fix bug related to linker

geppy/core/entity.py

@@ -454,7 +454,8 @@ def __init__(self, gene_gen, n_genes, linker=None):
         .. note:
             If a linker is specified, then it must accept *n_genes* arguments, each produced by one gene. If the
             *linker* parameter is the default value ``None``, then for a monogenic chromosome, no linking is applied,
-            while for a multigenic chromosome, the ``tuple`` function is used.
+            while for a multigenic chromosome, the ``tuple`` function is used, i.e., a tuple of values of all genes 
+            is returned.
         """
         list.__init__(self, (gene_gen() for _ in range(n_genes)))
         self._linker = linker
@@ -522,10 +523,13 @@ def kexpressions(self):
     @property
     def linker(self):
         """
-        Get the linking function.
+        Get the linking function. 
+
+        .. note:
+            If linker is `None`, then the actual linking function during evaluation of an individual
+            returns the value of the single gene for a single-gene (monogenic) chromosome or a tuple of values of all 
+            genes for a multi-gene chromosome.
         """
-        if self._linker is None and len(self) > 1:
-            return tuple
         return self._linker
 
     def __repr__(self):

geppy/support/visualization.py

@@ -72,7 +72,8 @@ def graph(genome, label_renaming_map=None):
             for gene in genome:
                 expr = gene.kexpression
                 sub_roots.append(starting_index)
-                sub_nodes, sub_edges, sub_labels = _graph_kexpression(expr, starting_index)
+                sub_nodes, sub_edges, sub_labels = _graph_kexpression(
+                    expr, starting_index)
                 nodes.extend(sub_nodes)
                 edges.extend(sub_edges)
                 labels.update(sub_labels)
@@ -114,7 +115,7 @@ def export_expression_tree(genome, label_renaming_map=None, file='tree.png'):
     import graphviz as gv
     import os.path
 
-    nodes, edges, labels = graph(genome, label_renaming_map)
+    _, edges, labels = graph(genome, label_renaming_map)
     file_name, ext = os.path.splitext(file)
     ext = ext.lstrip('.')
     g = gv.Graph(format=ext)
@@ -125,4 +126,4 @@ def export_expression_tree(genome, label_renaming_map=None, file='tree.png'):
     g.render(file_name)
 
 
-__all__ = ['graph', 'export_expression_tree']
+__all__ = ['graph', 'export_expression_tree']

geppy/tools/parser.py

@@ -42,12 +42,12 @@ def compile_(individual, pset):
     """
     fs = [_compile_gene(gene, pset) for gene in individual]
     linker = individual.linker
-    if linker is None:
+    if linker is None:  # return the gene itself for a monogenic one or tuple of all genes
         if len(fs) == 1:
             return fs[0]
         else:
             return lambda *x: tuple((f(*x) for f in fs))
     return lambda *x: linker(*(f(*x) for f in fs))
 
 
-__all__ = ['compile_']
+__all__ = ['compile_']