toil.test.src.environmentTest

Attributes

logger

Classes

EnvironmentTest

Test to make sure that Toil's environment variable save and restore system

Functions

signal_leader(job)	Make a file in the file store that the leader can see.
check_environment(job, try_name)	Fail if the test environment is wrong.
wait_a_bit(job)	Toil job that waits.
check_environment_repeatedly(job)	Toil job that checks the environment, waits, and checks it again, as
main([options])	Run the actual workflow with the given options.

Module Contents

toil.test.src.environmentTest.logger

class toil.test.src.environmentTest.EnvironmentTest(methodName='runTest')

Bases: toil.test.ToilTest

Test to make sure that Toil’s environment variable save and restore system (environment.pickle) works.

The environment should be captured once at the start of the workflow and should be sent through based on that, not base don the leader’s current environment when the job is launched.

test_environment()

toil.test.src.environmentTest.signal_leader(job)

Make a file in the file store that the leader can see.

toil.test.src.environmentTest.check_environment(job, try_name)

Fail if the test environment is wrong.

Parameters:

try_name (str)

toil.test.src.environmentTest.wait_a_bit(job)

Toil job that waits.

toil.test.src.environmentTest.check_environment_repeatedly(job)

Toil job that checks the environment, waits, and checks it again, as separate invocations.

toil.test.src.environmentTest.main(options=None)

Run the actual workflow with the given options.

Parameters:

options (Optional[argparse.Namespace])