iplotx 1.1.0__py3-none-any.whl → 1.2.1__py3-none-any.whl

iplotx/__init__.py

@@ -11,6 +11,7 @@ from .plotting import (
     network,
     graph,
     tree,
+    doubletree,
     plot,
 )
 import iplotx.artists as artists
@@ -20,6 +21,7 @@ import iplotx.style as style
 __all__ = [
     "network",
     "tree",
+    "doubletree",
     "plot",
     "graph",
     "artists",

iplotx/edge/__init__.py

@@ -274,6 +274,12 @@ class EdgeCollection(mpl.collections.PatchCollection):
         """Return mappable for colorbar."""
         return self
 
+    def shift(self, x: float, y: float) -> None:
+        """Shift the cascade by a certain amount."""
+        for path in self._paths:
+            path.vertices[:, 0] += x
+            path.vertices[:, 1] += y
+
     def _get_adjacent_vertices_info(self):
         index = self._vertex_collection.get_index()
         index = pd.Series(

iplotx/edge/arrow.py

@@ -2,7 +2,12 @@
 Module for edge arrows in iplotx.
 """
 
-from typing import Never, Optional
+import sys
+if sys.version_info < (3, 11):
+    from typing_extensions import Never
+else:
+    from typing import Never
+from typing import Optional
 
 from math import atan2, cos, sin
 import numpy as np

iplotx/ingest/__init__.py

@@ -2,16 +2,24 @@
 This module focuses on how to ingest network/tree data into standard data structures no matter what library they come from.
 """
 
-import pathlib
-import pkgutil
-import importlib
-import warnings
+import sys
 from typing import (
     Optional,
     Sequence,
-    Protocol,
 )
+
+# NOTE: __init__ in Protocols has had a difficult gestation
+# https://github.com/python/cpython/issues/88970
+if sys.version_info < (3, 11):
+    Protocol = object
+else:
+    from typing import Protocol
+
 from collections.abc import Hashable
+import pathlib
+import pkgutil
+import importlib
+import warnings
 import pandas as pd
 
 from ..typing import (
@@ -35,6 +43,9 @@ provider_protocols = {
 data_providers: dict[str, dict[str, Protocol]] = {kind: {} for kind in provider_protocols}
 for kind in data_providers:
     providers_path = pathlib.Path(__file__).parent.joinpath("providers").joinpath(kind)
+    if sys.version_info < (3, 11):
+        providers_path = str(providers_path)
+
     for importer, module_name, _ in pkgutil.iter_modules([providers_path]):
         module = importlib.import_module(f"iplotx.ingest.providers.{kind}.{module_name}")
         for key, val in module.__dict__.items():
@@ -138,11 +149,11 @@ def ingest_tree_data(
 
 
 # INTERNAL FUNCTIONS
-def _update_data_providers(kind):
-    """Update data provieders dynamically from external packages."""
+def _update_data_providers(kind: str):
+    """Update data providers dynamically from external packages."""
     discovered_providers = importlib.metadata.entry_points(group=f"iplotx.{kind}_data_providers")
     for entry_point in discovered_providers:
-        if entry_point.name not in data_providers["network"]:
+        if entry_point.name not in data_providers[kind]:
             try:
                 data_providers[kind][entry_point.name] = entry_point.load()
             except Exception as e:

iplotx/ingest/providers/tree/simple.py

@@ -3,7 +3,6 @@ from typing import (
     Optional,
     Sequence,
     Iterable,
-    Self,
 )
 
 from ...typing import (
@@ -19,12 +18,12 @@ class SimpleTree:
         branch_length: Length of the branch leading to this node/tree.
     """
 
-    children: Sequence[Self] = []
+    children: Sequence = []
     branch_length: float = 1
     name: str = ""
 
     @classmethod
-    def from_dict(cls, data: dict) -> Self:
+    def from_dict(cls, data: dict):
         """Create a SimpleTree from a dictionary.
 
         Parameters:

iplotx/ingest/typing.py

@@ -5,15 +5,20 @@ Networkx and trees are treated separately for practical reasons: many tree analy
 work as well on general networks.
 """
 
+import sys
 from typing import (
-    NotRequired,
-    TypedDict,
-    Protocol,
     Optional,
     Sequence,
     Any,
     Iterable,
 )
+# NOTE: __init__ in Protocols has had a difficult gestation
+# https://github.com/python/cpython/issues/88970
+if sys.version_info < (3, 11):
+    Protocol = object
+else:
+    from typing import Protocol
+
 from collections.abc import Hashable
 import numpy as np
 import pandas as pd
@@ -26,6 +31,11 @@ from .heuristics import (
     normalise_tree_layout,
 )
 
+if sys.version_info < (3, 11):
+    from typing_extensions import TypedDict, NotRequired
+else:
+    from typing import TypedDict, NotRequired
+
 
 class NetworkData(TypedDict):
     """Network data structure for iplotx."""

iplotx/network/__init__.py

@@ -1,7 +1,6 @@
 from typing import (
     Optional,
     Sequence,
-    Self,
 )
 import numpy as np
 import pandas as pd
@@ -103,8 +102,8 @@ class NetworkArtist(mpl.artist.Artist):
     @classmethod
     def from_other(
         cls: "NetworkArtist",  # NOTE: This is fixed in Python 3.14
-        other: Self,
-    ) -> Self:
+        other,
+    ):
         """Create a NetworkArtist as a copy of another one.
 
         Parameters:
@@ -123,7 +122,7 @@ class NetworkArtist(mpl.artist.Artist):
     def from_edgecollection(
         cls: "NetworkArtist",  # NOTE: This is fixed in Python 3.14
         edge_collection: EdgeCollection | Edge3DCollection,
-    ) -> Self:
+    ):
         """Create a NetworkArtist from iplotx artists.
 
         Parameters:

iplotx/plotting.py

@@ -1,4 +1,8 @@
-from typing import Optional, Sequence
+from typing import (
+    Optional,
+    Sequence,
+    Any,
+)
 from contextlib import nullcontext
 import numpy as np
 import pandas as pd
@@ -269,8 +273,86 @@ def tree(
     return artist
 
 
+def doubletree(
+    tree_left: Optional[TreeType] = None,
+    tree_right: Optional[TreeType] = None,
+    kwargs_left: Optional[dict[Any]] = None,
+    kwargs_right: Optional[dict[Any]] = None,
+    gap: float = 0,
+    ax: Optional[mpl.axes.Axes] = None,
+    title: Optional[str] = None,
+    aspect: Optional[str | float] = None,
+    margins: float | tuple[float, float] = 0,
+    strip_axes: bool = True,
+    figsize: Optional[tuple[float, float]] = None,
+) -> tuple[TreeArtist, TreeArtist]:
+    """Visualize two trees facing each other.
+
+    Parameters:
+        tree_left: The tree to plot on the left side.
+        tree_right: The tree to plot on the right side.
+        kwargs_left: Additional keyword arguments passed to the left tree plotting function.
+        kwargs_right: Additional keyword arguments passed to the right tree plotting function.
+        ax: The axis to plot on. If None, a new figure and axis will be created. Defaults to
+            None.
+        title: If not None, set the axes title to this value.
+        aspect: If not None, set the aspect ratio of the axis to this value. The most common
+            value is 1.0, which proportionates x- and y-axes.
+        margins: How much margin to leave around the plot. A higher value (e.g. 0.1) can be
+            used as a quick fix when some vertex shapes reach beyond the plot edge. This is
+            a fraction of the data limits, so 0.1 means 10% of the data limits will be left
+            as margin.
+        strip_axes: If True, remove axis spines and ticks.
+        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.
+    Returns:
+        A tuple with the left and right TreeArtist objects.
+    """
+    artist1 = tree(
+        tree_left,
+        layout="horizontal",
+        layout_orientation="right",
+        ax=ax,
+        strip_axes=False,
+        figsize=figsize,
+        **kwargs_left or {},
+    )
+
+    ax = artist1.axes
+
+    if kwargs_right is None:
+        kwargs_right = {}
+
+    had_layout_start = "layout_start" in kwargs_right
+
+    artist2 = tree(
+        tree_right,
+        layout="horizontal",
+        layout_orientation="left",
+        ax=ax,
+        title=title,
+        aspect=aspect,
+        strip_axes=False,
+        margins=margins,
+        **kwargs_right,
+    )
+
+    if not had_layout_start:
+        x2min = artist2.get_layout().values[:, 0].min()
+        x1max = artist1.get_layout().values[:, 0].max()
+        xshift = x1max - x2min + gap
+
+        artist2.shift(0.5 * xshift, 0)
+        artist1.shift(-0.5 * xshift, 0)
+
+    _postprocess_axes(ax, [artist1, artist2], strip=strip_axes, ignore_previous=True)
+
+    return (artist1, artist2)
+
+
 # INTERNAL ROUTINES
-def _postprocess_axes(ax, artists, strip=True, had_data=None):
+def _postprocess_axes(ax, artists, strip=True, had_data=None, ignore_previous=False):
     """Postprocess axis after plotting."""
 
     if strip:
@@ -309,7 +391,11 @@ def _postprocess_axes(ax, artists, strip=True, had_data=None):
         for art in artists:
             bboxes.append(art.get_datalim(ax.transData))
         bbox = mpl.transforms.Bbox.union(bboxes)
-        ax.update_datalim(bbox)
+
+        if not ignore_previous:
+            ax.update_datalim(bbox)
+        else:
+            ax.dataLim.update_from_data_xy(bbox.corners(), ignore=True)
 
         # Autoscale for x/y axis limits
         ax.autoscale_view()

iplotx/tree/__init__.py

@@ -219,6 +219,31 @@ class TreeArtist(mpl.artist.Artist):
         else:
             raise ValueError(f"Unknown layout kind: {kind}. Use 'vertex' or 'edge'.")
 
+    def shift(self, x: float, y: float) -> None:
+        """Shift layout coordinates for all tree elements.
+
+        Paramerers:
+            x: The shift in x direction.
+            y: The shift in y direction.
+        """
+        layout_columns = [f"_ipx_layout_{i}" for i in range(self._ipx_internal_data["ndim"])]
+        self._ipx_internal_data["vertex_df"][layout_columns[0]] += x
+        self._ipx_internal_data["vertex_df"][layout_columns[1]] += y
+
+        self.get_vertices()._layout.values[:, 0] += x
+        self.get_vertices()._layout.values[:, 1] += y
+        self.get_vertices()._update_offsets_from_layout()
+
+        self.get_edges().shift(x, y)
+
+        if hasattr(self, "_leaf_vertices"):
+            self.get_leaf_vertices()._layout.values[:, 0] += x
+            self.get_leaf_vertices()._layout.values[:, 1] += y
+            self.get_leaf_vertices()._update_offsets_from_layout()
+
+        if hasattr(self, "_cascades"):
+            self._cascades.shift(x, y)
+
     def get_datalim(self, transData, pad=0.15):
         """Get limits on x/y axes based on the graph layout data.
 

iplotx/tree/cascades.py

@@ -158,6 +158,12 @@ class CascadeCollection(mpl.collections.PatchCollection):
             zorder=zorder,
         )
 
+    def shift(self, x: float, y: float) -> None:
+        """Shift the cascade by a certain amount."""
+        for path in self._paths:
+            path.vertices[:, 0] += x
+            path.vertices[:, 1] += y
+
     def get_maxdepth(self) -> float:
         """Get the maxdepth of the cascades.
 

iplotx/version.py

@@ -2,4 +2,4 @@
 iplotx version information module.
 """
 
-__version__ = "1.1.0"
+__version__ = "1.2.1"

{iplotx-1.1.0.dist-info → iplotx-1.2.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: iplotx
-Version: 1.1.0
+Version: 1.2.1
 Summary: Plot networkx from igraph and networkx.
 Project-URL: Homepage, https://github.com/fabilab/iplotx
 Project-URL: Documentation, https://readthedocs.org/iplotx
@@ -26,8 +26,8 @@ Classifier: Programming Language :: Python :: 3.13
 Classifier: Topic :: Scientific/Engineering :: Visualization
 Classifier: Topic :: System :: Networking
 Classifier: Typing :: Typed
-Requires-Python: >=3.11
-Requires-Dist: matplotlib>=2.0.0
+Requires-Python: >=3.10
+Requires-Dist: matplotlib>=3.10.0
 Requires-Dist: numpy>=2.0.0
 Requires-Dist: pandas>=2.0.0
 Provides-Extra: igraph
@@ -78,8 +78,7 @@ import iplotx as ipx
 
 g = nx.Graph([(0, 1), (1, 2), (2, 3), (3, 4), (4, 0)])
 layout = nx.layout.circular_layout(g)
-fig, ax = plt.subplots(figsize=(3, 3))
-ipx.plot(g, ax=ax, layout=layout)
+ipx.plot(g, layout)
 ```
 
 ![Quick start image](/docs/source/_static/graph_basic.png)

{iplotx-1.1.0.dist-info → iplotx-1.2.1.dist-info}/RECORD

@@ -1,23 +1,23 @@
-iplotx/__init__.py,sha256=RzSct91jO8abrxOIn33rKEnDUgYpu1oj4olbObgX_hs,489
+iplotx/__init__.py,sha256=RKlRSSEAv2qECd6rCiovdLDu-4k1eXMGCOCPt0xwpFA,523
 iplotx/artists.py,sha256=2dBDT240zGwKb6tIc_y9pXeyU3LuYeF9wjj2tvi4KJo,730
 iplotx/label.py,sha256=7eS8ByadrhdIFOZz19U4VrS-oXY_ndFYNB-D4RZbFqI,9573
 iplotx/layout.py,sha256=S-iFxHaIOzhBDG2JUzl9_oDBRP5TYY1hXnEOs0h1Rck,5588
-iplotx/plotting.py,sha256=FvV33DCuEjJwO9ytiYJuQmfOywgF-cDANd6nEE5s8R0,13211
+iplotx/plotting.py,sha256=RyAdvaHSpuyJkf8DF3SJBvEXBrPmJEdovUyAlBWQvqU,16228
 iplotx/typing.py,sha256=QLdzV358IiD1CFe88MVp0D77FSx5sSAVUmM_2WPPE8I,1463
-iplotx/version.py,sha256=mrnbNTnvhHXH5H10Drqi5HLqPXOwoyNlRYIAv7vTAy0,66
+iplotx/version.py,sha256=2CsPuf8-y4qmmHpnn5_1DZwxypX8SRHYrsqTTmN1h5A,66
 iplotx/vertex.py,sha256=_yYyvusn4vYvi6RBEW6CHa3vnbv43GnZylnMIaK4bG0,16040
 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=lkrMkQFx9PNzorKc9trQ8MggC-nZSyALhvP78DMvhN4,26363
-iplotx/edge/arrow.py,sha256=U7vvBo7IMwo1qiyU9cyUEwraOaBcJLgdu9oU2OyoHL4,17453
+iplotx/edge/__init__.py,sha256=GlY_CmlMVD1DWJeOb5cFQEP_4K1pPneS_fRLqAxNGMk,26573
+iplotx/edge/arrow.py,sha256=ymup2YT_0GVYMtZw_DSKrZqFHG_ysYteEhmoL6T8Mu4,17563
 iplotx/edge/geometry.py,sha256=jkTMvQC5425GjB_fmGLIPJeSDAr_7NZF8zZDLTrSj34,15541
 iplotx/edge/leaf.py,sha256=SyGMv2PIOoH0pey8-aMVaZheK3hNe1Qz_okcyWbc4E4,4268
 iplotx/edge/ports.py,sha256=BpkbiEhX4mPBBAhOv4jcKFG4Y8hxXz5GRtVLCC0jbtI,1235
-iplotx/ingest/__init__.py,sha256=S0YfnXcFKseB7ZBQc4yRt0cNDsLlhqdom0TmSY3OY2E,4756
+iplotx/ingest/__init__.py,sha256=k1Q-7lSdotMR4RkF1x0t19RFsTknohX0L507Dw69WyU,5035
 iplotx/ingest/heuristics.py,sha256=715VqgfKek5LOJnu1vTo7RqPgCl-Bb8Cf6o7_Tt57fA,5797
-iplotx/ingest/typing.py,sha256=61LwNwrTHVh8eqqC778Gr81zPYcUKW61mDgGCCsuGSk,14181
+iplotx/ingest/typing.py,sha256=nk0UTqTuZoa9YE7F8RlOTqhxPw4OEYFTqrFFRWQs0jI,14488
 iplotx/ingest/providers/network/graph_tool.py,sha256=iTCf4zHe4Zmdd8Tlz6j7Xfo_FwfsIiK5JkQfH3uq7TM,3028
 iplotx/ingest/providers/network/igraph.py,sha256=WL9Yx2IF5QhUIoKMlozdyq5HWIZ-IJmNoeS8GOhL0KU,2945
 iplotx/ingest/providers/network/networkx.py,sha256=ehCg4npL073HX-eAG-VoP6refLPsMb3lYG51xt_rNjA,4636
@@ -26,20 +26,20 @@ iplotx/ingest/providers/tree/biopython.py,sha256=4N_54cVyHHPcASJZGr6pHKE2p5R3i8C
 iplotx/ingest/providers/tree/cogent3.py,sha256=JmELbDK7LyybiJzFNbmeqZ4ySJoDajvFfJebpNfFKWo,1073
 iplotx/ingest/providers/tree/dendropy.py,sha256=uRMe46PfDPUTeNInUO2Gbp4pVr-WIFIZQvrND2tovsg,1548
 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/simple.py,sha256=-T7Kf-G4F4niggy_tNZ8AafDf8fpDdthC-vlkjbEZso,2569
 iplotx/ingest/providers/tree/skbio.py,sha256=O1KUr8tYi28pZ3VVjapgO4Uj-YpMuix3GhOH5je8Lv4,822
-iplotx/network/__init__.py,sha256=oEv6f8oFYrtcI_NKabr8a_oIWTc1jXXTl_yO1xox_rE,13575
+iplotx/network/__init__.py,sha256=cJ6m6s157AOCqg-znUAlsumuZ2jiE9QsVQ3-GCK01wo,13543
 iplotx/network/groups.py,sha256=E_eYVXRHjv1DcyA4RupTkMa-rRFrIKkt9Rxn_Elw9Nc,6796
 iplotx/style/__init__.py,sha256=rf1GutrE8hHUhCoe4FGKYX-aNtHuu_U-kYQnqUxZNrY,10282
 iplotx/style/leaf_info.py,sha256=3xBn7xv9Uy2KAqdhM9S6ew5ZBJrGRTXRL3xXb8atfLw,1018
 iplotx/style/library.py,sha256=58Y8BlllGLsR4pQM7_PVCP5tH6_4GkchXZvJpqGHlcg,8534
-iplotx/tree/__init__.py,sha256=mFCgXSusB1dSMc-xN_zOc5PojpEf_XyP8yR3xeZVQMY,30065
-iplotx/tree/cascades.py,sha256=on5GyqbWasl1zgK7bYXYQE0LOSfHc1z-1hnm0GWd6aw,8184
+iplotx/tree/__init__.py,sha256=nV2iWrtpPhpGZnkEJqK8ydimMi7pJtRQ1Eqn5dgqUyA,31043
+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/style.py,sha256=vyNP80nDYVinqm6_9ltCJCtjK35ZcGlHvOskNv3eQBc,4225
-iplotx-1.1.0.dist-info/METADATA,sha256=BBWbFLjqgs00VaB3DXNSex39oA0iDplDgBeCmrO6hKw,5053
-iplotx-1.1.0.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
-iplotx-1.1.0.dist-info/RECORD,,
+iplotx-1.2.1.dist-info/METADATA,sha256=DVxutHflrg2vXCJfyzmPR83ywc4_5DfGdrViUMvV43E,5001
+iplotx-1.2.1.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
+iplotx-1.2.1.dist-info/RECORD,,