fixing docstrings

KarrLab · Nov 15, 2018 · d724511 · d724511
1 parent d4a7546
commit d724511
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Showing 4 changed files with 10 additions and 10 deletions.
diff --git a/datanator/api/lib/metabolite/manager.py b/datanator/api/lib/metabolite/manager.py
@@ -104,7 +104,7 @@ def _search_simple(self, value):
             value (:obj:`str`): string to search table for
 
         Returns:
-            :obj:`list` of `models.Metabolite`: List of found models.Metabolite objects (search parameters: 'metabolite_name')
+            :obj:`list` of :obj:`models.Metabolite`: List of found models.Metabolite objects (search parameters: 'metabolite_name')
 
         """
 
@@ -117,7 +117,7 @@ def _search_complex(self,value):
             value (:obj:`str`): string to search table for
 
         Returns:
-            :obj:`list` of `models.Metabolite`: List of found models.Metabolite objects search parameters: 'metabolite_name',  'description')
+            :obj:`list` of :obj:`models.Metabolite`: List of found models.Metabolite objects search parameters: 'metabolite_name',  'description')
             
         """
 

diff --git a/datanator/core/data_query.py b/datanator/core/data_query.py
@@ -351,20 +351,20 @@ class FilterResult(object):
     """ Represents the results of applying a list of filters to a dataset
 
     Attributes:
-        observed_results (:obj:`list` of `data_model.ObservedValue`): prioritized list of observed values
+        observed_results (:obj:`list` of :obj:`data_model.ObservedValue`): prioritized list of observed values
         scores (:obj:`numpy.ndarray`): matrix of scores (rows: observed values in same order as in `ordered_observed_results`; columns: filters, in same orders as in `filters`)
         observed_value_indices (:obj:`list` of :obj:`int`): indices of the ordered observed values in the input list of observed values
-        all_observed_results (:obj:`list` of `data_model.ObservedValue`): input list of observed values
+        all_observed_results (:obj:`list` of :obj:`data_model.ObservedValue`): input list of observed values
         all_scores (:obj:`numpy.ndarray`): matrix of scores (rows: observed values in same order as in `observed_results`; columns: filters, in same orders as in `filters`)
     """
 
     def __init__(self, observed_results, scores, observed_value_indices, all_observed_results, all_scores):
         """
         Args:
-            observed_results (:obj:`list` of `data_model.ObservedValue`): prioritized list of observed values
+            observed_results (:obj:`list` of :obj:`data_model.ObservedValue`): prioritized list of observed values
             scores (:obj:`numpy.ndarray`): matrix of scores (rows: observed values in same order as in `ordered_observed_results`; columns: filters, in same orders as in `filters`)
             observed_value_indices (:obj:`list` of :obj:`int`): indices of the ordered observed values in the input list of observed values
-            all_observed_results (:obj:`list` of `data_model.ObservedValue`): input list of observed values
+            all_observed_results (:obj:`list` of :obj:`data_model.ObservedValue`): input list of observed values
             all_scores (:obj:`numpy.ndarray`): matrix of scores (rows: observed values in same order as in `observed_results`; columns: filters, in same orders as in `filters`)
         """
         self.observed_results = observed_results

diff --git a/datanator/data_source/sabio_rk.py b/datanator/data_source/sabio_rk.py
@@ -1255,7 +1255,7 @@ def create_cross_references_from_sbml(self, sbml):
             sbml (:obj:`libsbml.SBase`): object in an SBML documentation
 
         Returns:
-            :obj:`list` of `Resource`: list of resources
+            :obj:`list` of :obj:`Resource`: list of resources
         """
         if not sbml.isSetAnnotation():
             return []

diff --git a/datanator/io.py b/datanator/io.py
@@ -62,7 +62,7 @@ def read_compartments(self, ws):
             ws (:obj:`openpyxl.Worksheet`): worksheet
 
         Returns:
-            :obj:`list` of `data_model.Compartment`: list of compartments
+            :obj:`list` of :obj:`data_model.Compartment`: list of compartments
         """
         compartments = []
         for i in range(2, ws.max_row + 1):
@@ -79,7 +79,7 @@ def read_species(self, ws):
             ws (:obj:`openpyxl.Worksheet`): worksheet
 
         Returns:
-            :obj:`list` of `data_model.Specie`: list of species
+            :obj:`list` of :obj:`data_model.Specie`: list of species
         """
         species = []
         for i in range(2, ws.max_row + 1):
@@ -99,7 +99,7 @@ def read_reactions(self, ws, compartments, species):
             species (:obj:`list` of :obj:`data_model.Specie`): list of species
 
         Returns:
-            :obj:`list` of `data_model.Reaction`: list of reactions
+            :obj:`list` of :obj:`data_model.Reaction`: list of reactions
         """
         reactions = []
         for i in range(2, ws.max_row + 1):