Updated qiime2 version in CI #76
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| name: ci | |
| on: | |
| push: | |
| branches: [main] | |
| pull_request: | |
| branches: [main] | |
| workflow_dispatch: | |
| jobs: | |
| build: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout code | |
| uses: actions/checkout@v2 | |
| - name: Setup Mamba | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| python-version: 3.8 | |
| miniconda-version: 'latest' | |
| mamba-version: "*" | |
| channels: conda-forge,defaults | |
| channel-priority: true | |
| - name: Create conda environment | |
| run: | | |
| wget https://data.qiime2.org/distro/core/qiime2-2023.7-py38-linux-conda.yml | |
| mamba env create -n makarsa-test --file qiime2-2023.7-py38-linux-conda.yml | |
| mamba init | |
| - name: Install SpiecEasi | |
| run: | | |
| source /home/runner/.bashrc | |
| mamba activate makarsa-test | |
| mamba install -y -c conda-forge -c bioconda r-spieceasi flake8 julia | |
| julia -e 'using Pkg; Pkg.add(["FlashWeave", "ArgParse", "GraphIO"])' | |
| - name: Install Makarsa | |
| run: | | |
| source /home/runner/.bashrc | |
| mamba activate makarsa-test | |
| pip install . | |
| - name: Run Flake8 | |
| run: | | |
| source /home/runner/.bashrc | |
| mamba activate makarsa-test | |
| flake8 | |
| - name: Run pytest | |
| run: | | |
| source /home/runner/.bashrc | |
| mamba activate makarsa-test | |
| pytest |