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self-hosted.yml
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name: Self-hosted CI
on:
pull_request:
branches: [main, master, develop]
paths-ignore:
- '**.md'
workflow_dispatch:
jobs:
########################################################################################
checkout:
name: Checkout
strategy:
matrix:
machine: [x64_linux, x64_mac, arm64_linux, arm64_mac]
runs-on: [self-hosted, clusty, '${{ matrix.machine }}']
steps:
- name: clean
run: rm -rf ${{ github.workspace }}/*
- uses: actions/checkout@v4
with:
submodules: recursive
- name: Get tags
run: |
cd ./libs/igraph
git fetch --prune --unshallow
echo exit code $?
git tag --list
continue-on-error: true
########################################################################################
make:
name: Make
needs: checkout
strategy:
fail-fast: false
matrix:
machine: [x64_linux, x64_mac, arm64_linux, arm64_mac]
compiler: [11, 12]
include:
- {machine: x64_linux, platform: avx2, compiler: 14}
- {machine: x64_linux, platform: avx2}
- {machine: arm64_linux, platform: arm8}
- {machine: x64_mac, platform: avx2}
- {machine: arm64_mac, platform: m1}
runs-on: [self-hosted, clusty, '${{ matrix.machine }}']
steps:
- name: make
run: |
gmake -j32 CXX=g++-${{matrix.compiler}} CC=gcc-${{matrix.compiler}} PLATFORM=${{ matrix.platform }} LEIDEN=true STATIC_LINK=true
cp ./bin/clusty ./clusty-${{matrix.compiler}}
gmake clean
########################################################################################
toy:
name: Toy example
needs: make
strategy:
fail-fast: false
matrix:
algo: [single]
machine: [x64_linux, x64_mac, arm64_linux, arm64_mac]
compiler: [11, 12]
include:
- {algo: single, machine: x64_linux, compiler: 14}
runs-on: [self-hosted, clusty, '${{ matrix.machine }}']
steps:
- name: help
run: ./clusty-${{matrix.compiler}}
- name: version
run: ./clusty-${{matrix.compiler}} --version
- name: ${{matrix.algo}} (no representatives, numeric ids, singletons in object file)
run: |
./clusty-${{matrix.compiler}} --objects-file ./test/toy.ids.tsv --algo ${{matrix.algo}} --id-cols idx1 idx2 --distance-col tani --similarity --numeric-ids --min tani 0.95 ./test/toy.ani.tsv toy.${{matrix.algo}}.tsv
python3 ./test/cmp.py toy.${{matrix.algo}}.tsv ./test/toy.${{matrix.algo}}.tsv
########################################################################################
vir61-linkage:
name: Vir61
needs: toy
strategy:
fail-fast: false
matrix:
algo: [single, complete]
threshold: [95, 70]
machine: [x64_linux, x64_mac, arm64_linux, arm64_mac]
compiler: [12]
include:
- {algo: single, threshold: 95, machine: x64_linux, compiler: 14}
- {algo: single, threshold: 70, machine: x64_linux, compiler: 14}
- {algo: complete, threshold: 95, machine: x64_linux, compiler: 14}
- {algo: complete, threshold: 70, machine: x64_linux, compiler: 14}
runs-on: [self-hosted, clusty, '${{ matrix.machine }}']
steps:
- name: ${{matrix.algo}}, ${{matrix.threshold}} (with representatives, reordered columns)
run: |
./clusty-${{matrix.compiler}} --algo ${{matrix.algo}} --objects-file ./test/vir61.list --similarity --min ani 0.${{matrix.threshold}} --id-cols id2 id1 --distance-col ani ./test/vir61.ani vir61.${{matrix.algo}}.${{matrix.threshold}} --out-representatives
python3 ./test/cmp.py vir61.${{matrix.algo}}.${{matrix.threshold}} ./test/vir61.${{matrix.algo}}.${{matrix.threshold}}.python.csv
########################################################################################
ictv-linkage:
name: ICTV (single and complete versus python clusterings)
needs: vir61-linkage
strategy:
fail-fast: false
matrix:
algo: [single, complete]
threshold: [95, 70]
machine: [x64_linux, x64_mac, arm64_linux, arm64_mac]
compiler: [12]
include:
- {algo: single, threshold: 95, machine: x64_linux, compiler: 14}
- {algo: single, threshold: 70, machine: x64_linux, compiler: 14}
- {algo: complete, threshold: 95, machine: x64_linux, compiler: 14}
- {algo: complete, threshold: 70, machine: x64_linux, compiler: 14}
runs-on: [self-hosted, clusty, '${{ matrix.machine }}']
steps:
- name: ${{matrix.algo}}, ${{matrix.threshold}} (no representatives)
run: |
./clusty-${{matrix.compiler}} --algo ${{matrix.algo}} --objects-file ./test/ictv.list --similarity --min ani 0.${{matrix.threshold}} ./test/ictv.ani ictv.${{matrix.algo}}.${{matrix.threshold}}
python3 ./test/cmp.py ictv.${{matrix.algo}}.${{matrix.threshold}} ./test/ictv.${{matrix.algo}}.${{matrix.threshold}}.python.csv
- name: ${{matrix.algo}}, ${{matrix.threshold}} (with representatives)
run: |
./clusty-${{matrix.compiler}} --algo ${{matrix.algo}} --objects-file ./test/ictv.list --similarity --min ani 0.${{matrix.threshold}} ./test/ictv.ani ictv.${{matrix.algo}}.${{matrix.threshold}}.reps --out-representatives
python3 ./test/cmp.py ictv.${{matrix.algo}}.${{matrix.threshold}}.reps ./test/ictv.${{matrix.algo}}.${{matrix.threshold}}.python.csv
- name: ${{matrix.algo}}, ${{matrix.threshold}} (no representatives, numeric ids)
run: |
./clusty-${{matrix.compiler}} --algo ${{matrix.algo}} --objects-file ./test/ictv.list --similarity --min ani 0.${{matrix.threshold}} ./test/ictv.num ictv.${{matrix.algo}}.${{matrix.threshold}}.num --numeric-ids
python3 ./test/cmp.py ictv.${{matrix.algo}}.${{matrix.threshold}}.num ./test/ictv.${{matrix.algo}}.${{matrix.threshold}}.python.csv
- name: ${{matrix.algo}}, ${{matrix.threshold}} (with representatives, numeric ids)
run: |
./clusty-${{matrix.compiler}} --algo ${{matrix.algo}} --objects-file ./test/ictv.list --similarity --min ani 0.${{matrix.threshold}} ./test/ictv.num ictv.${{matrix.algo}}.${{matrix.threshold}}.reps.num --out-representatives --numeric-ids
python3 ./test/cmp.py ictv.${{matrix.algo}}.${{matrix.threshold}}.reps.num ./test/ictv.${{matrix.algo}}.${{matrix.threshold}}.python.csv
########################################################################################
ictv-all:
name: ICTV (all algos versus our clusterings)
needs: ictv-linkage
strategy:
fail-fast: false
matrix:
algo: [single, complete, uclust, set-cover, cd-hit, leiden]
threshold: [70]
machine: [x64_linux, x64_mac, arm64_linux, arm64_mac]
compiler: [12]
include:
- {algo: single, threshold: 70, machine: x64_linux, compiler: 14}
- {algo: complete, threshold: 70, machine: x64_linux, compiler: 14}
- {algo: uclust, threshold: 70, machine: x64_linux, compiler: 14}
- {algo: set-cover, threshold: 70, machine: x64_linux, compiler: 14}
- {algo: cd-hit, threshold: 70, machine: x64_linux, compiler: 14}
- {algo: leiden, threshold: 70, machine: x64_linux, compiler: 14}
runs-on: [self-hosted, clusty, '${{ matrix.machine }}']
steps:
- name: ${{matrix.algo}}, ${{matrix.threshold}} (no representatives)
run: |
./clusty-${{matrix.compiler}} --algo ${{matrix.algo}} --objects-file ./test/ictv.list --similarity --min ani 0.${{matrix.threshold}} ./test/ictv.ani ictv.${{matrix.algo}}.${{matrix.threshold}}
cmp ictv.${{matrix.algo}}.${{matrix.threshold}} ./test/ictv.${{matrix.algo}}.${{matrix.threshold}}.csv
- name: ${{matrix.algo}}, ${{matrix.threshold}} (with representatives)
run: |
./clusty-${{matrix.compiler}} --algo ${{matrix.algo}} --objects-file ./test/ictv.list --similarity --min ani 0.${{matrix.threshold}} ./test/ictv.ani ictv.${{matrix.algo}}.${{matrix.threshold}}.reps --out-representatives
cmp ictv.${{matrix.algo}}.${{matrix.threshold}}.reps ./test/ictv.${{matrix.algo}}.${{matrix.threshold}}.reps.csv
- name: ${{matrix.algo}}, ${{matrix.threshold}} (with representatives, numeric ids)
run: |
./clusty-${{matrix.compiler}} --algo ${{matrix.algo}} --objects-file ./test/ictv.list --similarity --min ani 0.${{matrix.threshold}} ./test/ictv.num ictv.${{matrix.algo}}.${{matrix.threshold}}.reps.num --out-representatives --numeric-ids
cmp ictv.${{matrix.algo}}.${{matrix.threshold}}.reps.num ./test/ictv.${{matrix.algo}}.${{matrix.threshold}}.reps.csv