LoLab-VU / pysb / 906
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alubbock 
Updating sensitivity analysis class to be general for any model parameters (#426)

* Updating Sensitivity analysis class to be used with any parameters, not just initial conditions. Also added ability to pass a list of parameter names rather than requiring all from the model to be used.

* Adding check to if passed in list of parameters is actually in the model.

* Adding examples in documentation for sens_type='params' and with a list
 of parameters. Adding tests for parameter list.

* Adding test for using deprecated class name (InitialsSensitivity). This
will maintain compatibility.

* Fixing doc tests. Printing differences between python versions gave
some errors. They seem to be fixed.

* Adding last test case where sens_type=None and sample_list=None

* Removed a lot of the initializations of the solver. Not needed.
Added test to catch a non pysb simulator.

* Fixing logic in checking if sens_type sample_list is None and sens_type
is not in approved list.

* Addressing changes for pull request.

* Changing doctest to verify size of array, rather than printing.
Windows represents np.array.shape as type L, where on linux it
uses it uses int. This is due to differences in C types. Pointless fix
in the long run, but now it should pass doctests on python2 for windows.
It is discussed here.
https://github.com/numpy/numpy/issues/5809

* Adding attribute and parameter descriptions. I made some attributes
private that were supposed to be for internal calculations.

* Documentation fixes for sensitivity analysis class

7428 of 9408 relevant lines covered (78.95%)

2.35 hits per line

Jobs
ID Job ID Ran Files Coverage
1 906.1 (PYVER=2.7) 100
78.56
 Travis Job 906.1
2 906.2 (PYVER=3.6) 100
78.16
 Travis Job 906.2
3 906.3 (PYVER=3.7) 100
78.16
 Travis Job 906.3
Source Files on build 906