Workflow file for this run
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| # 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:9.5 | |
| 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: 3.9 | |
| - 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 = $pgport/" qiita-dev/qiita_core/support_files/config_test.cfg | |
| # PGPASSWORD is read by pg_restore, which is called by the build_db process. | |
| export PGPASSWORD=postgres | |
| # Setting up main qiita conda environment | |
| conda config --add channels conda-forge | |
| conda create -q --yes -n qiita python=3.9 libgfortran numpy nginx cython redis | |
| conda activate qiita | |
| pip install sphinx sphinx-bootstrap-theme nose-timer codecov Click | |
| - name: Qiita install | |
| shell: bash -l {0} | |
| run: | | |
| conda activate qiita | |
| pip install qiita-dev/ --no-binary redbiom | |
| mkdir ~/.qiita_plugins | |
| - name: Install Qiita plugins | |
| shell: bash -l {0} | |
| run: | | |
| conda config --add channels bioconda | |
| conda create --yes -n qp-fastp-minimap2 -c bioconda samtools=1.11 minimap2=2.17 fastp python=3.6 | |
| conda activate qp-fastp-minimap2 | |
| export QIITA_SERVER_CERT=`pwd`/qiita-dev/qiita_core/support_files/ci_rootca.crt | |
| export QIITA_CONFIG_FP=`pwd`/qiita-dev/qiita_core/support_files/config_test_local.cfg | |
| pip --quiet install -U pip | |
| pip --quiet install . | |
| pip --quiet install coveralls | |
| export QC_REFERENCE_DB=$PWD/qp_fastp_minimap2/support_files/databases/ | |
| for file in $(ls $QC_REFERENCE_DB/*.gz); do gunzip $file; done | |
| samtools_version=`samtools --version` | |
| minimap2_version=`minimap2 --version` | |
| fastp_version=$(fastp --version 2>&1) | |
| if [[ $samtools_version != *"1.11"* ]]; then echo "wrong samtools version", $samtools_version; exit 1; fi | |
| if [[ $minimap2_version != *"2.17"* ]]; then echo "wrong minimap2 version", $minimap2_version; exit 1; fi | |
| if [[ $fastp_version != *"23.4"* ]]; then echo "wrong fastp version", $fastp_version; exit 1; fi | |
| configure_qp_fastp_minimap2 --env-script "source ~/.bash_profile; conda activate qp-fastp-minimap2; export QC_REFERENCE_DB=${PWD}/qp_fastp_minimap2/support_files/databases/; export ENVIRONMENT='source ~/.bash_profile; source activate qp-fastp-minimap2; export QC_REFERENCE_DB=${PWD}/qp_fastp_minimap2/support_files/databases/'" --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: ${{ matrix.cover_package }} | |
| run: | | |
| conda activate qp-fastp-minimap2 | |
| export QIITA_SERVER_CERT=`pwd`/qiita-dev/qiita_core/support_files/ci_rootca.crt | |
| export QIITA_CONFIG_FP=`pwd`/qiita-dev/qiita_core/support_files/config_test_local.cfg | |
| export QC_REFERENCE_DB=$PWD/qp_fastp_minimap2/support_files/databases/ | |
| export ENVIRONMENT="source ~/.bash_profile; source activate qp-fastp-minimap2; export QC_REFERENCE_DB=${PWD}/qp_fastp_minimap2/support_files/databases/" | |
| nosetests --with-doctest --with-coverage -v --cover-package=qp_fastp_minimap2 | |
| - 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_fastp_minimap2 setup.py scripts/* |