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Merge pull request #15 from Mathics3/tweak-docs-for-measures-and-metrics
Go over docs for graph measures and metrics...
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‎pymathics/graph/__init__.py‎

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@@ -1,16 +1,40 @@
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"""
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Graphs - Vertices and Edges
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A Graph is a tuple of a set of Nodes and Edges.
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Mathics3 Module that provides functions and variables for working with graphs.
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Example:
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In[1]:= LoadModule["pymathics.graph"]
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Out[1]= pymathics.graph
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In[2]:= BinomialTree[3]
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In[3]:= BinomialTree[6]
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In[4]:= CompleteKaryTree[3, VertexLabels->True]
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Examples:
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>> LoadModule["pymathics.graph"]
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= pymathics.graph
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>> BinomialTree[3, DirectedEdges->True]
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= -Graph-
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>> BalancedTree[3, 3]
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= -Graph-
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>> g = Graph[{1 -> 2, 2 -> 3, 3 <-> 4}, VertexLabels->True]
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= -Graph-
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>> ConnectedComponents[g]
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= {{3, 4}, {2}, {1}}
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>> WeaklyConnectedComponents[g]
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= {{1, 2, 3, 4}}
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>> GraphDistance[g, 1, 4]
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= 3
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>> GraphDistance[g, 3, 2]
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= Infinity
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Networkx does the heavy lifting here.
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<url>
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:NetworkX:
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https://networkx.org</url> does the heavy lifting here.
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"""
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from pymathics.graph.base import (

‎pymathics/graph/base.py‎

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@@ -2,9 +2,6 @@
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"""
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Core routines for working with Graphs.
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A Graph is a tuple of a set of Nodes and Edges.
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networkx does all the heavy lifting.
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"""
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# uses networkx
@@ -1028,9 +1025,9 @@ def eval_patt(self, graph, patt, expression, evaluation, options):
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class AdjacencyList(_NetworkXBuiltin):
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"""
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<url>
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:Adjacenty list:
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:Adjacency list:
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https://en.wikipedia.org/wiki/Adjacency_list</url> (<url>
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:Networkx:
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:NetworkX:
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https://networkx.org/documentation/networkx-2.8.8/reference/readwrite/adjlist.html</url>,
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<url>
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:WMA:
@@ -1039,9 +1036,10 @@ class AdjacencyList(_NetworkXBuiltin):
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<dl>
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<dt>'AdjacencyList'[$graph$, $v$]
10411038
<dd>gives a list of vertices adjacent to $v$ in a 'Graph' \
1042-
or a list of edges $g$..
1039+
or a list of edges $g$.
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<dt>'AdjacencyList'[$graph$, $pattern$]
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<dd>gives a list of vertices adjacent to vertices \.
1042+
<dd>gives a list of vertices adjacent to vertices \
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matching $pattern$.
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</dl>
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@@ -1102,7 +1100,7 @@ class BetweennessCentrality(_Centrality):
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<url>
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:Betweenness centrality:
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https://en.wikipedia.org/wiki/Betweenness_centrality</url> (<url>
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:Networkx:
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:NetworkX:
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https://networkx.org/documentation/networkx-2.8.8/reference/algorithms/generated/\
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networkx.algorithms.centrality.betweenness_centrality.html</url>,
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<url>
@@ -1146,7 +1144,7 @@ class ClosenessCentrality(_Centrality):
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<url>
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:Betweenness centrality:
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https://en.wikipedia.org/wiki/Closeness_centrality</url> (<url>
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:Networkx:
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:NetworkX:
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https://networkx.org/documentation/networkx-2.8.8/reference/algorithms/generated/\
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networkx.algorithms.centrality.closeness_centrality.html</url>,
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<url>
@@ -1194,7 +1192,7 @@ class DegreeCentrality(_Centrality):
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<url>
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:Degree centrality:
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https://en.wikipedia.org/wiki/Degree_centrality</url> (<url>
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:Networkx:
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:NetworkX:
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https://networkx.org/documentation/networkx-2.8.8/reference/algorithms/generated/\
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networkx.algorithms.centrality.degree_centrality.html</url>,
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<url>
@@ -1252,7 +1250,7 @@ class DirectedEdge(Builtin):
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<url>
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:Directed edge:
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https://en.wikipedia.org/wiki/Directed_graph</url> (<url>
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:Networkx:
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:NetworkX:
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https://networkx.org/documentation/stable/reference/classes/digraph.html</url>,
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<url>
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:WMA:
@@ -1273,7 +1271,7 @@ class EdgeConnectivity(_NetworkXBuiltin):
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<url>
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:Edge connectivity:
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https://en.wikipedia.org/wiki/Directed_graph</url> (<url>
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:Networkx:
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:NetworkX:
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https://networkx.org/documentation/stable/reference/algorithms/\
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generated/networkx.algorithms.connectivity.connectivity.edge_connectivity.html</url>,
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<url>
@@ -1397,7 +1395,7 @@ class EigenvectorCentrality(_ComponentwiseCentrality):
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<url>
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:Eigenvector Centrality:
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https://en.wikipedia.org/wiki/Eigenvector_centrality</url> (<url>
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:Networkx:
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:NetworkX:
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https://networkx.org/documentation/networkx-2.8.8/reference/algorithms\
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/generated/networkx.algorithms.centrality.eigenvector_centrality.html</url>,
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<url>
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<url>
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:Shortest path problem:
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https://en.wikipedia.org/wiki/Shortest_path_problem</url> (<url>
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:Networkx:
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:NetworkX:
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https://networkx.org/documentation/networkx-2.8.8/reference/algorithms\
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/generated/networkx.algorithms.shortest_paths.generic.shortest_path.html</url>,
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<url>
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class HITSCentrality(_Centrality):
16481646
"""
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<url>
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:https://en.wikipedia.org/wiki/HITS_algorithm:
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https://en.wikipedia.org/wiki/HITS_centrality</url> (<url>
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:Networkx:
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:NetworkX:
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https://networkx.org/documentation/networkx-2.8.8/reference/algorithms/\
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generated/networkx.algorithms.link_analysis.hits_alg.hits.html</url>,
1655-
<url>
1650+
generated/networkx.algorithms.link_analysis.hits_alg.hits.html</url>, <url>
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:WMA:
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https://reference.wolfram.com/language/ref/HITSCentrality.html</url>)
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https://reference.wolfram.com/language/ref/HITSCentrality.html</url>
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<dl>
16601655
<dt>'HITSCentrality'[$g$]
@@ -1731,7 +1726,7 @@ class KatzCentrality(_ComponentwiseCentrality):
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<url>
17321727
:Katz Centrality:
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https://en.wikipedia.org/wiki/Katz_centrality</url> (<url>
1734-
:Networkx:
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:NetworkX:
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https://networkx.org/documentation/networkx-2.8.8/reference/algorithms\
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/generated/networkx.algorithms.centrality.katz_centrality.html\
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#networkx.algorithms.centrality.katz_centrality</url>, <url>
@@ -1793,7 +1788,7 @@ class PageRankCentrality(_Centrality):
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<url>
17941789
:Pagerank Centrality:
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https://en.wikipedia.org/wiki/Pagerank</url> (<url>
1796-
:Networkx:
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:NetworkX:
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https://networkx.org/documentation/networkx-2.8.8/reference/algorithms\
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/generated/networkx.algorithms.link_analysis.pagerank_alg.pagerank.html</url>,
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<url>
@@ -1814,6 +1809,7 @@ class PageRankCentrality(_Centrality):
18141809
# >> g = Graph[{a -> d, b -> c, d -> c, d -> a, e -> c, d -> c}]; PageRankCentrality[g, 0.2]
18151810
= {0.184502, 0.207565, 0.170664, 0.266605, 0.170664}
18161811
"""
1812+
18171813
summary_text = "get the page rank centralities"
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18191815
def eval_alpha_beta(self, graph, alpha, expression, evaluation, options):

‎pymathics/graph/measures_and_metrics.py‎

Lines changed: 16 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -55,7 +55,9 @@ def eval_patt(
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class EdgeCount(_PatternCount):
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"""
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<url>
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:WMA link:
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:NetworkX:
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https://networkx.org/documentation/latest/reference/generated/networkx.classes.function.edges.html#edges</url>, <url>
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:WMA:
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https://reference.wolfram.com/language/ref/EdgeCount.html</url>
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<dl>
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8385
class GraphDistance(_NetworkXBuiltin):
8486
"""
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<url>
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:NetworkX:
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https://networkx.org/documentation/latest/reference/algorithms/generated/networkx.algorithms.shortest_paths.generic.shortest_path_length.html</url>, <url>
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:WMA:
91+
https://reference.wolfram.com/language/ref/GraphDistance.html</url>
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8593
<dl>
8694
<dt>'GraphDistance'[$g$, $s$, $t$]
8795
<dd>returns the distance from source vertex $s$ to target vertex $t$ in the graph $g$.
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155163
class VertexCount(_PatternCount):
156164
"""
157165
<url>
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:WMA link:
166+
:NetworkX:
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https://networkx.org/documentation/latest/reference/generated/networkx.classes.function.nodes.html</url>, <url>
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:WMA:
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https://reference.wolfram.com/language/ref/VertexCount.html</url>
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<dl>
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193203
class VertexDegree(_NetworkXBuiltin):
194204
"""
195205
<url>
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:WMA link:
197-
https://reference.wolfram.com/language/ref/EdgeCount.html</url>
206+
:NetworkX:
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https://networkx.org/documentation/latest/reference/classes/generated/networkx.Graph.degree.html</url>, <url>
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:WMA:
209+
https://reference.wolfram.com/language/ref/VertexDegree.html</url>
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<dl>
200212
<dt>'VertexDegree[$g$]'

‎pymathics/graph/parametric.py‎

Lines changed: 4 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -320,9 +320,10 @@ def eval(self, r, n, expression, evaluation: Evaluation, options: dict):
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321321

322322
class GraphAtlas(_NetworkXBuiltin):
323-
"""<dl>
323+
"""
324+
<dl>
324325
<dt>'GraphAtlas[$n$]'
325-
<dd>Returns graph number $i$ from the Networkx's Graph \
326+
<dd>Returns graph number $i$ from the NetworkX's Graph \
326327
Atlas. There are about 1200 of them and get large as $i$ \
327328
increases.
328329
</dl>
@@ -334,7 +335,7 @@ class GraphAtlas(_NetworkXBuiltin):
334335
messages = {
335336
"ilsmp": "Expected a positive integer at position 1 in ``.",
336337
}
337-
summary_text = "build the i-esim graph from the Networkx atlas"
338+
summary_text = "build the i-esim graph from the NetworkX atlas"
338339

339340
def eval(self, n, expression, evaluation: Evaluation, options: dict):
340341
"%(name)s[n_Integer, OptionsPattern[%(name)s]]"

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