Fix the test suite

[mdunphy]

The test suite should be in working condition to be useful.

1. The tests are converted to pytest form on branch fix_tests -- run with python -m pytest

2. They are not all passing: 7 failed, 25 passed, 58 warnings

3. The test data generators don't reproduce the test data

Investigation needed: is the test data bad, or is there a code problem, or is it a random-seed situation, etc