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Fix a bug where a element of dict with empty values was left behind a… #6

Fix a bug where a element of dict with empty values was left behind a…

Fix a bug where a element of dict with empty values was left behind a… #6

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