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: Qiita Plugin CI | |
| on: | |
| push: | |
| branches: [ dev ] | |
| pull_request: | |
| jobs: | |
| # derived from https://github.com/actions/example-services/blob/master/.github/workflows/postgres-service.yml | |
| main: | |
| runs-on: ubuntu-latest | |
| 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: | |
| # Downloads a copy of the code in your repository before running CI tests | |
| - name: Check out repository code | |
| uses: actions/checkout@v2 | |
| - name: Setup for conda | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| auto-update-conda: true | |
| python-version: 3.6 | |
| - name: Basic dependencies install | |
| env: | |
| COVER_PACKAGE: ${{ matrix.cover_package }} | |
| shell: bash -l {0} | |
| run: | | |
| echo "Testing: " $COVER_PACKAGE | |
| # we need to download qiita directly so we have "easy" access to | |
| # all config files | |
| wget https://github.com/biocore/qiita/archive/dev.zip | |
| unzip dev.zip | |
| # pull out the port so we can modify the configuration file easily | |
| pgport=${{ job.services.postgres.ports[5432] }} | |
| sed -i "s/PORT = 5432/PORT = $pgport/" qiita-dev/qiita_core/support_files/config_test.cfg | |
| # PGPASSWORD is read by pg_restore, which is called by the build_db process. | |
| export PGPASSWORD=postgres | |
| # Setting up main qiita conda environment | |
| conda config --add channels conda-forge | |
| conda create -q --yes -n qiita python=3.9 pip libgfortran numpy nginx cython redis | |
| conda activate qiita | |
| pip install sphinx sphinx-bootstrap-theme nose-timer codecov Click | |
| - name: Qiita install | |
| shell: bash -l {0} | |
| run: | | |
| conda activate qiita | |
| export QIITA_SERVER_CERT=`pwd`/qiita-dev/qiita_core/support_files/server.crt | |
| export QIITA_CONFIG_FP=`pwd`/qiita-dev/qiita_core/support_files/config_test.cfg | |
| pip install qiita-dev/ --no-binary redbiom | |
| mkdir ~/.qiita_plugins | |
| - name: Install Qiita plugins | |
| shell: bash -l {0} | |
| run: | | |
| conda config --add channels anaconda | |
| conda config --add channels conda-forge | |
| conda config --add channels bioconda | |
| conda create -q --yes -n qp-meta python=3.9 biom-format sortmerna=2.1b samtools pigz | |
| conda activate qp-meta | |
| export QIITA_SERVER_CERT=`pwd`/qiita-dev/qiita_core/support_files/ci_rootca.crt | |
| export QIITA_CONFIG_FP=`pwd`/qiita-dev/qiita_core/support_files/config_test_local.cfg | |
| pip --quiet install -U pip | |
| pip --quiet install . | |
| pip --quiet install coveralls | |
| export QC_SORTMERNA_DB_DP=$PWD/qp_meta/sortmerna/databases/rRNA_databases/ | |
| pushd $QC_SORTMERNA_DB_DP | |
| for file in $(ls); do gunzip $file; done | |
| popd | |
| configure_meta --env-script "source /home/runner/.profile; conda activate qp-meta; export QC_SORTMERNA_DB_DP=$PWD/qp_meta/sortmerna/databases/rRNA_databases/; export ENVIRONMENT=\"source /home/runner/.profile; conda activate qp-meta\"" --server-cert $QIITA_SERVER_CERT | |
| echo "Available Qiita plugins" | |
| ls ~/.qiita_plugins/ | |
| - name: Starting Main Services | |
| shell: bash -l {0} | |
| run: | | |
| conda activate qiita | |
| export QIITA_SERVER_CERT=`pwd`/qiita-dev/qiita_core/support_files/ci_rootca.crt | |
| export QIITA_CONFIG_FP=`pwd`/qiita-dev/qiita_core/support_files/config_test_local.cfg | |
| sed "s#/home/runner/work/qiita/qiita#${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 10 | |
| cat /tmp/supervisord.log | |
| - name: Main tests | |
| shell: bash -l {0} | |
| env: | |
| COVER_PACKAGE: ${{ matrix.cover_package }} | |
| run: | | |
| conda activate qp-meta | |
| export QIITA_SERVER_CERT=`pwd`/qiita-dev/qiita_core/support_files/ci_rootca.crt | |
| export QIITA_CONFIG_FP=`pwd`/qiita-dev/qiita_core/support_files/config_test_local.cfg | |
| export QC_SORTMERNA_DB_DP=$PWD/qp_meta/sortmerna/databases/rRNA_databases/ | |
| export ENVIRONMENT="source /home/runner/.profile; conda activate qp-meta" | |
| export PYTHONWARNINGS="ignore:Certificate for localhost has no \`subjectAltName\`" | |
| nosetests --with-doctest --with-coverage --cover-package=qp_meta | |
| - uses: codecov/codecov-action@v1 | |
| with: | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| file: codecov.yml | |
| lint: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: flake8 | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: 3.9 | |
| - name: install dependencies | |
| run: python -m pip install --upgrade pip | |
| - name: Check out repository code | |
| uses: actions/checkout@v2 | |
| - name: lint | |
| run: | | |
| pip install -q flake8 | |
| flake8 qp_meta setup.py scripts/* |