Update in self-hosted tests. #24
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| 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: ['${{ matrix.machine }}'] | |
| env: | |
| REF_DIR: ./test/adeno_fiber | |
| INPUT: ./test/adeno_fiber/adeno_fiber | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| submodules: recursive | |
| - name: make | |
| run: | | |
| g++ --version | |
| make -j | |
| - name: copy sl->slink references | |
| run: | | |
| cp ./test/adeno_fiber/sl.fasta ./test/adeno_fiber/slink.fasta | |
| cp ./test/hemopexin/medoid-sl.fasta ./test/hemopexin/medoid-slink.fasta | |
| - name: tar artifacts | |
| run: tar -cvf famsa.tar ./famsa ./test | |
| - uses: actions/upload-artifact@v4 | |
| with: | |
| name: executable-artifact-${{ 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: ['${{ matrix.machine }}'] | |
| env: | |
| REF_DIR: ./test/adeno_fiber | |
| INPUT: ./test/adeno_fiber/adeno_fiber | |
| steps: | |
| - uses: actions/download-artifact@v4 | |
| with: | |
| name: executable-artifact-${{ 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: ['${{ matrix.machine }}'] | |
| env: | |
| REF_DIR: ./test/hemopexin | |
| INPUT: ./test/hemopexin/hemopexin | |
| steps: | |
| - uses: actions/download-artifact@v4 | |
| with: | |
| name: executable-artifact-${{ 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: ['${{ matrix.machine }}'] | |
| env: | |
| REF_DIR: ./test/adeno_fiber | |
| INPUT: ./test/adeno_fiber/adeno_fiber | |
| steps: | |
| - uses: actions/download-artifact@v4 | |
| with: | |
| name: executable-artifact-${{ 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 | |
| ######################################################################################## | |