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feat: add github action for test
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jiarong committed Nov 28, 2024
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37 changes: 37 additions & 0 deletions .github/workflows/test.yaml
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name: Test VirSorter2
on: [push, pull_request]

jobs:
miniconda:
name: Miniconda ${{ matrix.os }}
runs-on: ubuntu-latest
defaults:
run:
shell: bash -l {0}
strategy:
matrix:
python-version: ["3.10"]
steps:
- uses: actions/checkout@v4
- name: Set up environment with Python ${{ matrix.python-version }}
uses: conda-incubator/setup-miniconda@v3
with:
activate-environment: test
environment-file: vs2-external-deps.yaml
python-version: ${{ matrix.python-version }}
auto-activate-base: false
channels: conda-forge,bioconda
channel-priority: true
- run: |
conda info
conda list
conda config --set channel_priority strict
- name: Install VirSorter2
run: |
pip install -e .
- name: Run tests
run: |
virsorter --help
virsorter --version
virsorter setup -d db -j 4
virsorter run -w test/test.out -i test/8seq.fa all --dryrun

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