BayesianOpt fix - Githubissues

Pull Request Description

Closes #312 Closes #308

Re-implements Anthoney's original PR with only the changes necessary for BayesianOpt.

More work needs to be done to (1) set BayesianOpt as the default optimizer, (2) convert the workshop cases.

The following review must be completed by an authorized member of the Change Control Board.

[x] 1. Review all computer code.
[x] 2. If any changes occur to the input syntax, there must be an accompanying change to the user manual and xsd schema. If the input syntax change deprecates existing input files, a conversion script needs to be added (see Conversion Scripts).
[x] 3. Make sure the Python code and commenting standards are respected (camelBack, etc.) - See on the wiki for details.
[x] 4. Automated Tests should pass.
[x] 5. If significant functionality is added, there must be tests added to check this. Tests should cover all possible options. Multiple short tests are preferred over one large tes.
[x] 6. If the change modifies or adds a requirement or a requirement based test case, the Change Control Board's Chair or designee also needs to approve the change. The requirements and the requirements test shall be in sync.
[x] 7. The merge request must reference an issue. If the issue is closed, the issue close checklist shall be done.
[x] 8. If an analytic test is changed/added, the the analytic documentation must be updated/added.
[x] 9. If any test used as a basis for documentation examples have been changed, the associated documentation must be reviewed and assured the text matches the example.