This project is built using sbt: https://www.scala-sbt.org/1.0/docs/Setup.html

Start an sbt shell using the sbt command.

To compile the main code:

compile

To run all tests:

test

To test a specific suite:

testOnly *VCFDataSourceSuite

If you use IntelliJ, you'll want to set up scalafmt on save.

To test or testOnly in remote debug mode with IntelliJ IDEA set the remote debug configuration in IntelliJ to 'Attach to remote JVM' mode and a specific port number (here the default port number 5005 is used) and then modify the definition of options in groupByHash function in build.sbt to

val options = ForkOptions().withRunJVMOptions(Vector("-Xmx1024m")).withRunJVMOptions(Vector("-agentlib:jdwp=transport=dt_socket,server=y,suspend=y,address=5005"))

To run Python tests, you must install and activate the conda environment in python/environment.yml. You can then run tests from sbt:

python/test

These tests will run with the same Spark classpath as the Scala tests.