add functional test #8
Workflow file for this run
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| name: SEPP_github_tests | |
| on: | |
| push: | |
| branches: [ master ] | |
| pull_request: | |
| branches: [ master ] | |
| jobs: | |
| python_tests: | |
| strategy: | |
| matrix: | |
| python-version: ["3.9", "3.10"] | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout Repo | |
| uses: actions/checkout@v3 | |
| - name: setup conda | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| # This uses *miniforge*, rather than *minicond*. The primary difference | |
| # is that the defaults channel is not enabled at all | |
| miniforge-version: latest | |
| # These properties enable the use of mamba, which is much faster and far | |
| # less error prone than conda while being completely compatible with the | |
| # conda CLI | |
| use-mamba: true | |
| mamba-version: "*" | |
| python-version: ${{ matrix.python-version }} | |
| environment-file: ci/environment.yml | |
| auto-activate-base: true | |
| activate-environment: sepp_ci | |
| - name: install sepp | |
| shell: bash -el {0} | |
| run: | | |
| python setup.py config -c | |
| python setup.py install | |
| # - name: run tests | |
| # shell: bash -el {0} | |
| # run: | | |
| # conda list | |
| # nosetests -w test/unittest --with-doctest --with-coverage | |
| - name: functional test | |
| run: | | |
| sepp-package/run-sepp.sh test/unittest/data/q2-fragment-insertion/input_fragments.fasta funcTest -x 2 -a test/unittest/data/q2-fragment-insertion/reference_alignment_tiny.fasta -t test/unittest/data/q2-fragment-insertion/reference_phylogeny_tiny.nwk -r test/unittest/data/q2-fragment-insertion/RAxML_info-reference-gg-raxml-bl.info; cat *funcTest-err.log | |
| diff funcTest_placement.tog.relabelled.tre test/functionaltest/funcTest_q2-tiny_placement.tog.relabelled.tre | |
| # - name: convert coverage | |
| # shell: bash -el {0} | |
| # run: | | |
| # coverage lcov | |
| # - name: send coverage report. | |
| # uses: coverallsapp/github-action@master | |
| # with: | |
| # github-token: ${{ secrets.GITHUB_TOKEN }} | |
| # path-to-lcov: "coverage.lcov" | |
| linting: | |
| strategy: | |
| matrix: | |
| python-version: ["3.9", "3.10"] | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout Repo | |
| uses: actions/checkout@v3 | |
| - name: setup conda | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| # This uses *miniforge*, rather than *minicond*. The primary difference | |
| # is that the defaults channel is not enabled at all | |
| miniforge-version: latest | |
| # These properties enable the use of mamba, which is much faster and far | |
| # less error prone than conda while being completely compatible with the | |
| # conda CLI | |
| use-mamba: true | |
| mamba-version: "*" | |
| python-version: ${{ matrix.python-version }} | |
| environment-file: ci/env_lint.yml | |
| auto-activate-base: true | |
| activate-environment: sepp_lint | |
| - name: linting | |
| shell: bash -el {0} | |
| run: | | |
| flake8 setup.py split_sequences.py distribute_setup.py run_ensemble.py run_sepp.py run_upp.py merge_script.py test/unittest/ sepp/ |