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HasharaHashara
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update values for failing checks
1 parent 5c1c5b8 commit c9c09f4

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3 files changed

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-41
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3 files changed

+53
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‎test_scripts/test_data/expected_memory.tsv‎

Lines changed: 25 additions & 25 deletions
Original file line numberDiff line numberDiff line change
@@ -1,26 +1,26 @@
11
Command diff-threshold Linux-gcc-9 Linux-gcc-12 Linux-aarch64 mac-os-x86-64 mac-os-arm64 windows-x86
2-
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
3-
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
4-
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
5-
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
6-
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
7-
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
8-
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
9-
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
10-
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
11-
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
12-
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
13-
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
14-
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
15-
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
16-
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
17-
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
18-
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
19-
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
20-
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
21-
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
22-
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
23-
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
24-
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
25-
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
26-
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
2+
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
3+
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
4+
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
5+
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
6+
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
7+
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
8+
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
9+
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
10+
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
11+
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
12+
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
13+
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
14+
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
15+
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
16+
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
17+
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
18+
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
19+
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
20+
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
21+
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
22+
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
23+
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
24+
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
25+
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
26+
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

‎test_scripts/test_data/expected_runtimes.tsv‎

Lines changed: 12 additions & 12 deletions
Original file line numberDiff line numberDiff line change
@@ -2,21 +2,21 @@
22
turtle.fa.iqtree Total CPU time used 2 3.128169 3.299343 4.909145 4.93771 3.595236 3.21875
33
turtle.loci.iqtree Total CPU time used 2 3.376 3.6 4.561 5.737 2.786 3.359
44
turtle.merge.iqtree Total CPU time used 2 3.22134 3.336272 4.881305 4.074864 3.063053 3.34375
5-
turtle.mix.iqtree Total CPU time used 1 2.288 2.437 3.653 2.043 2.607 2.391
6-
turtle.mix.jc.link.iqtree Total CPU time used 1 0.678048 0.716485 1.05925 0.79052 0.798578 0.8125
7-
turtle.mix.link.iqtree Total CPU time used 1 0.765474 0.829717 1.19517 0.856055 0.868658 0.90625
8-
turtle.mixfinder.iqtree Total CPU time used 3 9.34105 9.95267 14.5544 9.57637 8.78048 8.40625
5+
turtle.mix.iqtree Total CPU time used 1 2.288 2.437 3.653 4.416 2.607 2.391
6+
turtle.mix.jc.link.iqtree Total CPU time used 1 0.678048 0.716485 1.05925 1.97384 0.798578 0.8125
7+
turtle.mix.link.iqtree Total CPU time used 1 0.765474 0.829717 1.19517 2.31644 0.868658 0.90625
8+
turtle.mixfinder.iqtree Total CPU time used 3 9.34105 9.95267 14.5544 13.1422 8.78048 8.40625
99
turtle.nex.constr.iqtree Total CPU time used 3 2.74033 2.88714 3.45122 4.30755 2.83421 2.85938
1010
turtle.nex.constr2.iqtree Total CPU time used 3 3.172122 3.296328 3.914713 4.247386 3.261848 3.484375
1111
turtle.nex.iqtree Total CPU time used 3 3.139167 3.257494 4.000374 4.824423 3.217744 3.578125
1212
turtle.test.iqtree Total CPU time used 1 0.235 0.242 0.349 0.192 0.225 0.234
1313
turtle.wpl.iqtree Total CPU time used 1 0.037859 0.036415 0.043837 0.041274 0.030318 0.015625
14-
turtle_aa.fasta.iqtree Total CPU time used 12 61.60878 61.761949 100.241028 44.144877 44.523198 34.46875
15-
turtle_aa.loci.iqtree Total CPU time used 12 55.21 56.31 89.16 32.3 45.828247 31.66
16-
turtle_aa.merge.iqtree Total CPU time used 12 65.057715 65.34153 106.422985 48.539932 47.526024 36.890625
17-
turtle_aa.nex.constr.iqtree Total CPU time used 12 60.3527 60.7689 98.7859 47.122 38.9924 34.4219
18-
turtle_aa.nex.constr2.iqtree Total CPU time used 12 82.473306 82.646098 135.013106 54.514873 58.861398 47.40625
19-
turtle_aa.nex.iqtree Total CPU time used 12 70.691887 71.079425 115.466386 54.95159 52.16108 40.890625
20-
turtle_aa.test.iqtree Total CPU time used 1 1.69 1.81 2.72 0.862 0.979 0.922
14+
turtle_aa.fasta.iqtree Total CPU time used 12 61.60878 61.761949 100.241028 56.571182 44.523198 34.46875
15+
turtle_aa.loci.iqtree Total CPU time used 12 55.21 56.31 89.16 54.17 45.828247 31.66
16+
turtle_aa.merge.iqtree Total CPU time used 12 65.057715 65.34153 106.422985 76.722846 47.526024 36.890625
17+
turtle_aa.nex.constr.iqtree Total CPU time used 12 60.3527 60.7689 98.7859 59.6715 38.9924 34.4219
18+
turtle_aa.nex.constr2.iqtree Total CPU time used 12 82.473306 82.646098 135.013106 85.280632 58.861398 47.40625
19+
turtle_aa.nex.iqtree Total CPU time used 12 70.691887 71.079425 115.466386 71.812495 52.16108 40.890625
20+
turtle_aa.test.iqtree Total CPU time used 1 1.69 1.81 2.72 2.24 0.979 0.922
2121
turtle_aa.wpl.iqtree Total CPU time used 3 1.6987 1.701 2.7838 0.89948 1.0239 0.96875
22-
turtle_aa.mix.iqtree Total CPU time used 3 12.8918 13.1371 21.3145 6.91331 9.35718 7.09375
22+
turtle_aa.mix.iqtree Total CPU time used 3 12.8918 13.1371 21.3145 10.1353 9.35718 7.09375

‎test_scripts/test_iqtree.ps1‎

Lines changed: 16 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -12,12 +12,18 @@ function Measure-IQTree {
1212

1313
$startTime = Get-Date
1414

15-
# Start the command in a child PowerShell process
16-
$proc = Start-Process -FilePath "powershell" -ArgumentList "-NoProfile", "-Command", $CommandLine -PassThru
15+
# Split command and arguments
16+
$exe, $args = $CommandLine -split '\s+', 2
17+
$tempOut = [System.IO.Path]::GetTempFileName()
18+
19+
# Start the process with output redirection
20+
$proc = Start-Process -FilePath $exe -ArgumentList $args `
21+
-RedirectStandardOutput $tempOut `
22+
-NoNewWindow -PassThru
23+
1724
$procId = $proc.Id
1825
$peakMemory = 0
1926

20-
# Monitor the child process's memory usage
2127
while (-not $proc.HasExited) {
2228
Start-Sleep -Milliseconds 200
2329
try {
@@ -33,8 +39,14 @@ function Measure-IQTree {
3339
$endTime = Get-Date
3440
$elapsed = [math]::Round(($endTime - $startTime).TotalSeconds, 2)
3541

36-
# Write timing and memory data to log
42+
# Show output
43+
Get-Content $tempOut
44+
45+
# Log timing and memory
3746
"$CommandLine`t$elapsed`t$([math]::Round($peakMemory, 2))" | Out-File -FilePath $LOGFILE -Append -Encoding utf8
47+
48+
# Cleanup
49+
Remove-Item $tempOut
3850
}
3951

4052

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