tempdir to before call #66
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| name: civet3 | |
| on: [push, pull_request] | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| jobs: | |
| run_civet3_test: | |
| name: Civet3 test on ${{ matrix.os }} | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| matrix: | |
| os: ["ubuntu-latest", "macos-latest"] | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| environment-file: environment.yml | |
| activate-environment: civet3 | |
| channels: conda-forge,bioconda,defaults | |
| mamba-version: "*" | |
| - name: Install civet3 | |
| run: pip install -e . | |
| - name: Check civet3 version | |
| run: civet --version | |
| - name: Check gofasta version | |
| run: gofasta --version | |
| - name: Test with example data | |
| run: civet --input-metadata civet/tests/outbreak_test.csv --input-sequences civet/tests/outbreak_test.fasta --timeline-dates symptom_onset,collection_date,upload_date --datadir civet/tests/action_test_data/ --no-temp --verbose | |
| - name: Test gisad_id based example | |
| run: civet -ids EPI_ISL_000001,EPI_ISL_000022,EPI_ISL_000033 --background-id-column gisaid_id --sequence-id-column sequence_name --datadir civet/tests/action_test_data/ &> test2.log | |
| - name: Test adm2 and date range example | |
| run: civet --from-metadata adm2=EDINBURGH sample_date=2020-03-01:2021-07-14 --datadir civet/tests/action_test_data/ --no-temp &> test3.log | |
| # add more tests here |