Fix test failures and warnings from pytest within test suite

brocksam commented 3 years ago

This PR addresses the failing tests and warnings raised by pytest when running the test suite using pytest. Included changes are as follows:

Issue #307 previously raised the failing of tests/test_ode.py::test_initial_parameters and specified that the reason for this failing was due to a too tight absolute tolerance on the numerical result of the fit. This test now passes by increasing the acceptable absolute numerical tolerance from 1e-8 to 5e-7.
DeprecationWarnings were being raised in a number of places, primarily resulting from the deprecation of the autogeneration of names for Parameters and Variables, as well as the use of the newly-preferred use of connectivity_mappings when instantiating CallableNumericalModels. The test suite has been refactored to use the new beast-practice approach, or to use a pytest.warns context manager in places where this makes more sense in the test to handle the DeprecationWarning.
Small refactors to certain tests (specifically what used to be tests/test_general::test_model_callable and tests/test_minimize.py::test_minimize) where "TODO" comments suggested splitting specific tests in to constituent parts would make sense.

pckroon commented 3 years ago

Ping @tBuLi I'll merge this on Friday if you don't have any complaints.

pckroon commented 3 years ago

Thanks again @brocksam, and sorry for the long wait.

tBuLi / symfit