DOC Fix markdown in docs #467
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: semibin_test | |
on: [push, pull_request] | |
jobs: | |
build: | |
runs-on: ubuntu-latest | |
strategy: | |
matrix: | |
os: [ubuntu-latest, macos-latest, windows-latest] | |
python-version: | |
- "3.7" | |
- "3.8" | |
- "3.9" | |
- "3.10" | |
- "3.11" | |
- "3.12" | |
steps: | |
- uses: actions/checkout@v2 | |
- name: Set up Python ${{ matrix.python-version }} | |
uses: actions/setup-python@v2 | |
with: | |
python-version: ${{ matrix.python-version }} | |
- uses: conda-incubator/setup-miniconda@v2 | |
with: | |
activate-environment: test | |
python-version: ${{ matrix.python-version }} | |
auto-activate-base: false | |
- name: Install dependencies | |
shell: bash -l {0} | |
run : | | |
conda install -c conda-forge numpy pandas pytest hypothesis python-igraph scikit-learn requests numexpr tqdm | |
conda install -c conda-forge -c bioconda bedtools hmmer fraggenescan prodigal samtools mmseqs2 | |
conda install -c pytorch -c nvidia pytorch pytorch-cuda=11.8 | |
pip install . | |
- name: Test with pytest | |
shell: bash -l {0} | |
run: | | |
python -m pytest ./test | |
- name: Test with SemiBin command | |
shell: bash -l {0} | |
run: | | |
for t in integration-tests/*.py; do | |
echo "Running $t ..." | |
python $t | |
done | |