Skip to content

DOC Fix markdown in docs #467

DOC Fix markdown in docs

DOC Fix markdown in docs #467

Workflow file for this run

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