iplotx 1.2.1__tar.gz → 1.3.0__tar.gz

{iplotx-1.2.1 → iplotx-1.3.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: iplotx
-Version: 1.2.1
+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
@@ -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-1.2.1 → 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-1.2.1 → iplotx-1.3.0}/docs/source/code_of_conduct.rst

@@ -1,6 +1,6 @@
 .. _scipy-coc:
 
-ilpotx Code of Conduct
+iplotx Code of Conduct
 ======================
 
 

{iplotx-1.2.1 → 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-1.2.1 → 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-1.2.1 → 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-1.2.1 → 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-1.2.1 → 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-1.2.1 → iplotx-1.3.0}/iplotx/ingest/providers/tree/simple.py

@@ -64,7 +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-1.2.1 → 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-1.2.1 → iplotx-1.3.0}/iplotx/ingest/typing.py

@@ -12,6 +12,7 @@ from typing import (
     Any,
     Iterable,
 )
+
 # NOTE: __init__ in Protocols has had a difficult gestation
 # https://github.com/python/cpython/issues/88970
 if sys.version_info < (3, 11):
@@ -156,8 +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.
@@ -235,8 +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:
@@ -244,7 +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.
@@ -253,7 +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
@@ -285,9 +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(),
@@ -304,8 +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",
+]

iplotx-1.3.0/iplotx/layout/tree/__init__.py

@@ -0,0 +1,72 @@
+"""
+Tree layout algorithms.
+"""
+
+from typing import (
+    Any,
+)
+from collections.abc import (
+    Hashable,
+    Callable,
+)
+
+from .rooted import (
+    _horizontal_tree_layout,
+    _vertical_tree_layout,
+    _radial_tree_layout,
+)
+from .unrooted import (
+    _equalangle_tree_layout,
+    _daylight_tree_layout,
+)
+
+
+def compute_tree_layout(
+    layout: str,
+    orientation: str,
+    root: Any,
+    preorder_fun: Callable,
+    postorder_fun: Callable,
+    levelorder_fun: Callable,
+    children_fun: Callable,
+    branch_length_fun: Callable,
+    leaves_fun: Callable,
+    **kwargs,
+) -> dict[Hashable, list[float]]:
+    """Compute the layout for a tree.
+
+    Parameters:
+        layout: The name of the layout, e.g. "horizontal", "vertical", or "radial".
+        orientation: The orientation of the layout, e.g. "right", "left", "descending",
+            "ascending", "clockwise", "anticlockwise".
+
+    Returns:
+        A layout dictionary with node positions.
+    """
+    kwargs["root"] = root
+    kwargs["preorder_fun"] = preorder_fun
+    kwargs["postorder_fun"] = postorder_fun
+    kwargs["levelorder_fun"] = levelorder_fun
+    kwargs["children_fun"] = children_fun
+    kwargs["orientation"] = orientation
+    kwargs["branch_length_fun"] = branch_length_fun
+    kwargs["leaves_fun"] = leaves_fun
+
+    # Angular or not, the vertex layout is unchanged. Since we do not
+    # currently compute an edge layout here, we can ignore the option.
+    kwargs.pop("angular", None)
+
+    if layout == "radial":
+        layout_dict = _radial_tree_layout(**kwargs)
+    elif layout == "horizontal":
+        layout_dict = _horizontal_tree_layout(**kwargs)
+    elif layout == "vertical":
+        layout_dict = _vertical_tree_layout(**kwargs)
+    elif layout == "equalangle":
+        layout_dict = _equalangle_tree_layout(**kwargs)
+    elif layout == "daylight":
+        layout_dict = _daylight_tree_layout(**kwargs)
+    else:
+        raise ValueError(f"Tree layout not available: {layout}")
+
+    return layout_dict

iplotx-1.2.1/iplotx/layout.py → iplotx-1.3.0/iplotx/layout/tree/rooted.py

@@ -1,5 +1,5 @@
 """
-Layout functions, currently limited to trees.
+Rooted tree layout for iplotx library.
 """
 
 from typing import (
@@ -14,55 +14,13 @@ from collections.abc import (
 import numpy as np
 
 
-def compute_tree_layout(
-    layout: str,
-    orientation: str,
-    root: Any,
-    preorder_fun: Callable,
-    postorder_fun: Callable,
-    children_fun: Callable,
-    branch_length_fun: Callable,
-    **kwargs,
-) -> dict[Hashable, list[float]]:
-    """Compute the layout for a tree.
-
-    Parameters:
-        layout: The name of the layout, e.g. "horizontal", "vertical", or "radial".
-        orientation: The orientation of the layout, e.g. "right", "left", "descending",
-            "ascending", "clockwise", "anticlockwise".
-
-    Returns:
-        A layout dictionary with node positions.
-    """
-    kwargs["root"] = root
-    kwargs["preorder_fun"] = preorder_fun
-    kwargs["postorder_fun"] = postorder_fun
-    kwargs["children_fun"] = children_fun
-    kwargs["branch_length_fun"] = branch_length_fun
-    kwargs["orientation"] = orientation
-
-    # Angular or not, the vertex layout is unchanged. Since we do not
-    # currently compute an edge layout here, we can ignore the option.
-    kwargs.pop("angular", None)
-
-    if layout == "radial":
-        layout_dict = _radial_tree_layout(**kwargs)
-    elif layout == "horizontal":
-        layout_dict = _horizontal_tree_layout(**kwargs)
-    elif layout == "vertical":
-        layout_dict = _vertical_tree_layout(**kwargs)
-    else:
-        raise ValueError(f"Tree layout not available: {layout}")
-
-    return layout_dict
-
-
 def _horizontal_tree_layout_right(
     root: Any,
     preorder_fun: Callable,
     postorder_fun: Callable,
     children_fun: Callable,
     branch_length_fun: Callable,
+    **kwargs,
 ) -> dict[Hashable, list[float]]:
     """Build a tree layout horizontally, left to right.
 
@@ -173,7 +131,7 @@ def _radial_tree_layout(
             360, it leaves a small gap at the end to ensure the first and last leaf
             are not overlapping.
     Returns:
-        A dictionary with the radial layout.
+        A dictionary with the layout.
     """
     # Short form
     th = start * np.pi / 180