Fix BP tree corruption due to numpy uints #261
Workflow file for this run
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| # Tests EMPress' Python and JS code within a QIIME 2 conda environment. | |
| # Also lints and stylechecks the code (both Python and JS). | |
| # When tests pass, this runs "make docs" to generate various test QIIME 2 | |
| # visualizations (.qzv files) and uploads them to McHelper. | |
| name: Main CI + McHelper | |
| # 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 | |
| # 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 | |
| - name: Set up Node.js | |
| uses: actions/setup-node@v1 | |
| with: | |
| # Can use a matrix of Node.js versions in the future if desired; | |
| # however, since Node.js should only be used when developing | |
| # EMPress, it's not an urgent priority (and should likely be done | |
| # separately from the Python CI stuff to save time) | |
| node-version: 14 | |
| - name: Install Node.js modules | |
| run: npm install -g qunit-puppeteer jshint [email protected] | |
| - name: Install flake8 | |
| run: conda run -n base pip install flake8 | |
| - name: Run linting and stylechecking | |
| run: | | |
| conda run -n base make stylecheck | |
| - name: Set up conda | |
| uses: s-weigand/setup-conda@v1 | |
| with: | |
| update-conda: true | |
| python-version: 3.6 | |
| conda-channels: anaconda, conda-forge | |
| - name: Create QIIME 2 conda environment | |
| run: | | |
| wget https://data.qiime2.org/distro/core/qiime2-2020.6-py36-linux-conda.yml | |
| conda env create -n qiime2-dev --file qiime2-2020.6-py36-linux-conda.yml | |
| - name: Install EMPress | |
| run: | | |
| conda run -n qiime2-dev pip uninstall emperor --yes | |
| conda run -n qiime2-dev pip install -e .[all] --verbose | |
| conda run -n qiime2-dev qiime dev refresh-cache | |
| - name: Run tests | |
| run: conda run -n qiime2-dev make test | |
| - name: Check development script | |
| run: | | |
| conda run -n qiime2-dev ./tests/python/make-dev-page.py | |
| conda run -n qiime2-dev ./tests/python/make-dev-page.py docs/moving-pictures/rooted-tree.qza docs/moving-pictures/table.qza docs/moving-pictures/sample_metadata.tsv docs/moving-pictures/taxonomy.qza | |
| conda run -n qiime2-dev ./tests/python/make-dev-page.py docs/moving-pictures/rooted-tree.qza docs/moving-pictures/table.qza docs/moving-pictures/sample_metadata.tsv docs/moving-pictures/taxonomy.qza docs/moving-pictures/unweighted_unifrac_pcoa_results.qza --filter-extra-samples | |
| conda run -n qiime2-dev ./tests/python/make-dev-page.py docs/moving-pictures/rooted-tree.qza docs/moving-pictures/table.qza docs/moving-pictures/sample_metadata.tsv docs/moving-pictures/taxonomy.qza docs/moving-pictures/biplot.qza --filter-extra-samples | |
| - name: Upload to McHelper | |
| run: | | |
| conda run -n qiime2-dev make docs | |
| curl -POST -F "files[]=@${PWD}/docs/moving-pictures/plain.qzv" -F "files[]=@${PWD}/docs/moving-pictures/just-fm.qzv" -F "files[]=@${PWD}/docs/moving-pictures/empress-tree.qzv" -F "files[]=@${PWD}/docs/moving-pictures/empire.qzv" -F "files[]=@${PWD}/docs/moving-pictures/empire-biplot.qzv" http://mchelper.ucsd.edu:8888/uploads/empress/${{env.BRANCH_NUMBER}}/ |