iplotx 0.6.7__tar.gz → 0.7.0__tar.gz

{iplotx-0.6.7 → iplotx-0.7.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: iplotx
-Version: 0.6.7
+Version: 0.7.0
 Summary: Plot networkx from igraph and networkx.
 Project-URL: Homepage, https://github.com/fabilab/iplotx
 Project-URL: Documentation, https://readthedocs.org/iplotx

{iplotx-0.6.7 → iplotx-0.7.0}/docs/source/api/complete_style_specification.md

@@ -7,8 +7,12 @@
 
 ```python
 {
-    # Vertex style
-    "vertex": {
+    # Vertex/node style
+    # NOTE: you can use "node" or "vertex" interchangeably. If both are specified
+    # at the SAME time, these styles are merged, with conflicts resolved in favour
+    # of "node". In other words, "vertex" is applied first, then "node" on top of it.
+
+    "vertex" | "node": {
         # Size of the vertex in points. If a pair, it indicates width and height
         # of the marker. If "label", set the size dynamically based on the vertex
         # label (a label is needed in this case)
@@ -74,7 +78,8 @@
 
         # Whether to leave any space between edge cap and vertex border. This is
         # in figure points and autoscales correctly with dpi.
-        "padding": float,
+        # DEPRECATED: "padding" is a synonym for this option, but it is deprecated.
+        "shrink": float,
 
         # Matplotlib color map used to map floating numbers into RGBA colors. Only
         # used when the previous option "color" is set to floats.

{iplotx-0.6.7 → iplotx-0.7.0}/docs/source/sg_execution_times.rst

@@ -6,7 +6,7 @@
 
 Computation times
 =================
-**00:00.109** total execution time for 71 files **from all galleries**:
+**00:00.798** total execution time for 72 files **from all galleries**:
 
 .. container::
 
@@ -32,8 +32,23 @@ Computation times
    * - Example
      - Time
      - Mem (MB)
-   * - :ref:`sphx_glr_gallery_basic_plot_loops.py` (``../../gallery/basic/plot_loops.py``)
-     - 00:00.109
+   * - :ref:`sphx_glr_gallery_biology_plot_animal_phylogeny.py` (``../../gallery/biology/plot_animal_phylogeny.py``)
+     - 00:00.614
+     - 0.0
+   * - :ref:`sphx_glr_gallery_network_science_plot_social_network_circles.py` (``../../gallery/network_science/plot_social_network_circles.py``)
+     - 00:00.051
+     - 0.0
+   * - :ref:`sphx_glr_gallery_basic_plot_house.py` (``../../gallery/basic/plot_house.py``)
+     - 00:00.049
+     - 0.0
+   * - :ref:`sphx_glr_gallery_style_plot_arrows.py` (``../../gallery/style/plot_arrows.py``)
+     - 00:00.037
+     - 0.0
+   * - :ref:`sphx_glr_gallery_other_plot_feedbacks.py` (``../../gallery/other/plot_feedbacks.py``)
+     - 00:00.025
+     - 0.0
+   * - :ref:`sphx_glr_gallery_style_plot_edgepadding.py` (``../../gallery/style/plot_edgepadding.py``)
+     - 00:00.021
      - 0.0
    * - :ref:`sphx_glr_gallery_basic_plot_basic.py` (``../../gallery/basic/plot_basic.py``)
      - 00:00.000
@@ -50,7 +65,7 @@ Computation times
    * - :ref:`sphx_glr_gallery_basic_plot_grouping.py` (``../../gallery/basic/plot_grouping.py``)
      - 00:00.000
      - 0.0
-   * - :ref:`sphx_glr_gallery_basic_plot_house.py` (``../../gallery/basic/plot_house.py``)
+   * - :ref:`sphx_glr_gallery_basic_plot_loops.py` (``../../gallery/basic/plot_loops.py``)
      - 00:00.000
      - 0.0
    * - :ref:`sphx_glr_gallery_basic_plot_simple_path.py` (``../../gallery/basic/plot_simple_path.py``)
@@ -128,9 +143,6 @@ Computation times
    * - :ref:`sphx_glr_gallery_network_science_plot_simple_networkx.py` (``../../gallery/network_science/plot_simple_networkx.py``)
      - 00:00.000
      - 0.0
-   * - :ref:`sphx_glr_gallery_network_science_plot_social_network_circles.py` (``../../gallery/network_science/plot_social_network_circles.py``)
-     - 00:00.000
-     - 0.0
    * - :ref:`sphx_glr_gallery_network_science_plot_traveling_salesman.py` (``../../gallery/network_science/plot_traveling_salesman.py``)
      - 00:00.000
      - 0.0
@@ -143,9 +155,6 @@ Computation times
    * - :ref:`sphx_glr_gallery_other_plot_edit_artists.py` (``../../gallery/other/plot_edit_artists.py``)
      - 00:00.000
      - 0.0
-   * - :ref:`sphx_glr_gallery_other_plot_feedbacks.py` (``../../gallery/other/plot_feedbacks.py``)
-     - 00:00.000
-     - 0.0
    * - :ref:`sphx_glr_gallery_other_plot_graph.py` (``../../gallery/other/plot_graph.py``)
      - 00:00.000
      - 0.0
@@ -155,12 +164,6 @@ Computation times
    * - :ref:`sphx_glr_gallery_other_plot_train.py` (``../../gallery/other/plot_train.py``)
      - 00:00.000
      - 0.0
-   * - :ref:`sphx_glr_gallery_style_plot_arrows.py` (``../../gallery/style/plot_arrows.py``)
-     - 00:00.000
-     - 0.0
-   * - :ref:`sphx_glr_gallery_style_plot_edgepadding.py` (``../../gallery/style/plot_edgepadding.py``)
-     - 00:00.000
-     - 0.0
    * - :ref:`sphx_glr_gallery_style_plot_elements.py` (``../../gallery/style/plot_elements.py``)
      - 00:00.000
      - 0.0

{iplotx-0.6.7 → iplotx-0.7.0}/gallery/basic/plot_house.py

@@ -31,7 +31,8 @@ ipx.plot(
             "alpha": 0.5,
             "linewidth": 6,
         },
-        "vertex": {
+        # You could use "vertex" instead of "node"
+        "node": {
             "size": G.nodes.data("size"),
             "facecolor": G.nodes.data("color"),
             "edgecolor": "k",

iplotx-0.7.0/gallery/biology/data/GN-tree.json

@@ -0,0 +1 @@
+{"identifier": "GN-tree.json", "data": "{\"newick\": \"((((((((FlyingFox,DogFaced)edge.0,((FreeTaile,LittleBro)edge.1,(TombBat,RoundEare)edge.2)edge.3)edge.4,(FalseVamp,LeafNose)edge.5)edge.6,(((Horse,Rhino)edge.7,(Pangolin,(Cat,Dog)edge.8)edge.9)edge.10,(Llama,(Pig,(Cow,(Hippo,(SpermWhale,HumpbackW)edge.11)edge.12)edge.13)edge.14)edge.15)edge.16)edge.17,(Mole,Hedgehog)edge.18)edge.19,(((TreeShrew,FlyingLem)edge.20,(Galago,(HowlerMon,(Rhesus,(Orangutan,(Gorilla,(Human,Chimpanzee)edge.21)edge.22)edge.23)edge.24)edge.25)edge.26)edge.27,(Jackrabbit,(FlyingSqu,(OldWorld,(Mouse,Rat)edge.28)edge.29)edge.30)edge.31)edge.32)edge.33,((NineBande,HairyArma)edge.34,(Anteater,Sloth)edge.35)edge.36)edge.37,(((Dugong,Manatee)edge.38,((AfricanEl,AsianElep)edge.39,(RockHyrax,TreeHyrax)edge.40)edge.41)edge.42,(Aardvark,((GoldenMol,(Madagascar,Tenrec)edge.43)edge.44,(LesserEle,GiantElep)edge.45)edge.46)edge.47)edge.48,(Caenolest,(Phascogale,(Wombat,Bandicoot)edge.49)edge.50)edge.51)root\", \"edge_attributes\": {\"FlyingFox\": {\"ENS\": 0.017741273670248456, \"paralinear\": 0.07436068151499686, \"mprobs\": {\"T\": 0.2294585662184629, \"C\": 0.18571261063637373, \"A\": 0.3654713959371184, \"G\": 0.21935742720804552}, \"G>T\": 0.5210606837133107, \"G>C\": 0.7751010590349916, \"G>A\": 4.592225166516715, \"T>C\": 3.047228461372764, \"T>A\": 0.8301683237233797, \"C>G\": 0.874076821592714, \"C>T\": 3.330613467509294, \"C>A\": 0.70891762217141, \"A>G\": 3.112164460742973, \"A>T\": 0.5926442300672324, \"A>C\": 1.0408659281719779}, \"DogFaced\": {\"ENS\": 0.036375233232148925, \"paralinear\": 0.15227833435933036, \"mprobs\": {\"T\": 0.22884598834630437, \"C\": 0.18693757218882817, \"A\": 0.3640014964856682, \"G\": 0.22021494297919972}, \"G>T\": 0.5210606837133107, \"G>C\": 0.7751010590349916, \"G>A\": 4.592225166516715, \"T>C\": 3.047228461372764, \"T>A\": 0.8301683237233797, \"C>G\": 0.874076821592714, \"C>T\": 3.330613467509294, \"C>A\": 0.70891762217141, \"A>G\": 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0.22015688115995305, \"C\": 0.20753895948805964, \"A\": 0.3397216247822709, \"G\": 0.23258253456971648}, \"G>T\": 0.5210606837133107, \"G>C\": 0.7751010590349916, \"G>A\": 4.592225166516715, \"T>C\": 3.047228461372764, \"T>A\": 0.8301683237233797, \"C>G\": 0.874076821592714, \"C>T\": 3.330613467509294, \"C>A\": 0.70891762217141, \"A>G\": 3.112164460742973, \"A>T\": 0.5926442300672324, \"A>C\": 1.0408659281719779}, \"Wombat\": {\"ENS\": 0.05341483216623319, \"paralinear\": 0.21825024546720062, \"mprobs\": {\"T\": 0.22068836088594349, \"C\": 0.20594850711460674, \"A\": 0.34156607462177296, \"G\": 0.23179705737767692}, \"G>T\": 0.5210606837133107, \"G>C\": 0.7751010590349916, \"G>A\": 4.592225166516715, \"T>C\": 3.047228461372764, \"T>A\": 0.8301683237233797, \"C>G\": 0.874076821592714, \"C>T\": 3.330613467509294, \"C>A\": 0.70891762217141, \"A>G\": 3.112164460742973, \"A>T\": 0.5926442300672324, \"A>C\": 1.0408659281719779}, \"Bandicoot\": {\"ENS\": 0.11802583598875109, \"paralinear\": 0.48157335693097103, \"mprobs\": {\"T\": 0.21990267870766467, \"C\": 0.20833443879699598, \"A\": 0.33880092648026205, \"G\": 0.2329619560150774}, \"G>T\": 0.5210606837133107, \"G>C\": 0.7751010590349916, \"G>A\": 4.592225166516715, \"T>C\": 3.047228461372764, \"T>A\": 0.8301683237233797, \"C>G\": 0.874076821592714, \"C>T\": 3.330613467509294, \"C>A\": 0.70891762217141, \"A>G\": 3.112164460742973, \"A>T\": 0.5926442300672324, \"A>C\": 1.0408659281719779}, \"edge.49\": {\"ENS\": 0.0023513667862750656, \"paralinear\": 0.009620615296157098, \"mprobs\": {\"T\": 0.2214474526120714, \"C\": 0.20381293871996006, \"A\": 0.34405046854094873, \"G\": 0.23068914012701983}, \"G>T\": 0.5210606837133107, \"G>C\": 0.7751010590349916, \"G>A\": 4.592225166516715, \"T>C\": 3.047228461372764, \"T>A\": 0.8301683237233797, \"C>G\": 0.874076821592714, \"C>T\": 3.330613467509294, \"C>A\": 0.70891762217141, \"A>G\": 3.112164460742973, \"A>T\": 0.5926442300672324, \"A>C\": 1.0408659281719779}, \"edge.50\": {\"ENS\": 0.018168822909575597, \"paralinear\": 0.07436246315938799, \"mprobs\": {\"T\": 0.22148332633799156, \"C\": 0.20371532109063575, \"A\": 0.3441642465169451, \"G\": 0.23063710605442758}, \"G>T\": 0.5210606837133107, \"G>C\": 0.7751010590349916, \"G>A\": 4.592225166516715, \"T>C\": 3.047228461372764, \"T>A\": 0.8301683237233797, \"C>G\": 0.874076821592714, \"C>T\": 3.330613467509294, \"C>A\": 0.70891762217141, \"A>G\": 3.112164460742973, \"A>T\": 0.5926442300672324, \"A>C\": 1.0408659281719779}, \"edge.51\": {\"ENS\": 0.437404074913319, \"paralinear\": 1.8127156513621356, \"mprobs\": {\"T\": 0.22176778200217562, \"C\": 0.20295053627457427, \"A\": 0.3450562954133852, \"G\": 0.230225386309865}, \"G>T\": 0.5210606837133107, \"G>C\": 0.7751010590349916, \"G>A\": 4.592225166516715, \"T>C\": 3.047228461372764, \"T>A\": 0.8301683237233797, \"C>G\": 0.874076821592714, \"C>T\": 3.330613467509294, \"C>A\": 0.70891762217141, \"A>G\": 3.112164460742973, \"A>T\": 0.5926442300672324, \"A>C\": 1.0408659281719779}, \"root\": {\"mprobs\": {\"T\": 0.2338215316192115, \"C\": 0.17739355857203987, \"A\": 0.3755275913395219, \"G\": 0.21325731846922674}}}, \"length_and_support\": {\"FlyingFox\": {\"length\": 0.017741273670248456, \"support\": null}, \"DogFaced\": {\"length\": 0.036375233232148925, \"support\": null}, \"edge.0\": {\"length\": 0.04627655860256909, \"support\": null}, \"FreeTaile\": {\"length\": 0.03763092526433395, \"support\": null}, \"LittleBro\": {\"length\": 0.05478868222706951, \"support\": null}, \"edge.1\": {\"length\": 0.01108010605652313, \"support\": null}, \"TombBat\": {\"length\": 0.0553127072328518, \"support\": null}, \"RoundEare\": {\"length\": 0.17376260163391286, \"support\": null}, \"edge.2\": {\"length\": 0.004811085287800328, \"support\": null}, \"edge.3\": {\"length\": 0.014436026647335837, \"support\": null}, \"edge.4\": {\"length\": 0.0021773549055771587, \"support\": null}, \"FalseVamp\": {\"length\": 0.06711224149743963, \"support\": null}, \"LeafNose\": {\"length\": 0.060568286302822724, \"support\": null}, \"edge.5\": {\"length\": 0.007149151015846594, \"support\": null}, \"edge.6\": {\"length\": 0.016175811942560764, \"support\": null}, \"Horse\": {\"length\": 0.0437020774610027, \"support\": null}, \"Rhino\": {\"length\": 0.03421064062929262, \"support\": null}, \"edge.7\": {\"length\": 0.015423667902144758, \"support\": null}, \"Pangolin\": {\"length\": 0.07724919751648576, \"support\": null}, \"Cat\": {\"length\": 0.054278226867084195, \"support\": null}, \"Dog\": {\"length\": 0.08124577241175945, \"support\": null}, \"edge.8\": {\"length\": 0.02640201982933406, \"support\": null}, \"edge.9\": {\"length\": 0.00532539297142259, \"support\": null}, \"edge.10\": {\"length\": 1.4916235222169097e-12, \"support\": null}, \"Llama\": {\"length\": 0.05751778972284968, \"support\": null}, \"Pig\": {\"length\": 0.07739856946657771, \"support\": null}, \"Cow\": {\"length\": 0.08777639231499659, \"support\": null}, \"Hippo\": {\"length\": 0.05237103842803992, \"support\": null}, \"SpermWhale\": {\"length\": 0.015086414806001838, \"support\": null}, \"HumpbackW\": {\"length\": 0.011148378728088007, \"support\": null}, \"edge.11\": {\"length\": 0.02311129371016991, \"support\": null}, \"edge.12\": {\"length\": 0.0017671228722700198, \"support\": null}, \"edge.13\": {\"length\": 0.009021829241666193, \"support\": null}, \"edge.14\": {\"length\": 0.006065726212199961, \"support\": null}, \"edge.15\": {\"length\": 0.0232983945107026, \"support\": null}, \"edge.16\": {\"length\": 4.0910086032102326e-12, \"support\": null}, \"edge.17\": {\"length\": 0.004462299380591719, \"support\": null}, \"Mole\": {\"length\": 0.10667843328437873, \"support\": null}, \"Hedgehog\": {\"length\": 0.15203511050694332, \"support\": null}, \"edge.18\": {\"length\": 0.017502977063435274, \"support\": null}, \"edge.19\": {\"length\": 0.012295342065535626, \"support\": null}, \"TreeShrew\": {\"length\": 0.12124168041750151, \"support\": null}, \"FlyingLem\": {\"length\": 0.05958767876443372, \"support\": null}, \"edge.20\": {\"length\": 0.0025361270506288514, \"support\": null}, \"Galago\": {\"length\": 0.13046860680133676, \"support\": null}, \"HowlerMon\": {\"length\": 0.04226893142237102, \"support\": null}, \"Rhesus\": {\"length\": 0.02203638164824187, \"support\": null}, \"Orangutan\": {\"length\": 0.007756254235291462, \"support\": null}, \"Gorilla\": {\"length\": 0.0024749249271206865, \"support\": null}, \"Human\": {\"length\": 0.0063856384285867485, \"support\": null}, \"Chimpanzee\": {\"length\": 0.002829346930370289, \"support\": null}, \"edge.21\": {\"length\": 3.0288845470928904e-12, \"support\": null}, \"edge.22\": {\"length\": 0.0032910959449209067, \"support\": null}, \"edge.23\": {\"length\": 0.011446772659536697, \"support\": null}, \"edge.24\": {\"length\": 0.010576268400132443, \"support\": null}, \"edge.25\": {\"length\": 0.04265551239205802, \"support\": null}, \"edge.26\": {\"length\": 0.011364290022017151, \"support\": null}, \"edge.27\": {\"length\": 0.0007791077607150512, \"support\": null}, \"Jackrabbit\": {\"length\": 0.13159844503570856, \"support\": null}, \"FlyingSqu\": {\"length\": 0.08768424057786249, \"support\": null}, \"OldWorld\": {\"length\": 0.2441999414569413, \"support\": null}, \"Mouse\": {\"length\": 0.06897933728712956, \"support\": null}, \"Rat\": {\"length\": 0.05491541685407963, \"support\": null}, \"edge.28\": {\"length\": 0.18388363230548743, \"support\": null}, \"edge.29\": {\"length\": 0.009794937976471138, \"support\": null}, \"edge.30\": {\"length\": 0.015292210767004136, \"support\": null}, \"edge.31\": {\"length\": 0.005076122245415853, \"support\": null}, \"edge.32\": {\"length\": 0.008549142959653054, \"support\": null}, \"edge.33\": {\"length\": 0.011774296515826487, \"support\": null}, \"NineBande\": {\"length\": 0.04106652871082478, \"support\": null}, \"HairyArma\": {\"length\": 0.02411886492701163, \"support\": null}, \"edge.34\": {\"length\": 0.020341174156229366, \"support\": null}, \"Anteater\": {\"length\": 0.060441339704554335, \"support\": null}, \"Sloth\": {\"length\": 0.04154194955535044, \"support\": null}, \"edge.35\": {\"length\": 0.008980091291957981, \"support\": null}, \"edge.36\": {\"length\": 0.027701154320570187, \"support\": null}, \"edge.37\": {\"length\": 0.003949441717156716, \"support\": null}, \"Dugong\": {\"length\": 0.008023138779536174, \"support\": null}, \"Manatee\": {\"length\": 0.007449617092641844, \"support\": null}, \"edge.38\": {\"length\": 0.025616406556216657, \"support\": null}, \"AfricanEl\": {\"length\": 0.0017346458044374493, \"support\": null}, \"AsianElep\": {\"length\": 0.002584417728248381, \"support\": null}, \"edge.39\": {\"length\": 0.04178294591089507, \"support\": null}, \"RockHyrax\": {\"length\": 0.006790858356137325, \"support\": null}, \"TreeHyrax\": {\"length\": 0.0067932248278529195, \"support\": null}, \"edge.40\": {\"length\": 0.11050523736329819, \"support\": null}, \"edge.41\": {\"length\": 0.005019872861390538, \"support\": null}, \"edge.42\": {\"length\": 0.012480902726092386, \"support\": null}, \"Aardvark\": {\"length\": 0.07884116968290134, \"support\": null}, \"GoldenMol\": {\"length\": 0.08673799739540111, \"support\": null}, \"Madagascar\": {\"length\": 0.053317056406054004, \"support\": null}, \"Tenrec\": {\"length\": 0.09500008597600096, \"support\": null}, \"edge.43\": {\"length\": 0.1623790434112199, \"support\": null}, \"edge.44\": {\"length\": 0.010471300968225242, \"support\": null}, \"LesserEle\": {\"length\": 0.11302469657727374, \"support\": null}, \"GiantElep\": {\"length\": 0.1361486451967194, \"support\": null}, \"edge.45\": {\"length\": 0.037611999311299646, \"support\": null}, \"edge.46\": {\"length\": 0.002092017352092417, \"support\": null}, \"edge.47\": {\"length\": 0.005079900667538481, \"support\": null}, \"edge.48\": {\"length\": 0.023477688198102677, \"support\": null}, \"Caenolest\": {\"length\": 0.1267199502010649, \"support\": null}, \"Phascogale\": {\"length\": 0.09821104059366854, \"support\": null}, \"Wombat\": {\"length\": 0.05341483216623319, \"support\": null}, \"Bandicoot\": {\"length\": 0.11802583598875109, \"support\": null}, \"edge.49\": {\"length\": 0.0023513667862750656, \"support\": null}, \"edge.50\": {\"length\": 0.018168822909575597, \"support\": null}, \"edge.51\": {\"length\": 0.437404074913319, \"support\": null}, \"root\": {\"length\": null, \"support\": null}}, \"type\": \"cogent3.core.tree.PhyloNode\", \"version\": \"2025.7.10a5\"}", "completed": true}

iplotx-0.7.0/gallery/biology/plot_animal_phylogeny.py

@@ -0,0 +1,81 @@
+"""
+Animal phylogeny
+================
+
+This example from ``cogent3`` shows how to use ``iplotx`` to visualise a phylogenetic tree of many animals.
+
+It also shows how to combine ``iplotx`` trees with other ``matplotlib`` artists such as annotations and
+scatter plots.
+"""
+
+from collections import defaultdict
+import cogent3
+import matplotlib.pyplot as plt
+import iplotx as ipx
+
+reader = cogent3.get_app("load_json")
+
+ens_tree = reader("data/GN-tree.json")
+
+# Customise the figure as you like
+fig, ax = plt.subplots(figsize=(8, 14))
+
+# Inject plot into the figure/axes
+tree_artist = ipx.tree(
+  ens_tree,
+  layout="horizontal",
+  ax=ax,
+  leaf_labels=True,
+  # Style options
+  layout_angular=False,
+  leaf_deep=True,
+  margins=(0.2, 0),
+  leafedge_color=defaultdict(lambda: "black", {
+      "Human": "tomato",
+      "Chimpanzee": "orange",
+      "Orangutan": "gold",
+      "Gorilla": "gold",
+      "Rhesus": "yellow",
+      "HowlerMon": "yellow",
+  }),
+  leafedge_linewidth=2,
+)
+
+# Add an annotation with an arrow towards the root
+layout = tree_artist.get_layout().values
+root_coords = layout[layout[:, 0] == 0][0]
+ax.annotate(
+    "Tree root",
+    root_coords,
+    (-0.1, 55),
+    xycoords="data",
+    textcoords="data",
+    arrowprops=dict(
+      color="grey",
+      arrowstyle="-|>",
+      shrinkA=4,
+      shrinkB=12,
+      linewidth=2,
+      connectionstyle="angle",
+    ),
+    bbox=dict(
+        boxstyle="round,rounding_size=0.2,pad=0.5",
+        facecolor="white",
+        edgecolor="grey",
+        linewidth=2,
+    ),
+    fontsize=12,
+)
+
+# Also add concentric circles at the root
+ax.scatter(
+    [root_coords[0]] * 3,
+    [root_coords[1]] * 3,
+    s=[50, 200, 500],
+    facecolor="none",
+    edgecolor="orchid",
+    linewidth=2,
+)
+
+# Ensure tight layout for minimal whitespace
+fig.tight_layout()

{iplotx-0.6.7 → iplotx-0.7.0}/gallery/network_science/plot_social_network_circles.py

@@ -62,7 +62,7 @@ ipx.network(
     ax=ax,
     vertex_marker="s",
     vertex_facecolor="red",
-    edge_padding=3,
+    edge_shrink=3,
     edge_zorder=2,
     vertex_zorder=3,
     vertex_label_color="black",

{iplotx-0.6.7 → iplotx-0.7.0}/gallery/other/plot_feedbacks.py

@@ -34,7 +34,7 @@ ipx.network(
     edge_arrow_width=30,
     edge_arrow_height=40,
     edge_arrow_marker=[")>", "|", "|"],
-    edge_padding=15,
+    edge_shrink=15,
     edge_curved=True,
     edge_tension=[2, 2, 2],
     vertex_facecolor=["#26677FFF", "#635C72FF", "#89374FFF"],

{iplotx-0.6.7 → iplotx-0.7.0}/gallery/style/plot_arrows.py

@@ -25,7 +25,7 @@ ipx.network(
     vertex_size=12,
     edge_arrow_marker=arrow_markers,
     edge_arrow_height="width",
-    edge_padding=8,
+    edge_shrink=8,
     edge_color="steelblue",
     title="Arrow markers",
 )

{iplotx-0.6.7 → iplotx-0.7.0}/gallery/style/plot_edgepadding.py

@@ -1,8 +1,8 @@
 """
-Edge padding
-============
+Edge shrink
+===========
 
-This example illustrates how to pad edges, i.e. leave a bit of empty space between
+This example illustrates how to shrink edges, i.e. leave a bit of empty space between
 edge cap (end) and the border of its source/target vertices.
 """
 
@@ -31,7 +31,7 @@ ipx.network(
     graph,
     layout,
     style="rededge",
-    edge_padding=5,
+    edge_shrink=5,
     vertex_labels=True,
     vertex_size={"A": 20, "B": 20, "C": 20, "D": 20, "E": 20, "Bingo": 50},
 )

{iplotx-0.6.7 → iplotx-0.7.0}/iplotx/edge/__init__.py

@@ -352,9 +352,9 @@ class EdgeCollection(mpl.collections.PatchCollection):
                 tension = 0
                 ports = None
 
-            # Scale padding by dpi
+            # Scale shrink by dpi
             dpi = self.figure.dpi if hasattr(self, "figure") else 72.0
-            padding = dpi / 72.0 * edge_stylei.pop("padding", 0)
+            shrink = dpi / 72.0 * edge_stylei.pop("shrink", 0)
 
             # False is a synonym for "none"
             waypoints = edge_stylei.get("waypoints", "none")
@@ -380,7 +380,7 @@ class EdgeCollection(mpl.collections.PatchCollection):
                 waypoints=waypoints,
                 ports=ports,
                 layout_coordinate_system=self._vertex_collection.get_layout_coordinate_system(),
-                padding=padding,
+                shrink=shrink,
             )
 
             offset = edge_stylei.get("offset", 0)
@@ -720,6 +720,8 @@ def make_stub_patch(**kwargs):
         "cmap",
         "norm",
         "split",
+        "shrink",
+        # DEPRECATED
         "padding",
     ]
     for prop in forbidden_props:

{iplotx-0.6.7 → iplotx-0.7.0}/iplotx/edge/arrow.py

@@ -2,7 +2,7 @@
 Module for edge arrows in iplotx.
 """
 
-from typing import Never
+from typing import Never, Optional
 
 import numpy as np
 import matplotlib as mpl
@@ -149,10 +149,35 @@ class EdgeArrowCollection(mpl.collections.PatchCollection):
         super().draw(renderer)
 
 
-def make_arrow_patch(marker: str = "|>", width: float = 8, **kwargs):
-    """Make a patch of the given marker shape and size."""
-    height = kwargs.pop("height", width * 1.3)
-    if height == "width":
+def make_arrow_patch(
+    marker: str = "|>",
+    width: float = 8,
+    height: Optional[float | str] = None,
+    **kwargs,
+):
+    """Make a patch of the given marker shape and size.
+
+    Parameters:
+        marker: The marker shape to use. Supported markers are:
+            "|>", "|/", "|\\", ">", "<", ">>", ")>", ")", "(", "]", "[", "|",
+            "x", "s", "d", "p", "q". Dashes at the start of this string will
+            be ignored, so "->" is equivalent to ">".
+        width: The width of the marker in points. Height is by default 1.3 the
+            width, unless specified separately.
+        height: The height of the marker in points. If not specified, it is
+            1.3 times the width. This can also be the string "width", in which
+            case the height will be equal to the width.
+        **kwargs: Additional keyword arguments passed to the PathPatch.
+
+    Returns:
+        A pair with the patch and the max size of the patch in points.
+    """
+    # Forget any leading dashes
+    marker = marker.lstrip("-")
+
+    if height is None:
+        height = width * 1.3
+    elif height == "width":
         height = width
 
     # Normalise by the max size, this is taken care of in _transforms