fix pydocstyle

tests/__init__.py

@@ -0,0 +1 @@
+"""yaml2sbml tests."""

tox.ini

@@ -20,10 +20,10 @@ envlist =
 [testenv]
 # Dependencies
 deps =
-    coverage
-    pytest
-    pytest-cov
-    pytest-console-scripts
+    coverage >= 5.5
+    pytest >= 6.2.2
+    pytest-cov >= 2.11.1
+    pytest-console-scripts >= 1.1.0
 
 # Sub-environments
 #  inherit settings defined in the base
@@ -54,7 +54,7 @@ commands =
     flake8 yaml2sbml tests setup.py
     pydocstyle yaml2sbml tests setup.py
 description =
-    Run flake8 with various plugins
+    Run flake8 with various plugins, and pydocstyle
 
 [testenv:unittests]
 commands =

yaml2sbml/YamlModel.py

@@ -181,16 +181,20 @@ def _get_reduced_model_dict(self) -> dict:
 
     # functionalities regarding the time
     def is_set_time(self):
+        """Check whether there is a time variable."""
         return 'variable' in self._yaml_model['time'].keys()
 
     def set_time(self,
                  time_variable: str):
+        """Set time variable."""
         self._yaml_model['time'] = {'variable': time_variable}
 
     def delete_time(self):
+        """Delete time variable."""
         self._yaml_model['time'] = {}
 
     def get_time(self):
+        """Get time variable."""
         if self.is_set_time():
             return self._yaml_model['time']['variable']
         else:

yaml2sbml/version.py

@@ -1 +1,3 @@
+"""yaml2sbml version."""
+
 __version__ = '0.2.1'

yaml2sbml/yaml2sbml.py

@@ -224,7 +224,6 @@ def _create_time(model: sbml.Model, time_var: str):
         model: the SBML model to which the species will be added.
         time_var: str, the time variable
     """
-
     if time_var == 'time':
         return