Merge pull request #47 from althonos/patch-1 #22
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| name: GitHub Actions CI | |
| on: | |
| push: | |
| branches: [ master, experimental, develop ] | |
| paths-ignore: | |
| - '**.md' | |
| workflow_dispatch: | |
| jobs: | |
| make-tests: | |
| name: Make | |
| strategy: | |
| matrix: | |
| machine: [ubuntu-latest, macOS-12] | |
| runs-on: ['${{ matrix.machine }}'] | |
| env: | |
| REF_DIR: ./test/adeno_fiber | |
| INPUT: ./test/adeno_fiber/adeno_fiber | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: make | |
| run: | | |
| g++ --version | |
| make -j | |
| - name: copy sl->slink references | |
| run: | | |
| cp ./test/adeno_fiber/sl.fasta ./test/adeno_fiber/slink.fasta | |
| cp ./test/hemopexin/medoid-sl.fasta ./test/hemopexin/medoid-slink.fasta | |
| - name: tar artifacts | |
| run: tar -cvf famsa.tar ./famsa ./test | |
| - uses: actions/upload-artifact@v2 | |
| with: | |
| name: executable-artifact-${{ matrix.machine }} | |
| path: ./famsa.tar | |
| ######################################################################################## | |
| full-tree: | |
| name: Full tree (adeno-fiber) | |
| needs: make-tests | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| tree: [sl, upgma] | |
| machine: [ubuntu-latest, macOS-12] | |
| runs-on: ['${{ matrix.machine }}'] | |
| env: | |
| REF_DIR: ./test/adeno_fiber | |
| INPUT: ./test/adeno_fiber/adeno_fiber | |
| steps: | |
| - uses: actions/download-artifact@v2 | |
| with: | |
| name: executable-artifact-${{ matrix.machine }} | |
| path: ./ | |
| - name: untar artifacts | |
| run: tar -xf famsa.tar | |
| - name: ${{matrix.tree}} (tree only) | |
| run: | | |
| ./famsa -v -gt ${{matrix.tree}} -gt_export ${INPUT} ${{matrix.tree}}.dnd | |
| cmp ${{matrix.tree}}.dnd ${REF_DIR}/${{matrix.tree}}.dnd | |
| - name: ${{matrix.tree}} (from tree) | |
| run: | | |
| ./famsa -v -gt import ${{matrix.tree}}.dnd ${INPUT} ${{matrix.tree}}.dnd.fasta | |
| cmp ${{matrix.tree}}.dnd.fasta ${REF_DIR}/${{matrix.tree}}.fasta | |
| - name: ${{matrix.tree}} (complete alignment) | |
| run: | | |
| ./famsa -v -gt ${{matrix.tree}} ${INPUT} ${{matrix.tree}}.fasta | |
| cmp ${{matrix.tree}}.fasta ${REF_DIR}/${{matrix.tree}}.fasta | |
| ######################################################################################## | |
| medoid-tree: | |
| name: Medoid tree (hemopexin) | |
| needs: full-tree | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| tree: [sl, upgma, nj] | |
| machine: [ubuntu-latest, macOS-12] | |
| runs-on: ['${{ matrix.machine }}'] | |
| env: | |
| REF_DIR: ./test/hemopexin | |
| INPUT: ./test/hemopexin/hemopexin | |
| steps: | |
| - uses: actions/download-artifact@v2 | |
| with: | |
| name: executable-artifact-${{ matrix.machine }} | |
| path: ./ | |
| - name: untar artifacts | |
| run: tar -xf famsa.tar | |
| - name: medoid + ${{matrix.tree}} (tree only) | |
| run: | | |
| ./famsa -medoidtree -gt ${{matrix.tree}} -gt_export ${INPUT} medoid-${{matrix.tree}}.dnd | |
| cmp medoid-${{matrix.tree}}.dnd ${REF_DIR}/medoid-${{matrix.tree}}.dnd | |
| - name: medoid + ${{matrix.tree}} (complete alignment) | |
| run: | | |
| ./famsa -medoidtree -gt ${{matrix.tree}} ${INPUT} medoid-${{matrix.tree}}.fasta | |
| cmp medoid-${{matrix.tree}}.fasta ${REF_DIR}/medoid-${{matrix.tree}}.fasta | |
| - name: medoid + ${{matrix.tree}} (from tree) | |
| run: | | |
| ./famsa -gt import medoid-${{matrix.tree}}.dnd ${INPUT} medoid-${{matrix.tree}}.dnd.fasta | |
| cmp medoid-${{matrix.tree}}.dnd.fasta ${REF_DIR}/medoid-${{matrix.tree}}.fasta | |
| - name: medoid + ${{matrix.tree}} (non-default params) | |
| run: | | |
| ./famsa -medoidtree -gt ${{matrix.tree}} -gt_export -subtree_size 10 -sample_size 100 -cluster_fraction 0.2 -cluster_iters 1 ${INPUT} medoid-${{matrix.tree}}-params.dnd | |
| cmp medoid-${{matrix.tree}}-params.dnd ${REF_DIR}/medoid-${{matrix.tree}}-params.dnd | |
| ######################################################################################## | |
| other-tests: | |
| name: Other tests (adeno-fiber) | |
| needs: medoid-tree | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| machine: [ubuntu-latest, macOS-12] | |
| runs-on: ['${{ matrix.machine }}'] | |
| env: | |
| REF_DIR: ./test/adeno_fiber | |
| INPUT: ./test/adeno_fiber/adeno_fiber | |
| steps: | |
| - uses: actions/download-artifact@v2 | |
| with: | |
| name: executable-artifact-${{ matrix.machine }} | |
| path: ./ | |
| - name: untar artifacts | |
| run: tar -xf famsa.tar | |
| - name: non-default gaps | |
| run: | | |
| ./famsa -go 10 -ge 2 -tgo 0.5 -tge 1.0 -gsd 3 -gsl 30 ${INPUT} gaps.fasta | |
| cmp gaps.fasta ${REF_DIR}/gaps.fasta | |
| - name: export distance | |
| run: | | |
| ./famsa -dist_export ${INPUT} dist.csv | |
| cmp dist.csv ${REF_DIR}/dist.csv | |
| - name: export distance (square) | |
| run: | | |
| ./famsa -dist_export -square_matrix ${INPUT} dist_sq.csv | |
| cmp dist_sq.csv ${REF_DIR}/dist_sq.csv | |
| - name: export pid | |
| run: | | |
| ./famsa -dist_export -pid ${INPUT} pid.csv | |
| cmp pid.csv ${REF_DIR}/pid.csv | |
| - name: export pid (square) | |
| run: | | |
| ./famsa -dist_export -square_matrix -pid ${INPUT} pid_sq.csv | |
| cmp pid_sq.csv ${REF_DIR}/pid_sq.csv | |
| ######################################################################################## | |