iplotx 0.6.7__py3-none-any.whl → 0.7.0__py3-none-any.whl

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/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

iplotx/edge/geometry.py

@@ -64,7 +64,7 @@ def _compute_loops_per_angle(nloops, angles):
     ]
 
 
-def _get_shorter_edge_coords(vpath, vsize, theta, padding=0):
+def _get_shorter_edge_coords(vpath, vsize, theta, shrink=0):
     # Bound theta from -pi to pi (why is that not guaranteed?)
     theta = (theta + pi) % (2 * pi) - pi
 
@@ -105,8 +105,8 @@ def _get_shorter_edge_coords(vpath, vsize, theta, padding=0):
 
     ve = ve * vsize
 
-    # Padding (assuming dpi scaling is already applied to the padding)
-    ve += padding * np.array([np.cos(theta), np.sin(theta)])
+    # Shrink (assuming dpi scaling is already applied to the shrink)
+    ve += shrink * np.array([np.cos(theta), np.sin(theta)])
 
     return ve
 
@@ -145,12 +145,12 @@ def _compute_loop_path(
     angle2,
     trans_inv,
     looptension,
-    padding=0,
+    shrink=0,
 ):
     # Shorten at starting angle
-    start = _get_shorter_edge_coords(vpath, vsize, angle1, padding) + vcoord_fig
+    start = _get_shorter_edge_coords(vpath, vsize, angle1, shrink) + vcoord_fig
     # Shorten at end angle
-    end = _get_shorter_edge_coords(vpath, vsize, angle2, padding) + vcoord_fig
+    end = _get_shorter_edge_coords(vpath, vsize, angle2, shrink) + vcoord_fig
 
     aux1 = (start - vcoord_fig) * looptension + vcoord_fig
     aux2 = (end - vcoord_fig) * looptension + vcoord_fig
@@ -182,7 +182,7 @@ def _compute_edge_path_straight(
     trans,
     trans_inv,
     layout_coordinate_system: str = "cartesian",
-    padding: float = 0,
+    shrink: float = 0,
     **kwargs,
 ):
     if layout_coordinate_system not in ("cartesian", "polar"):
@@ -211,11 +211,11 @@ def _compute_edge_path_straight(
     theta = atan2(*((vcoord_fig[1] - vcoord_fig[0])[::-1]))
 
     # Shorten at starting vertex
-    vs = _get_shorter_edge_coords(vpath_fig[0], vsize_fig[0], theta, padding) + vcoord_fig[0]
+    vs = _get_shorter_edge_coords(vpath_fig[0], vsize_fig[0], theta, shrink) + vcoord_fig[0]
     points.append(vs)
 
     # Shorten at end vertex
-    ve = _get_shorter_edge_coords(vpath_fig[1], vsize_fig[1], theta + pi, padding) + vcoord_fig[1]
+    ve = _get_shorter_edge_coords(vpath_fig[1], vsize_fig[1], theta + pi, shrink) + vcoord_fig[1]
     points.append(ve)
 
     codes = ["MOVETO", "LINETO"]
@@ -237,7 +237,7 @@ def _compute_edge_path_waypoints(
     layout_coordinate_system: str = "cartesian",
     points_per_curve: int = 30,
     ports: Pair[Optional[str]] = (None, None),
-    padding: float = 0,
+    shrink: float = 0,
     **kwargs,
 ):
     if not isinstance(waypoints, str):
@@ -263,7 +263,7 @@ def _compute_edge_path_waypoints(
 
             # Shorten at vertex border
             vshorts[i] = (
-                _get_shorter_edge_coords(vpath_fig[i], vsize_fig[i], thetas[i], padding)
+                _get_shorter_edge_coords(vpath_fig[i], vsize_fig[i], thetas[i], shrink)
                 + vcoord_fig[i]
             )
 
@@ -293,7 +293,7 @@ def _compute_edge_path_waypoints(
 
             # Shorten at vertex border
             vshorts[i] = (
-                _get_shorter_edge_coords(vpath_fig[i], vsize_fig[i], thetas[i], padding)
+                _get_shorter_edge_coords(vpath_fig[i], vsize_fig[i], thetas[i], shrink)
                 + vcoord_fig[i]
             )
 
@@ -343,7 +343,7 @@ def _compute_edge_path_waypoints(
 
             # Shorten at vertex border
             vshort = (
-                _get_shorter_edge_coords(vpath_fig[i], vsize_fig[i], theta, padding) + vcoord_fig[i]
+                _get_shorter_edge_coords(vpath_fig[i], vsize_fig[i], theta, shrink) + vcoord_fig[i]
             )
             thetas.append(theta)
             vshorts.append(vshort)
@@ -391,7 +391,7 @@ def _compute_edge_path_curved(
     trans,
     trans_inv,
     ports: Pair[Optional[str]] = (None, None),
-    padding: float = 0,
+    shrink: float = 0,
 ):
     """Shorten the edge path along a cubic Bezier between the vertex centres.
 
@@ -445,7 +445,7 @@ def _compute_edge_path_curved(
     for i in range(2):
         thetas[i] = atan2(*((auxs[i] - vcoord_fig[i])[::-1]))
         vs[i] = (
-            _get_shorter_edge_coords(vpath_fig[i], vsize_fig[i], thetas[i], padding) + vcoord_fig[i]
+            _get_shorter_edge_coords(vpath_fig[i], vsize_fig[i], thetas[i], shrink) + vcoord_fig[i]
         )
 
     path = {

iplotx/style/__init__.py

@@ -141,6 +141,27 @@ def merge_styles(
                     value,
                 )
 
+    def _sanitize_ambiguous(style: dict):
+        """Fix a few ambiguous cases in the style dict."""
+
+        # Accept "node" style as "vertex" style for user flexibility
+        if "node" in style:
+            style_node = style.pop("node")
+            if "vertex" not in style:
+                style["vertex"] = style_node
+            else:
+                # "node" style applies on TOP of "vertex" style
+                _update(style_node, style["vertex"])
+
+        # NOTE: Deprecate edge_padding for edge_shrink
+        for edgekey in ["edge", "leafedge"]:
+            if "padding" in style.get(edgekey, {}):
+                # shrink takes over
+                if "shrink" in style[edgekey]:
+                    del style[edgekey]["padding"]
+                else:
+                    style[edgekey]["shrink"] = style[edgekey].pop("padding")
+
     merged = {}
     for style in styles:
         if isinstance(style, str):
@@ -148,6 +169,7 @@ def merge_styles(
         else:
             _sanitize_leaves(style)
             unflatten_style(style)
+            _sanitize_ambiguous(style)
         _update(style, merged)
 
     return merged

iplotx/style/leaf_info.py

@@ -22,10 +22,12 @@ rotating_leaves = (
     "vpadding",
     "hmargin",
     "vmargin",
-    "padding",
     "ports",
     "width",
     "height",
+    "shrink",
+    # DEPRECATED
+    "padding",
 )
 
 # These properties are also terminal style properties, but they cannot be rotated.

iplotx/style/library.py

@@ -62,7 +62,7 @@ style_library = {
     "feedback": {
         "edge": {
             "linewidth": 4,
-            "padding": 10,
+            "shrink": 10,
             "arrow": {
                 "marker": ")>",
                 "width": 20,

iplotx/tree.py

@@ -311,13 +311,21 @@ class TreeArtist(mpl.artist.Artist):
         if not leaf_style.get("deep", True):
             return
 
+        # Given the conditions above, we should have leaf labels. If not,
+        # make a None series with a valid index
+        leaf_label_series = self._get_label_series("leaf")
+        if leaf_label_series is None:
+            leaf_label_series = self._ipx_internal_data["leaf_df"].copy()
+            leaf_label_series["label"] = None
+            leaf_label_series = leaf_label_series["label"]
+
         edge_style = get_style(
             ".leafedge",
         )
         default_style = {
             "linestyle": "--",
             "linewidth": 1,
-            "edgecolor": "#111",
+            "color": "#111",
         }
         for key, value in default_style.items():
             if key not in edge_style:
@@ -335,14 +343,24 @@ class TreeArtist(mpl.artist.Artist):
         else:
             cmap_fun = None
 
-        leaf_shallow_layout = self.get_layout("leaf")
-
         if "cmap" in edge_style:
             colorarray = []
         edgepatches = []
         adjacent_vertex_ids = []
-        for i, vid in enumerate(leaf_shallow_layout.index):
-            edge_stylei = rotate_style(edge_style, index=i, key=vid)
+        for i, (vid, label) in enumerate(leaf_label_series.items()):
+            # Use leaf label to compute backup key for style rotation
+            # NOTE: This is quite a common use case. Users typically
+            # refer to leaves via their labels because that's what you see
+            # on screen. While an object exact match should take priority
+            # for power users, a backup based on label is useful. Beginners
+            # won't stumble upon this anyway since it's only used if
+            # a dict-like property for leaf edges is provided, which is a
+            # decently advanced thing to do.
+            # NOTE: Multiple leaves might have the same label, in which case
+            # all leaves will be style matched to this *unless* the dict-like
+            # style object *also* matches on leaf objects directly, which
+            # takes precedence since key2 is only a fallback.
+            edge_stylei = rotate_style(edge_style, index=i, key=vid, key2=label)
 
             if cmap_fun is not None:
                 colorarray.append(edge_stylei["color"])

iplotx/version.py

@@ -2,4 +2,4 @@
 iplotx version information module.
 """
 
-__version__ = "0.6.7"
+__version__ = "0.7.0"

iplotx/vertex.py

@@ -247,7 +247,11 @@ class VertexCollection(PatchCollection):
         patches = []
         sizes = []
         for i, (vid, row) in enumerate(self._layout.iterrows()):
-            stylei = rotate_style(style, index=i, key=vid)
+            # Use vertex labels if present as a fallback key for style rotation
+            # This way one can be very specific via the exact object or cast
+            # a looser net with the label string
+            key2 = self._labels.iloc[i] if self._labels is not None else None
+            stylei = rotate_style(style, index=i, key=vid, key2=key2)
             if stylei.get("size", 20) == "label":
                 stylei["size"] = _get_label_width_height(
                     str(self._labels[vid]), **style.get("label", {})

{iplotx-0.6.7.dist-info → iplotx-0.7.0.dist-info}/METADATA

@@ -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.dist-info → iplotx-0.7.0.dist-info}/RECORD

@@ -6,13 +6,13 @@ iplotx/label.py,sha256=6am3a0ejcW_bWEXSOODE1Ke3AyCU1lJ45RfnXNbHAQw,8923
 iplotx/layout.py,sha256=KxmRLqjo8AYCBAmXez8rIiLU2sM34qhb6ox9AHYwRyE,4839
 iplotx/network.py,sha256=LaW9zQZ4sKiDVb25_icnquGNnN7HrKC7NO07o6PSmGI,11527
 iplotx/plotting.py,sha256=IEUxW1xzTljLjBfsVP2BNsOPCDpj5bEPZ99bzvD5-mo,10066
-iplotx/tree.py,sha256=Zzz7nCPZrSjh9_yHXFdd8hjbF-FYURTZs00rUHc4OT8,27304
+iplotx/tree.py,sha256=-69lpPjisRfigY4fDQcmVxzOAf1tGwMXviUcW6mZU6U,28508
 iplotx/typing.py,sha256=QLdzV358IiD1CFe88MVp0D77FSx5sSAVUmM_2WPPE8I,1463
-iplotx/version.py,sha256=1Mi-AUAfWTkSNROfIn7bWkeZBzSl_j_A7HmbA4LSs0c,66
-iplotx/vertex.py,sha256=-JZaQPjIAWWP8Wap1HyR4g4HXLNGLwjf4v6jyo994Tk,14671
-iplotx/edge/__init__.py,sha256=HlxeIs88RbRrTetJNLcoq9gjV7cBhOdqQoiVZFFylFc,27081
-iplotx/edge/arrow.py,sha256=C4XoHGCYou1z2alz5Q2VhdaWYEzgebtEF70zVYY_frk,15533
-iplotx/edge/geometry.py,sha256=tiaF4PzvsNBoROrEgcCsw0YdxxZr3oBxF4ord_k4ThA,15069
+iplotx/version.py,sha256=8BIMMcy91d9_BPlUuoNyMNeyj04-gejk1STd-SLsrT0,66
+iplotx/vertex.py,sha256=hqdlD9fRBSwH5bRvlpaaPu7jgUR4z9nob1SYfPWDxtI,14966
+iplotx/edge/__init__.py,sha256=AVnLsrDWWCkix1LVhrjpWKEKDxOp8joM4tF6RqEHC8I,27115
+iplotx/edge/arrow.py,sha256=ZKt3UNZ7XRa2S3KxpoQfd4q_6eSUHOS476BZNqlf2pw,16462
+iplotx/edge/geometry.py,sha256=wpFTi12-BaUaWr6Ie-nHV_SMAdSGJvjzJaqeEaSPf9w,15053
 iplotx/edge/leaf.py,sha256=SyGMv2PIOoH0pey8-aMVaZheK3hNe1Qz_okcyWbc4E4,4268
 iplotx/edge/ports.py,sha256=BpkbiEhX4mPBBAhOv4jcKFG4Y8hxXz5GRtVLCC0jbtI,1235
 iplotx/ingest/__init__.py,sha256=S0YfnXcFKseB7ZBQc4yRt0cNDsLlhqdom0TmSY3OY2E,4756
@@ -26,13 +26,13 @@ iplotx/ingest/providers/tree/cogent3.py,sha256=JmELbDK7LyybiJzFNbmeqZ4ySJoDajvFf
 iplotx/ingest/providers/tree/ete4.py,sha256=D7usSq0MOjzrk3EoLi834IlaDGwv7_qG6Qt0ptfKqfI,928
 iplotx/ingest/providers/tree/simple.py,sha256=aV9wGqBomJ5klM_aJQeuL_Q_J1pLCv6AFN98BPDiKUw,2593
 iplotx/ingest/providers/tree/skbio.py,sha256=O1KUr8tYi28pZ3VVjapgO4Uj-YpMuix3GhOH5je8Lv4,822
-iplotx/style/__init__.py,sha256=XMkQZ1U63wVNo98Zo5uJAn-uQgW2OTZABAizJqiuB3s,12253
-iplotx/style/leaf_info.py,sha256=JoX1cPjRM_k3f93jzUPQ3gPlVP4wY_n032nOVhrgelU,969
-iplotx/style/library.py,sha256=wO-eeY3EZfAl0v21aX9f5_MiZhHuL2kGsBYA3uJkIGs,8535
+iplotx/style/__init__.py,sha256=_LhOJ9WJzC3of_nbaJyAJX3k4paI8utrigTzYDZRSB8,13138
+iplotx/style/leaf_info.py,sha256=mcd6ewZl3jC0CPshmbeUkNp2geoihJW9515roGy2T8o,1000
+iplotx/style/library.py,sha256=58Y8BlllGLsR4pQM7_PVCP5tH6_4GkchXZvJpqGHlcg,8534
 iplotx/utils/geometry.py,sha256=6RrC6qaB0-1vIk1LhGA4CfsiMd-9JNniSPyL_l9mshE,9245
 iplotx/utils/internal.py,sha256=WWfcZDGK8Ut1y_tOHRGg9wSqY1bwSeLQO7dHM_8Tvwo,107
 iplotx/utils/matplotlib.py,sha256=wELE73quQv10-1w9uA5eDTgkZkylJvjg7pd3K5tZPOo,6294
 iplotx/utils/style.py,sha256=wMWxJykxBD-JmcN8-rSKlWcV6pMfwKgR4EzSpk_NX8k,547
-iplotx-0.6.7.dist-info/METADATA,sha256=O3tkLhtN4pM3FxyONC75a3CYvf1Ba6iU8bHRTgtBzgM,4908
-iplotx-0.6.7.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
-iplotx-0.6.7.dist-info/RECORD,,
+iplotx-0.7.0.dist-info/METADATA,sha256=vbdamou2U35GeUBn4_fG8kzeC9fTwYRzKeg2Ik9212Q,4908
+iplotx-0.7.0.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
+iplotx-0.7.0.dist-info/RECORD,,