Troubleshooting

If you’re running into problems, look for more information by including debug logging. To enable debug logging, set the environmental variable SF_LOGGING_LEVEL=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 troubleshoot environment or installation issues, start by running unit tests, which do not require any sample slides. Use the test.py script without any arguments:

$ python3 test.py

For a more comprehensive test of all pipeline functions, provide a path to a directory containing sample slides via --slides, setting --all=True to run all tests:

$ python3 test.py --slides=/path/to/slides --all=True

Individual tests can be manually skipped with the following syntax:

$ python3 test.py --slides=/path/to/slides --all=True --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. Be sure to include the following information:

• The version of Slideflow you are using, which can be displayed with sf.about():

$ python3 -c "import slideflow; slideflow.about()"
╭=======================╮
│       Slideflow       │
│    Version: 2.1.0     │
│  Backend: tensorflow  │
│ Slide Backend: cucim  │
│ https://slideflow.dev │
╰=======================╯

• The active deep learning backend (sf.backend()) and slide backend (sf.slide_backend())

• The version of Python you are using (python3 --version)

• The operating system you are using (uname -a)