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test.yaml
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name: Run tests
on:
push:
branches:
- main
pull_request:
branches:
- main
jobs:
test:
name: Run tests
runs-on: ubuntu-latest
timeout-minutes: 60
steps:
- name: checkout
uses: actions/checkout@v3
with:
lfs: true
- name: build conda environment
uses: conda-incubator/setup-miniconda@v2
with:
activate-environment: seqneut-pipeline
environment-file: environment.yml
auto-activate-base: false
auto-update-conda: true
channel-priority: strict
- name: lint code with ruff
# NOTE: must specify the shell so that conda init updates bashrc see:
# https://github.com/conda-incubator/setup-miniconda#IMPORTANT
shell: bash -el {0}
run: ruff check .
- name: lint Jupyter notebooks with ruff
shell: bash -el {0}
run: nbqa ruff .
- name: check code format with black
shell: bash -el {0}
run: black --check .
- name: check snakemake files format with snakefmt
shell: bash -el {0}
run: snakefmt --check .
- name: lint snakemake files with snakemake --lint
shell: bash -el {0}
run: cd test_example && snakemake --lint && cd ..
- name: run pipeline on test example
shell: bash -el {0}
run: >
rm -rf docs
&& cd test_example
&& rm -rf results
&& snakemake --use-conda -j 2
&& cd ..
- name: Upload log files in case of error
uses: actions/upload-artifact@v3
if: failure()
with:
name: log-files
path: test_example/results/logs
retention-days: 7