3.1.3. wc_test.core module
Methods for verifying models and simulations
- Author
Balazs Szigeti <balazs.szigeti@mssm.edu>
- Author
Jonathan Karr <jonrkarr@gmail.com>
- Date
2018-05-10
- Copyright
2018, Karr Lab
- License
MIT
TODO:
- all reaction methods: currently len(rate_laws)=1 assumed, generalize
- mod_parameters values are INTs in change_methods, but LISTs for sim_scan methods, synchornize
-
class
wc_test.core.KnowledgeBaseTestCase(methodName='runTest')[source]
Bases: unittest.case.TestCase
Methods for testing knowledge bases for WC models
-
kb[source]
knowledge base
- Type
wc_kb.KnowledgeBase
- Class attributes:
- KB (
wc_kb.KnowledgeBase or str): knowledge base or path to a knowledge base file
-
KB = None[source]
-
setUp()[source]
Hook method for setting up the test fixture before exercising it.
-
class
wc_test.core.ModelTestCase(methodName='runTest')[source]
Bases: unittest.case.TestCase
Methods for testing WC models
-
model[source]
model
- Type
wc_lang.Model
-
kb[source]
knowledge base
- Type
wc_kb.KnowledgeBase
-
results_dir[source]
path to directory where results will be stored
- Type
str
- Class attributes:
MODEL (wc_lang.Model or str): model or path to a model file
KB (wc_kb.KnowledgeBase or str): knowledge base or path to a
-
KB = None[source]
-
MODEL = None[source]
-
change_parameter_values(mod_parameters)[source]
-
change_reaction_k_cat_parameter_values(mod_reactions)[source]
-
change_species_mean_init_concentrations(mod_species)[source]
-
get_reaction(id)[source]
-
get_species(id)[source]
-
select_submodels(mod_submodels)[source]
Turn off all submodels, except the ones listed in submodel_ids
-
setUp()[source]
Hook method for setting up the test fixture before exercising it.
-
tearDown()[source]
Hook method for deconstructing the test fixture after testing it.
-
class
wc_test.core.SimulationTestCase(methodName='runTest')[source]
Bases: wc_test.core.ModelTestCase
Class to test simulations of models
-
avg_conc_runs(n, target_specie_ids, end_time)[source]
-
avg_conc_time(target_specie_ids, end_time, checkpoint_period)[source]
-
delta_conc(species, run_results)[source]
-
get_growth_rate(end_time)[source]
-
sim_scan_parameters(mod_parameters, end_time, checkpoint_period)[source]
-
sim_scan_reactions(mod_reactions, end_time, checkpoint_period)[source]
-
sim_scan_species(mod_species, end_time, checkpoint_period)[source]
-
simulate(end_time, checkpoint_period=None, n_sims=1)[source]