runtests.md

Running Tests

This document demonstrates how to run Cromshell's tests. All tests can be run from the Cromshell directory.

Linting files

As a reminder, linter is used to scan your code for styling corrections and issues that may lead to bugs. The main linting method can be executed is through Tox tox -e lint, which will run all the linting tools. However, It's possible to run the linting tools individually as seen below

# run all linting commands
tox -e lint

# reformat all project files
black src tests 

# sort imports in project files
isort -rc src tests 

# check pep8 against all project files
flake8 src tests 

# lint python code for common errors and codestyle issues
pylint src

Running Tests

To run tests in the /tests directory use the Tox commands below.

# run all linting and test
tox

# run only unit tests
tox -e unit

# run only integration tests 
tox -e integration

Integration Testing
Running integration tests isn't as simple as running unit tests. Some integration tests (e.g. submit command) are running Cromshell in a way that will require access to a local Cromwell server and will fail unless it finds a server. This can be easily remedied by running a containerized local cromshell server with the following command:

docker run -d -p 8000:8000 broadinstitute/cromwell:67 server