fix merge

Author: mmatera

.github/workflows/consistency-checks.yml

@@ -15,14 +15,14 @@ jobs:
     steps:
     - uses: actions/checkout@v3
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
         python -m pip install pytest
-        python -m pip install -e git+https://github.com/Mathics3/mathics-scanner#egg=Mathics-Scanner[full]	
+        python -m pip install -e git+https://github.com/Mathics3/mathics-scanner#egg=Mathics-Scanner[full]
         git clone https://github.com/Mathics3/mathics-core
         (cd mathics-core && make)
         (cd mathics-core && python -m pip install -e .[full])

.github/workflows/ubuntu.yml

@@ -15,19 +15,17 @@ jobs:
     steps:
     - uses: actions/checkout@v3
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
         python -m pip install pytest
         # Can comment out when next Mathics core and Mathics-scanner are released
-        python -m pip install -e git+https://github.com/Mathics3/mathics-scanner#egg=Mathics-Scanner[full]
+        # python -m pip install -e git+https://github.com/Mathics3/mathics-scanner#egg=Mathics-Scanner[full]
         python -m pip install -e git+https://github.com/Mathics3/mathics-core#egg=Mathics3[full]
         (cd src/mathics3 && bash ./admin-tools/make-op-tables.sh)
-        # python -m pip install Mathics3[full]
-        python -m pip install -e .
     - name: install pymathics graph
       run: |
         make develop

.gitignore

@@ -1,4 +1,5 @@
 *~
+/.hypothesis
 /.python-version
 /ChangeLog
 /build

Makefile

@@ -61,7 +61,7 @@ pytest:
 
 #: Run tests that appear in docstring in the code.
 doctest:
-	MATHICS_CHARACTER_ENCODING="ASCII" $(PYTHON) -m mathics.docpipeline -l pymathics.graph $o
+	MATHICS_CHARACTER_ENCODING="ASCII" $(PYTHON) -m mathics.docpipeline -l pymathics.graph -c  'Graphs - Vertices and Edges' $o
 
 # #: Make Mathics PDF manual
 # doc mathics.pdf: mathics/doc/tex/data

NEWS.md

@@ -1,3 +1,22 @@
+6.0.0
+-----
+
+Revise for 6.0.0 Mathics3 API and current Mathics3 builtin standards
+described in [Guidelines for Writing
+Documentation](https://mathics-development-guide.readthedocs.io/en/latest/extending/developing-code/extending/documentation-markup.html#guidelines-for-writing-documentation).
+
+This package has undergone a major overhaul. Modules have been split out along into logical groups following the documentation structure.
+
+We have gradually been rolling in more Python type annotations and
+have been using current Python practices. Tools such as using
+``isort``, ``black`` and ``flake8`` are used as well.
+
+Evaluation methods of built-in functions start ``eval_`` not
+``apply_``.
+
+There is more refactoring more to do here, Upgrade to NetworkX is also
+desirable.
+
 5.0.0.alpha0
 ------------
 

admin-tools/pyenv-versions

@@ -5,4 +5,4 @@ if [[ $0 == ${BASH_SOURCE[0]} ]] ; then
     echo "This script should be *sourced* rather than run directly through bash"
     exit 1
 fi
-export PYVERSIONS='3.6.13 3.7.13 3.8.13 3.9.13 3.10.5'
+export PYVERSIONS='3.6.15 3.7.16 3.8.16 3.9.16 3.10.10'

pymathics/graph/base.py

@@ -15,6 +15,7 @@
 from mathics.core.convert.expression import ListExpression, from_python, to_mathics_list
 from mathics.core.element import BaseElement
 from mathics.core.expression import Expression
+from mathics.core.pattern import pattern_objects
 from mathics.core.symbols import Symbol, SymbolList, SymbolTrue
 from mathics.core.systemsymbols import (
     SymbolBlank,
@@ -81,7 +82,7 @@ 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 +125,7 @@ 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 +174,15 @@ 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):
@@ -840,7 +841,6 @@ class AdjacencyList(_NetworkXBuiltin):
           matching $pattern$.
     </dl>
 
-    >> LoadModule["pymathics.graph"];
     >> AdjacencyList[{1 -> 2, 2 -> 3}, 3]
      = {2}
 
@@ -854,8 +854,6 @@ class AdjacencyList(_NetworkXBuiltin):
     summary_text = "list the adjacent vertices"
 
     def _retrieve(self, graph, what, neighbors, expression, evaluation):
-        from mathics.core.pattern import pattern_objects
-
         if what.get_head_name() in pattern_objects:
             collected = set()
             match = Matcher(what).match
@@ -897,12 +895,11 @@ def neighbors(v):
 
 class DirectedEdge(Builtin):
     """
-    <url>
-    :Directed edge:
+    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>
+    https://networkx.org/documentation/networkx-2.8.8/reference/classes/digraph.html</url>, <url>
     :WMA:
     https://reference.wolfram.com/language/ref/DirectedEdge.html</url>)
 
@@ -920,11 +917,10 @@ class EdgeConnectivity(_NetworkXBuiltin):
     """
     <url>
     :Edge connectivity:
-    https://en.wikipedia.org/wiki/Directed_graph</url> (<url>
+    https://en.wikipedia.org/wiki/Directed_graph#Directed_graph_connectivity</url> (<url>
     :NetworkX:
     https://networkx.org/documentation/networkx-2.8.8/reference/algorithms/\
-    generated/networkx.algorithms.connectivity.connectivity.edge_connectivity.html</url>,
-    <url>
+generated/networkx.algorithms.connectivity.connectivity.edge_connectivity.html</url>, <url>
     :WMA:
     https://reference.wolfram.com/language/ref/EdgeConnectivity.html</url>)
 
@@ -970,7 +966,7 @@ def eval_st(self, graph, s, t, expression, evaluation, options):
 class EdgeIndex(_NetworkXBuiltin):
     """
     <url>
-    :WMA:
+    :WMA link:
     https://reference.wolfram.com/language/ref/EdgeIndex.html</url>
 
     <dl>
@@ -998,7 +994,7 @@ def eval(self, graph, v, expression, evaluation, options):
 class EdgeList(_PatternList):
     """
     <url>
-    :WMA:
+    :WMA link:
     https://reference.wolfram.com/language/ref/EdgeList.html</url>
 
     <dl>
@@ -1016,7 +1012,7 @@ def _items(self, graph):
 class EdgeRules(_NetworkXBuiltin):
     """
     <url>
-    :WMA:
+    :WMA link:
     https://reference.wolfram.com/language/ref/EdgeRules.html</url>
 
     <dl>
@@ -1048,8 +1044,7 @@ class FindShortestPath(_NetworkXBuiltin):
     https://en.wikipedia.org/wiki/Shortest_path_problem</url> (<url>
     :NetworkX:
     https://networkx.org/documentation/networkx-2.8.8/reference/algorithms\
-    /generated/networkx.algorithms.shortest_paths.generic.shortest_path.html</url>,
-    <url>
+    /generated/networkx.algorithms.shortest_paths.generic.shortest_path.html</url>, <url>
     :WMA:
     https://reference.wolfram.com/language/ref/FindShortestPath.html</url>)
 
@@ -1083,7 +1078,7 @@ class FindShortestPath(_NetworkXBuiltin):
     summary_text = "find the shortest path between two vertices"
 
     def eval_s_t(self, graph, s, t, expression, evaluation, options):
-        "%(name)s[graph_, s_, t_, OptionsPattern[%(name)s]]"
+        "FindShortestPath[graph_, s_, t_, OptionsPattern[FindShortestPath]]"
         graph = self._build_graph(graph, evaluation, options, expression)
         if not graph:
             return
@@ -1169,8 +1164,7 @@ def eval_st(self, graph, s, t, expression, evaluation, options):
 
 class GraphAtom(AtomBuiltin):
     """
-    <url>:Graph:https://en.wikipedia.org/wiki/graph</url> (
-    <url>:WMA:
+    <url>:Graph:https://en.wikipedia.org/wiki/graph</url> (<url>:WMA:
     https://reference.wolfram.com/language/ref/Graph.html</url>)
     <dl>
       <dt>'Graph[{$e1, $e2, ...}]'
@@ -1224,7 +1218,7 @@ def eval_1(self, vertices, edges, evaluation, options):
 class HighlightGraph(_NetworkXBuiltin):
     """
     <url>
-    :WMA:
+    :WMA link:
     https://reference.wolfram.com/language/ref/HighlightGraph.html</url>
 
     <dl>
@@ -1264,7 +1258,7 @@ def parse(item):
 class Property(Builtin):
     """
     <url>
-    :WMA:
+    :WMA link:
     https://reference.wolfram.com/language/ref/Property.html</url>
 
     <dl>
@@ -1280,7 +1274,7 @@ class Property(Builtin):
 class PropertyValue(Builtin):
     """
     <url>
-    :WMA:
+    :WMA link:
     https://reference.wolfram.com/language/ref/PropertyValue.html</url>
 
     <dl>
@@ -1323,7 +1317,7 @@ def eval(self, graph, item, name, evaluation):
 class VertexAdd(_NetworkXBuiltin):
     """
     <url>
-    :WMA:
+    :WMA link:
     https://reference.wolfram.com/language/ref/VertexAdd.html</url>
 
     <dl>
@@ -1343,7 +1337,7 @@ class VertexAdd(_NetworkXBuiltin):
     summary_text = "add a vertex"
 
     def eval(self, graph: Expression, what, expression, evaluation, options):
-        "%(name)s[graph_, what_, OptionsPattern[%(name)s]]"
+        "VertexAdd[graph_, what_, OptionsPattern[VertexAdd]]"
         mathics_graph = self._build_graph(graph, evaluation, options, expression)
         if mathics_graph:
             if what.get_head_name() == "System`List":
@@ -1357,7 +1351,7 @@ def eval(self, graph: Expression, what, expression, evaluation, options):
 class VertexConnectivity(_NetworkXBuiltin):
     """
     <url>
-    :WMA:
+    :WMA link:
     https://reference.wolfram.com/language/ref/VertexConnectivity.html</url>
 
     <dl>
@@ -1408,7 +1402,7 @@ def eval_st(self, graph, s, t, expression, evaluation, options):
 class VertexDelete(_NetworkXBuiltin):
     """
     <url>
-    :WMA:
+    :WMA link:
     https://reference.wolfram.com/language/ref/VertexDelete.html</url>
 
     <dl>
@@ -1431,8 +1425,6 @@ def eval(self, graph, what, expression, evaluation, options) -> Optional[Graph]:
         "VertexDelete[graph_, what_, OptionsPattern[VertexDelete]]"
         graph = self._build_graph(graph, evaluation, options, expression)
         if graph:
-            from mathics.core.pattern import pattern_objects
-
             head_name = what.get_head_name()
             if head_name in pattern_objects:
                 cases = Expression(
@@ -1449,7 +1441,7 @@ def eval(self, graph, what, expression, evaluation, options) -> Optional[Graph]:
 class VertexIndex(_NetworkXBuiltin):
     """
     <url>
-    :WMA:
+    :WMA link:
     https://reference.wolfram.com/language/ref/VertexIndex.html</url>
     <dl>
       <dt>'VertexIndex'['g', 'v']
@@ -1477,7 +1469,7 @@ def eval(self, graph, v, expression, evaluation, options):
 class VertexList(_PatternList):
     """
     <url>
-    :WMA:
+    :WMA link:
     https://reference.wolfram.com/language/ref/VertexList.html</url>
     <dl>
       <dt>'VertexList[$edgelist$]'
@@ -1495,7 +1487,7 @@ class VertexList(_PatternList):
      = {10}
     """
 
-    summary_text = "list the vertex"
+    summary_text = "list the vertices of a graph"
 
     def _items(self, graph):
         return graph.vertices
@@ -1504,7 +1496,7 @@ def _items(self, graph):
 class UndirectedEdge(Builtin):
     """
     <url>
-    :WMA:
+    :WMA link:
     https://reference.wolfram.com/language/ref/UndirectedEdge.html</url>
 
     <dl>
@@ -1544,9 +1536,9 @@ class UndirectedEdge(Builtin):
 
 class EdgeDelete(_NetworkXBuiltin):
     """
-    <url>
+    Delete an Edge (<url>
     :WMA:
-    https://reference.wolfram.com/language/ref/EdgeDelete.html</url>
+    https://reference.wolfram.com/language/ref/EdgeDelete.html</url>)
 
     <dl>
       <dt>'EdgeDelete'[$g$, $edge$]
@@ -1572,8 +1564,6 @@ def eval(self, graph, what, expression, evaluation, options) -> Optional[Graph]:
         "EdgeDelete[graph_, what_, OptionsPattern[EdgeDelete]]"
         graph = self._build_graph(graph, evaluation, options, expression)
         if graph:
-            from mathics.core.pattern import pattern_objects
-
             head_name = what.get_head_name()
             if head_name in pattern_objects:
                 cases = Expression(

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