Fix docstring (#191)

biomass-dev · Sep 6, 2022 · 0101941 · 0101941
1 parent 7fc8a6a
commit 0101941
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Showing 3 changed files with 19 additions and 19 deletions.
diff --git a/biomass/construction/text2model.py b/biomass/construction/text2model.py
@@ -896,7 +896,7 @@ def register_word(
         Parameters
         ----------
         terminology : Dict[str, List[str]], optional
-            Rule to which users register a new rule word and list of user-defined rule words.
+            Pair of reaction rule and user-defined rule words.
 
         Examples
         --------
@@ -967,7 +967,7 @@ def static_plot(
     ) -> None:
         """Saves a static image of the network.
 
-        Static image is created using pygraphviz.
+        Static image is created using ``pygraphviz``.
 
         Parameters
         ----------
@@ -1019,17 +1019,17 @@ def dynamic_plot(
         which_controls: Optional[List[str]] = None,
     ) -> None:
         """Saves a dynamic and interactive image of the network graph.
-        Graph is read by pyvis. Using pyvis a dynamic and interactive representation of the biological network
+        Graph is read by ``pyvis``. Using ``pyvis`` a dynamic and interactive representation of the biological network
         is created in html format.
 
         Parameters
         ----------
         show: bool, default=True
-            If true the plot will immediately be displayed in the webbrowser.
+            If :obj:`True` the plot will immediately be displayed in the webbrowser.
         annotate_nodes : bool, default=True
-            If true nodes will be scaled according to number of edges and hovering over a node will show interaction partners.
+            If :obj:`True` nodes will be scaled according to number of edges and hovering over a node will show interaction partners.
         show_controls : bool, default=False
-            If true control buttons will be displayed.
+            If :obj:`True` control buttons will be displayed.
         which_controls : List(str), optional, default=None
             Used to specify which control buttons should be displayed. If empty all buttons will be displayed.
 

diff --git a/biomass/estimation/optimizer.py b/biomass/estimation/optimizer.py
@@ -55,12 +55,12 @@ class Optimizer(object):
     Examples
     --------
     >>> from scipy.optimize import differential_evolution
-    >>> from biomass import Model
-    >>> from biomass.estimation import ExternalOptimizer
+    >>> from biomass import create_model
+    >>> from biomass.estimation import Optimizer
     >>> from biomass.models import Nakakuki_Cell_2010
-    >>> model = Model(Nakakuki_Cell_2010.__package__).create()
+    >>> model = create_model(Nakakuki_Cell_2010.__package__)
     >>> param_idx = 1
-    >>> optimizer = ExternalOptimizer(model, differential_evolution, param_idx)
+    >>> optimizer = Optimizer(model, differential_evolution, param_idx)
     >>> def obj_fun(x):
     ...    '''Objective function to be minimized.'''
     ...    return optimizer.get_obj_val(x)
@@ -217,7 +217,7 @@ def generate(self, n_proc: int = 1, progress: bool = False) -> np.ndarray:
 
         Returns
         -------
-        population : numpy.ndarray
+        population : ``numpy.ndarray``
             Array specifying the initial population.
             The array should have shape (M, len(x)),
             where M is the total population size and len(x) is the number of parameters.

diff --git a/biomass/model_object.py b/biomass/model_object.py
@@ -17,11 +17,11 @@ class ModelObject(object):
 
     Examples
     --------
-    >>> from biomass import Model
+    >>> from biomass import create_model
     >>> from biomass.models import mapk_cascade
-    >>> model = Model(mapk_cascade.__package__).create()
+    >>> model = create_model(mapk_cascade.__package__)
     >>> type(model)
-    <class 'biomass.exec_model.ModelObject'>
+    <class 'biomass.model_object.ModelObject'>
     >>> print('Parameters:', len(model.parameters))
     Parameters: 22
     >>> print('Species:', len(model.species))
@@ -73,7 +73,7 @@ def get_individual(self, paramset_id: int) -> np.ndarray:
 
         Returns
         -------
-        best_individual : numpy.ndarray
+        best_individual : ``numpy.ndarray``
             Estimated parameter values.
         """
         best_generation = np.load(
@@ -105,7 +105,7 @@ def load_param(self, paramset: int) -> OptimizedValues:
 
         Returns
         -------
-        optimized_values : OptimizedValues
+        optimized_values : :class:`biomass.model_object.OptimizedValues`
             Optimized parameter/initial values.
         """
         best_individual = self.get_individual(paramset)
@@ -151,12 +151,12 @@ def gene2val(self, indiv_gene: np.ndarray) -> np.ndarray:
 
         Parameters
         ----------
-        indiv_gene : ``numpy.ndarray```
+        indiv_gene : ``numpy.ndarray``
             Individual gene.
 
         Returns
         -------
-        indiv_values : ``numpy.ndarray```
+        indiv_values : ``numpy.ndarray``
             Corresponding values.
         """
         bounds = self.problem.get_region()
@@ -169,7 +169,7 @@ def get_obj_val(self, indiv_gene: np.ndarray) -> float:
 
         Parameters
         ----------
-        indiv_gene : numpy.ndarray
+        indiv_gene : ``numpy.ndarray``
             Genes, not parameter values.
 
         Returns