Merge pull request #70 from akikuno/develop-0.5.6 #11
Workflow file for this run
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: E2E test for Tyr substitution | |
| on: | |
| push: | |
| jobs: | |
| build: | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| max-parallel: 2 | |
| matrix: | |
| os: [ubuntu-latest, macos-latest] | |
| python-version: ["3.13"] | |
| name: Python ${{ matrix.python-version }} on ${{ matrix.os }} | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Miniconda | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| miniconda-version: "latest" | |
| activate-environment: test-env | |
| channels: bioconda, conda-forge, defaults | |
| - name: Create and activate conda environment | |
| run: | | |
| conda create -y -n env-dajin2 python=${{ matrix.python-version }} pip pytest | |
| conda activate env-dajin2 | |
| - name: Install DAJIN2 and dependencies | |
| run: | | |
| pip install -e . # Install DAJIN2 in editable mode | |
| - name: Download and prepare example dataset | |
| run: | | |
| if [ ! -d example_batch ]; then | |
| curl -LJO https://github.com/akikuno/DAJIN2/raw/main/examples/example_batch.tar.gz | |
| tar -xf example_batch.tar.gz | |
| fi | |
| - name: Modify batch file and execute DAJIN2 batch test | |
| env: | |
| PYTHONPATH: src | |
| run: | | |
| TODAY=$(date -u "+%Y%m%d") | |
| sed "s|tyr_c230gt|tyr_c230gt_${TODAY}|" example_batch/batch.csv > /tmp/tmp_batch.csv | |
| time DAJIN2 batch --file /tmp/tmp_batch.csv --threads 4 --debug || exit 1 |