Fix BP tree corruption due to numpy uints #166
Workflow file for this run
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| # Tests EMPress' Python code, when installed outside of a QIIME 2 conda | |
| # environment. See https://github.com/biocore/empress/issues/496 for a | |
| # description of why this is useful. | |
| name: Standalone CI | |
| # Controls when the action will run. | |
| on: | |
| # Triggers the workflow on pull request and push events, only on the master | |
| # branch | |
| pull_request: | |
| branches: [ master ] | |
| push: | |
| branches: [ master ] | |
| jobs: | |
| # name of job | |
| build: | |
| # The type of runner that the job will run on (available options are window/macOS/linux) | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| # based roughly on https://github.com/conda-incubator/setup-miniconda#example-1-basic-usage | |
| python-version: ["3.6", "3.7", "3.8", "3.9"] | |
| # used in McHelper (similar to TRAVIS_PULL_REQUEST variable) | |
| env: | |
| BRANCH_NUMBER: ${{ github.event.number }} | |
| # Steps represent a sequence of tasks that will be executed as part of the job | |
| steps: | |
| # first grab branch from github | |
| - uses: actions/checkout@v2 | |
| with: | |
| persist-credentials: false | |
| fetch-depth: 0 | |
| # https://github.com/conda-incubator/setup-miniconda#example-1-basic-usage | |
| - uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| activate-environment: empress | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install conda packages | |
| shell: bash -l {0} | |
| run: conda install flake8 nose | |
| - name: Install Cython & NumPy | |
| shell: bash -l {0} | |
| run: pip install cython "numpy >= 1.12.0" | |
| - name: Install EMPress | |
| shell: bash -l {0} | |
| run: pip install -e .[all] | |
| # tests that don't import QIIME 2 dependencies | |
| - name: Run (non-QIIME 2) Python tests | |
| shell: bash -l {0} | |
| run: > | |
| nosetests | |
| ./tests/python/test_cli.py | |
| ./tests/python/test_compression_utils.py | |
| ./tests/python/test_core.py | |
| ./tests/python/test_taxonomy_utils.py | |
| ./tests/python/test_tools.py | |
| ./tests/python/test_tree.py |