Turn Logger into a container for storing issues that can be returned to user

[CiaranWelsh]

An API that makes it easy to get a list of issues, the level of each issue, and the message associated with each issue would be helpful. This would avoid the need to setup a log file and then parse the log file for errors. I don't have a strong opinion about exactly what this needs to look like.

Methods such as these would be fine:

• log.get_num_issues()
• log.get_issue_level(i_message)
• log.get_issue_message(i_message)

Here's one example from libCellML: https://libcellml.org/documentation/api/v0.2.0/classlibcellml_1_1Logger.
Another is libSBML: http://sbml.org/Software/libSBML/5.18.0/docs/python-api/classlibsbml_1_1_s_b_m_l_error_log.html.

Originally posted by @jonrkarr in #102 (comment)

[CiaranWelsh]

Implemented in v1.2.13. See docs.

[jonrkarr]

This will be very helpful.