Fix seppJsonMerger.jar #26
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: ${{ matrix.python-version }} | |
| environment-file: ci/environment.yml | |
| auto-activate-base: true | |
| activate-environment: sepp_ci | |
| - name: install sepp | |
| shell: bash -el {0} | |
| run: | | |
| python setup.py config -c | |
| python setup.py install | |
| - name: run tests | |
| shell: bash -el {0} | |
| run: | | |
| conda list | |
| nosetests -w test/unittest --with-doctest --with-coverage | |
| - name: functional test | |
| shell: bash -el {0} | |
| run: | | |
| mkdir -p sepp-package/sepp/.sepp/ functional_tests/ | |
| cp ./.sepp/main.config sepp-package/sepp/.sepp/main.config | |
| cd functional_tests | |
| ../sepp-package/run-sepp.sh ../test/unittest/data/q2-fragment-insertion/input_fragments.fasta funcTest -x 2 -a ../test/unittest/data/q2-fragment-insertion/reference_alignment_tiny.fasta -t ../test/unittest/data/q2-fragment-insertion/reference_phylogeny_tiny.nwk -r ../test/unittest/data/q2-fragment-insertion/RAxML_info-reference-gg-raxml-bl.info -b 1 | |
| diff funcTest_placement.tog.relabelled.tre ../test/functionaltest/funcTest_q2-tiny_placement.tog.relabelled.tre | |
| cd .. | |
| - name: Archive functional test results for local debugging | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: SEPP_functional_tests_${{ matrix.python-version }} | |
| path: functional_tests | |
| - name: functional test pplacer 1.1.alpha17 | |
| shell: bash -el {0} | |
| run: | | |
| mkdir -p sepp-package/sepp/.sepp/ functional_tests/ | |
| cp ./.sepp/main.config sepp-package/sepp/.sepp/main.config | |
| cd functional_tests | |
| rm -v `find ~/ -type f -name pplacer` | |
| wget "https://github.com/matsen/pplacer/releases/download/v1.1.alpha17/pplacer-Linux-v1.1.alpha17.zip" | |
| unzip pplacer-Linux-v1.1.alpha17.zip | |
| mv -v pplacer-Linux-v1.1.alpha17/pplacer ../.sepp/bundled-v4.5.5/pplacer | |
| rm -rf pplacer-Linux-v1.1.alpha17* | |
| ../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 -b 1 | |
| cat ../test/functionaltest/funcTest_q2-tiny_placement.tog.relabelled.tre | sed "s/((163164:0.0792419/((163164:0.079242/" | sed "s/1024637:0.0283109)'nodeid_321248':0.0224664/1024637:0.0283109)'nodeid_321248':0.0224708/" | sed "s/testseqe:0.0964783):0.195875)'nodeid_320633':0.0493007/testseqe:0.096466):0.195871)'nodeid_320633':0.0493007/" | sed "s/(272555:0.0600304/(272555:0.0600251/" | sed "s/testseqg:0.0321409):0.0609292)'nodeid_335817':0.281379)'nodeid_335169':0.00443657/testseqg:0.032141):0.0609345)'nodeid_335817':0.281379)'nodeid_335169':0.00443657/" > funcTest_q2-tiny_placement.tog.relabelled.tre | |
| diff funcTest_placement.tog.relabelled.tre funcTest_q2-tiny_placement.tog.relabelled.tre | |
| cd .. | |
| - 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/ |