Troubleshooting

If you’re running into problems, look for more information by including debug logging. To enable debug logging, set the environmental variable SF_BACKEND=10.

To check for errors in your environment or installation, you can also use the test script test.py, which uses the testing suite slideflow.test.TestSuite to execute all pipeline functions on a set of provided slides.

Testing

To test all pipeline functions, use the test.py script, providing a path to a directory containing slides to use for testing:

$ python3 test.py --slides /path/to/slides

Individual tests can be manually skipped with the following syntax:

$ python3 test.py --slides /path/to/slides --reader=False

To view a list of all tests that will be run (and thus can be skipped), pass the argument --help.

Issue Reporting

If the issue is still unclear, please submit an Issue on the project Github page.