Merge pull request #8 from Mathics3/mathics-6.0.0

Mathics 6.0.0

Author: rocky

.pre-commit-config.yaml

@@ -9,15 +9,20 @@ repos:
       stages: [commit]
     - id: end-of-file-fixer
       stages: [commit]
-    - id: trailing-whitespace
+# -   repo: https://github.com/pycqa/isort
+#     rev: 5.10.1
+#     hooks:
+#       - id: isort
+#         stages: [commit]
 -   repo: https://github.com/psf/black
     rev: 22.3.0
     hooks:
     - id: black
       language_version: python3
       exclude: 'pymathics/graph/version.py'
--   repo: https://github.com/pycqa/flake8
-    rev: 3.9.2
-    hooks:
-      - id: flake8
-        stages: [commit]
+      stages: [commit]
+# -   repo: https://github.com/pycqa/flake8
+#     rev: 3.9.2
+#     hooks:
+#       - id: flake8
+#         stages: [commit]

Makefile

@@ -5,8 +5,8 @@
 # remake --tasks to shows the targets and the comments
 
 GIT2CL ?= admin-tools/git2cl
-PYTHON ?= python3
-PIP ?= pip3
+PYTHON ?= python
+PIP ?= $(PYTHON) -m pip
 RM  ?= rm
 
 .PHONY: all build \
@@ -40,7 +40,7 @@ install: pypi-setup
 	$(PYTHON) setup.py install
 
 # Run tests
-check: pytest doctest
+test check: pytest
 
 #: Remove derived files
 clean: clean-pyc
@@ -51,7 +51,7 @@ clean-pyc:
 
 #: Run py.test tests. Use environment variable "o" for pytest options
 pytest:
-	py.test test $o
+	$(PYTHON) -m pytest test $o
 
 
 # #: Create data that is used to in Django docs and to build TeX PDF

README.rst

@@ -8,13 +8,13 @@ Example Session
 ::
 
    $ mathicsscript
-   Mathicscript: 5.0.0, Mathics 5.0.0
+   Mathicscript: 5.0.0, Mathics 6.0.0
    on CPython 3.10.4 (main, Jun 29 2022, 12:14:53) [GCC 11.2.0]
    using SymPy 1.9, mpmath 1.2.1, numpy 1.21.5
    matplotlib 3.5.2,
    Asymptote version 2.81
 
-   Copyright (C) 2011-2022 The Mathics Team.
+   Copyright (C) 2011-2023 The Mathics3 Team.
    This program comes with ABSOLUTELY NO WARRANTY.
    This is free software, and you are welcome to redistribute it
    under certain conditions.
@@ -23,7 +23,6 @@ Example Session
    Quit by pressing CONTROL-D
 
    In[1]:= LoadModule["pymathics.graph"]
-
    Out[1]= pymathics.graph
    In[2]:= BinomialTree[3]
    In[3]:= BinomialTree[6]

pymathics/graph/__init__.py

@@ -1,24 +1,64 @@
-"""Pymathics Graph - Working with Graphs (Vertices and Edges)
+"""
+Graphs - Vertices and Edges
 
-This module provides functions and variables for workting with
-graphs.
+A Pymathics module that provides functions and variables for working 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]
+
+Networkx does the heavy lifting here.
 """
 
-from pymathics.graph.__main__ import *  # noqa
+from pymathics.graph.base import (
+    AcyclicGraphQ,
+    BetweennessCentrality,
+    ClosenessCentrality,
+    ConnectedGraphQ,
+    DegreeCentrality,
+    DirectedEdge,
+    DirectedGraphQ,
+    EdgeConnectivity,
+    EdgeIndex,
+    EdgeList,
+    EdgeRules,
+    EigenvectorCentrality,
+    FindShortestPath,
+    FindVertexCut,
+    Graph,
+    GraphBox,
+    HITSCentrality,
+    HighlightGraph,
+    KatzCentrality,
+    LoopFreeGraphQ,
+    MixedGraphQ,
+    MultigraphQ,
+    PageRankCentrality,
+    PlanarGraphQ,
+    PathGraphQ,
+    Property,
+    PropertyValue,
+    SimpleGraphQ,
+    UndirectedEdge,
+    VertexAdd,
+    VertexConnectivity,
+    VertexDelete,
+    VertexIndex,
+    VertexList,
+)
+
+from pymathics.graph.measures_and_metrics import EdgeCount, VertexCount, VertexDegree
+
 from pymathics.graph.algorithms import *  # noqa
 from pymathics.graph.generators import *  # noqa
 from pymathics.graph.tree import *  # noqa
 from pymathics.graph.version import __version__  # noqa
 
 pymathics_version_data = {
-    "author": "The Mathics Team",
+    "author": "The Mathics3 Team",
     "version": __version__,
     "name": "Graph",
     "requires": ["networkx"],

pymathics/graph/algorithms.py

@@ -1,18 +1,19 @@
 # -*- coding: utf-8 -*-
 """
-Algorithms on Graphs.
-
-networkx does all the heavy lifting.
+Algorithms on Graphs
 """
 
+from typing import Optional
+
 from mathics.core.convert.expression import to_mathics_list
 from mathics.core.convert.python import from_python
+from mathics.core.evaluation import Evaluation
 from mathics.core.expression import Expression
 from mathics.core.list import ListExpression
 from mathics.core.symbols import SymbolFalse
 from mathics.core.systemsymbols import SymbolDirectedInfinity
 
-from pymathics.graph.__main__ import (
+from pymathics.graph.base import (
     DEFAULT_GRAPH_OPTIONS,
     SymbolDirectedEdge,
     SymbolUndirectedEdge,
@@ -25,7 +26,7 @@
 class ConnectedComponents(_NetworkXBuiltin):
     """
     ## >> g = Graph[{1 -> 2, 2 -> 3, 3 <-> 4}]; ConnectedComponents[g]
-    ##  = {{4, 3}, {2}, {1}}
+    ##  = {{3, 4}, {2}, {1}}
 
     ## >> g = Graph[{1 -> 2, 2 -> 3, 3 -> 1}]; ConnectedComponents[g]
     ## = {{1, 2, 3}}
@@ -34,7 +35,9 @@ class ConnectedComponents(_NetworkXBuiltin):
     ##  = {{4, 5}, {1, 2, 3}}
     """
 
-    def apply(self, graph, expression, evaluation, options):
+    def eval(
+        self, graph, expression, evaluation: Evaluation, options: dict
+    ) -> Optional[ListExpression]:
         "ConnectedComponents[graph_, OptionsPattern[%(name)s]]"
         graph = self._build_graph(graph, evaluation, options, expression)
         if graph:
@@ -54,10 +57,10 @@ def apply(self, graph, expression, evaluation, options):
 #       <dd>returns a Hamiltonian path in the given tournament graph.
 #       </dl>
 #     """
-#     def apply_(self, graph, expression, evaluation, options):
-#         "%(name)s[graph_, OptionsPattern[%(name)s]]"
+#     def eval_(self, graph, expression, evaluation: Evaluation, options):
+#         "FindHamiltonianPath[graph_, OptionsPattern[FindHamiltonPath]]"
 
-#         graph = self._build_graph(graph, evaluation, options, expression)
+#         graph = self._build_graph(graph, evaluation: Evaluation, options, expression)
 #         if graph:
 #             # FIXME: for this to work we need to fill in all O(n^2) edges as an adjacency matrix?
 #             path = nx.algorithms.tournament.hamiltonian_path(graph.G)
@@ -106,17 +109,19 @@ class GraphDistance(_NetworkXBuiltin):
      = GraphDistance[{1 -> 2}, 3, 4]
     """
 
-    def apply_s(self, graph, s, expression, evaluation, options):
-        "%(name)s[graph_, s_, OptionsPattern[%(name)s]]"
+    def eval_s(
+        self, graph, s, expression, evaluation: Evaluation, options: dict
+    ) -> Optional[ListExpression]:
+        "GraphDistance[graph_, s_, OptionsPattern[GraphDistance]]"
         graph = self._build_graph(graph, evaluation, options, expression)
         if graph:
             weight = graph.update_weights(evaluation)
             d = nx.shortest_path_length(graph.G, source=s, weight=weight)
             inf = Expression(SymbolDirectedInfinity, 1)
             return to_mathics_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]]"
+    def eval_s_t(self, graph, s, t, expression, evaluation: Evaluation, options: dict):
+        "GraphDistance[graph_, s_, t_, OptionsPattern[GraphDistance]]"
         graph = self._build_graph(graph, evaluation, options, expression)
         if not graph:
             return
@@ -147,7 +152,7 @@ class FindSpanningTree(_NetworkXBuiltin):
 
     options = DEFAULT_GRAPH_OPTIONS
 
-    def apply(self, graph, expression, evaluation, options):
+    def eval(self, graph, expression, evaluation: Evaluation, options: dict):
         "%(name)s[graph_, OptionsPattern[%(name)s]]"
         graph = self._build_graph(graph, evaluation, options, expression)
         if graph:
@@ -182,8 +187,8 @@ class PlanarGraphQ(_NetworkXBuiltin):
 
     options = DEFAULT_GRAPH_OPTIONS
 
-    def apply(self, graph, expression, evaluation, options):
-        "%(name)s[graph_, OptionsPattern[%(name)s]]"
+    def eval(self, graph, expression, evaluation: Evaluation, options: dict):
+        "PlanarGraphQ[graph_, OptionsPattern[PlanarGraphQ]]"
         graph = self._build_graph(graph, evaluation, options, expression)
         if not graph:
             return SymbolFalse
@@ -203,8 +208,8 @@ class WeaklyConnectedComponents(_NetworkXBuiltin):
      = {{1, 2, 3, 4, 5}, {6, 7, 8}}
     """
 
-    def apply(self, graph, expression, evaluation, options):
-        "WeaklyConnectedComponents[graph_, OptionsPattern[%(name)s]]"
+    def eval(self, graph, expression, evaluation: Evaluation, options):
+        "WeaklyConnectedComponents[graph_, OptionsPattern[WeaklyConnectedComponents]]"
         graph = self._build_graph(graph, evaluation, options, expression)
         if graph:
             components = nx.connected_components(graph.G.to_undirected())