Merge pull request #26 from Mathics3/misc-fixes

Doc and type corrections

pymathics/graph/base.py

@@ -81,7 +81,7 @@ def graph_helper(
     graph_generator_func: Callable,
     options: dict,
     can_digraph: bool,
-    graph_layout: str,
+    graph_layout: Optional[str],
     evaluation,
     root: Optional[int] = None,
     *args,
@@ -124,7 +124,7 @@ def graph_helper(
 
 
 def has_directed_option(options: dict) -> bool:
-    return options.get("System`DirectedEdges", False).to_python()
+    return options.get("System`DirectedEdges", False)
 
 
 def _process_graph_options(g, options: dict) -> None:
@@ -173,15 +173,15 @@ def _process_graph_options(g, options: dict) -> None:
 
 
 def _circular_layout(G):
-    return nx.drawing.circular_layout(G, scale=1.5)
+    return nx.drawing.circular_layout(G, scale=1)
 
 
 def _spectral_layout(G):
-    return nx.drawing.spectral_layout(G, scale=2.0)
+    return nx.drawing.spectral_layout(G, scale=2)
 
 
 def _shell_layout(G):
-    return nx.drawing.shell_layout(G, scale=2.0)
+    return nx.drawing.shell_layout(G, scale=2)
 
 
 def _generic_layout(G, warn):

pymathics/graph/collections.py

@@ -7,6 +7,9 @@
 
 from pymathics.graph.graphsymbols import SymbolDirectedEdge
 
+# There is no user-facing documentation here.
+no_doc = True
+
 
 def _count_edges(counts, edges, sign):
     n_directed, n_undirected = counts

pymathics/graph/components.py

@@ -16,8 +16,12 @@
 class ConnectedComponents(_NetworkXBuiltin):
     """
     <url>
-    :WMA:https://reference.wolfram.com/language/ref/ConnectedComponents.html
-    </url>
+    :Strongly connected components:
+    https://en.wikipedia.org/wiki/Strongly_connected_component</url> (<url>
+    :NetworkX:
+    https://networkx.org/documentation/networkx-2.8.8/reference/algorithms/\
+generated/networkx.algorithms.components.strongly_connected_components.html</url>, <url>
+:WMA:https://reference.wolfram.com/language/ref/ConnectedComponents.html</url>)
 
     <dl>
       <dt>'ConnectedComponents'[$g$]
@@ -83,8 +87,13 @@ def eval(
 class WeaklyConnectedComponents(_NetworkXBuiltin):
     """
     <url>
-    :WMA:https://reference.wolfram.com/language/ref/WeaklyConnectedComponents.html
-    </url>
+    :Weak components:
+    https://en.wikipedia.org/wiki/Weak_component</url> (<url>
+    :NetworkX:
+    https://networkx.org/documentation/networkx-2.8.8/reference/algorithms/\
+generated/networkx.algorithms.components.weakly_connected_components.html</url>, <url>
+    :WMA:
+    https://reference.wolfram.com/language/ref/WeaklyConnectedComponents.html</url>)
 
     <dl>
       <dt>'WeaklyConnectedComponents'[$g$]

pymathics/graph/curated.py

@@ -3,6 +3,7 @@
 """
 
 import networkx as nx
+from typing import Callable, Dict, Optional, Tuple
 from mathics.core.evaluation import Evaluation
 
 from pymathics.graph.base import Graph, _NetworkXBuiltin, graph_helper
@@ -11,8 +12,7 @@
 class GraphData(_NetworkXBuiltin):
     """
     <url>
-    :WMA:https://reference.wolfram.com/language/ref/GraphData.html
-    </url>
+    :WMA link:https://reference.wolfram.com/language/ref/GraphData.html</url>
 
     <dl>
       <dt>'GraphData[$name$]'
@@ -25,7 +25,9 @@ class GraphData(_NetworkXBuiltin):
 
     summary_text = "create a graph by name"
 
-    def eval(self, name, expression, evaluation: Evaluation, options: dict) -> Graph:
+    def eval(
+        self, name, expression, evaluation: Evaluation, options: dict
+    ) -> Optional[Graph]:
         "GraphData[name_String, OptionsPattern[GraphData]]"
         py_name = name.get_string_value()
         fn, layout = WL_TO_NETWORKX_FN.get(py_name, (None, None))
@@ -42,12 +44,13 @@ def eval(self, name, expression, evaluation: Evaluation, options: dict) -> Graph
             # if len([p for p in list(parameters) if p.kind in [inspect.Parameter.POSITIONAL_ONLY, inspect.Parameter.POSITIONAL_OR_KEYWORD]]) != 0:
             #     return
         if fn:
-            g = graph_helper(fn, options, False, evaluation, layout)
-            g.G.name = py_name
+            g = graph_helper(fn, options, False, layout, evaluation)
+            if g is not None:
+                g.G.name = py_name
             return g
 
 
-WL_TO_NETWORKX_FN = {
+WL_TO_NETWORKX_FN: Dict[str, Tuple[Callable, Optional[str]]] = {
     "DodecahedralGraph": (nx.dodecahedral_graph, None),
     "DiamondGraph": (nx.diamond_graph, "spring"),
     "PappusGraph": (nx.pappus_graph, "circular"),

pymathics/graph/parametric.py

@@ -140,10 +140,12 @@ def eval(
 class BinomialTree(_NetworkXBuiltin):
     """
     <url>
+    :Binomial tree:
+    https://en.wikipedia.org/wiki/Binomial_heap</url> (<url>
     :NetworkX:
     https://networkx.org/documentation/networkx-2.8.8/reference/\
 generated/networkx.generators.classic.binomial_tree.html</url>, <url>
-    :WMA:https://reference.wolfram.com/language/ref/BinomialTree.html</url>
+    :WMA:https://reference.wolfram.com/language/ref/BinomialTree.html</url>)
 
     <dl>
       <dt>'BinomialTree[$n$]'