Merge pull request #161 from ICB-DCM/develop

Release 0.0.7

doc/releasenotes.rst

@@ -6,6 +6,13 @@ Release notes
 ..........
 
 
+0.0.7 (2019-03-21)
+------------------
+
+* Support noise models in Petab and Amici.
+* Minor Petab update bug fixes.
+
+
 0.0.6 (2019-03-13)
 ------------------
 

pypesto/objective/petab_import.py

@@ -182,7 +182,11 @@ def compile_model(self):
         observables = self.petab_problem.get_observables()
 
         # sigmas
-        sigmas = self.petab_problem.get_sigmas()
+        sigmas = self.petab_problem.get_sigmas(remove=True)
+
+        # noise distributions
+        noise_distrs = _to_amici_noise_distributions(
+            self.petab_problem.get_noise_distributions())
 
         # model to string
         sbml_string = libsbml.SBMLWriter().writeSBMLToString(
@@ -197,7 +201,8 @@ def compile_model(self):
             output_dir=self.output_folder,
             observables=observables,
             constantParameters=constant_parameter_ids,
-            sigmas=sigmas
+            sigmas=sigmas,
+            noise_distributions=noise_distrs
         )
 
     def create_solver(self, model=None):
@@ -346,7 +351,6 @@ def create_objective(self,
                 measurement_df=self.petab_problem.measurement_df,
                 parameter_df=self.petab_problem.parameter_df,
                 sbml_model=self.petab_problem.sbml_model,
-                par_opt_ids=par_opt_ids,
                 par_sim_ids=par_sim_ids,
                 simulation_conditions=simulation_conditions,
             )
@@ -594,6 +598,22 @@ def _find_output_folder_name(petab_problem: petab.Problem):
     return output_folder
 
 
+def _to_amici_noise_distributions(noise_distributions):
+    """
+    Map from the petab to the amici format of noise distribution
+    identifiers.
+    """
+    amici_distrs = {}
+    for id_, val in noise_distributions.items():
+        amici_val = ''
+        if val['observableTransformation']:
+            amici_val += val['observableTransformation'] + '-'
+        if val['noiseDistribution']:
+            amici_val += val['noiseDistribution']
+        amici_distrs[id_] = amici_val
+    return amici_distrs
+
+
 def _find_model_name(output_folder):
     """
     Just re-use the last part of the output folder.

pypesto/version.py

@@ -1 +1 @@
-__version__ = "0.0.6"
+__version__ = "0.0.7"

setup.py

@@ -28,8 +28,8 @@ def read(fname):
                         'pandas>=0.23.4',
                         'matplotlib>=2.2.3',
                         'cloudpickle>=0.7.0',
-                        'petab>=0.0.0a11'],
+                        'petab>=0.0.0a12'],
       tests_require=['pytest', 'flake8>=3.7.1', 'gitpython'],
-      extras_require={'amici': ['amici>=0.10.2']},
+      extras_require={'amici': ['amici>=0.10.4']},
       python_requires='>=3.6',
       )