abi2fastq Testing #68
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name: abi2fastq Testing | |
on: | |
workflow_dispatch: | |
push: | |
branches: | |
- main | |
- dev | |
- refactoring | |
paths: | |
- bioconvert/abi2fastq.py | |
- .github/workflows/abi2fastq.yml | |
pull_request: | |
branches-ignore: [] | |
paths: | |
- bioconvert/abi2fastq.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 | |
# mamba install -c conda-forge -c bioconda --quiet -y samtools bedtools bamtools mosdepth pbzip2 pigz dsrc sambamba squizz | |
- 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.abi2fastq test/test_abi2fastq.py |