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Merged
bqminh merged 4 commits into from
May 19, 2026
Merged

Bugfix4 #167

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958436d
Update CI to use clang22
thomaskf May 18, 2026
a8c9135
Addressed the fluctration on memory usage
thomaskf May 18, 2026
a15d325
Update the memory threshold
thomaskf May 18, 2026
25866dd
Remove clang 13
thomaskf May 19, 2026
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19 changes: 13 additions & 6 deletions .github/workflows/ci.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -14,25 +14,32 @@ concurrency:

jobs:
build-linux-x86-64:
name: Linux x86-64 clang-${{ matrix.clang-version }} cmake-${{ matrix.cmake-version }}
name: Linux x86-64
runs-on: ubuntu-22.04
env:
# Disable glibc tcache to make peak RSS deterministic across runs.
GLIBC_TUNABLES: glibc.malloc.tcache_count=0
strategy:
fail-fast: false
matrix:
include:
- clang-version: 13
cmake-version: 3.14.7
upload: true
- clang-version: 15
- clang-version: 22
cmake-version: latest
upload: false
upload: true

steps:
- name: Checkout
uses: actions/checkout@v4
with:
submodules: "recursive"

- name: Add LLVM apt repository
if: matrix.clang-version >= 16
run: |
wget -qO- https://apt.llvm.org/llvm-snapshot.gpg.key | sudo gpg --dearmor -o /usr/share/keyrings/llvm.gpg
echo "deb [signed-by=/usr/share/keyrings/llvm.gpg] http://apt.llvm.org/jammy/ llvm-toolchain-jammy-${{ matrix.clang-version }} main" | sudo tee /etc/apt/sources.list.d/llvm.list
sudo apt-get update -q -y

- name: Install dependencies
run: |
sudo apt-get update -q -y
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2 changes: 1 addition & 1 deletion test_scripts/test_data/expected_memory.tsv
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Expand Up @@ -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 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 12 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.tree --prefix test_scripts/test_data/turtle_aa.nex.constr -T 1 -seed 73073 20 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 7 63.79 70.88 26.53 23.55 16.72 26.39
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