Remove tube+liquid mass from config #666
Workflow file for this run
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| name: Metapool 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 | |
| - dev | |
| push: | |
| branches: | |
| - master | |
| - dev | |
| 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 | |
| # we can add more versions of node.js in the future | |
| strategy: | |
| matrix: | |
| python-version: ['3.9'] | |
| services: | |
| postgres: | |
| # Docker Hub image | |
| image: postgres:13.4 | |
| env: | |
| POSTGRES_DB: postgres | |
| POSTGRES_USER: postgres | |
| POSTGRES_PASSWORD: postgres | |
| COVER_PACKAGE: ${{ matrix.cover_package }} | |
| # Set health checks to wait until postgres has started | |
| options: >- | |
| --health-cmd pg_isready | |
| --health-interval 10s | |
| --health-timeout 5s | |
| --health-retries 5 | |
| ports: | |
| # based on https://github.com/actions/example-services/blob/master/.github/workflows/postgres-service.yml#L44-L72 | |
| - 5432/tcp | |
| # 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 enviroment | |
| uses: actions/setup-node@v1 | |
| with: | |
| node-version: 14 | |
| - uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| activate-environment: tester | |
| python-version: ${{ matrix.python-version }} | |
| conda-channels: anaconda, conda-forge, bioconda | |
| auto-update-conda: true | |
| - name: Install Qiita | |
| env: | |
| COVER_PACKAGE: ${{ matrix.cover_package }} | |
| shell: bash -l {0} | |
| run: | | |
| # we need to download qiita directly so we have "easy" access to | |
| # all config files | |
| wget https://github.com/biocore/qiita/archive/dev.zip --secure-protocol=TLSv1_2 | |
| unzip dev.zip | |
| # pull out the port so we can modify the configuration file easily | |
| pgport=${{ job.services.postgres.ports[5432] }} | |
| sed -i "s/PORT = 5432/PORT = $pgport/" qiita-dev/qiita_core/support_files/config_test.cfg | |
| # PGPASSWORD is read by pg_restore, which is called by the build_db process. | |
| export PGPASSWORD=postgres | |
| # Setting up main qiita conda environment | |
| conda config --add channels conda-forge | |
| conda create -q --yes -n qiita python=3.9 libgfortran numpy nginx cython redis | |
| conda activate qiita | |
| pip install sphinx sphinx-bootstrap-theme nose-timer codecov Click | |
| conda activate qiita | |
| pip install qiita-dev/ --no-binary redbiom | |
| mkdir ~/.qiita_plugins | |
| - name: Starting Qiita Services | |
| shell: bash -l {0} | |
| run: | | |
| conda activate qiita | |
| export QIITA_ROOTCA_CERT=`pwd`/qiita-dev/qiita_core/support_files/ci_rootca.crt | |
| export QIITA_CONFIG_FP=`pwd`/qiita-dev/qiita_core/support_files/config_test_local.cfg | |
| sed "s#/home/runner/work/qiita/qiita#${PWD}/qiita-dev/#g" `pwd`/qiita-dev/qiita_core/support_files/config_test.cfg > ${QIITA_CONFIG_FP} | |
| export REDBIOM_HOST="http://localhost:7379" | |
| echo "1. Setting up redis" | |
| redis-server --daemonize yes --port 7777 | |
| echo "2. Setting up nginx" | |
| mkdir -p ${CONDA_PREFIX}/var/run/nginx/ | |
| export NGINX_FILE=`pwd`/qiita-dev/qiita_pet/nginx_example.conf | |
| export NGINX_FILE_NEW=`pwd`/qiita-dev/qiita_pet/nginx_example_local.conf | |
| sed "s#/home/runner/work/qiita/qiita#${PWD}/qiita-dev/#g" ${NGINX_FILE} > ${NGINX_FILE_NEW} | |
| nginx -c ${NGINX_FILE_NEW} | |
| echo "3. Setting up qiita" | |
| qiita-env make --no-load-ontologies | |
| qiita plugins update | |
| qiita-test-install | |
| echo "4. Starting supervisord => multiple qiita instances" | |
| supervisord -c ${PWD}/qiita-dev/qiita_pet/supervisor_example.conf | |
| sleep 5 | |
| cat /tmp/supervisord.log | |
| - name: Install metapool | |
| shell: bash -l {0} | |
| run: | | |
| conda config --add channels bioconda | |
| conda create --yes -n metapool python=${{ matrix.python-version }} scikit-learn pandas numpy nose pep8 flake8 matplotlib jupyter notebook 'seaborn>=0.7.1' pip openpyxl seqtk | |
| conda activate metapool | |
| pip install coveralls flake8 | |
| pip install -e ".[all]" | |
| # create local Qiita connection | |
| export QIITA_ROOTCA_CERT=`pwd`/qiita-dev/qiita_core/support_files/ci_rootca.crt | |
| echo -e "[qiita-oauth2]\nURL=https://localhost:8383\nCLIENT_ID=yKDgajoKn5xlOA8tpo48Rq8mWJkH9z4LBCx2SvqWYLIryaan2u\nCLIENT_SECRET=9xhU5rvzq8dHCEI5sSN95jesUULrZi6pT6Wuc71fDbFbsrnWarcSq56TJLN4kP4hH\nSERVER_CERT=${QIITA_ROOTCA_CERT}" > qiita.oauth2.cfg.local | |
| - name: Run tests and measure coverage | |
| shell: bash -l {0} | |
| run: | | |
| conda activate metapool | |
| nosetests --with-coverage --cover-inclusive --cover-package metapool | |
| coverage report | |
| - name: Python linter | |
| shell: bash -l {0} | |
| run: | | |
| conda activate metapool | |
| flake8 metapool setup.py | |
| - name: Coveralls | |
| uses: AndreMiras/coveralls-python-action@develop | |
| with: | |
| parallel: true | |
| flag-name: Unit Test | |
| coveralls_finish: | |
| needs: build | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Coveralls Finished | |
| uses: AndreMiras/coveralls-python-action@develop | |
| with: | |
| parallel-finished: true |