Fix a bug where a element of dict with empty values was left behind a… #6
Workflow file for this run
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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 |