Fix tests

[martinghunt]

• Tests are failing on GitHub actions. Change everything from classes and setup/teardown to using pytest.fixtures. This should fix it, but will find out on creating this PR
• Make sure all tests are discoverable with pytest (some were not and were never running)
• Fix a bug in probe generation where probes with context variants could have mismatching ref and alt probes. The probe sequences were correct, but not in the same order between ref and alt probes. Reinstated the test that checked these probes, since it was not running
• Ran black on all changed files
• Looks like more changes than it really is: moving the tests out of classes made the indentation one level less, plus running black means diff looks big