Get ready for release 2.3.0

Fix lint errors

.editorconfig

@@ -0,0 +1,28 @@
+# THis is an EditorConfig file
+# https://EditorConfig.org
+
+root = true
+
+[*]
+end_of_line = lf
+insert_final_newline = true
+charset = utf-8
+indent_style = tab
+indent_size = 4
+insert_final_newline = true
+
+[*.yml]
+indent_style = space
+indent_size = 2
+end_of_line = lf
+insert_final_newline = true
+
+[*.py]
+indent_style = space
+indent_size = 4
+end_of_line = lf
+insert_final_newline = true
+
+# Tab indentation (no size specified)
+[Makefile]
+indent_style = tab

.pre-commit-config.yaml

@@ -0,0 +1,12 @@
+repos:
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v2.0.0
+    hooks:
+    - id: debug-statements
+    - id: end-of-file-fixer
+-   repo: https://github.com/psf/black
+    rev: 20.8b1
+    hooks:
+    - id: black
+      language_version: python3
+      exclude: 'mathicsscript/version.py'

NEWS.md

@@ -1,3 +1,12 @@
+2.3.0
+-----
+
+Small API changes to track Mathics 3.0.0.
+
+Blacken everything
+
+
+
 2.2.0
 -----
 

README.rst

@@ -8,11 +8,11 @@ Example Session
 ::
 
    $ mathicsscript
-   Mathics 1.1.1
+   Mathics 3.0.1
    on CPython 3.6.12 (default, Oct 24 2020, 10:34:18)
-   using SymPy 1.8.dev, mpmath 1.1.0, cython 0.29.21
+   using SymPy 1.8, mpmath 1.2.1, cython 0.29.22
 
-   Copyright (C) 2011-2020 The Mathics Team.
+   Copyright (C) 2011-2021 The Mathics Team.
    This program comes with ABSOLUTELY NO WARRANTY.
    This is free software, and you are welcome to redistribute it
    under certain conditions.

pymathics/graph/__init__.py

@@ -1,15 +1,21 @@
-"""Pymathics Graph - Working with Graphs (Vertices and Edgies)
+"""Pymathics Graph - Working with Graphs (Vertices and Edges)
 
 This module provides functions and variables for workting with
 graphs.
-"""
 
+Example:
+   In[1]:= LoadModule["pymathics.graph"]
+   Out[1]= pymathics.graph
+   In[2]:= BinomialTree[3]
+   In[3]:= BinomialTree[6]
+   In[4]:= CompleteKaryTree[3, VertexLabels->True]
+"""
 
 from pymathics.graph.version import __version__
-from pymathics.graph.__main__ import *
-from pymathics.graph.tree import *
-from pymathics.graph.generators import *
-from pymathics.graph.algorithms import *
+from pymathics.graph.__main__ import *  # noqa
+from pymathics.graph.tree import *  # qoqa
+from pymathics.graph.generators import *  # noqa
+from pymathics.graph.algorithms import *  # noqa
 
 pymathics_version_data = {
     "author": "The Mathics Team",

pymathics/graph/__main__.py

@@ -10,13 +10,12 @@
 # uses networkx
 
 from mathics.builtin.base import Builtin, AtomBuiltin
-from mathics.builtin.graphics import GraphicsBox
+from mathics.builtin.box.graphics import GraphicsBox
 from mathics.core.expression import (
     Atom,
     Expression,
     Integer,
     Real,
-    String,
     Symbol,
 )
 from mathics.builtin.patterns import Matcher
@@ -730,7 +729,7 @@ def full_new_edge_properties(new_edge_style):
             attr_dict = attr_dict or empty_dict
             G.add_edge(u, v, **attr_dict)
 
-    edge_collection = _EdgeCollection(
+    _EdgeCollection(
         edges,
         edge_properties,
         n_directed=len(directed_edges),
@@ -1804,7 +1803,7 @@ def apply_s_t(self, graph, s, t, expression, evaluation, options):
 def _convert_networkx_graph(G, options):
     mapping = dict((v, Integer(i)) for i, v in enumerate(G.nodes))
     G = nx.relabel_nodes(G, mapping)
-    edges = [Expression("System`UndirectedEdge", u, v) for u, v in G.edges]
+    [Expression("System`UndirectedEdge", u, v) for u, v in G.edges]
     return Graph(
         G,
         **options,

pymathics/graph/algorithms.py

@@ -22,6 +22,7 @@
 # SymbolFalse = Symbol("System`False")
 # SymbolTrue = Symbol("System`True")
 
+
 class ConnectedComponents(_NetworkXBuiltin):
     """
     >> g = Graph[{1 -> 2, 2 -> 3, 3 <-> 4}]; ConnectedComponents[g]
@@ -38,10 +39,12 @@ def apply(self, graph, expression, evaluation, options):
         "ConnectedComponents[graph_, OptionsPattern[%(name)s]]"
         graph = self._build_graph(graph, evaluation, options, expression)
         if graph:
-            connect_fn = nx.strongly_connected_components if graph.G.is_directed() else nx.connected_components
-            components = [
-                Expression("List", *c) for c in connect_fn(graph.G)
-            ]
+            connect_fn = (
+                nx.strongly_connected_components
+                if graph.G.is_directed()
+                else nx.connected_components
+            )
+            components = [Expression("List", *c) for c in connect_fn(graph.G)]
             return Expression("List", *components)
 
 
@@ -63,6 +66,7 @@ def apply(self, graph, expression, evaluation, options):
 #                 # int_path = map(Integer, path)
 #                 return Expression("List", *path)
 
+
 class GraphDistance(_NetworkXBuiltin):
     """
     <dl>
@@ -110,9 +114,7 @@ def apply_s(self, graph, s, expression, evaluation, options):
             weight = graph.update_weights(evaluation)
             d = nx.shortest_path_length(graph.G, source=s, weight=weight)
             inf = Expression("DirectedInfinity", 1)
-            return Expression(
-                "List", *[d.get(v, inf) for v in graph.vertices]
-            )
+            return Expression("List", *[d.get(v, inf) for v in graph.vertices])
 
     def apply_s_t(self, graph, s, t, expression, evaluation, options):
         "%(name)s[graph_, s_, t_, OptionsPattern[%(name)s]]"
@@ -133,6 +135,7 @@ def apply_s_t(self, graph, s, t, expression, evaluation, options):
             except nx.exception.NetworkXNoPath:
                 return Expression("DirectedInfinity", 1)
 
+
 class FindSpanningTree(_NetworkXBuiltin):
     """
     <dl>
@@ -144,14 +147,18 @@ class FindSpanningTree(_NetworkXBuiltin):
     """
 
     options = DEFAULT_GRAPH_OPTIONS
+
     def apply(self, graph, expression, evaluation, options):
         "%(name)s[graph_, OptionsPattern[%(name)s]]"
         graph = self._build_graph(graph, evaluation, options, expression)
         if graph:
             weight = graph.update_weights(evaluation)
             edge_type = "DirectedEdge" if graph.G.is_directed() else "UndirectedEdge"
             # FIXME: put in edge to Graph conversion function?
-            edges = [Expression("UndirectedEdge", u, v) for u, v in nx.minimum_spanning_edges(graph.G, data=False)]
+            edges = [
+                Expression("UndirectedEdge", u, v)
+                for u, v in nx.minimum_spanning_edges(graph.G, data=False)
+            ]
             g = _create_graph(edges, [None] * len(edges), options)
             if not hasattr(g.G, "graph_layout"):
                 if hasattr(graph.G, "graph_layout"):
@@ -160,6 +167,7 @@ def apply(self, graph, expression, evaluation, options):
                     g.G.graph_layout = "tree"
             return g
 
+
 class PlanarGraphQ(_NetworkXBuiltin):
     """
     <dl>
@@ -174,6 +182,7 @@ class PlanarGraphQ(_NetworkXBuiltin):
     """
 
     options = DEFAULT_GRAPH_OPTIONS
+
     def apply(self, graph, expression, evaluation, options):
         "%(name)s[graph_, OptionsPattern[%(name)s]]"
         graph = self._build_graph(graph, evaluation, options, expression)
@@ -182,6 +191,7 @@ def apply(self, graph, expression, evaluation, options):
         is_planar, _ = nx.check_planarity(graph.G)
         return Symbol("System`True") if is_planar else Symbol("System`False")
 
+
 class WeaklyConnectedComponents(_NetworkXBuiltin):
     """
     >> g = Graph[{1 -> 2, 2 -> 3, 3 <-> 4}]; WeaklyConnectedComponents[g]

pymathics/graph/generators.py

@@ -6,11 +6,9 @@
 """
 
 from mathics.builtin.numbers.randomnumbers import RandomEnv
-from mathics.core.expression import String
 
 from pymathics.graph.__main__ import (
     Graph,
-    WL_MARKER_TO_NETWORKX,
     _NetworkXBuiltin,
     _convert_networkx_graph,
     _graph_from_list,
@@ -32,6 +30,7 @@ def graph_helper(
     options: dict,
     can_digraph: bool,
     graph_layout: str,
+    evaluation,
     root: Optional[int] = None,
     *args,
     **kwargs
@@ -94,7 +93,7 @@ def apply(self, r, h, expression, evaluation, options):
             return None
 
         args = (py_r, py_h)
-        g = graph_helper(nx.balanced_tree, options, True, "tree", 0, *args)
+        g = graph_helper(nx.balanced_tree, options, True, "tree", evaluation, 0, *args)
         if not g:
             return None
         g.G.r = r
@@ -133,7 +132,7 @@ def apply(self, m1, m2, expression, evaluation, options):
             return
 
         args = (py_m1, py_m2)
-        g = graph_helper(nx.barbell_graph, options, False, "spring", None, *args)
+        g = graph_helper(nx.barbell_graph, options, False, "spring", evaluation, None, *args)
         if not g:
             return None
 
@@ -205,7 +204,7 @@ def apply(self, n, expression, evaluation, options):
             return
 
         args = (py_n,)
-        g = graph_helper(binomial_tree, options, True, "tree", 0, *args)
+        g = graph_helper(binomial_tree, options, True, "tree", evaluation, 0, *args)
         if not g:
             return None
         g.G.n = n
@@ -220,7 +219,7 @@ def complete_graph_apply(self, n, expression, evaluation, options):
         return
 
     args = (py_n,)
-    g = graph_helper(nx.complete_graph, options, False, "circular", None, *args)
+    g = graph_helper(nx.complete_graph, options, False, "circular", evaluation, None, *args)
     if not g:
         return None
 
@@ -333,7 +332,7 @@ def f_r_t_apply(self, r, n, expression, evaluation, options):
         return
 
     args = (py_r, py_n)
-    g = graph_helper(nx.full_rary_tree, options, True, "tree", 0, *args)
+    g = graph_helper(nx.full_rary_tree, options, True, "tree", evaluation, 0, *args)
     if not g:
         return None
 
@@ -395,7 +394,7 @@ def apply(self, n, expression, evaluation, options):
             return
 
         args = (py_n,)
-        g = graph_helper(nx.graph_atlas, options, False, "spring", None, *args)
+        g = graph_helper(nx.graph_atlas, options, False, "spring", evaluation, None, *args)
         if not g:
             return None
         g.n = n
@@ -417,7 +416,7 @@ def hkn_harary_apply(self, k, n, expression, evaluation, options):
     from pymathics.graph.harary import hkn_harary_graph
 
     args = (py_k, py_n)
-    g = graph_helper(hkn_harary_graph, options, False, "circular", None, *args)
+    g = graph_helper(hkn_harary_graph, options, False, "circular", evaluation, None, *args)
     if not g:
         return None
     g.k = py_k
@@ -490,7 +489,7 @@ def apply(self, n, m, expression, evaluation, options):
         from pymathics.graph.harary import hnm_harary_graph
 
         args = (py_n, py_m)
-        g = graph_helper(hmn_harary_graph, options, False, "circular", None, *args)
+        g = graph_helper(hnm_harary_graph, options, False, "circular", evaluation, None, *args)
         if not g:
             return None
         g.n = py_n
@@ -557,12 +556,13 @@ def apply(self, n, expression, evaluation, options):
             return
 
         args = (py_n,)
-        g = graph_helper(nx.ladder_graph, options, False, "spring", 0, *args)
+        g = graph_helper(nx.ladder_graph, options, False, "spring", evaluation, 0, *args)
         if not g:
             return None
         g.G.n = n
         return g
 
+
 class PathGraph(_NetworkXBuiltin):
     """
     <dl>
@@ -582,7 +582,9 @@ def edges():
                 yield Expression("UndirectedEdge", u, v)
 
         g = _graph_from_list(edges(), options)
-        g.G.graph_layout = options["System`GraphLayout"].get_string_value() or "spiral_equidistant"
+        g.G.graph_layout = (
+            options["System`GraphLayout"].get_string_value() or "spiral_equidistant"
+        )
         return g
 
 
@@ -645,7 +647,7 @@ def apply(self, n, expression, evaluation, options):
             return
 
         args = (py_n,)
-        g = graph_helper(nx.random_tree, options, False, "tree", 0, *args)
+        g = graph_helper(nx.random_tree, options, False, "tree", evaluation, 0, *args)
         if not g:
             return None
         g.G.n = n
@@ -676,12 +678,13 @@ def apply(self, n, expression, evaluation, options):
             return
 
         args = (py_n,)
-        g = graph_helper(nx.star_graph, options, False, "spring", 0, *args)
+        g = graph_helper(nx.star_graph, options, False, "spring", evaluation, 0, *args)
         if not g:
             return None
         g.G.n = n
         return g
 
+
 WL_TO_NETWORKX_FN = {
     "DodecahedralGraph": (nx.dodecahedral_graph, None),
     "DiamondGraph": (nx.diamond_graph, "spring"),
@@ -690,6 +693,7 @@ def apply(self, n, expression, evaluation, options):
     "PetersenGraph": (nx.petersen_graph, None),
 }
 
+
 class GraphData(_NetworkXBuiltin):
     """
     <dl>
@@ -699,6 +703,7 @@ class GraphData(_NetworkXBuiltin):
 
     >> GraphData["PappusGraph"]
     """
+
     def apply(self, name, expression, evaluation, options):
         "%(name)s[name_String, OptionsPattern[%(name)s]]"
         py_name = name.get_string_value()
@@ -710,11 +715,12 @@ def apply(self, name, expression, evaluation, options):
                 # These graphs require parameters
                 return
             import inspect
+
             fn = dict(inspect.getmembers(nx, inspect.isfunction)).get(py_name, None)
             # parameters = inspect.signature(nx.diamond_graph).parameters.values()
             # 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, layout)
+            g = graph_helper(fn, options, False, evaluation, layout)
             g.G.name = py_name
             return g