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black linting

black linting #157

Workflow file for this run

name: tests ci
# This workflow runs the pipeline with the minimal test dataset to check
# is completed without any errors
on:
pull_request:
push:
jobs:
test_analyze_schema:
runs-on: ubuntu-latest
steps:
- name: Checkout repository
uses: actions/checkout@v4
- name: Set up Miniconda
uses: conda-incubator/setup-miniconda@v3
with:
activate-environment: taranis_env
environment-file: environment.yml
- name: Verify Conda environment
run: conda env list
- name: Activate env and install taranis
run: |
source $CONDA/etc/profile.d/conda.sh
conda activate taranis_env
python -m pip install .
taranis analyze-schema -i test/MLST_listeria/analyze_schema -o analyze_schema_test --cpus 1 --output-allele-annot --remove-no-cds --remove-duplicated --remove-subset
- name: Testing Reference allele
run: |
source $CONDA/etc/profile.d/conda.sh
conda activate taranis_env
taranis reference-alleles -s test/MLST_listeria/reference_allele -o reference_allele_test --cpus 1