documentation change

copasi · Dec 20, 2024 · bc91928 · bc91928
1 parent a4ebfa0
commit bc91928
Show file tree

Hide file tree

Showing 3 changed files with 10 additions and 21 deletions.
diff --git a/.gitignore b/.gitignore
@@ -144,4 +144,7 @@ $RECYCLE.BIN/
 /tests/test_data/observ*
 /tests/test_data/parameter*
 temp_dir
+temp_selection
+tmp_selection
+famos*
 .DS_Store
diff --git a/basico/petab/select.py b/basico/petab/select.py
@@ -47,15 +47,11 @@ def copasi_aic():
 def default_evaluation():
     """Default evaluation of current model:
 
-    * runs particle swarm for 600 iterations followed by
-    * levenberg marquardt
-
+    * runs genetic algorithm for 30 generations
+    * refines using nl2sol for 1000 iterations
 
     :return: found parameter values
     """
-    #logger.debug('running ps\n')
-    #basico.run_parameter_estimation(method='Particle Swarm', update_model=True,
-    #                                settings={'method': {'Iteration Limit': 600}})
     logger.debug('running ga, 30gens\n')
     basico.run_parameter_estimation(method=basico.PE.GENETIC_ALGORITHM_SR, update_model=True,
                                     settings={'method': {
@@ -69,8 +65,6 @@ def default_evaluation():
                                                 'Iteration Limit': 1000,
                                             }}
                                           )
-    # logger.debug('running lm')
-    # sol = basico.run_parameter_estimation(method='Levenberg - Marquardt', update_model=True)
     logger.debug('evaluation done')
     return sol
 

diff --git a/docs/notebooks/Working_with_PEtab.ipynb b/docs/notebooks/Working_with_PEtab.ipynb