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name: GitHub Actions CI | ||
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on: | ||
push: | ||
branches: [ main, master, develop ] | ||
paths-ignore: | ||
- '**.md' | ||
workflow_dispatch: | ||
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jobs: | ||
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######################################################################################## | ||
make: | ||
name: Make | ||
strategy: | ||
fail-fast: false | ||
matrix: | ||
machine: [ubuntu-latest, macOS-12] | ||
compiler: [g++-11] | ||
runs-on: ['${{ matrix.machine }}'] | ||
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steps: | ||
- uses: actions/checkout@v2 | ||
with: | ||
submodules: recursive | ||
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- name: get tags | ||
run: | | ||
cd ./libs/igraph | ||
git fetch --tags origin | ||
- name: make | ||
run: | | ||
make -j32 CXX=${{matrix.compiler}} | ||
cp ./clusty ./clusty-${{matrix.compiler}} | ||
make clean | ||
- name: tar artifacts | ||
run: tar -cvf clusty.tar ./clusty-${{matrix.compiler}} ./test/cmp.py ./test/vir61.* | ||
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- uses: actions/upload-artifact@v2 | ||
with: | ||
name: executable-artifact-${{ matrix.machine }} | ||
path: ./clusty.tar | ||
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######################################################################################## | ||
vir61-linkage: | ||
name: Vir61 | ||
needs: make | ||
strategy: | ||
fail-fast: false | ||
matrix: | ||
machine: [ubuntu-latest, macOS-12] | ||
compiler: [g++-11] | ||
algo: [single, complete] | ||
threshold: [95, 70] | ||
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runs-on: ['${{ matrix.machine }}'] | ||
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steps: | ||
- uses: actions/download-artifact@v2 | ||
with: | ||
name: executable-artifact-${{ matrix.machine }} | ||
path: ./ | ||
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- name: untar artifacts | ||
run: | | ||
tar -xf clusty.tar | ||
- 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 | ||
python ./test/cmp.py vir61.${{matrix.algo}}.${{matrix.threshold}} ./test/vir61.${{matrix.algo}}.${{matrix.threshold}}.python.csv | ||
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name: Self-hosted CI | ||
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on: | ||
pull_request: | ||
branches: [main, master, develop] | ||
paths-ignore: | ||
- '**.md' | ||
workflow_dispatch: | ||
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jobs: | ||
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######################################################################################## | ||
checkout: | ||
name: Checkout | ||
strategy: | ||
matrix: | ||
machine: [xeon, mac-i7, mac-m1] | ||
runs-on: [self-hosted, clusty, '${{ matrix.machine }}'] | ||
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steps: | ||
- uses: actions/checkout@v2 | ||
with: | ||
submodules: recursive | ||
- name: Get tags | ||
run: | | ||
cd ./libs/igraph | ||
git fetch --tags origin | ||
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######################################################################################## | ||
make: | ||
name: Make | ||
needs: checkout | ||
strategy: | ||
fail-fast: false | ||
matrix: | ||
machine: [xeon, mac-i7, mac-m1] | ||
compiler: [g++-11] | ||
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runs-on: [self-hosted, clusty, '${{ matrix.machine }}'] | ||
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steps: | ||
- name: make | ||
run: | | ||
make -j32 CXX=${{matrix.compiler}} | ||
cp ./clusty ./clusty-${{matrix.compiler}} | ||
make clean | ||
######################################################################################## | ||
make-leiden: | ||
name: make (Leiden) | ||
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needs: checkout | ||
strategy: | ||
fail-fast: false | ||
matrix: | ||
compiler: [g++-11] | ||
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runs-on: [self-hosted, clusty] | ||
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steps: | ||
- name: make | ||
run: | | ||
make -j32 CXX=${{matrix.compiler}} LEIDEN=true | ||
cp ./clusty ./clusty-leiden-${{matrix.compiler}} | ||
make clean | ||
######################################################################################## | ||
toy: | ||
name: Toy example | ||
needs: make | ||
strategy: | ||
fail-fast: false | ||
matrix: | ||
machine: [xeon, mac-i7, mac-m1] | ||
compiler: [g++-11] | ||
algo: [single] | ||
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runs-on: [self-hosted, clusty, '${{ matrix.machine }}'] | ||
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steps: | ||
- 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 | ||
######################################################################################## | ||
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vir61-linkage: | ||
name: Vir61 | ||
needs: make | ||
strategy: | ||
fail-fast: false | ||
matrix: | ||
machine: [xeon, mac-i7, mac-m1] | ||
compiler: [g++-11] | ||
algo: [single, complete] | ||
threshold: [95, 70] | ||
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||
runs-on: [self-hosted, clusty, '${{ matrix.machine }}'] | ||
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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: make | ||
strategy: | ||
fail-fast: false | ||
matrix: | ||
machine: [xeon, mac-i7, mac-m1] | ||
compiler: [g++-11] | ||
algo: [single, complete] | ||
threshold: [95, 70] | ||
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runs-on: [self-hosted, clusty, '${{ matrix.machine }}'] | ||
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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: make | ||
strategy: | ||
fail-fast: false | ||
matrix: | ||
machine: [xeon, mac-i7, mac-m1] | ||
compiler: [g++-11] | ||
algo: [single, complete, uclust, set-cover, cd-hit] | ||
threshold: [70] | ||
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runs-on: [self-hosted, clusty, '${{ matrix.machine }}'] | ||
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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 | ||
######################################################################################## | ||
ictv-leiden: | ||
name: ICTV (leiden) | ||
needs: make-leiden | ||
strategy: | ||
fail-fast: false | ||
matrix: | ||
compiler: [g++-11] | ||
algo: [leiden] | ||
threshold: [70] | ||
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runs-on: [self-hosted, clusty, '${{ matrix.machine }}'] | ||
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steps: | ||
- name: ${{matrix.algo}}, ${{matrix.threshold}} (no representatives) | ||
run: | | ||
./clusty-leiden-${{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}}, ${{matrix.threshold}} (with representatives) | ||
run: | | ||
./clusty-leiden-${{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}}, ${{matrix.threshold}} (with representatives, numeric ids) | ||
run: | | ||
./clusty-keiden-${{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 | ||
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/src/x64 | ||
/src/_release/ | ||
/src/_debug/ | ||
/src/.vs/rapid-cluster/v17 | ||
/src/.vs/rapid-cluster/FileContentIndex | ||
/src/.vs/clusty/v17 | ||
/src/.vs/clusty/FileContentIndex | ||
/libs/winflexbison | ||
/src/clusty/x64/Debug/clusty.tlog | ||
/src/clusty/x64/Debug | ||
/src |
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[submodule "libs/mimalloc"] | ||
path = libs/mimalloc | ||
url = https://github.com/refresh-bio-dependencies/mimalloc.git | ||
[submodule "libs/igraph"] | ||
path = libs/igraph | ||
url = https://github.com/refresh-bio-dependencies/igraph |
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