iplotx 1.2.0__tar.gz → 1.3.0__tar.gz

{iplotx-1.2.0 → iplotx-1.3.0}/.github/workflows/test.yml

@@ -12,7 +12,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.11", "3.12", "3.13"]
+        python-version: ["3.10", "3.11", "3.12", "3.13"]
 
     steps:
     - uses: actions/checkout@v5

{iplotx-1.2.0 → iplotx-1.3.0}/.gitignore

@@ -179,3 +179,7 @@ cython_debug/
 
 # PyPI configuration file
 .pypirc
+
+# vim backup files
+*.swp
+*.swo

{iplotx-1.2.0 → iplotx-1.3.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: iplotx
-Version: 1.2.0
+Version: 1.3.0
 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
@@ -36,9 +36,9 @@ Provides-Extra: networkx
 Requires-Dist: networkx>=2.0.0; extra == 'networkx'
 Description-Content-Type: text/markdown
 
-![Github Actions](https://github.com/fabilab/iplotx/actions/workflows/test.yml/badge.svg)
-![PyPI - Version](https://img.shields.io/pypi/v/iplotx)
-![RTD](https://readthedocs.org/projects/iplotx/badge/?version=latest)
+[![Github Actions](https://github.com/fabilab/iplotx/actions/workflows/test.yml/badge.svg)](https://github.com/fabilab/iplotx/actions/workflows/test.yml)
+[![PyPI - Version](https://img.shields.io/pypi/v/iplotx)](https://pypi.org/project/iplotx/)
+[![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)
@@ -89,6 +89,13 @@ See [readthedocs](https://iplotx.readthedocs.io/en/latest/) for the full documen
 ## Gallery
 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):
+
+```
+F. Zanini. (2025). Unified network visualisation in Python. Zenodo [PREPRINT]. https://doi.org/10.5281/zenodo.16599333
+```
+
 ## Features
 - Plot networks from multiple libraries including networkx, igraph and graph-tool, using Matplotlib. ✅
 - Plot trees from multiple libraries such as cogent3, ETE4, skbio, biopython, and dendropy. ✅

{iplotx-1.2.0 → iplotx-1.3.0}/README.md

@@ -1,6 +1,6 @@
-![Github Actions](https://github.com/fabilab/iplotx/actions/workflows/test.yml/badge.svg)
-![PyPI - Version](https://img.shields.io/pypi/v/iplotx)
-![RTD](https://readthedocs.org/projects/iplotx/badge/?version=latest)
+[![Github Actions](https://github.com/fabilab/iplotx/actions/workflows/test.yml/badge.svg)](https://github.com/fabilab/iplotx/actions/workflows/test.yml)
+[![PyPI - Version](https://img.shields.io/pypi/v/iplotx)](https://pypi.org/project/iplotx/)
+[![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)
@@ -51,6 +51,13 @@ See [readthedocs](https://iplotx.readthedocs.io/en/latest/) for the full documen
 ## Gallery
 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):
+
+```
+F. Zanini. (2025). Unified network visualisation in Python. Zenodo [PREPRINT]. https://doi.org/10.5281/zenodo.16599333
+```
+
 ## Features
 - Plot networks from multiple libraries including networkx, igraph and graph-tool, using Matplotlib. ✅
 - Plot trees from multiple libraries such as cogent3, ETE4, skbio, biopython, and dendropy. ✅

iplotx-1.3.0/docs/source/code_of_conduct.rst

@@ -0,0 +1,145 @@
+.. _scipy-coc:
+
+iplotx Code of Conduct
+======================
+
+
+Introduction
+------------
+
+This code of conduct applies to all spaces managed by the iplotx project,
+including all public and private mailing lists, issue trackers, wikis, blogs,
+and any other communication channel used by our community. The iplotx
+project does not organize in-person events, however, events related to our
+community should have a code of conduct similar in spirit to this one.
+
+This code of conduct should be honored by everyone who participates in
+the iplotx community formally or informally, or claims any affiliation with the
+project, in any project-related activities, and, especially, when representing the
+project, in any role.
+
+This code is neither exhaustive nor complete. It serves to distill our common
+understanding of a collaborative, shared environment and goals. Please try to
+follow this code in spirit as much as in letter, to create a friendly and
+productive environment that enriches the surrounding community.
+
+
+Specific guidelines
+-------------------
+
+We strive to:
+
+1. Be open. We invite anyone to participate in our community. We prefer to use
+   public methods of communication for project-related messages, unless
+   discussing something sensitive. This applies to messages for help or
+   project-related support, too; not only is a public-support request much more
+   likely to result in an answer to a question, it also ensures that any
+   inadvertent mistakes in answering are more easily detected and corrected.
+
+2. Be empathetic, welcoming, friendly, and patient. We work together to resolve
+   conflict, and assume good intentions. We may all experience some frustration
+   from time to time, but we do not allow frustration to turn into a personal
+   attack. A community where people feel uncomfortable or threatened is not a
+   productive one.
+
+3. Be collaborative. Our work will be used by other people, and in turn we will
+   depend on the work of others. When we make something for the benefit of the
+   project, we are willing to explain to others how it works, so that they can
+   build on the work to make it even better. Any decision we make will affect
+   users and colleagues, and we take those consequences seriously when making
+   decisions.
+
+4. Be inquisitive. Nobody knows everything! Asking questions early avoids many
+   problems later, so we encourage questions, although we may direct them to
+   the appropriate forum. We will try hard to be responsive and helpful.
+
+5. Be careful in the words that we choose. We are careful and respectful in
+   our communication and we take responsibility for our own speech. Be kind to
+   others. Do not insult or put down other participants. We will not accept
+   harassment or other exclusionary behavior, such as:
+
+  - Violent threats or language directed against another person.
+  - Sexist, racist, or otherwise discriminatory jokes and language.
+  - Posting sexually explicit or violent material.
+  - Posting (or threatening to post) other people's personally identifying information ("doxing").
+  - Sharing private content, such as emails sent privately or non-publicly,
+    or unlogged forums, such as IRC channel history, without the sender's consent.
+  - Personal insults, especially those using racist or sexist terms.
+  - Unwelcome sexual attention.
+  - Excessive profanity. Please avoid swearwords; people differ greatly in their sensitivity to swearing.
+  - Repeated harassment of others. In general, if someone asks you to stop, then stop.
+  - Advocating for, or encouraging, any of the above behavior.
+
+
+Diversity statement
+-------------------
+
+The iplotx project welcomes and encourages participation by everyone. We are
+committed to being a community that everyone enjoys being part of. Although
+we may not always be able to accommodate each individual's preferences, we try
+our best to treat everyone kindly.
+
+No matter how you identify yourself or how others perceive you: we welcome you.
+Though no list can hope to be comprehensive, we explicitly honor diversity in:
+age, culture, ethnicity, genotype, gender identity or expression, language,
+national origin, neurotype, phenotype, political beliefs, profession, race,
+religion, sexual orientation, socioeconomic status, subculture and technical
+ability, to the extent that these do not conflict with this code of conduct.
+
+
+Though we welcome people fluent in all languages, iplotx development is
+conducted in English.
+
+Standards for behavior in the iplotx community are detailed in the Code of
+Conduct above. Participants in our community should uphold these standards
+in all their interactions and help others to do so as well (see next section).
+
+
+Reporting guidelines
+--------------------
+
+We know that it is painfully common for internet communication to start at or
+devolve into obvious and flagrant abuse. We also recognize that sometimes
+people may have a bad day, or be unaware of some of the guidelines in this Code
+of Conduct. Please keep this in mind when deciding on how to respond to a
+breach of this Code.
+
+For clearly intentional breaches, report those to the Code of Conduct committee
+(see below). For possibly unintentional breaches, you may reply to the person
+and point out this Code of Conduct (either in public or in private, whatever is
+most appropriate). If you would prefer not to do that, please feel free to
+report to the Code of Conduct committee directly, or ask the committee for
+advice, in confidence.
+
+You can report issues to the iplotx core developer Fabio Zanini, at
+fabio.zanini@unsw.edu.au.
+
+
+Incident reporting resolution & Code of Conduct enforcement
+-----------------------------------------------------------
+
+We will investigate and respond to all complaints. This Code of Conduct
+Committee  will protect the identity of the reporter, and treat the content
+of complaints as confidential (unless the reporter requests otherwise).
+
+In case of severe and obvious breaches, e.g., personal threat or violent, sexist
+or racist language, we will immediately do our utmost to disconnect the
+originator from iplotx communication channels; please see the manual for details.
+
+In cases not involving clear severe and obvious breaches of this code of
+conduct, the process for acting on any received code of conduct violation
+report will be:
+
+1. Acknowledgement that the report has been received
+2. Reasonable discussion/feedback
+3. Mediation (if feedback didn't help, and only if both reporter and reportee agree to this)
+4. Enforcement via transparent decision by the Code of Conduct Committee
+
+The committee will respond to any report as soon as possible, and at most
+within 72 hours.
+
+
+Endnotes
+--------
+
+This document was adapted from the `SciPy Code of Conduct <https://scipy.github.io/devdocs/dev/conduct/code_of_conduct.html>`_.

{iplotx-1.2.0 → iplotx-1.3.0}/docs/source/index.md

@@ -36,4 +36,5 @@ Plotting API <api/plotting>
 Style API <api/style>
 Artist hierarchy <api/artists>
 Data provider protocols <api/providers>
+Code of conduct <code_of_conduct>
 ```

{iplotx-1.2.0 → iplotx-1.3.0}/docs/source/sg_execution_times.rst

@@ -6,7 +6,7 @@
 
 Computation times
 =================
-**00:00.565** total execution time for 77 files **from all galleries**:
+**00:00.514** total execution time for 78 files **from all galleries**:
 
 .. container::
 
@@ -32,8 +32,8 @@ Computation times
    * - Example
      - Time
      - Mem (MB)
-   * - :ref:`sphx_glr_gallery_tree_plot_double_tree.py` (``../../gallery/tree/plot_double_tree.py``)
-     - 00:00.565
+   * - :ref:`sphx_glr_gallery_tree_plot_equalangle.py` (``../../gallery/tree/plot_equalangle.py``)
+     - 00:00.514
      - 0.0
    * - :ref:`sphx_glr_gallery_basic_plot_3d.py` (``../../gallery/basic/plot_3d.py``)
      - 00:00.000
@@ -221,6 +221,9 @@ Computation times
    * - :ref:`sphx_glr_gallery_tree_plot_dendropy.py` (``../../gallery/tree/plot_dendropy.py``)
      - 00:00.000
      - 0.0
+   * - :ref:`sphx_glr_gallery_tree_plot_double_tree.py` (``../../gallery/tree/plot_double_tree.py``)
+     - 00:00.000
+     - 0.0
    * - :ref:`sphx_glr_gallery_tree_plot_elements_tree.py` (``../../gallery/tree/plot_elements_tree.py``)
      - 00:00.000
      - 0.0

iplotx-1.3.0/gallery/tree/plot_equalangle.py

@@ -0,0 +1,35 @@
+"""
+Equal angle layout
+==================
+
+This example showcases the "equal angle" layout. This layout is inspired by the `ggtree <https://yulab-smu.top/treedata-book/chapter4.html>`_ layout with the same name, which originally comes from Joseph Felsenstein's book "Inferring Phylogenies".
+"""
+
+from cogent3.phylo import nj
+import numpy as np
+import iplotx as ipx
+import matplotlib.pyplot as plt
+
+nleaves = 14
+distance_dict = {}
+for i in range(nleaves):
+    for j in range(i):
+        distance_dict[(str(i), str(j))] = np.random.rand()
+tree = nj.nj(distance_dict)
+
+ipx.plotting.tree(
+    tree,
+    layout="equalangle",
+)
+
+
+# %%
+# The "equal daylight" layout is an adjustment of the equal angle layout that attempts to spread out leaves more evenly
+# for imbalanced trees. ``iplotx`` has an experimental implementation of this layout.
+#
+# .. warning:: "Experimental" means you can use it but the API and resulting layout may change in future releases.
+
+ipx.plotting.tree(
+    tree,
+    layout="daylight",
+)

{iplotx-1.2.0 → iplotx-1.3.0}/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-1.2.0 → iplotx-1.3.0}/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-1.2.0 → iplotx-1.3.0}/iplotx/ingest/providers/tree/biopython.py

@@ -21,8 +21,9 @@ class BiopythonDataProvider(TreeDataProvider):
 
     preorder = partialmethod(_traverse, order="preorder")
     postorder = partialmethod(_traverse, order="postorder")
+    levelorder = partialmethod(_traverse, order="level")
 
-    def get_leaves(self) -> Sequence[Any]:
+    def _get_leaves(self) -> Sequence[Any]:
         return self.tree.get_terminals()
 
     @staticmethod

{iplotx-1.2.0 → iplotx-1.3.0}/iplotx/ingest/providers/tree/cogent3.py

@@ -16,7 +16,10 @@ class Cogent3DataProvider(TreeDataProvider):
     def postorder(self) -> Sequence[Any]:
         return self.tree.postorder()
 
-    def get_leaves(self) -> Sequence[Any]:
+    def levelorder(self) -> Sequence[Any]:
+        return self.tree.levelorder()
+
+    def _get_leaves(self) -> Sequence[Any]:
         return self.tree.tips()
 
     @staticmethod

{iplotx-1.2.0 → iplotx-1.3.0}/iplotx/ingest/providers/tree/dendropy.py

@@ -36,7 +36,16 @@ class DendropyDataProvider(TreeDataProvider):
             return self.tree.postorder_node_iter()
         return self.tree.postorder_iter()
 
-    def get_leaves(self) -> Sequence[Any]:
+    def levelorder(self) -> Any:
+        """Levelorder traversal of the tree.
+
+        NOTE: This will work on both entire Trees and Nodes (which means a subtree including self).
+        """
+        if hasattr(self.tree, "levelorder_node_iter"):
+            return self.tree.levelorder_node_iter()
+        return self.tree.levelorder_iter()
+
+    def _get_leaves(self) -> Sequence[Any]:
         """Get a list of leaves."""
         return self.tree.leaf_nodes()
 

{iplotx-1.2.0 → iplotx-1.3.0}/iplotx/ingest/providers/tree/ete4.py

@@ -18,8 +18,9 @@ class Ete4DataProvider(TreeDataProvider):
 
     preorder = partialmethod(_traverse, order="preorder")
     postorder = partialmethod(_traverse, order="postorder")
+    levelorder = partialmethod(_traverse, order="levelorder")
 
-    def get_leaves(self) -> Sequence[Any]:
+    def _get_leaves(self) -> Sequence[Any]:
         return self.tree.leaves()
 
     @staticmethod

{iplotx-1.2.0 → iplotx-1.3.0}/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:
@@ -65,7 +64,17 @@ class SimpleTreeDataProvider(TreeDataProvider):
 
         yield from _recur(self.tree)
 
-    def get_leaves(self) -> Sequence[Any]:
+    def levelorder(self) -> Iterable[dict[dict | str, Any]]:
+        from collections import deque
+
+        queue = deque([self.get_root()])
+        while queue:
+            node = queue.popleft()
+            for child in self.get_children(node):
+                queue.append(child)
+            yield node
+
+    def _get_leaves(self) -> Sequence[Any]:
         def _recur(node):
             if len(node.children) == 0:
                 yield node

{iplotx-1.2.0 → iplotx-1.3.0}/iplotx/ingest/providers/tree/skbio.py

@@ -16,7 +16,10 @@ class SkbioDataProvider(TreeDataProvider):
     def postorder(self) -> Sequence[Any]:
         return self.tree.postorder()
 
-    def get_leaves(self) -> Sequence[Any]:
+    def levelorder(self) -> Sequence[Any]:
+        return self.tree.levelorder()
+
+    def _get_leaves(self) -> Sequence[Any]:
         return self.tree.tips()
 
     @staticmethod

{iplotx-1.2.0 → iplotx-1.3.0}/iplotx/ingest/typing.py

@@ -5,15 +5,21 @@ 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 +32,11 @@ 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."""
@@ -146,8 +157,32 @@ class TreeDataProvider(Protocol):
                 return root_attr
         return self.tree.get_root()
 
-    def get_leaves(self) -> Sequence[Any]:
-        """Get the tree leaves/tips in a provider-specific data structure.
+    def get_subtree(self, node: TreeType):
+        """Get the subtree rooted at the given node.
+
+        Parameters:
+            node: The node to get the subtree from.
+        Returns:
+            The subtree rooted at the given node.
+        """
+        return self.__class__(node)
+
+    def get_leaves(self, node: Optional[TreeType] = None) -> Sequence[Any]:
+        """Get the leaves of the entire tree or a subtree.
+
+        Parameters:
+            node: The node to get the leaves from. If None, get from the entire
+                tree.
+        Returns:
+            The leaves or tips of the tree or node-anchored subtree.
+        """
+        if node is None:
+            return self._get_leaves()
+        else:
+            return self.get_subtree(node)._get_leaves()
+
+    def _get_leaves(self) -> Sequence[Any]:
+        """Get the whole tree leaves/tips in a provider-specific data structure.
 
         Returns:
             The leaves or tips of the tree.
@@ -225,8 +260,6 @@ class TreeDataProvider(Protocol):
         NOTE: individual providers may implement more efficient versions of
         this function if desired.
         """
-        provider = self.__class__
-
         # Find leaves of the selected nodes
         leaves = set()
         for node in nodes:
@@ -234,7 +267,7 @@ class TreeDataProvider(Protocol):
             if len(self.get_children(node)) == 0:
                 leaves.add(node)
             else:
-                leaves |= set(provider(node).get_leaves())
+                leaves |= set(self.get_leaves(node))
 
         # Look for nodes with the same set of leaves, starting from the bottom
         # and stopping at the first (i.e. lowest) hit.
@@ -243,7 +276,7 @@ class TreeDataProvider(Protocol):
             if len(self.get_children(node)) == 0:
                 leaves_node = {node}
             else:
-                leaves_node = set(provider(node).get_leaves())
+                leaves_node = set(self.get_leaves(node))
             if leaves <= leaves_node:
                 root = node
                 break
@@ -275,9 +308,26 @@ class TreeDataProvider(Protocol):
                 orientation = "right"
             elif layout == "vertical":
                 orientation = "descending"
-            elif layout == "radial":
+            elif layout in ("radial", "equalangle", "daylight"):
                 orientation = "clockwise"
 
+        # Validate orientation
+        valid = (layout == "horizontal") and (orientation in ("right", "left"))
+        valid |= (layout == "vertical") and (orientation in ("ascending", "descending"))
+        valid |= (layout == "radial") and (
+            orientation in ("clockwise", "counterclockwise", "left", "right")
+        )
+        valid |= (layout == "equalangle") and (
+            orientation in ("clockwise", "counterclockwise", "left", "right")
+        )
+        valid |= (layout == "daylight") and (
+            orientation in ("clockwise", "counterclockwise", "left", "right")
+        )
+        if not valid:
+            raise ValueError(
+                f"Orientation '{orientation}' is not valid for layout '{layout}'.",
+            )
+
         tree_data = {
             "root": self.get_root(),
             "rooted": self.is_rooted(),
@@ -294,8 +344,10 @@ class TreeDataProvider(Protocol):
             root=tree_data["root"],
             preorder_fun=self.preorder,
             postorder_fun=self.postorder,
+            levelorder_fun=self.levelorder,
             children_fun=self.get_children,
             branch_length_fun=self.get_branch_length_default_to_one,
+            leaves_fun=self.get_leaves,
             **layout_style,
         )
         if layout in ("radial",):

iplotx-1.3.0/iplotx/layout/__init__.py

@@ -0,0 +1,9 @@
+"""
+Layout functions.
+"""
+
+from .tree import compute_tree_layout
+
+__all__ = [
+    "compute_tree_layout",
+]