iplotx 1.5.1__py3-none-any.whl → 1.7.0__py3-none-any.whl

iplotx/edge/__init__.py

@@ -367,21 +367,13 @@ class EdgeCollection(mpl.collections.PatchCollection):
 
             # Leaf rotation
             edge_stylei = rotate_style(self._style, index=i, key=(v1, v2))
-            if edge_stylei.get("curved", False):
-                tension = edge_stylei.get("tension", 5)
-                ports = edge_stylei.get("ports", (None, None))
-            elif edge_stylei.get("arc", False):
-                tension = edge_stylei.get("tension", 1)
-                ports = None
-            else:
-                tension = 0
-                ports = None
 
             # Scale shrink by dpi
             dpi = self.figure.dpi if hasattr(self, "figure") else 72.0
             shrink = dpi / 72.0 * edge_stylei.pop("shrink", 0)
 
-            # False is a synonym for "none"
+            # Edge geometry and waypoints
+            # waypoints: False is a synonym for "none"
             waypoints = edge_stylei.get("waypoints", "none")
             if waypoints is False or waypoints is np.False_:
                 waypoints = "none"
@@ -391,10 +383,32 @@ class EdgeCollection(mpl.collections.PatchCollection):
                 raise ValueError(
                     "Could not determine automatically type of edge waypoints.",
                 )
-            if waypoints != "none":
-                ports = edge_stylei.get("ports", (None, None))
 
+            # Waypoints, curved, and arc have a complex logic
+            # TODO: This could be simplified I suppose
+            has_waypoints = waypoints != "none"
+            curved = edge_stylei.get("curved", False)
             arc = edge_stylei.get("arc", False)
+            ports = edge_stylei.get("ports", (None, None))
+
+            # For now, we establish a hierarchy from the most specialised to
+            # the most common cases. Each specialisation silences lower levels
+            # Tension and ports are entirely enslaved to the
+            # waypoint/arc/curved geometry settings.
+            # NOTE: The idea here is to not punish users for slight style
+            # inconsistencies that may well stem from fallback libraries
+            if has_waypoints:
+                tension = 0
+                arc = False
+            elif arc:
+                tension = edge_stylei.get("tension", 1)
+                ports = None
+                curved = False
+            elif curved:
+                tension = edge_stylei.get("tension", 5)
+            else:
+                tension = 0
+                ports = None
 
             # Compute actual edge path
             path, angles = _compute_edge_path(
@@ -406,6 +420,7 @@ class EdgeCollection(mpl.collections.PatchCollection):
                 tension=tension,
                 waypoints=waypoints,
                 ports=ports,
+                curved=curved,
                 arc=arc,
                 layout_coordinate_system=self._vertex_collection.get_layout_coordinate_system(),
                 shrink=shrink,

iplotx/edge/geometry.py

@@ -239,6 +239,7 @@ def _compute_edge_path_straight(
 
 def _compute_edge_path_waypoints(
     waypoints,
+    curved,
     vcoord_data,
     vpath_fig,
     vsize_fig,
@@ -277,8 +278,19 @@ def _compute_edge_path_waypoints(
                 + vcoord_fig[i]
             )
 
-        points = [vshorts[0]] + list(waypoints) + [vshorts[1]]
-        codes = ["MOVETO"] + ["LINETO"] * len(waypoints) + ["LINETO"]
+        if not curved:
+            points = [vshorts[0]] + list(waypoints) + [vshorts[1]]
+            codes = ["MOVETO"] + ["LINETO"] * len(waypoints) + ["LINETO"]
+        else:
+            points = [vshorts[0]]
+            for i, waypoint in enumerate(waypoints):
+                if i != 0:
+                    points.append(0.5 * (points[-1] + waypoint))
+                points.append(waypoint)
+                points.append(waypoint)
+            points.append(vshorts[1])
+            codes = ["MOVETO"] + ["CURVE4"] * (len(points) - 1)
+
         angles = tuple(thetas)
 
     elif waypoints in ("x0y1", "y0x1"):
@@ -587,6 +599,7 @@ def _compute_edge_path(
     tension: float = 0,
     waypoints: str | tuple[float, float] | Sequence[tuple[float, float]] | np.ndarray = "none",
     ports: Pair[Optional[str]] = (None, None),
+    curved: bool = False,
     arc: bool = False,
     layout_coordinate_system: str = "cartesian",
     **kwargs,
@@ -600,6 +613,7 @@ def _compute_edge_path(
     if waypoints != "none":
         return _compute_edge_path_waypoints(
             waypoints,
+            curved,
             *args,
             layout_coordinate_system=layout_coordinate_system,
             ports=ports,

iplotx/plotting.py

@@ -20,6 +20,7 @@ from .network import NetworkArtist
 from .network.groups import GroupingCollection
 from .tree import TreeArtist
 from .style import context
+from .utils.matplotlib import _heuristic_show
 
 
 def network(
@@ -36,6 +37,7 @@ def network(
     margins: float | tuple[float, float] | tuple[float, float, float] = 0,
     strip_axes: bool = True,
     figsize: Optional[tuple[float, float]] = None,
+    show: Optional[bool] = None,
     **kwargs,
 ) -> list[mpl.artist.Artist]:
     """Plot this network and/or vertex grouping using the specified layout.
@@ -70,6 +72,9 @@ def network(
         figsize: If ax is None, a new matplotlib Figure is created. This argument specifies
             the (width, height) dimension of the figure in inches. If ax is not None, this
             argument is ignored. If None, the default matplotlib figure size is used.
+        show: If True, call plt.show() after plotting. If False, do not call plt.show(). If
+            None (default), try to guess based on the environment and do not show in case of
+            doubt.
         kwargs: Additional arguments are treated as an alternate way to specify style. If
             both "style" and additional **kwargs are provided, they are both applied in that
             order (style, then **kwargs).
@@ -78,7 +83,12 @@ def network(
         A list of mpl.artist.Artist objects, set as a direct child of the matplotlib Axes.
         The list can have one or two elements, depending on whether you are requesting to
         plot a network, a grouping, or both.
+
+    NOTE: If your plots are now showing to screen, try passing show=True.
     """
+    if show is None:
+        show = _heuristic_show()
+
     # Equivalence of node_labels and vertex_labels
     if node_labels is not None:
         vertex_labels = node_labels
@@ -164,6 +174,9 @@ def network(
         if (margins[0] != 0) or (margins[1] != 0) or ((len(margins) == 3) and (margins[2] != 0)):
             ax.margins(*margins)
 
+        if show:
+            plt.show()
+
         return artists
 
 
@@ -187,6 +200,7 @@ def tree(
     margins: float | tuple[float, float] = 0,
     strip_axes: bool = True,
     figsize: Optional[tuple[float, float]] = None,
+    show: Optional[bool] = None,
     **kwargs,
 ) -> TreeArtist:
     """Plot a tree using the specified layout.
@@ -226,13 +240,21 @@ def tree(
         figsize: If ax is None, a new matplotlib Figure is created. This argument specifies
             the (width, height) dimension of the figure in inches. If ax is not None, this
             argument is ignored. If None, the default matplotlib figure size is used.
+        show: If True, call plt.show() after plotting. If False, do not call plt.show(). If
+            None (default), try to guess based on the environment and do not show in case of
+            doubt.
         kwargs: Additional arguments are treated as an alternate way to specify style. If
             both "style" and additional **kwargs are provided, they are both applied in that
             order (style, then **kwargs).
 
     Returns:
         A TreeArtist object, set as a direct child of the matplotlib Axes.
+
+    NOTE: If your plots are now showing to screen, try passing show=True.
     """
+    if show is None:
+        show = _heuristic_show()
+
     # Equivalence of node_labels and vertex_labels
     if node_labels is not None:
         vertex_labels = node_labels
@@ -270,6 +292,9 @@ def tree(
         if (margins[0] != 0) or (margins[1] != 0):
             ax.margins(*margins)
 
+        if show:
+            plt.show()
+
     return artist
 
 
@@ -285,6 +310,7 @@ def doubletree(
     margins: float | tuple[float, float] = 0,
     strip_axes: bool = True,
     figsize: Optional[tuple[float, float]] = None,
+    show: Optional[bool] = None,
 ) -> tuple[TreeArtist, TreeArtist]:
     """Visualize two trees facing each other.
 
@@ -306,9 +332,26 @@ def doubletree(
         figsize: If ax is None, a new matplotlib Figure is created. This argument specifies
             the (width, height) dimension of the figure in inches. If ax is not None, this
             argument is ignored. If None, the default matplotlib figure size is used.
+        show: If True, call plt.show() after plotting. If False, do not call plt.show(). If
+            None (default), try to guess based on the environment and do not show in case of
+            doubt.
     Returns:
         A tuple with the left and right TreeArtist objects.
+
+    NOTE: If your plots are now showing to screen, try passing show=True.
     """
+    if show is None:
+        show = _heuristic_show()
+
+    if kwargs_left is None:
+        kwargs_left = {}
+    if "show" not in kwargs_left:
+        kwargs_left["show"] = False
+    if kwargs_right is None:
+        kwargs_right = {}
+    if "show" not in kwargs_right:
+        kwargs_right["show"] = False
+
     artist1 = tree(
         tree_left,
         layout="horizontal",
@@ -316,14 +359,11 @@ def doubletree(
         ax=ax,
         strip_axes=False,
         figsize=figsize,
-        **kwargs_left or {},
+        **kwargs_left,
     )
 
     ax = artist1.axes
 
-    if kwargs_right is None:
-        kwargs_right = {}
-
     had_layout_start = "layout_start" in kwargs_right
 
     artist2 = tree(
@@ -348,6 +388,9 @@ def doubletree(
 
     _postprocess_axes(ax, [artist1, artist2], strip=strip_axes, ignore_previous=True)
 
+    if show:
+        plt.show()
+
     return (artist1, artist2)
 
 

iplotx/utils/matplotlib.py

@@ -282,3 +282,8 @@ def _get_data_scale(X, Y, Z):
     ptp_y = Y.max() - Y.min()
     ptp_z = Z.max() - Z.min()
     return np.sqrt(ptp_x**2 + ptp_y**2 + ptp_z**2)
+
+
+def _heuristic_show():
+    """Try guessing whether plt.show() should be called automatically."""
+    return False

iplotx/version.py

@@ -2,4 +2,4 @@
 iplotx version information module.
 """
 
-__version__ = "1.5.1"
+__version__ = "1.7.0"

{iplotx-1.5.1.dist-info → iplotx-1.7.0.dist-info}/METADATA

@@ -1,7 +1,7 @@
 Metadata-Version: 2.4
 Name: iplotx
-Version: 1.5.1
-Summary: Plot networkx from igraph and networkx.
+Version: 1.7.0
+Summary: Universal network and tree visualisation library.
 Project-URL: Homepage, https://github.com/fabilab/iplotx
 Project-URL: Documentation, https://readthedocs.org/iplotx
 Project-URL: Repository, https://github.com/fabilab/iplotx.git
@@ -41,7 +41,7 @@ Description-Content-Type: text/markdown
 [![RTD](https://readthedocs.org/projects/iplotx/badge/?version=latest)](https://iplotx.readthedocs.io/en/latest/)
 [![Coverage Status](https://coveralls.io/repos/github/fabilab/iplotx/badge.svg?branch=main)](https://coveralls.io/github/fabilab/iplotx?branch=main)
 ![pylint](assets/pylint.svg)
-[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.16599333.svg)](https://doi.org/10.5281/zenodo.16599333)
+[DOI](https://f1000research.com/articles/14-1377)
 
 
 # iplotx
@@ -90,10 +90,10 @@ See [readthedocs](https://iplotx.readthedocs.io/en/latest/) for the full documen
 See [gallery](https://iplotx.readthedocs.io/en/latest/gallery/index.html).
 
 ## Citation
-If you use `iplotx` for publication figures, please cite the [zenodo preprint](https://doi.org/10.5281/zenodo.16599333):
+If you use `iplotx` for publication figures, please cite:
 
 ```
-F. Zanini. (2025). Unified network visualisation in Python. Zenodo [PREPRINT]. https://doi.org/10.5281/zenodo.16599333
+F. Zanini. A universal tool for visualisation of networks and trees in Python. F1000Research 2025, 14:1377. https://doi.org/10.12688/f1000research.173131.1
 ```
 
 ## Features

{iplotx-1.5.1.dist-info → iplotx-1.7.0.dist-info}/RECORD

@@ -1,17 +1,17 @@
 iplotx/__init__.py,sha256=RKlRSSEAv2qECd6rCiovdLDu-4k1eXMGCOCPt0xwpFA,523
 iplotx/artists.py,sha256=2dBDT240zGwKb6tIc_y9pXeyU3LuYeF9wjj2tvi4KJo,730
 iplotx/label.py,sha256=7eS8ByadrhdIFOZz19U4VrS-oXY_ndFYNB-D4RZbFqI,9573
-iplotx/plotting.py,sha256=RyAdvaHSpuyJkf8DF3SJBvEXBrPmJEdovUyAlBWQvqU,16228
+iplotx/plotting.py,sha256=QlXCh3t1J9YmzkqrS6ozwSilFxZ1hwBHHWW-kpd-7zM,17679
 iplotx/typing.py,sha256=QLdzV358IiD1CFe88MVp0D77FSx5sSAVUmM_2WPPE8I,1463
-iplotx/version.py,sha256=2-ElWE7kiH17_8qfp3S7cxPYli-UBakrm7tAh8DbG2E,66
+iplotx/version.py,sha256=7dTkHVHx2G_FnFiWdcEX1gkeNeCO9nu53SE10IwwwKM,66
 iplotx/vertex.py,sha256=Ta48M_6ZT8xKQWdI5XHiRxTt2LlJ9vshiDk34OzKYlY,16585
 iplotx/art3d/vertex.py,sha256=Xf8Um30X2doCd8KdNN7332F6BxC4k72Mb_GeRAuzQfQ,2545
 iplotx/art3d/edge/__init__.py,sha256=uw1U_mMXqcZAvea-7JbU1PUKULQD1CMMrbwY02tiWRQ,8529
 iplotx/art3d/edge/arrow.py,sha256=14BFXY9kDOUGPZl2fMD9gRVGyaaN5kyd-l6ikBg6WHU,3601
 iplotx/art3d/edge/geometry.py,sha256=76VUmpPG-4Mls7x_994dMwdDPrWWnjT7nHJsHfwK_hA,2467
-iplotx/edge/__init__.py,sha256=8iHtkrEaxseh308VWlTgbZ7OJECqkRwSq-oJzejxH5U,26837
+iplotx/edge/__init__.py,sha256=mp_JRGeJWPXZNpQ6vTgTdzgVO1YxcZMKuVKarJGuLnY,27522
 iplotx/edge/arrow.py,sha256=ymup2YT_0GVYMtZw_DSKrZqFHG_ysYteEhmoL6T8Mu4,17563
-iplotx/edge/geometry.py,sha256=Vt1Y_wH2Fto_rgrQbuhXUzsfBpjQLti8Qws-oAGLcUw,19745
+iplotx/edge/geometry.py,sha256=Qyi7Q7sOGAFXU6gFeWFLm6OoGetEasrfv8HzgSWO2gY,20210
 iplotx/edge/leaf.py,sha256=SyGMv2PIOoH0pey8-aMVaZheK3hNe1Qz_okcyWbc4E4,4268
 iplotx/edge/ports.py,sha256=BpkbiEhX4mPBBAhOv4jcKFG4Y8hxXz5GRtVLCC0jbtI,1235
 iplotx/ingest/__init__.py,sha256=k1Q-7lSdotMR4RkF1x0t19RFsTknohX0L507Dw69WyU,5035
@@ -41,8 +41,8 @@ iplotx/tree/cascades.py,sha256=Wwqhy46QGeb4LNGUuz_-bgNWUMz6PFzs_dIxIb1dtqc,8394
 iplotx/tree/scalebar.py,sha256=Yxt_kF8JdTwKGa8Jzqt3qVePPK5ZBG8P0EiONrsh3E8,11863
 iplotx/utils/geometry.py,sha256=6RrC6qaB0-1vIk1LhGA4CfsiMd-9JNniSPyL_l9mshE,9245
 iplotx/utils/internal.py,sha256=WWfcZDGK8Ut1y_tOHRGg9wSqY1bwSeLQO7dHM_8Tvwo,107
-iplotx/utils/matplotlib.py,sha256=p_53Oamof0RI4mtV8HrdDtZbgVqUxeUZ_KDvLZSiBUQ,8604
+iplotx/utils/matplotlib.py,sha256=T-jiqy8KxF1Q4BofT1rZbbdtmSC-j_kjNRcOg_IZpYM,8720
 iplotx/utils/style.py,sha256=vyNP80nDYVinqm6_9ltCJCtjK35ZcGlHvOskNv3eQBc,4225
-iplotx-1.5.1.dist-info/METADATA,sha256=8-x0TGoqdL4oRbC3MtMnYii8ZNbiRZmATGze3RbW3mE,5407
-iplotx-1.5.1.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
-iplotx-1.5.1.dist-info/RECORD,,
+iplotx-1.7.0.dist-info/METADATA,sha256=gItmBkiLmtBY73aY3IIycXX61yghAdv0wBmMXsDBpSw,5333
+iplotx-1.7.0.dist-info/WHEEL,sha256=WLgqFyCfm_KASv4WHyYy0P3pM_m7J5L9k2skdKLirC8,87
+iplotx-1.7.0.dist-info/RECORD,,

{iplotx-1.5.1.dist-info → iplotx-1.7.0.dist-info}/WHEEL

@@ -1,4 +1,4 @@
 Wheel-Version: 1.0
-Generator: hatchling 1.27.0
+Generator: hatchling 1.28.0
 Root-Is-Purelib: true
 Tag: py3-none-any