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add workflow
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‎.github/workflows/qiita-plugin-ci.yml

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# name: Qiita Plugin CI
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on:
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push:
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branches: [ dev ]
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pull_request:
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jobs:
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# derived from https://github.com/actions/example-services/blob/master/.github/workflows/postgres-service.yml
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main:
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runs-on: ubuntu-latest
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services:
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postgres:
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# Docker Hub image
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image: postgres:9.5
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env:
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POSTGRES_DB: postgres
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POSTGRES_USER: postgres
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POSTGRES_PASSWORD: postgres
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COVER_PACKAGE: ${{ matrix.cover_package }}
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# Set health checks to wait until postgres has started
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options: >-
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--health-cmd pg_isready
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--health-interval 10s
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--health-timeout 5s
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--health-retries 5
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ports:
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# based on https://github.com/actions/example-services/blob/master/.github/workflows/postgres-service.yml#L44-L72
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- 5432/tcp
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steps:
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# Downloads a copy of the code in your repository before running CI tests
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- name: Check out repository code
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uses: actions/checkout@v2
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- name: Setup for conda
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uses: conda-incubator/setup-miniconda@v2
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with:
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auto-update-conda: true
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python-version: 3.6
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- name: Basic dependencies install
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env:
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COVER_PACKAGE: ${{ matrix.cover_package }}
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shell: bash -l {0}
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run: |
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echo "Testing: " $COVER_PACKAGE
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# we need to download qiita directly so we have "easy" access to
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# all config files
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wget https://github.com/biocore/qiita/archive/dev.zip
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unzip dev.zip
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# pull out the port so we can modify the configuration file easily
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pgport=${{ job.services.postgres.ports[5432] }}
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sed -i "s/PORT = 5432/PORT = $pgport/" qiita-dev/qiita_core/support_files/config_test.cfg
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# PGPASSWORD is read by pg_restore, which is called by the build_db process.
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export PGPASSWORD=postgres
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# Setting up main qiita conda environment
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conda config --add channels conda-forge
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conda create -q --yes -n qiita python=3.6 pip libgfortran numpy nginx cython redis
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conda activate qiita
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pip install sphinx sphinx-bootstrap-theme nose-timer codecov Click
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- name: Qiita install
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shell: bash -l {0}
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run: |
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conda activate qiita
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pip install qiita-dev/ --no-binary redbiom
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mkdir ~/.qiita_plugins
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- name: Install Qiita plugins
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shell: bash -l {0}
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run: |
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conda create -q --yes -n qtp-job-output-folder python=3.6
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conda activate qtp-job-output-folder
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export QIITA_SERVER_CERT=`pwd`/qiita-dev/qiita_core/support_files/server.crt
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export QIITA_CONFIG_FP=`pwd`/qiita-dev/qiita_core/support_files/config_test_local.cfg
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pip --quiet install -U pip
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pip --quiet install .
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pip --quiet install coveralls
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configure_qtp_job_output_folder --env-script "source /home/runner/.profile; conda activate qtp-job-output-folder" --server-cert $QIITA_SERVER_CERT
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echo "Available Qiita plugins"
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ls ~/.qiita_plugins/
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- name: Starting Main Services
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shell: bash -l {0}
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run: |
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conda activate qiita
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export QIITA_SERVER_CERT=`pwd`/qiita-dev/qiita_core/support_files/server.crt
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export QIITA_CONFIG_FP=`pwd`/qiita-dev/qiita_core/support_files/config_test_local.cfg
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sed "s#/home/runner/work/qiita/qiita#${PWD}/qiita-dev/#g" `pwd`/qiita-dev/qiita_core/support_files/config_test.cfg > ${QIITA_CONFIG_FP}
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export REDBIOM_HOST="http://localhost:7379"
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echo "1. Setting up redis"
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redis-server --daemonize yes --port 7777
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echo "2. Setting up nginx"
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mkdir -p ${CONDA_PREFIX}/var/run/nginx/
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export NGINX_FILE=`pwd`/qiita-dev/qiita_pet/nginx_example.conf
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export NGINX_FILE_NEW=`pwd`/qiita-dev/qiita_pet/nginx_example_local.conf
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sed "s#/home/runner/work/qiita/qiita#${PWD}/qiita-dev/#g" ${NGINX_FILE} > ${NGINX_FILE_NEW}
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nginx -c ${NGINX_FILE_NEW}
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echo "3. Setting up qiita"
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qiita-env make --no-load-ontologies
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qiita plugins update
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qiita-test-install
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echo "4. Starting supervisord => multiple qiita instances"
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supervisord -c ${PWD}/qiita-dev/qiita_pet/supervisor_example.conf
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sleep 10
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cat /tmp/supervisord.log
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- name: Main tests
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shell: bash -l {0}
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env:
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COVER_PACKAGE: ${{ matrix.cover_package }}
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run: |
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conda activate klp
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export QIITA_SERVER_CERT=`pwd`/qiita-dev/qiita_core/support_files/server.crt
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export QIITA_CONFIG_FP=`pwd`/qiita-dev/qiita_core/support_files/config_test_local.cfg
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export PYTHONWARNINGS="ignore:Certificate for localhost has no \`subjectAltName\`"
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nosetests --with-doctest --with-coverage -v --cover-package=qp_klp
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- uses: codecov/codecov-action@v1
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with:
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token: ${{ secrets.CODECOV_TOKEN }}
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file: codecov.yml
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lint:
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runs-on: ubuntu-latest
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steps:
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- name: flake8
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uses: actions/setup-python@v2
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with:
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python-version: 3.6
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- name: install dependencies
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run: python -m pip install --upgrade pip
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- name: Check out repository code
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uses: actions/checkout@v2
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- name: lint
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run: |
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pip install -q flake8
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flake8 qtp_job_output_folder setup.py scripts/*

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