Extending and testing the AMR-based modeling API

[bgyori]

Note: this is redoing the PR #238 by @nanglo123 against the main branch.

New MIRA Operations in mira/modeling/askenet/ops.py

• replace_rate_law_mathml
• add_parameter
  • Currently, we only add parameters that are present in rate laws. Thus newly added parameters using this method are not present in the output amr file. @bgyori will decide how to handle adding parameters not present in any rate laws.
• remove_X where X is an observable or parameter
  • If X is an observable, we simply just pop the observable object from the dict of observables
  • If X is a parameter, we remove the parameter from the list of parameters in the output amr file and replace every instance of the replaced parameter with the replacement value
• add_transition
  • Currently, new states and parameters present in the rate law passed in when adding a transition are not added to the list of states and parameters repsectively of the output amr file
• add_observable
• replace_x_expression
  • Added 2 versions of the method in which we either pass in a Sympy object or xml string (mathml object) representing the rate law

Unit tests for MIRA operations in tests/test_modeling/test_askenet.py

• Added passing unit tests for all previously defined MIRA operations. Added passing unit tests for all newly added operations except for add_parameter. Currently, the unit test for add_transition doesn't test for the presence of newly added states and parameters.

Bug Fixes

• Fixed a bug in commit e9cb3dc where changed parameters after calling replace_parameter_id were not showing in output amr['semantics']['ode']['parameters']

• Fixed a bug in commit 0ae9ed0 and commit a1e6381 where observables in the output amr had identical values for their name and id field (template model-> amr). Also fixed an issue where template models constructed from an amr file (amr -> template model) used a observables['id'] for the name and display_name of a concept. Now the name field will take the display_name attribute associated with a concept and id will take the id attribute associated with a oncept.