2.72	0.862	0.979	0.922
+turtle_aa.fasta.iqtree	Total CPU time used	12	61.60878	61.761949	100.241028	56.571182	44.523198	34.46875
+turtle_aa.loci.iqtree	Total CPU time used	12	55.21	56.31	89.16	54.17	45.828247	31.66
+turtle_aa.merge.iqtree	Total CPU time used	12	65.057715	65.34153	106.422985	76.722846	47.526024	36.890625
+turtle_aa.nex.constr.iqtree	Total CPU time used	12	60.3527	60.7689	98.7859	59.6715	38.9924	34.4219
+turtle_aa.nex.constr2.iqtree	Total CPU time used	12	82.473306	82.646098	135.013106	85.280632	58.861398	47.40625
+turtle_aa.nex.iqtree	Total CPU time used	12	70.691887	71.079425	115.466386	71.812495	52.16108	40.890625
+turtle_aa.test.iqtree	Total CPU time used	1	1.69	1.81	2.72	2.24	0.979	0.922
 turtle_aa.wpl.iqtree	Total CPU time used	3	1.6987	1.701	2.7838	0.89948	1.0239	0.96875
-turtle_aa.mix.iqtree	Total CPU time used	3	12.8918	13.1371	21.3145	6.91331	9.35718	7.09375
\ No newline at end of file
+turtle_aa.mix.iqtree	Total CPU time used	3	12.8918	13.1371	21.3145	10.1353	9.35718	7.09375
\ No newline at end of file
diff --git a/test_scripts/test_iqtree.ps1 b/test_scripts/test_iqtree.ps1
index 22ed581a..ac3b5e16 100755
--- a/test_scripts/test_iqtree.ps1
+++ b/test_scripts/test_iqtree.ps1
@@ -12,12 +12,18 @@ function Measure-IQTree {
 
     $startTime = Get-Date
 
-    # Start the command in a child PowerShell process
-    $proc = Start-Process -FilePath "powershell" -ArgumentList "-NoProfile", "-Command", $CommandLine -PassThru
+    # Split command and arguments
+    $exe, $args = $CommandLine -split '\s+', 2
+    $tempOut = [System.IO.Path]::GetTempFileName()
+
+    # Start the process with output redirection
+    $proc = Start-Process -FilePath $exe -ArgumentList $args `
+        -RedirectStandardOutput $tempOut `
+        -NoNewWindow -PassThru
+
     $procId = $proc.Id
     $peakMemory = 0
 
-    # Monitor the child process's memory usage
     while (-not $proc.HasExited) {
         Start-Sleep -Milliseconds 200
         try {
@@ -33,8 +39,14 @@ function Measure-IQTree {
     $endTime = Get-Date
     $elapsed = [math]::Round(($endTime - $startTime).TotalSeconds, 2)
 
-    # Write timing and memory data to log
+    # Show output
+    Get-Content $tempOut
+
+    # Log timing and memory
     "$CommandLine`t$elapsed`t$([math]::Round($peakMemory, 2))" | Out-File -FilePath $LOGFILE -Append -Encoding utf8
+
+    # Cleanup
+    Remove-Item $tempOut
 }
 
 

From e7115b81ca6e68bbbc7a1d15847c9f2f73df4e49 Mon Sep 17 00:00:00 2001
From: Hashara <kumarasinghe.k.a.s.h@gmail.com>
Date: Mon, 7 Jul 2025 11:00:24 +1000
Subject: [PATCH 10/16] resolve copilot suggestions

---
 test_scripts/verify_memory.ps1 | 1 -
 test_scripts/verify_memory.sh  | 6 ++----
 2 files changed, 2 insertions(+), 5 deletions(-)

diff --git a/test_scripts/verify_memory.ps1 b/test_scripts/verify_memory.ps1
index 5d7e2f28..d9574a96 100644
--- a/test_scripts/verify_memory.ps1
+++ b/test_scripts/verify_memory.ps1
@@ -33,7 +33,6 @@ for ($i = 0; $i -lt $selectedColumns.Count; $i++) {
 $combinedLines | Set-Content $finalFile
 
 # Now compare
-Write-Host "`nCommand`tExpected`tThreshold`tActual`tExceededBy"
 $failCount = 0
 $finalLines = Get-Content $finalFile
 
diff --git a/test_scripts/verify_memory.sh b/test_scripts/verify_memory.sh
index f7c12cef..dc0c997e 100644
--- a/test_scripts/verify_memory.sh
+++ b/test_scripts/verify_memory.sh
@@ -15,8 +15,6 @@ paste "$selected_columns_file" /tmp/reported_column.tsv > "$final_file"
 
 fail_count=0
 
-echo -e "Command\tExpected\tThreshold\tActual\tExceededBy"
-
 # Skip header
 while IFS=$'\t' read -r command threshold expected reported; do
     allowed=$(echo "$expected + $threshold" | bc -l)
@@ -25,12 +23,12 @@ while IFS=$'\t' read -r command threshold expected reported; do
     if [ "$is_exceed" = "1" ]; then
         diff=$(echo "$reported - $expected" | bc -l)
         echo "❌ $command exceeded the allowed memory usage."
-        echo "Expected: $expected MB, Threshold: $threshold MB, Reported: $reported MB"
+        echo "Expected: $expected MB, Threshold: $threshold MB, Reported: $reported MB, Difference: $diff MB"
         ((fail_count++))
     else
         echo "✅ $command passed the memory check."
         diff=$(echo "$reported - $expected" | bc -l)
-        echo "Expected: $expected MB, Threshold: $threshold MB, Reported: $reported MB"
+        echo "Expected: $expected MB, Threshold: $threshold MB, Reported: $reported MB, Difference: $diff MB"
     fi
 done < <(tail -n +2 "$final_file")
 

From fea468f03190d375ae711fc0ae7e9743f9fc8c25 Mon Sep 17 00:00:00 2001
From: Hashara <kumarasinghe.k.a.s.h@gmail.com>
Date: Mon, 7 Jul 2025 11:13:16 +1000
Subject: [PATCH 11/16] replace column index to column name for verify memory

---
 .github/workflows/ci.yaml     | 12 ++++++------
 test_scripts/verify_memory.sh | 12 +++++++++++-
 2 files changed, 17 insertions(+), 7 deletions(-)

diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
index 8f3537d1..8e20b284 100644
--- a/.github/workflows/ci.yaml
+++ b/.github/workflows/ci.yaml
@@ -25,13 +25,13 @@ jobs:
             cmake-version: 3.14.7
             upload: true
             runtime-arg: 4
-            memory-arg: 3
+            memory-arg: Linux-gcc-9
           # Latest supported gcc and cmake versions
           - gcc-version: 12
             cmake-version: latest
             upload: false
             runtime-arg: 5
-            memory-arg: 4
+            memory-arg: Linux-gcc-12
 
     steps:
       - name: Checkout
@@ -137,7 +137,7 @@ jobs:
       - name: Run verify_memory.sh
         run: |
           chmod +x test_scripts/verify_memory.sh
-          ./test_scripts/verify_memory.sh 5
+          ./test_scripts/verify_memory.sh Linux-aarch64
 
   compile-linux-universal:
     name: Linux Universal
@@ -227,7 +227,7 @@ jobs:
       - name: Run verify_memory.sh
         run: |
           chmod +x test_scripts/verify_memory.sh
-          ./test_scripts/verify_memory.sh 6
+          ./test_scripts/verify_memory.sh mac-os-x86-64
 
   build-macos-arm:
     name: Mac OS ARM64
@@ -280,7 +280,7 @@ jobs:
       - name: Run verify_memory.sh
         run: |
           chmod +x test_scripts/verify_memory.sh
-          ./test_scripts/verify_memory.sh 7
+          ./test_scripts/verify_memory.sh mac-os-arm64
 
   compile-mac-universal:
     name: Mac OS Universal
@@ -394,6 +394,6 @@ jobs:
         run: |
           ./test_scripts/verify_runtime.ps1
 
-      - name: Run verify_memory.sh
+      - name: Run verify_memory.ps1
         run: |
           ./test_scripts/verify_memory.ps1
\ No newline at end of file
diff --git a/test_scripts/verify_memory.sh b/test_scripts/verify_memory.sh
index dc0c997e..54701cac 100644
--- a/test_scripts/verify_memory.sh
+++ b/test_scripts/verify_memory.sh
@@ -5,7 +5,17 @@ WD="test_scripts/test_data"
 input_file="${WD}/expected_memory.tsv"
 reported_file="time_log.tsv"
 selected_columns_file="${WD}/selected_columns.tsv"
-cut -f1,2,"$expected_column" "$input_file" > "${selected_columns_file}"
+
+# Get the column index (1-based) of the expected column name
+col_index=$(head -1 "$input_file" | tr '\t' '\n' | awk -v col="$expected_column" '{if ($0 == col) print NR}')
+
+# Check if column was found
+if [[ -z "$col_index" ]]; then
+  echo "Column '$expected_column' not found in $input_file"
+  exit 1
+fi
+
+cut -f1,2,"$col_index" "$input_file" > "${selected_columns_file}"
 final_file="${WD}/combined_with_reported.tsv"
 
 # assuming the reported file and expected file have the same order of commands

From ee115db9de23dc693156d3828254aad2b5e46ca7 Mon Sep 17 00:00:00 2001
From: Hashara <kumarasinghe.k.a.s.h@gmail.com>
Date: Mon, 7 Jul 2025 12:05:49 +1000
Subject: [PATCH 12/16] add ps1 file to process with the column name update
 expected_memory.tsv for failing values update the verify_runtime.sh to check
 with usr/bin/time

---
 .github/workflows/ci.yaml                   | 10 +--
 test_scripts/test_data/expected_memory.tsv  |  4 +-
 test_scripts/test_data/expected_runtime.tsv | 26 ++++++++
 test_scripts/verify_memory.ps1              | 18 ++++--
 test_scripts/verify_memory.sh               |  2 +-
 test_scripts/verify_runtime.sh              | 68 +++++++++------------
 6 files changed, 77 insertions(+), 51 deletions(-)
 create mode 100644 test_scripts/test_data/expected_runtime.tsv

diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
index 8e20b284..4ca8feb9 100644
--- a/.github/workflows/ci.yaml
+++ b/.github/workflows/ci.yaml
@@ -24,13 +24,13 @@ jobs:
           - gcc-version: 9
             cmake-version: 3.14.7
             upload: true
-            runtime-arg: 4
+            runtime-arg: Linux-gcc-9
             memory-arg: Linux-gcc-9
           # Latest supported gcc and cmake versions
           - gcc-version: 12
             cmake-version: latest
             upload: false
-            runtime-arg: 5
+            runtime-arg: Linux-gcc-12
             memory-arg: Linux-gcc-12
 
     steps:
@@ -132,7 +132,7 @@ jobs:
       - name: Run verify_runtimes.sh
         run: |
           chmod +x test_scripts/verify_runtime.sh
-          ./test_scripts/verify_runtime.sh 6
+          ./test_scripts/verify_runtime.sh Linux-aarch64
 
       - name: Run verify_memory.sh
         run: |
@@ -222,7 +222,7 @@ jobs:
       - name: Run verify_runtimes.sh
         run: |
           chmod +x test_scripts/verify_runtime.sh
-          ./test_scripts/verify_runtime.sh 7
+          ./test_scripts/verify_runtime.sh mac-os-x86-64
 
       - name: Run verify_memory.sh
         run: |
@@ -275,7 +275,7 @@ jobs:
       - name: Run verify_runtimes.sh
         run: |
           chmod +x test_scripts/verify_runtime.sh
-          ./test_scripts/verify_runtime.sh 8
+          ./test_scripts/verify_runtime.sh mac-os-arm64
 
       - name: Run verify_memory.sh
         run: |
diff --git a/test_scripts/test_data/expected_memory.tsv b/test_scripts/test_data/expected_memory.tsv
index c4ac1eec..cacb9473 100644
--- a/test_scripts/test_data/expected_memory.tsv
+++ b/test_scripts/test_data/expected_memory.tsv
@@ -14,8 +14,8 @@ build/iqtree3 -s test_scripts/test_data/turtle.fa -p test_scripts/test_data/turt
 build/iqtree3 -s test_scripts/test_data/turtle.fa -p test_scripts/test_data/turtle.nex -g test_scripts/test_data/turtle.constr.tree2 -B 1000 -alrt 1000 --prefix test_scripts/test_data/turtle.nex.constr2 -T 1 -seed 73073	3	18.82	18.70	17.55	13.29	14.00	19.74
 build/iqtree3 -s test_scripts/test_data/turtle.fa -m MIX+MF --prefix test_scripts/test_data/turtle.mixfinder -T 1 -seed 73073	3	14.55	15.50	11.68	9.21	9.28	20.19
 build/iqtree3 -s test_scripts/test_data/turtle_aa.fasta -B 1000 -T 1 -seed 73073	3	25.57	25.66	24.47	21.26	15.77	22.72
-build/iqtree3 -s test_scripts/test_data/turtle_aa.fasta -p test_scripts/test_data/turtle_aa.nex -B 1000 -T 1 -seed 73073	3	76.22	67.05	26.73	23.80	16.39	24.45
-build/iqtree3 -s test_scripts/test_data/turtle_aa.fasta -p test_scripts/test_data/turtle_aa.nex -B 1000 -T 1 -m MFP+MERGE -rcluster 10 --prefix test_scripts/test_data/turtle_aa.merge -seed 73073	3	41.34	31.46	26.11	22.30	16.56	25.05
+build/iqtree3 -s test_scripts/test_data/turtle_aa.fasta -p test_scripts/test_data/turtle_aa.nex -B 1000 -T 1 -seed 73073	3	76.22	67.05	26.73	23.80	16.39	28.9
+build/iqtree3 -s test_scripts/test_data/turtle_aa.fasta -p test_scripts/test_data/turtle_aa.nex -B 1000 -T 1 -m MFP+MERGE -rcluster 10 --prefix test_scripts/test_data/turtle_aa.merge -seed 73073	3	41.34	31.46	26.11	22.30	16.56	28.35
 build/iqtree3 -s test_scripts/test_data/turtle_aa.fasta -p test_scripts/test_data/turtle_aa.merge.best_scheme.nex -z test_scripts/test_data/turtle_aa.trees -zb 10000 -au -n 0 --prefix test_scripts/test_data/turtle_aa.test -seed 73073 -T 1	3	33.53	33.46	32.43	31.32	30.30	33.82
 build/iqtree3 -s test_scripts/test_data/turtle_aa.fasta -p test_scripts/test_data/turtle_aa.nex.best_scheme.nex -z test_scripts/test_data/turtle_aa.trees -n 0 -wpl --prefix test_scripts/test_data/turtle_aa.wpl -seed 73073 -T 1	3	18.26	18.32	16.95	14.17	12.81	14.99
 build/iqtree3 -s test_scripts/test_data/turtle_aa.fasta -S test_scripts/test_data/turtle_aa.nex --prefix test_scripts/test_data/turtle_aa.loci -T 1 -seed 73073	3	16.49	16.11	13.53	11.07	9.69	14.96
diff --git a/test_scripts/test_data/expected_runtime.tsv b/test_scripts/test_data/expected_runtime.tsv
new file mode 100644
index 00000000..98ebe004
--- /dev/null
+++ b/test_scripts/test_data/expected_runtime.tsv
@@ -0,0 +1,26 @@
+Command	diff-threshold	Linux-gcc-9	Linux-gcc-12	Linux-aarch64	mac-os-x86-64	mac-os-arm64	windows-x86
+build/iqtree3 -s test_scripts/test_data/turtle.fa -B 1000 -T 1 -seed 73073	2	3.24	3.32	5.03	3.62	2.96	4.55
+build/iqtree3 -s test_scripts/test_data/turtle.fa -p test_scripts/test_data/turtle.nex -B 1000 -T 1 -seed 73073	2	3.46	3.59	4.32	3.63	2.74	4.06
+build/iqtree3 -s test_scripts/test_data/turtle.fa -p test_scripts/test_data/turtle.nex -B 1000 -T 1 -m MFP+MERGE -rcluster 10 --prefix test_scripts/test_data/turtle.merge -seed 73073	2	3.35	3.49	5.01	4.14	3.00	3.86
+build/iqtree3 -s test_scripts/test_data/turtle.fa -p test_scripts/test_data/turtle.merge.best_scheme.nex -z test_scripts/test_data/turtle.trees -zb 10000 -au -n 0 --prefix test_scripts/test_data/turtle.test -seed 73073 -T 1	2	1.34	1.31	0.74	0.85	0.78	3.26
+build/iqtree3 -s test_scripts/test_data/turtle.fa -m GTR+F+I+R3+T -te test_scripts/test_data/turtle.trees -T 1 --prefix test_scripts/test_data/turtle.mix -seed 73073	2	2.43	2.36	3.76	2.29	2.52	2.85
+build/iqtree3 -s test_scripts/test_data/turtle.fa -p test_scripts/test_data/turtle.nex.best_scheme.nex -z test_scripts/test_data/turtle.trees -n 0 -wpl --prefix test_scripts/test_data/turtle.wpl -seed 73073 -T 1	2	0.05	0.05	0.05	0.13	0.04	0.62
+build/iqtree3 -s test_scripts/test_data/turtle.fa -S test_scripts/test_data/turtle.nex --prefix test_scripts/test_data/turtle.loci -T 1 -seed 73073	2	3.64	3.82	4.88	3.90	2.94	3.86
+build/iqtree3 -t test_scripts/test_data/turtle.nex.treefile --gcf test_scripts/test_data/turtle.loci.treefile -s test_scripts/test_data/turtle.fa --scf 100 -seed 73073 -T 1	1	0.01	0.01	0.01	0.02	0.01	0.4
+build/iqtree3 -t test_scripts/test_data/turtle.fa.treefile --gcf test_scripts/test_data/turtle.loci.treefile -s test_scripts/test_data/turtle.fa --scf 100 -seed 73073 -T 1	1	0.01	0.01	0.01	0.02	0.01	0.41
+build/iqtree3 -s test_scripts/test_data/turtle.fa -m MIX{GTR+FO,GTR+FO} --link-exchange-rates --prefix test_scripts/test_data/turtle.mix.link -seed 73073 -T 1	2	0.79	0.82	1.23	0.69	0.64	0.4
+build/iqtree3 -s test_scripts/test_data/turtle.fa -m MIX{GTR{1,1,1,1,1,1}+FO,GTR{1,1,1,1,1,1}+FO} --link-exchange-rates --prefix test_scripts/test_data/turtle.mix.jc.link -seed 73073 -T 1	2	0.70	0.74	1.09	0.82	0.71	0.41
+build/iqtree3 -s test_scripts/test_data/turtle.fa -p test_scripts/test_data/turtle.nex -g test_scripts/test_data/turtle.constr.tree --prefix test_scripts/test_data/turtle.nex.constr -T 1 -seed 73073	2	3.05	3.17	3.83	3.62	2.22	3.47
+build/iqtree3 -s test_scripts/test_data/turtle.fa -p test_scripts/test_data/turtle.nex -g test_scripts/test_data/turtle.constr.tree2 -B 1000 -alrt 1000 --prefix test_scripts/test_data/turtle.nex.constr2 -T 1 -seed 73073	2	3.50	3.58	4.25	3.95	2.49	4.27
+build/iqtree3 -s test_scripts/test_data/turtle.fa -m MIX+MF --prefix test_scripts/test_data/turtle.mixfinder -T 1 -seed 73073	3	9.15	8.47	14.31	9.81	8.20	0.42
+build/iqtree3 -s test_scripts/test_data/turtle_aa.fasta -B 1000 -T 1 -seed 73073	12	62.06	65.05	100.61	35.56	40.99	35.76
+build/iqtree3 -s test_scripts/test_data/turtle_aa.fasta -p test_scripts/test_data/turtle_aa.nex -B 1000 -T 1 -seed 73073	12	71.33	72.66	116.11	44.03	46.82	41.86
+build/iqtree3 -s test_scripts/test_data/turtle_aa.fasta -p test_scripts/test_data/turtle_aa.nex -B 1000 -T 1 -m MFP+MERGE -rcluster 10 --prefix test_scripts/test_data/turtle_aa.merge -seed 73073	12	65.65	67.02	106.90	39.94	40.45	37.61
+build/iqtree3 -s test_scripts/test_data/turtle_aa.fasta -p test_scripts/test_data/turtle_aa.merge.best_scheme.nex -z test_scripts/test_data/turtle_aa.trees -zb 10000 -au -n 0 --prefix test_scripts/test_data/turtle_aa.test -seed 73073 -T 1	2	2.66	2.61	3.17	1.43	1.61	3.26
+build/iqtree3 -s test_scripts/test_data/turtle_aa.fasta -p test_scripts/test_data/turtle_aa.nex.best_scheme.nex -z test_scripts/test_data/turtle_aa.trees -n 0 -wpl --prefix test_scripts/test_data/turtle_aa.wpl -seed 73073 -T 1	2	1.80	1.83	2.92	1.08	1.27	1.62
+build/iqtree3 -s test_scripts/test_data/turtle_aa.fasta -S test_scripts/test_data/turtle_aa.nex --prefix test_scripts/test_data/turtle_aa.loci -T 1 -seed 73073	12	55.46	56.38	89.44	34.67	35.94	32.52
+build/iqtree3 -t test_scripts/test_data/turtle_aa.nex.treefile --gcf test_scripts/test_data/turtle_aa.loci.treefile -s test_scripts/test_data/turtle_aa.fasta --scf 100 -seed 73073 -T 1	1	0.01	0.01	0.01	0.02	0.02	0.4
+build/iqtree3 -t test_scripts/test_data/turtle_aa.fasta.treefile --gcf test_scripts/test_data/turtle_aa.loci.treefile -s test_scripts/test_data/turtle_aa.fasta --scf 100 -seed 73073 -T 1	1	0.01	0.01	0.01	0.02	0.01	0.41
+build/iqtree3 -s test_scripts/test_data/turtle_aa.fasta -m MIX{LG+F,WAG+F} --prefix test_scripts/test_data/turtle_aa.mix -seed 73073 -T 1	3	13.04	13.33	21.36	7.23	8.97	0.41
+build/iqtree3 -s test_scripts/test_data/turtle_aa.fasta -p test_scripts/test_data/turtle_aa.nex -g test_scripts/test_data/turtle.constr.tree --prefix test_scripts/test_data/turtle_aa.nex.constr -T 1 -seed 73073	12	61.22	61.69	99.07	37.95	39.54	35.39
+build/iqtree3 -s test_scripts/test_data/turtle_aa.fasta -p test_scripts/test_data/turtle_aa.nex -g test_scripts/test_data/turtle.constr.tree2 -B 1000 -alrt 1000 --prefix test_scripts/test_data/turtle_aa.nex.constr2 -T 1 -seed 73073	12	82.86	85.39	135.76	49.92	53.91	48.37
diff --git a/test_scripts/verify_memory.ps1 b/test_scripts/verify_memory.ps1
index d9574a96..d830604f 100644
--- a/test_scripts/verify_memory.ps1
+++ b/test_scripts/verify_memory.ps1
@@ -1,5 +1,5 @@
 param (
-    [int]   $ExpectedColumn = 8
+    [string] $ExpectedColumnName = "windows-x86"
 )
 
 $WD = "test_scripts/test_data"
@@ -9,11 +9,21 @@ $selectedColumnsFile = Join-Path $WD "selected_columns.tsv"
 $reportedColumnFile = "$env:TEMP\reported_column.tsv"
 $finalFile = Join-Path $WD "combined_with_reported.tsv"
 
-# Read expected: Command, Threshold, ExpectedColumn
+# Get the header and find the index of the expected column name
+$header = Get-Content $expectedFile -TotalCount 1
+$columns = $header -split "`t"
+$columnIndex = $columns.IndexOf($ExpectedColumnName)
+
+if ($columnIndex -lt 0) {
+    Write-Error "Column '$ExpectedColumnName' not found in $expectedFile"
+    exit 1
+}
+
+# Adjust to 0-based indexing for arrays
 $expectedLines = Get-Content $expectedFile | Select-Object -Skip 1
 $selectedColumns = foreach ($line in $expectedLines) {
     $parts = $line -split "`t"
-    "$($parts[0])`t$($parts[1])`t$($parts[$ExpectedColumn - 1])"
+    "$($parts[0])`t$($parts[1])`t$($parts[$columnIndex])"
 }
 $selectedColumns | Set-Content $selectedColumnsFile
 
@@ -59,7 +69,7 @@ foreach ($line in $finalLines) {
 Write-Host ""
 
 if ($failCount -eq 0) {
-    Write-Host "✅ All runtime/memory checks passed."
+    Write-Host "✅ All memory checks passed."
     exit 0
 } else {
     Write-Host "❌ $failCount checks failed."
diff --git a/test_scripts/verify_memory.sh b/test_scripts/verify_memory.sh
index 54701cac..03643cf6 100644
--- a/test_scripts/verify_memory.sh
+++ b/test_scripts/verify_memory.sh
@@ -43,7 +43,7 @@ while IFS=$'\t' read -r command threshold expected reported; do
 done < <(tail -n +2 "$final_file")
 
 if [ "$fail_count" -eq 0 ]; then
-    echo "✅ All runtime checks passed."
+    echo "✅ All memory checks passed."
 else
     echo "❌ $fail_count checks failed."
     exit 1
diff --git a/test_scripts/verify_runtime.sh b/test_scripts/verify_runtime.sh
index f20f0790..14c2ced4 100644
--- a/test_scripts/verify_runtime.sh
+++ b/test_scripts/verify_runtime.sh
@@ -2,56 +2,46 @@
 expected_column="$1"
 
 WD="test_scripts/test_data"
-input_file="${WD}/expected_runtimes.tsv"
-selected_colums_file="${WD}/selected_columns.tsv"
-cut -f1,2,3,"$expected_column" "$input_file" > "${selected_colums_file}"
+input_file="${WD}/expected_runtime.tsv"
+reported_file="time_log.tsv"
+selected_columns_file="${WD}/selected_columns.tsv"
 
-fail_count=0
-line_num=0
-
-while IFS=$'\t' read -r iqtree_file field_name threshold expected_value || [ -n "$iqtree_file" ]; do
-    ((line_num++))
+# Get the column index (1-based) of the expected column name
+col_index=$(head -1 "$input_file" | tr '\t' '\n' | awk -v col="$expected_column" '{if ($0 == col) print NR}')
 
-    # Skip header (first line)
-    if [ "$line_num" -eq 1 ]; then
-        continue
-    fi
+# Check if column was found
+if [[ -z "$col_index" ]]; then
+  echo "Column '$expected_column' not found in $input_file"
+  exit 1
+fi
 
-    iqtree_file="${WD}/${iqtree_file}"
+cut -f1,2,"$col_index" "$input_file" > "${selected_columns_file}"
+final_file="${WD}/combined_with_reported.tsv"
 
-    if [ ! -f "$iqtree_file" ]; then
-        echo "File not found: $iqtree_file"
-        continue
-    fi
+# assuming the reported file and expected file have the same order of commands
+cut -f2 "$reported_file" > /tmp/reported_column.tsv
+paste "$selected_columns_file" /tmp/reported_column.tsv > "$final_file"
 
-    # Look for the line containing the field name
-    report_line=$(grep -F "$field_name" "$iqtree_file")
-    if [ -z "$report_line" ]; then
-        echo "Field not found in $iqtree_file: $field_name"
-        continue
-    fi
 
-    # Extract the first numeric value from the matched line
-    report_value=$(echo "$report_line" | grep -Eo '[-+]?[0-9]+(\.[0-9]+)?([eE][-+]?[0-9]+)?' | head -n1)
-    if [ -z "$report_value" ]; then
-        echo "No numeric value found in line: $report_line"
-        continue
-    fi
+fail_count=0
 
-    # Compute report value less than the highest value
-    higest_value=$(echo "$expected_value + $threshold"  | bc -l)
-    result=$(echo "$report_value <= $higest_value" | bc -l)
+# Skip header
+while IFS=$'\t' read -r command threshold expected reported; do
+    allowed=$(echo "$expected + $threshold" | bc -l)
+    is_exceed=$(echo "$reported > $allowed" | bc -l)
 
-    if [ "$result" -eq 1 ]; then
-        echo "PASS: $iqtree_file -- Expected: ${expected_value}, Reported: ${report_value}, Threshold: $threshold"
-    else
-        echo "FAIL: $iqtree_file ($field_name)"
-        echo "  Expected: ${expected_value}, Reported: ${report_value}, Threshold: $threshold"
+    if [ "$is_exceed" = "1" ]; then
+        diff=$(echo "$reported - $expected" | bc -l)
+        echo "❌ $command exceeded the allowed runtime usage."
+        echo "Expected: $expected S, Threshold: $threshold S, Reported: $reported S, Difference: $diff S"
         ((fail_count++))
+    else
+        echo "✅ $command passed the runtime check."
+        diff=$(echo "$reported - $expected" | bc -l)
+        echo "Expected: $expected S, Threshold: $threshold S, Reported: $reported S, Difference: $diff S"
     fi
-done < "$selected_colums_file"
+done < <(tail -n +2 "$final_file")
 
-echo
 if [ "$fail_count" -eq 0 ]; then
     echo "✅ All runtime checks passed."
 else

From 4ff421ce88d1f22c110ebff4d29b199996c4fcbf Mon Sep 17 00:00:00 2001
From: Hashara <kumarasinghe.k.a.s.h@gmail.com>
Date: Mon, 7 Jul 2025 12:39:33 +1000
Subject: [PATCH 13/16] add verify_runtime.ps1 file to process with the column
 name remove expected_runtimes.tsv

---
 test_scripts/test_data/expected_runtimes.tsv |  22 ----
 test_scripts/verify_runtime.ps1              | 100 +++++++++++--------
 2 files changed, 57 insertions(+), 65 deletions(-)
 delete mode 100644 test_scripts/test_data/expected_runtimes.tsv

diff --git a/test_scripts/test_data/expected_runtimes.tsv b/test_scripts/test_data/expected_runtimes.tsv
deleted file mode 100644
index a025d890..00000000
--- a/test_scripts/test_data/expected_runtimes.tsv
+++ /dev/null
@@ -1,22 +0,0 @@
-#file name	key-words	diff-threshold	Linux-gcc-9	Linux-gcc-12	Linux-aarch64	mac-os-x86-64	mac-os-arm64	windows-x86
-turtle.fa.iqtree	Total CPU time used	2	3.128169	3.299343	4.909145	4.93771	3.595236	3.21875
-turtle.loci.iqtree	Total CPU time used	2	3.376	3.6	4.561	5.737	2.786	3.359
-turtle.merge.iqtree	Total CPU time used	2	3.22134	3.336272	4.881305	4.074864	3.063053	3.34375
-turtle.mix.iqtree	Total CPU time used	1	2.288	2.437	3.653	4.416	2.607	2.391
-turtle.mix.jc.link.iqtree	Total CPU time used	1	0.678048	0.716485	1.05925	1.97384	0.798578	0.8125
-turtle.mix.link.iqtree	Total CPU time used	1	0.765474	0.829717	1.19517	2.31644	0.868658	0.90625
-turtle.mixfinder.iqtree	Total CPU time used	3	9.34105	9.95267	14.5544	13.1422	8.78048	8.40625
-turtle.nex.constr.iqtree	Total CPU time used	3	2.74033	2.88714	3.45122	4.30755	2.83421	2.85938
-turtle.nex.constr2.iqtree	Total CPU time used	3	3.172122	3.296328	3.914713	4.247386	3.261848	3.484375
-turtle.nex.iqtree	Total CPU time used	3	3.139167	3.257494	4.000374	4.824423	3.217744	3.578125
-turtle.test.iqtree	Total CPU time used	1	0.235	0.242	0.349	0.192	0.225	0.234
-turtle.wpl.iqtree	Total CPU time used	1	0.037859	0.036415	0.043837	0.041274	0.030318	0.015625
-turtle_aa.fasta.iqtree	Total CPU time used	12	61.60878	61.761949	100.241028	56.571182	44.523198	34.46875
-turtle_aa.loci.iqtree	Total CPU time used	12	55.21	56.31	89.16	54.17	45.828247	31.66
-turtle_aa.merge.iqtree	Total CPU time used	12	65.057715	65.34153	106.422985	76.722846	47.526024	36.890625
-turtle_aa.nex.constr.iqtree	Total CPU time used	12	60.3527	60.7689	98.7859	59.6715	38.9924	34.4219
-turtle_aa.nex.constr2.iqtree	Total CPU time used	12	82.473306	82.646098	135.013106	85.280632	58.861398	47.40625
-turtle_aa.nex.iqtree	Total CPU time used	12	70.691887	71.079425	115.466386	71.812495	52.16108	40.890625
-turtle_aa.test.iqtree	Total CPU time used	1	1.69	1.81	2.72	2.24	0.979	0.922
-turtle_aa.wpl.iqtree	Total CPU time used	3	1.6987	1.701	2.7838	0.89948	1.0239	0.96875
-turtle_aa.mix.iqtree	Total CPU time used	3	12.8918	13.1371	21.3145	10.1353	9.35718	7.09375
\ No newline at end of file
diff --git a/test_scripts/verify_runtime.ps1 b/test_scripts/verify_runtime.ps1
index 188fe902..ea97ea1b 100755
--- a/test_scripts/verify_runtime.ps1
+++ b/test_scripts/verify_runtime.ps1
@@ -1,63 +1,77 @@
-param(
-    [int]   $ExpectedColumn = 8,                                # 1-based index of the threshold column
-    [string]$input_file     = "test_scripts/test_data/expected_runtimes.tsv"
+param (
+    [string] $ExpectedColumnName = "windows-x86"
 )
 
-$fail_count = 0
-$line_num = 0
+$WD = "test_scripts/test_data"
+$expectedFile = Join-Path $WD "expected_runtime.tsv"
+$reportedFile = "time_log.tsv"
+$selectedColumnsFile = Join-Path $WD "selected_columns.tsv"
+$reportedColumnFile = "$env:TEMP\reported_column.tsv"
+$finalFile = Join-Path $WD "combined_with_reported.tsv"
 
-Get-Content $input_file | ForEach-Object {
-    $line = $_.Trim()
-    $line_num++
+# Get the header and find the index of the expected column name
+$header = Get-Content $expectedFile -TotalCount 1
+$columns = $header -split "`t"
+$columnIndex = $columns.IndexOf($ExpectedColumnName)
 
-    if ($line_num -eq 1 -or $line -eq "") {
-        return  # skip header or empty line
-    }
-
-    $columns = $line -split "`t"
-    if ($columns.Count -lt 4) {
-        Write-Host "Skipping malformed line: $line"
-        return
-    }
+if ($columnIndex -lt 0) {
+    Write-Error "Column '$ExpectedColumnName' not found in $expectedFile"
+    exit 1
+}
 
-    $iqtree_file = Join-Path "test_scripts/test_data" $columns[0]
-    $field_name = $columns[1]
-    $expected_value = [double]$columns[$ExpectedColumn]
-    $threshold = [double]$columns[2]
+# Adjust to 0-based indexing for arrays
+$expectedLines = Get-Content $expectedFile | Select-Object -Skip 1
+$selectedColumns = foreach ($line in $expectedLines) {
+    $parts = $line -split "`t"
+    "$($parts[0])`t$($parts[1])`t$($parts[$columnIndex])"
+}
+$selectedColumns | Set-Content $selectedColumnsFile
 
-    if (-not (Test-Path $iqtree_file)) {
-        Write-Host "File not found: ${iqtree_file}"
-        return
-    }
+# Read reported column from time_log.tsv (column 3 = RealTime, 4 = Memory)
+$reportedLines = Get-Content $reportedFile | Select-Object -Skip 1
+$reportedColumn = foreach ($line in $reportedLines) {
+    $parts = $line -split "`t"
+    $parts[1]  # column 2 = runtime (0-based index)
+}
+$reportedColumn | Set-Content $reportedColumnFile
 
-    $actual_line = Select-String -Path $iqtree_file -Pattern ([regex]::Escape($field_name))
-    if (-not $actual_line) {
-        Write-Host "Field not found in ${iqtree_file}: ${field_name}"
-        return
-    }
+# Combine both files
+$combinedLines = @()
+for ($i = 0; $i -lt $selectedColumns.Count; $i++) {
+    $combinedLines += "$($selectedColumns[$i])`t$($reportedColumn[$i])"
+}
+$combinedLines | Set-Content $finalFile
 
-    $match = [regex]::Match($actual_line.Line, '[-+]?\d+(\.\d+)?([eE][-+]?\d+)?')
+# Now compare
+$failCount = 0
+$finalLines = Get-Content $finalFile
 
-    if (-not $match.Success) {
-        Write-Host "No numeric value found in line: $($actual_line.Line)"
-        return
-    }
+foreach ($line in $finalLines) {
+    $parts = $line -split "`t"
+    $command = $parts[0]
+    $threshold = [double]$parts[1]
+    $expected = [double]$parts[2]
+    $reported = [double]$parts[3]
 
-    $actual_value = [double]$match.Value
-    $highest_value = $expected_value + $threshold
+    $allowed = $expected + $threshold
+    $exceededBy = $reported - $expected
 
-    if ($actual_value -le $highest_value) {
-        Write-Host "PASS: ${iqtree_file} -- Expected: ${expected_value}, Reported: ${actual_value}, Threshold: ${threshold}"
+    if ($reported -gt $allowed) {
+        Write-Host "❌ $command exceeded the allowed usage."
+        Write-Host "Expected: $expected S, Threshold: $threshold S, Reported: $reported S"
+        $failCount++
     } else {
-        Write-Host "FAIL: ${iqtree_file} -- Expected: ${expected_value}, Reported: ${actual_value}, Threshold: ${threshold}"
-        $fail_count++
+        Write-Host "✅ $command passed the check."
+        Write-Host "Expected: $expected S, Threshold: $threshold S, Reported: $reported S"
     }
 }
 
 Write-Host ""
-if ($fail_count -eq 0) {
+
+if ($failCount -eq 0) {
     Write-Host "✅ All runtime checks passed."
+    exit 0
 } else {
-    Write-Host "❌ ${fail_count} checks failed."
+    Write-Host "❌ $failCount checks failed."
     exit 1
 }

From 57e62c969252b1e1f28e092104a36163a204991b Mon Sep 17 00:00:00 2001
From: Hashara <kumarasinghe.k.a.s.h@gmail.com>
Date: Mon, 7 Jul 2025 13:00:50 +1000
Subject: [PATCH 14/16] update values of failing checks

---
 test_scripts/test_data/expected_memory.tsv  | 4 ++--
 test_scripts/test_data/expected_runtime.tsv | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/test_scripts/test_data/expected_memory.tsv b/test_scripts/test_data/expected_memory.tsv
index cacb9473..04dbdebd 100644
--- a/test_scripts/test_data/expected_memory.tsv
+++ b/test_scripts/test_data/expected_memory.tsv
@@ -13,7 +13,7 @@ build/iqtree3 -s test_scripts/test_data/turtle.fa -m MIX{GTR{1,1,1,1,1,1}+FO,GTR
 build/iqtree3 -s test_scripts/test_data/turtle.fa -p test_scripts/test_data/turtle.nex -g test_scripts/test_data/turtle.constr.tree --prefix test_scripts/test_data/turtle.nex.constr -T 1 -seed 73073	3	10.57	10.45	8.80	5.86	6.78	10.43
 build/iqtree3 -s test_scripts/test_data/turtle.fa -p test_scripts/test_data/turtle.nex -g test_scripts/test_data/turtle.constr.tree2 -B 1000 -alrt 1000 --prefix test_scripts/test_data/turtle.nex.constr2 -T 1 -seed 73073	3	18.82	18.70	17.55	13.29	14.00	19.74
 build/iqtree3 -s test_scripts/test_data/turtle.fa -m MIX+MF --prefix test_scripts/test_data/turtle.mixfinder -T 1 -seed 73073	3	14.55	15.50	11.68	9.21	9.28	20.19
-build/iqtree3 -s test_scripts/test_data/turtle_aa.fasta -B 1000 -T 1 -seed 73073	3	25.57	25.66	24.47	21.26	15.77	22.72
+build/iqtree3 -s test_scripts/test_data/turtle_aa.fasta -B 1000 -T 1 -seed 73073	3	25.57	25.66	24.47	21.26	15.77	26.65
 build/iqtree3 -s test_scripts/test_data/turtle_aa.fasta -p test_scripts/test_data/turtle_aa.nex -B 1000 -T 1 -seed 73073	3	76.22	67.05	26.73	23.80	16.39	28.9
 build/iqtree3 -s test_scripts/test_data/turtle_aa.fasta -p test_scripts/test_data/turtle_aa.nex -B 1000 -T 1 -m MFP+MERGE -rcluster 10 --prefix test_scripts/test_data/turtle_aa.merge -seed 73073	3	41.34	31.46	26.11	22.30	16.56	28.35
 build/iqtree3 -s test_scripts/test_data/turtle_aa.fasta -p test_scripts/test_data/turtle_aa.merge.best_scheme.nex -z test_scripts/test_data/turtle_aa.trees -zb 10000 -au -n 0 --prefix test_scripts/test_data/turtle_aa.test -seed 73073 -T 1	3	33.53	33.46	32.43	31.32	30.30	33.82
@@ -23,4 +23,4 @@ build/iqtree3 -t test_scripts/test_data/turtle_aa.nex.treefile --gcf test_script
 build/iqtree3 -t test_scripts/test_data/turtle_aa.fasta.treefile --gcf test_scripts/test_data/turtle_aa.loci.treefile -s test_scripts/test_data/turtle_aa.fasta --scf 100 -seed 73073 -T 1	3	6.29	6.55	5.93	2.29	3.09	6.64
 build/iqtree3 -s test_scripts/test_data/turtle_aa.fasta -m MIX{LG+F,WAG+F} --prefix test_scripts/test_data/turtle_aa.mix -seed 73073 -T 1	3	11.79	11.80	10.67	6.39	6.78	11.94
 build/iqtree3 -s test_scripts/test_data/turtle_aa.fasta -p test_scripts/test_data/turtle_aa.nex -g test_scripts/test_data/turtle.constr.tree --prefix test_scripts/test_data/turtle_aa.nex.constr -T 1 -seed 73073	3	59.79	60.66	18.28	18.67	10.61	16.95
-build/iqtree3 -s test_scripts/test_data/turtle_aa.fasta -p test_scripts/test_data/turtle_aa.nex -g test_scripts/test_data/turtle.constr.tree2 -B 1000 -alrt 1000 --prefix test_scripts/test_data/turtle_aa.nex.constr2 -T 1 -seed 73073	3	50.73	70.88	26.53	23.55	16.72	26.39
+build/iqtree3 -s test_scripts/test_data/turtle_aa.fasta -p test_scripts/test_data/turtle_aa.nex -g test_scripts/test_data/turtle.constr.tree2 -B 1000 -alrt 1000 --prefix test_scripts/test_data/turtle_aa.nex.constr2 -T 1 -seed 73073	3	63.79	70.88	26.53	23.55	16.72	26.39
diff --git a/test_scripts/test_data/expected_runtime.tsv b/test_scripts/test_data/expected_runtime.tsv
index 98ebe004..d4aa8392 100644
--- a/test_scripts/test_data/expected_runtime.tsv
+++ b/test_scripts/test_data/expected_runtime.tsv
@@ -21,6 +21,6 @@ build/iqtree3 -s test_scripts/test_data/turtle_aa.fasta -p test_scripts/test_dat
 build/iqtree3 -s test_scripts/test_data/turtle_aa.fasta -S test_scripts/test_data/turtle_aa.nex --prefix test_scripts/test_data/turtle_aa.loci -T 1 -seed 73073	12	55.46	56.38	89.44	34.67	35.94	32.52
 build/iqtree3 -t test_scripts/test_data/turtle_aa.nex.treefile --gcf test_scripts/test_data/turtle_aa.loci.treefile -s test_scripts/test_data/turtle_aa.fasta --scf 100 -seed 73073 -T 1	1	0.01	0.01	0.01	0.02	0.02	0.4
 build/iqtree3 -t test_scripts/test_data/turtle_aa.fasta.treefile --gcf test_scripts/test_data/turtle_aa.loci.treefile -s test_scripts/test_data/turtle_aa.fasta --scf 100 -seed 73073 -T 1	1	0.01	0.01	0.01	0.02	0.01	0.41
-build/iqtree3 -s test_scripts/test_data/turtle_aa.fasta -m MIX{LG+F,WAG+F} --prefix test_scripts/test_data/turtle_aa.mix -seed 73073 -T 1	3	13.04	13.33	21.36	7.23	8.97	0.41
+build/iqtree3 -s test_scripts/test_data/turtle_aa.fasta -m MIX{LG+F,WAG+F} --prefix test_scripts/test_data/turtle_aa.mix -seed 73073 -T 1	3	13.04	13.33	21.36	7.23	8.97	7.53
 build/iqtree3 -s test_scripts/test_data/turtle_aa.fasta -p test_scripts/test_data/turtle_aa.nex -g test_scripts/test_data/turtle.constr.tree --prefix test_scripts/test_data/turtle_aa.nex.constr -T 1 -seed 73073	12	61.22	61.69	99.07	37.95	39.54	35.39
 build/iqtree3 -s test_scripts/test_data/turtle_aa.fasta -p test_scripts/test_data/turtle_aa.nex -g test_scripts/test_data/turtle.constr.tree2 -B 1000 -alrt 1000 --prefix test_scripts/test_data/turtle_aa.nex.constr2 -T 1 -seed 73073	12	82.86	85.39	135.76	49.92	53.91	48.37

From 230ea88a6ff00aad818e40f6e30ea9daf76555b1 Mon Sep 17 00:00:00 2001
From: Hashara <kumarasinghe.k.a.s.h@gmail.com>
Date: Mon, 7 Jul 2025 14:04:59 +1000
Subject: [PATCH 15/16] add comment to clarify what are the expected inputs

---
 test_scripts/verify_memory.sh  | 1 +
 test_scripts/verify_runtime.sh | 1 +
 2 files changed, 2 insertions(+)

diff --git a/test_scripts/verify_memory.sh b/test_scripts/verify_memory.sh
index 03643cf6..2e42a24b 100644
--- a/test_scripts/verify_memory.sh
+++ b/test_scripts/verify_memory.sh
@@ -1,4 +1,5 @@
 #!/bin/bash
+# expect the first argument to be the column name : contain what platform(OS) is running the script
 expected_column="$1"
 
 WD="test_scripts/test_data"
diff --git a/test_scripts/verify_runtime.sh b/test_scripts/verify_runtime.sh
index 14c2ced4..f42513bd 100644
--- a/test_scripts/verify_runtime.sh
+++ b/test_scripts/verify_runtime.sh
@@ -1,4 +1,5 @@
 #!/bin/bash
+# expect the first argument to be the column name : contain what platform(OS) is running the script
 expected_column="$1"
 
 WD="test_scripts/test_data"

From 5dcdf010455f55b6eb1d6cb11014872377274d54 Mon Sep 17 00:00:00 2001
From: Hashara Kumarasinghe <47107459+Hashara@users.noreply.github.com>
Date: Mon, 7 Jul 2025 14:36:34 +1000
Subject: [PATCH 16/16] Update test_scripts/verify_memory.sh

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
---
 test_scripts/verify_memory.sh | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/test_scripts/verify_memory.sh b/test_scripts/verify_memory.sh
index 2e42a24b..ae23f9b9 100644
--- a/test_scripts/verify_memory.sh
+++ b/test_scripts/verify_memory.sh
@@ -20,8 +20,10 @@ cut -f1,2,"$col_index" "$input_file" > "${selected_columns_file}"
 final_file="${WD}/combined_with_reported.tsv"
 
 # assuming the reported file and expected file have the same order of commands
-cut -f3 "$reported_file" > /tmp/reported_column.tsv
-paste "$selected_columns_file" /tmp/reported_column.tsv > "$final_file"
+temp_reported_column=$(mktemp)
+cut -f3 "$reported_file" > "$temp_reported_column"
+paste "$selected_columns_file" "$temp_reported_column" > "$final_file"
+rm -f "$temp_reported_column"
 
 
 fail_count=0