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pymathics/graph/boxes.py

@@ -8,51 +8,47 @@
 
 import base64
 import tempfile
-
-
 from typing import Tuple
 
 from mathics.core.element import BaseElement, BoxElementMixin
 
-
 from pymathics.graph.format import png_format_graph, svg_format_graph
 
 no_doc = True
 
+
 class GraphBox(BoxElementMixin):
     def __init__(self, G, **options):
         self.G = G
         self.options = options
 
-    def boxes_to_b64text(
-        self, elements: Tuple[BaseElement] = None, **options
-    ) -> Tuple[bytes, Tuple[int, int]]:
+    def to_b64text(self, **options) -> Tuple[bytes, Tuple[int, int]]:
         """
         Produces a base64 png representation and a tuple with the size of the pillow image
         associated to the object.
         """
-        contents, size = self.boxes_to_png(elements, **options)
+        contents, size = self.to_png(**options)
         encoded = base64.b64encode(contents)
         encoded = b"data:image/png;base64," + encoded
         return encoded, size
 
-    def boxes_to_png(self, elements=None, **options) -> Tuple[bytes, Tuple[int, int]]:
+    def to_png(self, **options) -> Tuple[bytes, Tuple[int, int]]:
         """
         returns a tuple with the set of bytes with a png representation of the image
         and the scaled size.
         """
         return png_format_graph(self.G, **self.options), (800, 600)
 
-    def boxes_to_svg(self, elements=None, **options):
+    def to_svg(self, **options):
         return svg_format_graph(self.G, **self.options), (400, 300)
 
-    def boxes_to_tex(self, elements=None, **options) -> str:
+    def to_tex(self, **options) -> str:
         """
         Store the associated image as a png file and return
         a LaTeX command for including it.
         """
 
-        data, size = self.boxes_to_png(elements, **options)
+        data, size = self.to_png(elements, **options)
         res = 100  # pixels/cm
         width_str, height_str = (str(n / res).strip() for n in size)
         head = rf"\includegraphics[width={width_str}cm,height={height_str}cm]"
@@ -69,11 +65,11 @@ def boxes_to_tex(self, elements=None, **options) -> str:
 
         return head + "{" + format(path) + "}"
 
-    def boxes_to_text(self, elements=None, **options):
+    def to_text(self, **options):
         return "-Graph-"
 
-    def boxes_to_mathml(self, elements=None, **options):
-        encoded, size = self.boxes_to_b64text(elements, **options)
+    def to_mathml(self, **options):
+        encoded, size = self.to_b64text(**options)
         decoded = encoded.decode("utf8")
         # see https://tools.ietf.org/html/rfc2397
         return f'<mglyph src="{decoded}" width="50%" height="50%" />'

pymathics/graph/format.py

@@ -115,7 +115,6 @@ def get_png_graph() -> BytesIO:
 def hierarchy_pos(
     G, root=None, width=1.0, vert_gap=0.2, vert_loc=0, leaf_vs_root_factor=0.5
 ):
-
     """Position nodes in tree layout. The root is at the top.
 
     Based on Joel's answer at https://stackoverflow.com/a/29597209/2966723,

pyproject.toml

@@ -1,11 +1,10 @@
 [build-system]
 requires = [
 	"setuptools", # CVE-2024-38335 recommends this
-        "Mathics3>9.0.0",
+        "mathics-core >= 9.0.1",
         "Mathics3-Module-Base",
         "networkx>=3.0.0",
         "matplotlib",
-        "Mathics3-Module-Base",
 ]
 build-backend = "setuptools.build_meta"
 

test/helper.py

@@ -12,9 +12,7 @@
 # Set up a Mathics session with definitions.
 # For consistency set the character encoding ASCII which is
 # the lowest common denominator available on all systems.
-session = MathicsSession(
-    character_encoding="ASCII"
-)
+session = MathicsSession(character_encoding="ASCII")
 
 
 def reset_session(add_builtin=True, catch_interrupt=False):
@@ -115,7 +113,7 @@ def check_evaluation(
         assert (
             expected_len == got_len
         ), f"expected {expected_len}; got {got_len}. Messages: {outs}"
-        for (out, msg) in zip(outs, msgs):
+        for out, msg in zip(outs, msgs):
             if out != msg:
                 print(f"out:<<{out}>>")
                 print(" and ")

test/test_fixme.py

@@ -5,77 +5,78 @@
 from test.helper import check_evaluation, evaluate, evaluate_value
 import pytest
 
+
 def setup_module(module):
     """Load pymathics.graph"""
     assert evaluate_value('LoadModule["pymathics.graph"]') == "pymathics.graph"
     evaluate("SortList[list_] := Sort[Map[Sort, list]]")
 
 
-
 @pytest.mark.skip("Wrong result. Investigate me.")
 def test_EdgeList():
     check_evaluation(
-     "EdgeList[{1 -> 2, 2 <-> 3}]",
-     "{DirectedEdge[1, 2], UndirectedEdge[2, 3]}"
-     )
+        "EdgeList[{1 -> 2, 2 <-> 3}]", "{DirectedEdge[1, 2], UndirectedEdge[2, 3]}"
+    )
 
 
-
 @pytest.mark.skip("Wrong result. Investigate me.")
 def test_FindShortestPath():
-     check_evaluation(
-         (
-             "g = Graph[{1 -> 2, 2 -> 3, 1 -> 3}, EdgeWeight -> {0.5, a, 3}];"
-             "a = 0.5; FindShortestPath[g, 1, 3]'"),
-         "{1, 2, 3}")
-     check_evaluation("a = 10; FindShortestPath[g, 1, 3]", "{1, 3}")
-     check_evaluation("a = .;", "Null")
-
-
+    check_evaluation(
+        (
+            "g = Graph[{1 -> 2, 2 -> 3, 1 -> 3}, EdgeWeight -> {0.5, a, 3}];"
+            "a = 0.5; FindShortestPath[g, 1, 3]'"
+        ),
+        "{1, 2, 3}",
+    )
+    check_evaluation("a = 10; FindShortestPath[g, 1, 3]", "{1, 3}")
+    check_evaluation("a = .;", "Null")
 
 
 @pytest.mark.skip("This finds d<->a in the position 4 instead 2.")
 def test_EdgeIndex():
-    check_evaluation("EdgeIndex[{c <-> d, d <-> a, a -> e}, d <-> a]",
-                     "2")
+    check_evaluation("EdgeIndex[{c <-> d, d <-> a, a -> e}, d <-> a]", "2")
+
 
-
 @pytest.mark.parametrize(
     ("str_expr", "str_expect"),
     [
         (
-            ("g = Graph[{1 -> 2, 2 -> 3}, DirectedEdges -> True];"
-             "EdgeCount[g, _DirectedEdge]"), 
-            "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, _DirectedEdge]"
+            ),
+            "0",
         ),
-        ("EdgeCount[g, _UndirectedEdge]","2")
-    ]
+        ("EdgeCount[g, _UndirectedEdge]", "2"),
+    ],
 )
 @pytest.mark.skip("This finds d<->a in the position 4 instead 2.")
 def test_edgecount(str_expr, str_expect):
     check_evaluation(str_expr, str_expect)
 
-    
+
 @pytest.mark.skip("This finds d<->a in the position 4 instead 2.")
 def test_EdgeIndex():
-    check_evaluation("EdgeIndex[{c <-> d, d <-> a, a -> e}, d <-> a]",
-                     "2")
+    check_evaluation("EdgeIndex[{c <-> d, d <-> a, a -> e}, d <-> a]", "2")
+
 
 @pytest.mark.skip("This is not properly evaluated. Investigate me")
 def test_HITSCentrality():
-     check_evaluation("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}}")
+    check_evaluation(
+        "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}}",
+    )
+
 
 @pytest.mark.skip("Investigate me.")
 def test_EdgeRules():
     check_evaluation(
-        "EdgeRules[{1 <-> 2, 2 -> 3, 3 <-> 4}]",
-     "{1 -> 2, 2 -> 3, 3 -> 4}"
+        "EdgeRules[{1 <-> 2, 2 -> 3, 3 <-> 4}]", "{1 -> 2, 2 -> 3, 3 -> 4}"
     )
-