Merge pull request #205 from PEtab-dev/release_0.2.1

Release 0.2.1

Author: dweindl

CHANGELOG.md

@@ -2,6 +2,12 @@
 
 ## 0.2 series
 
+### 0.2.1
+
+Fixes:
+* Fixed an issue in `Problem.to_files(model_file=...)` (#204)
+* Fixed `PySBModel.get_parameter_value`, which incorrectly returned the parameter name instead of its value (#203)
+
 ### 0.2.0
 
 Note: petab 0.2.0 requires Python>=3.9

README.md

@@ -22,7 +22,7 @@ and the easiest way to install it is running
 
     pip3 install petab
 
-It will require Python>=3.8 to run. (We are following the
+It will require Python>=3.9 to run. (We are following the
 [numpy Python support policy](https://numpy.org/neps/nep-0029-deprecation_policy.html)).
 
 Development versions of the PEtab library can be installed using

petab/models/pysb_model.py

@@ -83,7 +83,7 @@ def get_parameter_ids(self) -> Iterable[str]:
 
     def get_parameter_value(self, id_: str) -> float:
         try:
-            return self.model.parameters[id_].name
+            return self.model.parameters[id_].value
         except KeyError as e:
             raise ValueError(f"Parameter {id_} does not exist.") from e
 

petab/problem.py

@@ -411,7 +411,7 @@ def to_files_generic(
             if not isinstance(self.model, SbmlModel):
                 raise NotImplementedError("Saving non-SBML models is "
                                           "currently not supported.")
-            filenames['sbml_file'] = 'model.xml'
+            filenames['model_file'] = 'model.xml'
 
         filenames['yaml_file'] = 'problem.yaml'
 
@@ -542,7 +542,7 @@ def error(name: str) -> ValueError:
 
         if yaml_file:
             yaml.create_problem_yaml(
-                sbml_files=sbml_file,
+                sbml_files=model_file,
                 condition_files=condition_file,
                 measurement_files=measurement_file,
                 parameter_file=parameter_file,

petab/version.py

@@ -1,2 +1,2 @@
 """PEtab library version"""
-__version__ = '0.2.0'
+__version__ = '0.2.1'