Bug fixes for Joint-RPCA #60
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| # much of this is taken from the Empress main.yml file | |
| name: Main CI | |
| on: | |
| pull_request: | |
| branches: | |
| - master | |
| - phylo-rclr | |
| push: | |
| branches: | |
| - master | |
| - phylo-rclr | |
| jobs: | |
| build: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v2 | |
| with: | |
| persist-credentials: false | |
| fetch-depth: 0 | |
| - name: Download Q2 file | |
| run: wget -q https://raw.githubusercontent.com/qiime2/environment-files/master/latest/staging/qiime2-latest-py38-linux-conda.yml | |
| - uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| activate-environment: q2 | |
| environment-file: qiime2-latest-py38-linux-conda.yml | |
| - name: Install conda reqs | |
| shell: bash -l {0} | |
| run: conda install --file ci/conda_requirements.txt -c biocore | |
| - name: Install auxillary conda CI packages | |
| shell: bash -l {0} | |
| run: conda install -c conda-forge coveralls flake8 nose | |
| - name: Install auxillary pip CI packages | |
| shell: bash -l {0} | |
| run: pip install iow tax2tree | |
| - name: Install gemelli | |
| shell: bash -l {0} | |
| run: pip install -e . | |
| - name: Check style | |
| shell: bash -l {0} | |
| run: flake8 gemelli/*.py gemelli/tests/*.py setup.py | |
| - name: Run tests & coverage | |
| shell: bash -l {0} | |
| run: nosetests -v gemelli --with-coverage --cover-package=gemelli |