upgrade nltk #1050
Workflow file for this run
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| # name: Qiita 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 | |
| strategy: | |
| matrix: | |
| include: | |
| - cover_package: "qiita_db" | |
| - cover_package: "qiita_pet qiita_core qiita_ware" | |
| 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: '3.9' | |
| - name: Basic dependencies install | |
| env: | |
| COVER_PACKAGE: ${{ matrix.cover_package }} | |
| shell: bash -l {0} | |
| run: | | |
| echo "Testing: " $COVER_PACKAGE | |
| # pull out the port so we can modify the configuration file easily | |
| pgport=${{ job.services.postgres.ports[5432] }} | |
| sed -i "s/PORT = 5432/PORT = $pgport/" qiita_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 deactivate | |
| conda create --quiet --yes -n qiita python=3.9 pip libgfortran numpy nginx cython redis | |
| conda env list | |
| conda activate qiita | |
| pip install -U pip | |
| pip install sphinx sphinx-bootstrap-theme nose-timer Click coverage | |
| # Configuring SSH | |
| cp /etc/ssh/sshd_config sshd_config | |
| echo "RSAAuthentication yes" > sshd_config | |
| echo "PubkeyAuthentication yes" > sshd_config | |
| echo "StrictModes no" > sshd_config | |
| sudo mv sshd_config /etc/ssh/sshd_config | |
| sudo systemctl restart ssh | |
| - name: Webdis install | |
| shell: bash -l {0} | |
| run: | | |
| sudo apt-get -y install libevent-dev | |
| git clone https://github.com/nicolasff/webdis | |
| cd webdis | |
| make | |
| - name: Main install | |
| shell: bash -l {0} | |
| run: | | |
| conda activate qiita | |
| export QIITA_ROOTCA_CERT=`pwd`/qiita_core/support_files/ci_rootca.crt | |
| export QIITA_CONFIG_FP=`pwd`/qiita_core/support_files/config_test.cfg | |
| export REDBIOM_HOST="http://localhost:7379" | |
| pip install . --no-binary redbiom | |
| # 10.2022 | |
| # this is for redbiom / biom-format (so fine to delete in the future) | |
| pip install future | |
| pwd | |
| mkdir ~/.qiita_plugins | |
| - name: Install plugins | |
| shell: bash -l {0} | |
| run: | | |
| conda env create -n qtp-biom --file https://data.qiime2.org/distro/amplicon/qiime2-amplicon-2024.5-py39-linux-conda.yml | |
| export QIITA_ROOTCA_CERT=`pwd`/qiita_core/support_files/ci_rootca.crt | |
| export QIITA_CONFIG_FP=`pwd`/qiita_core/support_files/config_test.cfg | |
| export REDBIOM_HOST="http://localhost:7379" | |
| conda activate qtp-biom | |
| pip install -U pip | |
| pip install https://github.com/qiita-spots/qiita_client/archive/master.zip | |
| pip install https://github.com/qiita-spots/qtp-biom/archive/master.zip | |
| # if QIITA_ROOTCA_CERT is appended to certifi's cacert.pem file, | |
| # then --server-cert does not need to be specified to any plugin, | |
| # including configure_biom. | |
| # echo `python -c "import certifi;print(certifi.where())"` | |
| configure_biom --env-script "source /home/runner/.profile; conda activate qtp-biom" --server-cert $QIITA_ROOTCA_CERT | |
| - name: Starting services | |
| shell: bash -l {0} | |
| run: | | |
| conda activate qiita | |
| export QIITA_ROOTCA_CERT=`pwd`/qiita_core/support_files/ci_rootca.crt | |
| export QIITA_CONFIG_FP=`pwd`/qiita_core/support_files/config_test.cfg | |
| export REDBIOM_HOST="http://localhost:7379" | |
| echo "1. Setting up redis" | |
| redis-server --daemonize yes --port 7777 | |
| redis-server --daemonize yes --port 6379 | |
| echo "2. Starting webdis" | |
| pushd webdis | |
| ./webdis & | |
| popd | |
| echo "3. Starting redbiom: " $REDBIOM_HOST | |
| curl -s http://localhost:7379/FLUSHALL > /dev/null | |
| redbiom --version | |
| redbiom admin scripts-writable | |
| redbiom admin create-context --name "qiita-test" --description "qiita-test context" | |
| redbiom admin load-sample-metadata --metadata `pwd`/qiita_db/support_files/test_data/templates/1_19700101-000000.txt | |
| redbiom admin load-sample-metadata-search --metadata `pwd`/qiita_db/support_files/test_data/templates/1_19700101-000000.txt | |
| redbiom admin load-sample-data --table `pwd`/qiita_db/support_files/test_data/processed_data/1_study_1001_closed_reference_otu_table.biom --context qiita-test --tag 4 | |
| redbiom admin load-sample-data --table `pwd`/qiita_db/support_files/test_data/processed_data/1_study_1001_closed_reference_otu_table-for_redbiom_tests.biom --context qiita-test --tag 5 | |
| echo "4. Setting up nginx" | |
| mkdir -p /usr/share/miniconda/envs/qiita/var/run/nginx/ | |
| nginx -c ${PWD}/qiita_pet/nginx_example.conf | |
| echo "5. Setting up qiita" | |
| conda activate qiita | |
| qiita-env make --no-load-ontologies | |
| qiita-test-install | |
| qiita plugins update | |
| echo "6. Starting supervisord => multiple qiita instances" | |
| supervisord -c ${PWD}/qiita_pet/supervisor_example.conf | |
| sleep 10 | |
| cat /tmp/supervisord.log | |
| echo "7. Starting plugins" | |
| conda deactivate | |
| conda activate qtp-biom | |
| export QIITA_CLIENT_DEBUG_LEVEL=DEBUG | |
| start_biom https://localhost:8383 register ignored | |
| conda deactivate | |
| echo "8. Setting up SSH" | |
| ssh-keygen -t rsa -b 4096 -N '' -f $PWD/qiita_ware/test/test_data/test_key | |
| mkdir ~/.ssh/ | |
| cp $PWD/qiita_ware/test/test_data/test_key* ~/.ssh/ | |
| cat ~/.ssh/test_key.pub > ~/.ssh/authorized_keys | |
| chmod 600 $PWD/qiita_ware/test/test_data/test_key* | |
| chmod 600 ~/.ssh/* | |
| chmod 700 ~/.ssh/ | |
| echo "Connecting as $USER@localhost" | |
| # this line (and the -o StrictHostKeyChecking=no) is so the server | |
| # is added to the list of known servers | |
| scp -O -o StrictHostKeyChecking=no -i $PWD/qiita_ware/test/test_data/test_key $USER@localhost:/home/runner/work/qiita/qiita/qiita_ware/test/test_data/random_key /home/runner/work/qiita/qiita/qiita_ware/test/test_data/random_key_copy_1 | |
| - name: Main tests | |
| shell: bash -l {0} | |
| env: | |
| COVER_PACKAGE: ${{ matrix.cover_package }} | |
| run: | | |
| conda activate qiita | |
| export QIITA_ROOTCA_CERT=`pwd`/qiita_core/support_files/ci_rootca.crt | |
| export QIITA_CONFIG_FP=`pwd`/qiita_core/support_files/config_test.cfg | |
| # for testing we only need to have this set, not actually exist | |
| export QIITA_JOB_SCHEDULER_EPILOGUE=`/path/to/epilogue/file` | |
| export REDBIOM_HOST="http://localhost:7379" | |
| nosetests $COVER_PACKAGE --with-doctest --with-coverage --with-timer -v --cover-package=${COVER_PACKAGE// / --cover-package=} -e 'test_submit_EBI_parse_EBI_reply_failure' -e 'test_full_submission' | |
| # killing the qiita server to run the next commands | |
| QIITA_PID=`cat /tmp/supervisord.pid` | |
| kill $QIITA_PID | |
| sleep 10 | |
| # due to qiita_db tests being more complex and taking longer than | |
| # the other tests we will only add some extra tests to the run that is | |
| # not testing qiita_db | |
| if [[ "$COVER_PACKAGE" != *"qiita_db"* ]]; then | |
| # 1. testing that we can add some "dummy" studies to the db via | |
| # CLI | |
| test_data_studies/commands.sh; | |
| # 2. making sure that all qiita cron jobs complete as expected | |
| all-qiita-cron-job; | |
| # 3. making sure than a production system has the expected rows | |
| # in all our tables; steps: a. drop test db, b. change $QIITA_CONFIG_FP | |
| # c. create new production system, c. count rows in the db. | |
| qiita-env drop; | |
| cp $QIITA_CONFIG_FP ${QIITA_CONFIG_FP}.bk | |
| sed 's/TEST_ENVIRONMENT = TRUE/TEST_ENVIRONMENT = FALSE/g' ${QIITA_CONFIG_FP}.bk > $QIITA_CONFIG_FP; | |
| qiita-env make --no-load-ontologies; | |
| export PGPASSWORD=postgres | |
| pgport=${{ job.services.postgres.ports[5432] }} | |
| row_counts=`psql -h localhost -U postgres -d qiita_test -p $pgport -c "SELECT SUM(c.reltuples) FROM pg_class c JOIN pg_namespace n on n.oid = c.relnamespace WHERE n.nspname = 'qiita' AND c.relkind = 'r' AND n.nspname NOT IN ('information_schema', 'pg_catalog');"` | |
| if [[ `echo $row_counts` != *" 0 "* ]]; then | |
| echo "***********"; | |
| echo "The number of rows in a production system is not what's expected:"; | |
| echo $row_counts; | |
| echo "***********"; | |
| exit 1 | |
| fi | |
| fi | |
| - name: Submit coveralls | |
| uses: AndreMiras/coveralls-python-action@develop | |
| with: | |
| github-token: ${{ secrets.github_token }} | |
| flag-name: "${{ matrix.cover_package }}" | |
| parallel: true | |
| coveralls_finish: | |
| needs: main | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Coveralls Finished | |
| uses: AndreMiras/coveralls-python-action@develop | |
| with: | |
| github-token: ${{ secrets.github_token }} | |
| parallel-finished: true | |
| 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 qiita_* setup.py scripts/qiita* notebooks/*/*.py |