bam2cov Testing #102
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| name: bam2cov Testing | |
| on: | |
| workflow_dispatch: | |
| push: | |
| branches: | |
| - main | |
| - dev | |
| - refactoring | |
| paths: | |
| - bioconvert/bam2cov.py | |
| - .github/workflows/bam2cov.yml | |
| pull_request: | |
| branches-ignore: [] | |
| paths: | |
| - bioconvert/bam2cov.py | |
| schedule: | |
| - cron: '0 0 13 * *' | |
| jobs: | |
| build-linux: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| max-parallel: 5 | |
| matrix: | |
| python: [3.8, 3.9, '3.10'] | |
| fail-fast: false | |
| steps: | |
| - name: install graphviz and curl | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install -y graphviz-dev | |
| sudo apt-get install libcurl4-gnutls-dev | |
| - name: checkout git repo | |
| uses: actions/checkout@v2 | |
| - name: conda/mamba | |
| uses: mamba-org/provision-with-micromamba@main | |
| with: | |
| cache-downloads: true | |
| environment-file: false | |
| environment-name: installation | |
| channels: | |
| conda-forge,bioconda,defaults,r | |
| extra-specs: | | |
| python=${{ matrix.python }} | |
| easydev | |
| biosniff | |
| colorlog | |
| deeptools | |
| gffread | |
| pandas | |
| biopython>=1.70 | |
| mappy | |
| matplotlib-base | |
| networkx | |
| pyyaml | |
| pysam | |
| pyexcel | |
| pyexcel-ods3 | |
| pyexcel-xls | |
| pyexcel-xlsx | |
| pyBigWig | |
| py2bit | |
| statsmodels | |
| tqdm | |
| bamtools | |
| bcftools | |
| bedtools | |
| bedops | |
| dsrc | |
| go==1.10.3 | |
| goalign | |
| gotree | |
| mosdepth | |
| pbzip2 | |
| pigz | |
| plink | |
| sambamba | |
| samtools>=1.9 | |
| seqtk | |
| seqkit | |
| squizz | |
| sra-tools | |
| ucsc-wigtobigwig | |
| ucsc-twobittofa | |
| ucsc-fatotwobit | |
| ucsc-bedgraphtobigwig | |
| ucsc-bigwigtobedgraph | |
| wiggletools | |
| sed | |
| mawk | |
| xlrd | |
| - name: Install with pip | |
| shell: bash -l {0} | |
| run: | | |
| pip install .[testing] | |
| - name: testing | |
| shell: bash -l {0} | |
| run: | | |
| pytest -n 1 --cov-report term --cov=bioconvert.bam2cov test/test_bam2cov.py |