Add thirty models#13
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…tch to draw_graph
…arkov-builder into fix_transition_matrix
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## master #13 +/- ##
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+ Coverage 89.71% 93.30% +3.59%
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Files 5 22 +17
Lines 554 837 +283
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+ Hits 497 781 +284
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Add sundials install to workflow
MichaelClerx
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MichaelClerx
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Hi Joey,
Won't have time for an in-depth review (if you want that) till June or after.
Few small comments. And comparison 2 looks plain wrong?
Would plot an error for these 3 cases too (signal1 - signal2)
…arkov-builder into fix_transition_matrix
You'll have to show me those Joey! And do a pull request on the 30 models repo? |
| 'b2': ('p11 * exp(-p12*V)',), | ||
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| open_state = 'O' |
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| class TestThirtyModels(unittest.TestCase): | ||
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| def setUp(self): |
There was a problem hiding this comment.
Did you mean setUpClass here?
The difference is that setUp gets called before every test_x method in your class, while setUpClass is called just once
| self.output_dir = test_output_dir | ||
| logging.info("outputting to " + test_output_dir) | ||
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| self.models = [model_00, model_01, model_02, model_03, model_04, |
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[f'model_{i:02}' for i in self.model_indices] ?
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I think this is all fine now. I think we should get it merged in soon because I'm using this branch for other projects |
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If it is something special I would take that out and just rename all the variables, throwing an error if you call one 'O' (or any SymPy keyword or whatever the problem is!) |
3 participants
Description
Add models 1-11 and 30 from CardiacModelling/hergModels/tree/master/models_myokit. These models are tested by comparing Myokit Simulation output form the original .mmt files with those generated through the Markov_builder.
The newly added models make extensive use of the shared_variables_dict. The behaviour of parameterise_rates was modified to make it more convenient to set these variables to numerical values.
These changes exposed some issues with reversibility checking and transition matrix calculation which have now been fixed.
The new models can be easily generated by users and modified to include drug-trapping or additional states/parameters.
Types of changes
Testing
Documentation checklist