192 bug excluded inputs regex argument is not respected #195
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| --- | |
| on: | |
| push: | |
| branches: | |
| - main | |
| pull_request: | |
| workflow_dispatch: | |
| name: Extra checks with DBs | |
| jobs: | |
| ###################################### | |
| # R CMD check with Databases running # | |
| ###################################### | |
| test-coverage: | |
| name: Checks with DBs 🛠 & Coverage 📔 | |
| runs-on: ${{ matrix.config.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| config: | |
| - {os: ubuntu-latest, r: 'release'} | |
| timeout-minutes: 30 | |
| ############################################### | |
| # Environment variables so tests with DBs run # | |
| ############################################### | |
| env: | |
| # MariaDB | |
| TEST_MARIADB_USER: root | |
| TEST_MARIADB_PASSWORD: root | |
| TEST_MARIADB_PORT: 3306 | |
| TEST_MARIADB_DBNAME: shiny_telemetry | |
| TEST_MARIADB_HOSTNAME: '127.0.0.1' | |
| # PostgreSQL | |
| TEST_POSTGRESQL_USER: postgres | |
| TEST_POSTGRESQL_PASSWORD: mysecretpassword | |
| TEST_POSTGRESQL_PORT: 5432 | |
| TEST_POSTGRESQL_DBNAME: shiny_telemetry | |
| TEST_POSTGRESQL_HOSTNAME: '127.0.0.1' | |
| # MS SQL | |
| TEST_MSSQLSERVER_USER: sa | |
| TEST_MSSQLSERVER_PASSWORD: 'my-Secr3t_Password' | |
| TEST_MSSQLSERVER_PORT: 1433 | |
| TEST_MSSQLSERVER_DBNAME: shiny_telemetry | |
| TEST_MSSQLSERVER_HOSTNAME: '127.0.0.1' | |
| TEST_MSSQLSERVER_TRUST_SERVER_CERTIFICATE: 'YES' | |
| TEST_MSSQLSERVER_DRIVER: 'ODBC Driver 18 for SQL Server' | |
| ## MongoDb | |
| TEST_MONGODB_USER: 'mongodb' | |
| TEST_MONGODB_PASSWORD: 'mysecretpassword' | |
| TEST_MONGODB_HOST: '127.0.0.1' | |
| TEST_MONGODB_PORT: 27017 | |
| TEST_MONGODB_DBNAME: 'shiny_telemetry' | |
| TEST_MONGODB_COLLECTION: 'event_log' | |
| ########################################### | |
| # Services container to run with main job # | |
| ########################################### | |
| services: | |
| # Label used to access the service container | |
| postgres: | |
| # Docker Hub image | |
| image: postgres | |
| # Provide the password for postgres | |
| env: | |
| POSTGRES_PASSWORD: mysecretpassword | |
| POSTGRES_USER: postgres | |
| POSTGRES_DB: shiny_telemetry | |
| # Set health checks to wait until postgres has started | |
| ports: | |
| - 5432:5432 | |
| options: >- | |
| --health-cmd pg_isready | |
| --health-interval 10s | |
| --health-timeout 5s | |
| --health-retries 5 | |
| mssql: | |
| image: mcr.microsoft.com/mssql/server | |
| ports: | |
| - 1433:1433 | |
| env: | |
| ACCEPT_EULA: Y | |
| MSSQL_SA_PASSWORD: 'my-Secr3t_Password' | |
| mongodb: | |
| image: mongo | |
| env: | |
| MONGO_INITDB_ROOT_USERNAME: mongodb | |
| MONGO_INITDB_ROOT_PASSWORD: mysecretpassword | |
| ports: | |
| - 27017:27017 | |
| steps: | |
| ################## | |
| # Load all steps # | |
| ################## | |
| - name: Checkout repository | |
| ########################## | |
| # Checkout the code base # | |
| ########################## | |
| uses: actions/checkout@v3 | |
| - name: Install R | |
| ############# | |
| # Install R # | |
| ############# | |
| uses: r-lib/actions/setup-r@v2 | |
| with: | |
| r-version: ${{ matrix.config.r }} | |
| - name: Install R package dependencies | |
| ########################## | |
| # Install R Dependencies # | |
| ########################## | |
| uses: r-lib/actions/setup-r-dependencies@v2 | |
| with: | |
| # Necessary to avoid object usage linter errors. | |
| extra-packages: | | |
| local::. | |
| any::rcmdcheck | |
| any::spelling | |
| any::lintr | |
| any::covr | |
| - name: Install Microsoft ODBC | |
| ################################### | |
| # Install MS SQL driver and tools # | |
| ################################### | |
| run: sudo ACCEPT_EULA=Y apt-get install msodbcsql18 mssql-tools18 -y | |
| - name: Create MSSQL database | |
| ########################## | |
| # Create MS SQL database # | |
| ########################## | |
| run: | | |
| sqlcmd -e -U $TEST_MSSQLSERVER_USER -P $TEST_MSSQLSERVER_PASSWORD -H $TEST_MSSQLSERVER_HOSTNAME:TEST_MSSQLSERVER_PORT -C -Q "CREATE DATABASE $TEST_MSSQLSERVER_DBNAME" | |
| - name: Start MySQL | |
| ################## | |
| # Start MySQL DB # | |
| ################## | |
| run: | | |
| sudo /etc/init.d/mysql start | |
| mysql -e "CREATE DATABASE IF NOT EXISTS $TEST_MARIADB_DBNAME;" -u$TEST_MARIADB_USER -p$TEST_MARIADB_PASSWORD | |
| - name: R CMD check | |
| ########################### | |
| # Perform the R CMD check # | |
| ########################### | |
| if: always() | |
| uses: r-lib/actions/check-r-package@v2 | |
| with: | |
| error-on: '"note"' | |
| - name: Test coverage | |
| ########################### | |
| # Perform the R CMD check # | |
| ########################### | |
| run: | | |
| Rscript -e 'covr::codecov()' |