Merge pull request #14 from Mathics3/cleaning_tests_and_adding_workflows

Cleaning tests and adding workflows

Author: rocky

.github/workflows/consistency-checks.yml

@@ -0,0 +1,34 @@
+name: Pymathics-Graph (Consistency Checks)
+
+on:
+  push:
+    branches: [ master ]
+  pull_request:
+    branches: [ master ]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ['3.10']
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v2
+      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]	
+        git clone https://github.com/Mathics3/mathics-core
+        (cd mathics-core && make)
+        (cd mathics-core && python -m pip install -e .[full])
+    - name: Install Pymathics.graph with minimum dependencies
+      run: |
+        make develop
+    - name: Test Mathics Consistency and Style
+      run: |
+        make check-consistency-and-style

.github/workflows/ubuntu.yml

@@ -0,0 +1,36 @@
+name: Pymathics.graph (ubuntu)
+
+on:
+  push:
+    branches: [ master ]
+  pull_request:
+    branches: '**'
+
+jobs:
+  build:
+    runs-on: ubuntu-20.04
+    strategy:
+      matrix:
+        python-version: ['3.9', '3.10']
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v2
+      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-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
+    - name: Test Mathics
+      run: |
+        make -j3 check

Makefile

@@ -74,3 +74,8 @@ rmChangeLog:
 #: Create a ChangeLog from git via git log and git2cl
 ChangeLog: rmChangeLog
 	git log --pretty --numstat --summary | $(GIT2CL) >$@
+
+
+#: Run pytest consistency and style checks
+check-consistency-and-style:
+	MATHICS_LINT=t $(PYTHON) -m pytest test/consistency-and-style

pymathics/graph/base.py

@@ -540,6 +540,8 @@ class Graph(Atom):
     def __init__(self, G, **kwargs):
         super(Graph, self).__init__()
         self.G = G
+        self.mixed = kwargs.get("mixed", False)
+        print("creating", self.G, self.mixed)
 
     def __hash__(self):
         return hash(("Pymathics`Graph", self.G))
@@ -636,12 +638,17 @@ def empty(self):
     def head(self):
         return SymbolGraph
 
+    def is_directed(self):
+        if self.G.is_directed():
+            return not self.mixed
+        return False
+    
     def is_loop_free(self):
         return not any(True for _ in nx.nodes_with_selfloops(self.G))
 
     # networkx graphs can't be for mixed
     def is_mixed_graph(self):
-        return False
+        return self.mixed
         # return self.edges. ... is_mixed()
 
     def is_multigraph(self):
@@ -900,6 +907,7 @@ def full_new_edge_properties(new_edge_style):
         return None
 
     empty_dict = {}
+    mixed = False
     if directed_edges:
         G = nx.MultiDiGraph() if multigraph[0] else nx.DiGraph()
         nodes_seen = set()
@@ -913,6 +921,8 @@ def full_new_edge_properties(new_edge_style):
         for v in unseen_vertices:
             G.add_node(v)
 
+        if undirected_edges:
+            mixed = True
         for u, v, attr_dict in undirected_edges:
             attr_dict = attr_dict or empty_dict
             G.add_edge(u, v, **attr_dict)
@@ -931,7 +941,7 @@ def full_new_edge_properties(new_edge_style):
         n_undirected=len(undirected_edges),
     )
 
-    g = Graph(G)
+    g = Graph(G, mixed=mixed)
     _process_graph_options(g, options)
     return g
 
@@ -1209,6 +1219,10 @@ class DirectedEdge(Builtin):
 
 class DirectedGraphQ(_NetworkXBuiltin):
     """
+    <dl>
+      <dt>'DirectedGraphQ'[$graph$]
+      <dd>True if $graph$ is a 'Graph' and all the edges are directed.
+    </dl>
     >> g = Graph[{1 -> 2, 2 -> 3}]; DirectedGraphQ[g]
      = True
 
@@ -1226,8 +1240,7 @@ def eval(self, graph, expression, evaluation, options):
         "%(name)s[graph_, OptionsPattern[%(name)s]]"
         graph = self._build_graph(graph, evaluation, options, expression, quiet=True)
         if graph:
-            directed = graph.G.is_directed() and not graph.is_mixed_graph()
-            return from_python(directed)
+            return from_python(graph.is_directed())
         else:
             return SymbolFalse
 
@@ -1268,8 +1281,11 @@ def eval_st(self, graph, s, t, expression, evaluation, options):
 
 class EdgeIndex(_NetworkXBuiltin):
     """
-    >> EdgeIndex[{c <-> d, d <-> a, a -> e}, d <-> a]
-     = 2
+    <dl>
+    <dt>'EdgeIndex['graph', 'edge']'
+    <dd>gives the position of the 'edge' in the list of edges associated \
+    to the graph.
+    </dl>
     """
 
     def eval(self, graph, v, expression, evaluation, options):
@@ -1287,8 +1303,10 @@ def eval(self, graph, v, expression, evaluation, options):
 
 class EdgeList(_PatternList):
     """
-    >> EdgeList[{1 -> 2, 2 <-> 3}]
-     = {DirectedEdge[1, 2], UndirectedEdge[2, 3]}
+    <dl>
+      <dt>'EdgeList'[$g$]
+      <dd>gives the list of edges that defines $g$
+    </dl>
     """
 
     def _items(self, graph):
@@ -1301,17 +1319,13 @@ class EdgeRules(_NetworkXBuiltin):
       <dt>'EdgeRules'[$g$]
       <dd> gives the list of edge rules for the graph $g$.
     </dl>
-
-    >> EdgeRules[{1 <-> 2, 2 -> 3, 3 <-> 4}]
-     = {1 -> 2, 2 -> 3, 3 -> 4}
     """
     summary_text = "list the edge rules"
 
     def eval(self, graph, expression, evaluation, options):
         "%(name)s[graph_, OptionsPattern[%(name)s]]"
         graph = self._build_graph(graph, evaluation, options, expression)
         if graph:
-
             def rules():
                 for edge in graph.edges:
                     u, v = edge
@@ -1396,11 +1410,6 @@ class FindShortestPath(_NetworkXBuiltin):
      = {}
 
     >> g = Graph[{1 -> 2, 2 -> 3, 1 -> 3}, EdgeWeight -> {0.5, a, 3}];
-    >> a = 0.5; FindShortestPath[g, 1, 3]
-     = {1, 2, 3}
-    >> a = 10; FindShortestPath[g, 1, 3]
-     = {1, 3}
-    >> a=.;
 
     #> FindShortestPath[{}, 1, 2]
      : The vertex at position 2 in FindShortestPath[{}, 1, 2] does not belong to the graph at position 1.
@@ -1519,14 +1528,6 @@ class GraphAtom(AtomBuiltin):
     >> Graph[{{1 -> 2}}]
      = Graph[{{1 -> 2}}]
 
-    >> g = Graph[{1 -> 2, 2 -> 3}, DirectedEdges -> True];
-    >> EdgeCount[g, _DirectedEdge]
-     = 2
-    >> g = Graph[{1 -> 2, 2 -> 3}, DirectedEdges -> False];
-    >> EdgeCount[g, _DirectedEdge]
-     = 0
-    >> EdgeCount[g, _UndirectedEdge]
-     = 2
     """
 
     # requires = ("networkx",)
@@ -1583,8 +1584,6 @@ class HITSCentrality(_Centrality):
           the vertices in the graph $g$.
     </dl>
 
-    >> g = Graph[{a -> d, b -> c, d -> c, d -> a, e -> c}]; HITSCentrality[g]
-     = {{0.292893, 0., 0., 0.707107, 0.}, {0., 1., 0.707107, 0., 0.707107}}
     """
 
     summary_text = "HITS centrality"