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track module change in mathics-core...
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Also, use annotations more often. Remove links to older NetworkX 2.8 docs
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@rocky
rocky committed Nov 27, 2024
1 parent 57522db commit 588e037
Showing 1 changed file with 149 additions and 136 deletions.
285 changes: 149 additions & 136 deletions pymathics/graph/base.py
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Original file line number Diff line number Diff line change
Expand Up @@ -4,13 +4,13 @@
Core routines for working with Graphs.
"""

# uses networkx
# uses NetworkX

from collections import defaultdict
from inspect import isgenerator
from typing import Callable, Optional, Union

from mathics.builtin.no_meaning import (
from mathics.builtin.no_meaning.infix_extra import (
DirectedEdge as GenericDirectedEdge,
UndirectedEdge as GenericUndirectedEdge,
)
Expand All @@ -19,6 +19,7 @@
from mathics.core.atoms import Atom, Integer, Integer0, Integer1, Integer2, String
from mathics.core.convert.expression import ListExpression, from_python, to_mathics_list
from mathics.core.element import BaseElement
from mathics.core.evaluation import Evaluation
from mathics.core.expression import Expression
from mathics.core.pattern import pattern_objects
from mathics.core.symbols import Symbol, SymbolList, SymbolTrue
Expand Down Expand Up @@ -133,133 +134,6 @@ def has_directed_option(options: dict) -> bool:
return options.get("System`DirectedEdges", False)


def _process_graph_options(g, options: dict) -> None:
"""
Handle common graph-related options like VertexLabels, PlotLabel, VertexShape, etc.
"""
# FIXME: for now we are adding both to both g and g.G.
# g is where it is used in format. However we should wrap this as our object.
# Access in G which might be better, currently isn't used.
g.G.vertex_labels = g.vertex_labels = (
options["System`VertexLabels"].to_python()
if "System`VertexLabels" in options
else False
)
shape = (
options["System`VertexShape"].get_string_value()
if "System`VertexShape" in options
else "Circle"
)

g.G.node_shape = g.node_shape = WL_MARKER_TO_NETWORKX.get(shape, shape)

color = (
options["System`VertexStyle"].get_string_value()
if "System`VertexStyle" in options
else "Blue"
)

g.graph_layout = (
options["System`GraphLayout"].get_string_value()
if "System`GraphLayout" in options
else ""
)

g.G.graph_layout = g.graph_layout = WL_LAYOUT_TO_NETWORKX.get(
g.graph_layout, g.graph_layout
)

g.G.node_color = g.node_color = WL_COLOR_TO_NETWORKX.get(color, color)

g.G.title = g.title = (
options["System`PlotLabel"].get_string_value()
if "System`PlotLabel" in options
else None
)


def _circular_layout(G):
return nx.drawing.circular_layout(G, scale=1)


def _spectral_layout(G):
return nx.drawing.spectral_layout(G, scale=2)


def _shell_layout(G):
return nx.drawing.shell_layout(G, scale=2)


def _generic_layout(G, warn):
return nx.nx_pydot.graphviz_layout(G, prog="dot")


def _path_layout(G, root):
v = root
x = 0
y = 0

k = 0
d = 0

pos = {}
neighbors = G.neighbors(v)

for _ in range(len(G)):
pos[v] = (x, y)

if not neighbors:
break
try:
v = next(neighbors) if isgenerator(neighbors) else neighbors[0]
except StopIteration:
break
neighbors = G.neighbors(v)

if k == 0:
if d < 1 or neighbors:
d += 1
x += d
elif k == 1:
y += d
elif k == 2:
if neighbors:
d += 1
x -= d
elif k == 3:
y -= d

k = (k + 1) % 4

return pos


def _auto_layout(G, warn):
path_root = None

for v, d in G.degree(G.nodes):
if d == 1 and G.neighbors(v):
path_root = v
elif d > 2:
path_root = None
break

if path_root is not None:
return _path_layout(G, path_root)
else:
return _generic_layout(G, warn)


def _convert_networkx_graph(G, options):
mapping = dict((v, Integer(i)) for i, v in enumerate(G.nodes))
G = nx.relabel_nodes(G, mapping)
[Expression(SymbolUndirectedEdge, u, v) for u, v in G.edges]
return Graph(
G,
**options,
)


_default_minimum_distance = 0.3


Expand Down Expand Up @@ -424,7 +298,7 @@ def __hash__(self):
def __str__(self):
return "-Graph-"

def atom_to_boxes(self, f, evaluation) -> "GraphBox":
def atom_to_boxes(self, f, evaluation: Evaluation) -> "GraphBox":
return GraphBox(self.G)

def add_edges(self, new_edges, new_edge_properties):
Expand All @@ -439,7 +313,7 @@ def add_vertices(self, *vertices_to_add):
G.add_nodes_from(vertices_to_add)
return Graph(G)

def coalesced_graph(self, evaluation):
def coalesced_graph(self, evaluation: Evaluation):
if not isinstance(self.G, (nx.MultiDiGraph, nx.MultiGraph)):
return self.G, "WEIGHT"

Expand Down Expand Up @@ -603,6 +477,133 @@ def _graph_from_list(rules, options, new_vertices=None):
)


def _process_graph_options(g: Graph, options: dict) -> None:
"""
Handle common graph-related options like VertexLabels, PlotLabel, VertexShape, etc.
"""
# FIXME: for now we are adding both to both g and g.G.
# g is where it is used in format. However we should wrap this as our object.
# Access in G which might be better, currently isn't used.
g.G.vertex_labels = g.vertex_labels = (
options["System`VertexLabels"].to_python()
if "System`VertexLabels" in options
else False
)
shape = (
options["System`VertexShape"].get_string_value()
if "System`VertexShape" in options
else "Circle"
)

g.G.node_shape = g.node_shape = WL_MARKER_TO_NETWORKX.get(shape, shape)

color = (
options["System`VertexStyle"].get_string_value()
if "System`VertexStyle" in options
else "Blue"
)

g.graph_layout = (
options["System`GraphLayout"].get_string_value()
if "System`GraphLayout" in options
else ""
)

g.G.graph_layout = g.graph_layout = WL_LAYOUT_TO_NETWORKX.get(
g.graph_layout, g.graph_layout
)

g.G.node_color = g.node_color = WL_COLOR_TO_NETWORKX.get(color, color)

g.G.title = g.title = (
options["System`PlotLabel"].get_string_value()
if "System`PlotLabel" in options
else None
)


def _circular_layout(G: Graph):
return nx.drawing.circular_layout(G, scale=1)


def _spectral_layout(G: Graph):
return nx.drawing.spectral_layout(G, scale=2)


def _shell_layout(G: Graph):
return nx.drawing.shell_layout(G, scale=2)


def _generic_layout(G, warn):
return nx.nx_pydot.graphviz_layout(G, prog="dot")


def _path_layout(G, root):
v = root
x = 0
y = 0

k = 0
d = 0

pos = {}
neighbors = G.neighbors(v)

for _ in range(len(G)):
pos[v] = (x, y)

if not neighbors:
break
try:
v = next(neighbors) if isgenerator(neighbors) else neighbors[0]
except StopIteration:
break
neighbors = G.neighbors(v)

if k == 0:
if d < 1 or neighbors:
d += 1
x += d
elif k == 1:
y += d
elif k == 2:
if neighbors:
d += 1
x -= d
elif k == 3:
y -= d

k = (k + 1) % 4

return pos


def _auto_layout(G: Graph, warn):
path_root = None

for v, d in G.degree(G.nodes):
if d == 1 and G.neighbors(v):
path_root = v
elif d > 2:
path_root = None
break

if path_root is not None:
return _path_layout(G, path_root)
else:
return _generic_layout(G, warn)


def _convert_networkx_graph(G: Graph, options: dict):
mapping = dict((v, Integer(i)) for i, v in enumerate(G.nodes))
G = nx.relabel_nodes(G, mapping)
[Expression(SymbolUndirectedEdge, u, v) for u, v in G.edges]
return Graph(
G,
**options,
)


def _create_graph(
new_edges, new_edge_properties, options, from_graph=None, new_vertices=None
):
Expand Down Expand Up @@ -813,7 +814,9 @@ def full_new_edge_properties(new_edge_style):


class _PatternList(_NetworkXBuiltin):
def eval(self, graph, expression, evaluation, options):
def eval(
self, graph, expression: Expression, evaluation: Evaluation, options: dict
):
"%(name)s[graph_, OptionsPattern[%(name)s]]"
graph = self._build_graph(graph, evaluation, options, expression)
if graph:
Expand Down Expand Up @@ -903,8 +906,6 @@ class DirectedEdge(GenericDirectedEdge):
Edge of a <url>
:Directed graph:
https://en.wikipedia.org/wiki/Directed_graph</url> (<url>
:NetworkX:
https://networkx.org/documentation/networkx-2.8.8/reference/classes/digraph.html</url>, <url>
:WMA:
https://reference.wolfram.com/language/ref/DirectedEdge.html</url>)
Expand All @@ -921,6 +922,10 @@ class DirectedEdge(GenericDirectedEdge):
= a → b
"""

# attributes change from the default, so we need to
# specify this below. Other things like "formats",
# "operator" and "summary" do not change from the default.

attributes = A_PROTECTED | A_READ_PROTECTED


Expand Down Expand Up @@ -1088,7 +1093,9 @@ class FindShortestPath(_NetworkXBuiltin):

summary_text = "find the shortest path between two vertices"

def eval_s_t(self, graph, s, t, expression, evaluation, options):
def eval_s_t(
self, graph, s, t, expression: Expression, evaluation: Evaluation, options: dict
):
"FindShortestPath[graph_, s_, t_, OptionsPattern[FindShortestPath]]"
graph = self._build_graph(graph, evaluation, options, expression)
if not graph:
Expand Down Expand Up @@ -1507,7 +1514,9 @@ def _items(self, graph):

class UndirectedEdge(GenericUndirectedEdge):
"""
<url>
Edge of a <url>
:Undirected graph:
https://en.wikipedia.org/wiki/Graph_(discrete_mathematics)#Undirected_graph</url> <url>
:WMA link:
https://reference.wolfram.com/language/ref/UndirectedEdge.html</url>
Expand All @@ -1520,6 +1529,10 @@ class UndirectedEdge(GenericUndirectedEdge):
= ...
"""

# attributes change from the default, so we need to
# specify this below. Other things like "formats",
# "operator" and "summary" do not change from the default.

attributes = A_PROTECTED | A_READ_PROTECTED


Expand Down

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