CI #1092
Workflow file for this run
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| name: CI | |
| on: | |
| pull_request: | |
| branches: | |
| - '*' | |
| paths: | |
| # if any of this files or directory changed, trigger the CI | |
| # The only case where it is not triggerd is when docs/ is modified | |
| - 'tests/**' | |
| - 'testingDataset/**' | |
| - '.github/**' | |
| - 'ppanggolin/**' | |
| - 'MANIFEST.in' | |
| - 'VERSION' | |
| - 'ppanggolin_env.yaml' | |
| - 'pyproject.toml' | |
| - 'setup.py' | |
| # Allows you to run this workflow manually from the Actions tab | |
| workflow_dispatch: | |
| env: | |
| NUM_CPUS: 1 | |
| # A workflow run is made up of one or more jobs that can run sequentially or in parallel | |
| jobs: | |
| test: | |
| name: test PPanGGOLiN on ${{ matrix.os }} with python ${{ matrix.python-version }} | |
| # The type of runner that the job will run on | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| matrix: | |
| os: ['macos-14'] | |
| python-version: ['3.10', '3.12'] | |
| steps: | |
| # Get number of cpu available on the current runner | |
| - name: Get core number on linux | |
| if: matrix.os == 'ubuntu-latest' | |
| run: | | |
| nb_cpu_linux=`nproc` | |
| echo "Number of cores avalaible on the current linux runner $nb_cpu_linux" | |
| echo "NUM_CPUS=$nb_cpu_linux" >> "$GITHUB_ENV" | |
| - name: Get core number on macos | |
| if: matrix.os == 'macos-14' | |
| run: | | |
| nb_cpu_macos=`sysctl -n hw.ncpu` | |
| echo "Number of cores avalaible on the current macos runner $nb_cpu_macos" | |
| echo "NUM_CPUS=$nb_cpu_macos" >> "$GITHUB_ENV" | |
| # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it | |
| - uses: actions/checkout@v4 | |
| # # Install requirements with miniconda | |
| # - uses: conda-incubator/setup-miniconda@v3 | |
| # with: | |
| # python-version: ${{ matrix.python-version }} | |
| # channels: conda-forge,bioconda,defaults | |
| # environment-file: ppanggolin_env.yaml | |
| # activate-environment: ppanggolin | |
| - name: Set up Python environment | |
| run: | | |
| python${{ matrix.python-version }} -m venv ppgg | |
| source ppgg/bin/activate | |
| - name: Install dependencies with Homebrew | |
| run: | | |
| brew update | |
| brew upgrade | |
| brew install mmseqs2 | |
| brew install mafft | |
| brew install python-setuptools | |
| # brew install infernal | |
| # brew install aragorn | |
| - name: Install ppanggolin | |
| run: | | |
| # Activate the Python environment again in the correct directory | |
| source ppgg/bin/activate | |
| python -V | |
| python -m pip install pytest | |
| python -m pip install .[python_deps] | |
| # - name: Install ppanggolin | |
| # shell: bash -l {0} | |
| # run: | | |
| # pip install .[test] | |
| # mmseqs version | |
| # Check that it is installed and displays help without error | |
| - name: Check that PPanGGOLiN is installed | |
| shell: bash -l {0} | |
| run: | | |
| source ppgg/bin/activate | |
| ppanggolin --version | |
| ppanggolin --help | |
| # Check that unit tests are all passing | |
| - name: Unit tests | |
| shell: bash -l {0} | |
| run: | | |
| source ppgg/bin/activate | |
| pytest | |
| - name: gbff parsing and MSA computing | |
| shell: bash -l {0} | |
| run: | | |
| source ppgg/bin/activate | |
| cd testingDataset | |
| mkdir info_to_test | |
| ppanggolin workflow --cpu $NUM_CPUS --anno genomes.gbff.list --output myannopang | |
| ppanggolin msa --pangenome myannopang/pangenome.h5 --source dna --partition core -o myannopang/ -f --use_gene_id --phylo --single_copy --cpu $NUM_CPUS | |
| ppanggolin info --pangenome myannopang/pangenome.h5 > info_to_test/myannopang_info.yaml | |
| cat info_to_test/myannopang_info.yaml | |
| echo "$(grep 'myannopang/gene_families.tsv' expected_info_files/checksum.txt | cut -d' ' -f1) myannopang/gene_families.tsv" | shasum -a 256 -c - || { echo 'Checksum verification failed.' >&2; exit 1; } | |
| shasum -a 256 myannopang/gene_families.tsv >> info_to_test/checksum.txt | |
| cd - | |
| - name: clusters reading from external file | |
| shell: bash -l {0} | |
| run: | | |
| source ppgg/bin/activate | |
| cd testingDataset | |
| ppanggolin panrgp --anno genomes.gbff.list --cluster clusters.tsv --output readclusterpang --cpu $NUM_CPUS | |
| ppanggolin annotate --anno genomes.gbff.list --output readclusters --cpu $NUM_CPUS | |
| awk 'BEGIN{FS=OFS="\t"} {$1 = $1 OFS $1} 1' clusters.tsv > clusters_with_reprez.tsv; | |
| ppanggolin cluster --clusters clusters_with_reprez.tsv -p readclusters/pangenome.h5 --cpu $NUM_CPUS | |
| ppanggolin msa --pangenome readclusterpang/pangenome.h5 --partition persistent --phylo -o readclusterpang/msa/ -f --cpu $NUM_CPUS | |
| echo "$(grep 'readclusterpang/gene_families.tsv' expected_info_files/checksum.txt | cut -d' ' -f1) readclusterpang/gene_families.tsv" | shasum -a 256 -c - || { echo 'Checksum verification failed.' >&2; exit 1; } | |
| shasum -a 256 readclusterpang/gene_families.tsv >> info_to_test/checksum.txt | |
| cd - | |
| - name: testing context command | |
| shell: bash -l {0} | |
| run: | | |
| source ppgg/bin/activate | |
| cd testingDataset | |
| ppanggolin context --pangenome myannopang/pangenome.h5 --sequences some_chlam_proteins.fasta --output test_context --fast --cpu $NUM_CPUS | |
| # test from gene family ids. Test here with one family of module 1. The context should find all families of module 1 | |
| echo AP288_RS05055 > one_family_of_module_1.txt | |
| ppanggolin context --pangenome myannopang/pangenome.h5 --family one_family_of_module_1.txt --output test_context_from_id --cpu $NUM_CPUS | |
| cd - | |
| - name: testing config file | |
| shell: bash -l {0} | |
| run: | | |
| source ppgg/bin/activate | |
| cd testingDataset | |
| ppanggolin utils --default_config panrgp -o panrgp_default_config.yaml | |
| cut -f1,2 clusters.tsv > clusters_without_frag.tsv | |
| ppanggolin panrgp --anno genomes.gbff.list --cluster clusters_without_frag.tsv -o test_config --config panrgp_default_config.yaml --cpu $NUM_CPUS | |
| echo "$(grep 'test_config/gene_families.tsv' expected_info_files/checksum.txt | cut -d' ' -f1) test_config/gene_families.tsv" | shasum -a 256 -c - || { echo 'Checksum verification failed.' >&2; exit 1; } | |
| shasum -a 256 test_config/gene_families.tsv >> info_to_test/checksum.txt | |
| cd - | |
| - name: testing projection cmd | |
| shell: bash -l {0} | |
| run: | | |
| source ppgg/bin/activate | |
| cd testingDataset | |
| head genomes.fasta.list | sed 's/^/input_genome_/g' > genomes.fasta.head.list | |
| # ppanggolin projection --pangenome myannopang/pangenome.h5 -o projection_from_list_of_fasta --fasta genomes.fasta.head.list --gff --proksee --cpu $NUM_CPUS | |
| # projection of a plasmid with chevron that have been added manually to test chevron handeling in GFF | |
| ppanggolin projection --pangenome myannopang/pangenome.h5 --anno GBFF/plasmid_NZ_CP007132_with_manually_added_chevrons.gff.gz --cpu $NUM_CPUS -o projection_plasmid_with_chevron | |
| echo GFF_plasmid_No_seq$'\t'GBFF/plasmid_GCF_000093005.1_ASM9300v1.gff.gz >> genomes.gbff.h3_and_GFFplasmidNoSeq.list | |
| echo GFF_plasmid_No_seq$'\t'GBFF/plasmid_GCF_000093005.1_ASM9300v1.fna.gz >> genomes.fna.GFFplasmidNoSeq.list | |
| ppanggolin projection -p myannopang/pangenome.h5 --anno genomes.gbff.h3_and_GFFplasmidNoSeq.list --fasta genomes.fna.GFFplasmidNoSeq.list | |
| - name: Archive diff files | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: comparison-results_${{ matrix.os }}_python${{ matrix.python-version }} | |
| path: testingDataset/info_to_test/* | |