iplotx 1.0.0__tar.gz → 1.1.0__tar.gz

iplotx-1.1.0/.github/workflows/test.yml

@@ -0,0 +1,86 @@
+# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
+
+name: Python package
+
+on:
+  [push, pull_request]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.11", "3.12", "3.13"]
+
+    steps:
+    - uses: actions/checkout@v5
+
+    - name: Install uv
+      uses: astral-sh/setup-uv@v6
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Install the project
+      run: uv sync --all-extras --group test
+
+    - name: Run pytest
+      run: uv run pytest --cov-report term-missing --cov=iplotx tests
+
+    - name: Coveralls
+      uses: coverallsapp/github-action@v2
+      with:
+        fail-on-error: false
+
+    - name: Run flake8
+      run: uv run flake8 iplotx --count --exit-zero --max-complexity=20 --max-line-length=127 --statistics
+
+  build_graph_tool:
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.11", "3.12", "3.13"]
+
+    steps:
+    - uses: actions/checkout@v5
+
+    - uses: conda-incubator/setup-miniconda@v3
+      with:
+        auto-activate-base: false
+        auto-update-conda: true
+        python-version: ${{ matrix.python-version }}
+        activate-environment: gt
+        miniforge-version: latest
+        channels: conda-forge
+        conda-remove-defaults: true
+    - name: Conda info
+      shell: bash -el {0}
+      run: conda info
+    - name: Conda list
+      shell: bash -el {0}
+      run: conda list
+    - name: Install graph-tool
+      shell: bash -el {0}
+      run: conda install -c conda-forge graph-tool
+    - name: Install pip
+      shell: bash -el {0}
+      run: conda install -c conda-forge pip
+    - name: Upgrade pip to >= 25.1 (which has dependency groups)
+      shell: bash -el {0}
+      run: pip install --upgrade pip
+    - name: Install deps and package
+      shell: bash -el {0}
+      run: pip install --group test .
+    - name: Check pytest
+      shell: bash -el {0}
+      run: which pytest
+    - name: Run pytest (graph-tool)
+      shell: bash -el {0}
+      run: pytest tests/test_graph_tool.py

{iplotx-1.0.0 → iplotx-1.1.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: iplotx
-Version: 1.0.0
+Version: 1.1.0
 Summary: Plot networkx from igraph and networkx.
 Project-URL: Homepage, https://github.com/fabilab/iplotx
 Project-URL: Documentation, https://readthedocs.org/iplotx
@@ -53,14 +53,15 @@ Supports:
 - **networks**:
   - [networkx](https://networkx.org/)
   - [igraph](igraph.readthedocs.io/)
-  - [minimal network data structure](https://iplotx.readthedocs.io/en/latest/gallery/plot_simplenetworkdataprovider.html#sphx-glr-gallery-plot-simplenetworkdataprovider-py) (zero dependency)
+  - [graph-tool](https://graph-tool.skewed.de/)
+  - [zero-dependency](https://iplotx.readthedocs.io/en/latest/gallery/plot_simplenetworkdataprovider.html#sphx-glr-gallery-plot-simplenetworkdataprovider-py)
 - **trees**:
   - [ETE4](https://etetoolkit.github.io/ete/)
   - [cogent3](https://cogent3.org/)
   - [Biopython](https://biopython.org/)
   - [scikit-bio](https://scikit.bio)
   - [dendropy](https://jeetsukumaran.github.io/DendroPy/index.html)
-  - [minimal tree data structure](https://iplotx.readthedocs.io/en/latest/gallery/tree/plot_simpletreedataprovider.html#sphx-glr-gallery-tree-plot-simpletreedataprovider-py) (zero dependency)
+  - [zero-dependency](https://iplotx.readthedocs.io/en/latest/gallery/tree/plot_simpletreedataprovider.html#sphx-glr-gallery-tree-plot-simpletreedataprovider-py)
 
 In addition to the above, *any* network or tree analysis library can register an [entry point](https://iplotx.readthedocs.io/en/latest/providers.html#creating-a-custom-data-provider) to gain compatibility with `iplotx` with no intervention from our side.
 
@@ -81,7 +82,7 @@ fig, ax = plt.subplots(figsize=(3, 3))
 ipx.plot(g, ax=ax, layout=layout)
 ```
 
-![Quick start image](docs/source/_static/graph_basic.png)
+![Quick start image](/docs/source/_static/graph_basic.png)
 
 ## Documentation
 See [readthedocs](https://iplotx.readthedocs.io/en/latest/) for the full documentation.
@@ -90,11 +91,11 @@ See [readthedocs](https://iplotx.readthedocs.io/en/latest/) for the full documen
 See [gallery](https://iplotx.readthedocs.io/en/latest/gallery/index.html).
 
 ## Features
-- Plot networks from multiple libraries including networkx and igraph, using matplotlib as a backend. ✅
+- 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. ✅
 - Flexible yet easy styling, including an internal library of styles ✅
 - Interactive plotting, e.g. zooming and panning after the plot is created. ✅
-- Store the plot to disk thanks to the many matplotlib backends (SVG, PNG, PDF, etc.). ✅
+- Store the plot to disk in many formats (SVG, PNG, PDF, GIF, etc.). ✅
 - 3D network visualisation with depth shading. ✅
 - Efficient plotting of large graphs (up to ~1 million nodes on a laptop). ✅
 - Edit plotting elements after the plot is created, e.g. changing node colors, labels, etc. ✅

{iplotx-1.0.0 → iplotx-1.1.0}/README.md

@@ -15,14 +15,15 @@ Supports:
 - **networks**:
   - [networkx](https://networkx.org/)
   - [igraph](igraph.readthedocs.io/)
-  - [minimal network data structure](https://iplotx.readthedocs.io/en/latest/gallery/plot_simplenetworkdataprovider.html#sphx-glr-gallery-plot-simplenetworkdataprovider-py) (zero dependency)
+  - [graph-tool](https://graph-tool.skewed.de/)
+  - [zero-dependency](https://iplotx.readthedocs.io/en/latest/gallery/plot_simplenetworkdataprovider.html#sphx-glr-gallery-plot-simplenetworkdataprovider-py)
 - **trees**:
   - [ETE4](https://etetoolkit.github.io/ete/)
   - [cogent3](https://cogent3.org/)
   - [Biopython](https://biopython.org/)
   - [scikit-bio](https://scikit.bio)
   - [dendropy](https://jeetsukumaran.github.io/DendroPy/index.html)
-  - [minimal tree data structure](https://iplotx.readthedocs.io/en/latest/gallery/tree/plot_simpletreedataprovider.html#sphx-glr-gallery-tree-plot-simpletreedataprovider-py) (zero dependency)
+  - [zero-dependency](https://iplotx.readthedocs.io/en/latest/gallery/tree/plot_simpletreedataprovider.html#sphx-glr-gallery-tree-plot-simpletreedataprovider-py)
 
 In addition to the above, *any* network or tree analysis library can register an [entry point](https://iplotx.readthedocs.io/en/latest/providers.html#creating-a-custom-data-provider) to gain compatibility with `iplotx` with no intervention from our side.
 
@@ -43,7 +44,7 @@ fig, ax = plt.subplots(figsize=(3, 3))
 ipx.plot(g, ax=ax, layout=layout)
 ```
 
-![Quick start image](docs/source/_static/graph_basic.png)
+![Quick start image](/docs/source/_static/graph_basic.png)
 
 ## Documentation
 See [readthedocs](https://iplotx.readthedocs.io/en/latest/) for the full documentation.
@@ -52,11 +53,11 @@ See [readthedocs](https://iplotx.readthedocs.io/en/latest/) for the full documen
 See [gallery](https://iplotx.readthedocs.io/en/latest/gallery/index.html).
 
 ## Features
-- Plot networks from multiple libraries including networkx and igraph, using matplotlib as a backend. ✅
+- 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. ✅
 - Flexible yet easy styling, including an internal library of styles ✅
 - Interactive plotting, e.g. zooming and panning after the plot is created. ✅
-- Store the plot to disk thanks to the many matplotlib backends (SVG, PNG, PDF, etc.). ✅
+- Store the plot to disk in many formats (SVG, PNG, PDF, GIF, etc.). ✅
 - 3D network visualisation with depth shading. ✅
 - Efficient plotting of large graphs (up to ~1 million nodes on a laptop). ✅
 - Edit plotting elements after the plot is created, e.g. changing node colors, labels, etc. ✅

{iplotx-1.0.0 → iplotx-1.1.0}/docs/source/index.md

@@ -17,7 +17,7 @@
   :::
 ```
 
-[iplotx](https://github.com/fabilab/iplotx) is a Python library to display graphs/networks and trees with [matplotlib](https://matplotlib.org/). It natively supports [networkx](https://networkx.org/) and [igraph](https://python.igraph.org/) networks and [biopython](https://biopython.org/), [scikit-bio](https://scikit.bio/), [cogent3](https://cogent3.org/), [ETE4](https://etetoolkit.github.io/ete/), and [dendropy](https://jeetsukumaran.github.io/DendroPy/index.html) trees. It can also plot networks and trees from simple, pure Python data structures for zero-dependency visualisation.
+[iplotx](https://github.com/fabilab/iplotx) is a Python library to display graphs/networks and trees with [matplotlib](https://matplotlib.org/). It natively supports [networkx](https://networkx.org/), [igraph](https://python.igraph.org/), and [graph-tool](https://graph-tool.skewed.de/) networks and [biopython](https://biopython.org/), [scikit-bio](https://scikit.bio/), [cogent3](https://cogent3.org/), [ETE4](https://etetoolkit.github.io/ete/), and [dendropy](https://jeetsukumaran.github.io/DendroPy/index.html) trees. It can also plot networks and trees from simple Python data structures for zero-dependency visualisation.
 
 `iplotx` guarantees the **exact same visual appearance** independently of what library you used to construct the network/tree.
 

{iplotx-1.0.0 → iplotx-1.1.0}/docs/source/sg_execution_times.rst

@@ -6,7 +6,7 @@
 
 Computation times
 =================
-**00:00.497** total execution time for 76 files **from all galleries**:
+**00:00.542** total execution time for 77 files **from all galleries**:
 
 .. container::
 
@@ -32,8 +32,8 @@ Computation times
    * - Example
      - Time
      - Mem (MB)
-   * - :ref:`sphx_glr_gallery_tree_plot_scalebar.py` (``../../gallery/tree/plot_scalebar.py``)
-     - 00:00.497
+   * - :ref:`sphx_glr_gallery_tree_plot_double_tree.py` (``../../gallery/tree/plot_double_tree.py``)
+     - 00:00.542
      - 0.0
    * - :ref:`sphx_glr_gallery_basic_plot_3d.py` (``../../gallery/basic/plot_3d.py``)
      - 00:00.000
@@ -233,6 +233,9 @@ Computation times
    * - :ref:`sphx_glr_gallery_tree_plot_leafedges_and_cascades.py` (``../../gallery/tree/plot_leafedges_and_cascades.py``)
      - 00:00.000
      - 0.0
+   * - :ref:`sphx_glr_gallery_tree_plot_scalebar.py` (``../../gallery/tree/plot_scalebar.py``)
+     - 00:00.000
+     - 0.0
    * - :ref:`sphx_glr_gallery_tree_plot_skbio_tree.py` (``../../gallery/tree/plot_skbio_tree.py``)
      - 00:00.000
      - 0.0

iplotx-1.1.0/gallery/tree/plot_double_tree.py

@@ -0,0 +1,56 @@
+"""
+Double tree
+===========
+
+This example shows how to use `iplotx` to plot two trees facing each other, which is typical in coevolutionary studies.
+"""
+
+from ete4 import Tree
+from matplotlib import pyplot as plt
+import iplotx as ipx
+
+tree1 = Tree(
+    "((),((),(((),()),((),()))));",
+)
+
+
+tree2 = Tree(
+    "((),((),(),((),())),());",
+)
+
+fig, ax = plt = plt.subplots(figsize=(9, 4))
+
+# Plot first tree on the left
+ipx.plotting.tree(
+    tree1,
+    ax=ax,
+    aspect=1,
+    edge_color="tomato",
+    leaf_deep=True,
+)
+
+# Plot second tree on the right, facing left
+ipx.plotting.tree(
+    tree2,
+    ax=ax,
+    aspect=1,
+    edge_color="steelblue",
+    layout="horizontal",
+    layout_orientation="left",
+    layout_start=(11, 0),
+    leaf_deep=True,
+)
+
+# Add lines connecting corresponding leaves
+matches = [
+    (0, 0),
+    (1, 4),
+    (2, 5),
+    (3, 2),
+    (4, 1),
+    (5, 5),
+]
+for y1, y2 in matches:
+    ax.plot(
+        [5.2, 6.8], [y1, y2], color="gray", linewidth=2,
+    )

iplotx-1.1.0/iplotx/ingest/providers/network/graph_tool.py

@@ -0,0 +1,100 @@
+from typing import (
+    Optional,
+    Sequence,
+)
+from collections.abc import Hashable
+import importlib
+import numpy as np
+import pandas as pd
+
+from ....typing import (
+    LayoutType,
+)
+from ...heuristics import (
+    normalise_layout,
+)
+from ...typing import (
+    NetworkDataProvider,
+    NetworkData,
+)
+from ....utils.internal import (
+    _make_layout_columns,
+)
+
+
+class GraphToolDataProvider(NetworkDataProvider):
+    def __call__(
+        self,
+        layout: Optional[LayoutType] = None,
+        vertex_labels: Optional[Sequence[str] | dict[Hashable, str] | pd.Series] = None,
+        edge_labels: Optional[Sequence[str] | dict[str]] = None,
+    ) -> NetworkData:
+        """Create network data object for iplotx from an igraph object."""
+
+        # Get layout
+        vertex_df = normalise_layout(
+            layout,
+            network=self.network,
+            nvertices=self.number_of_vertices(),
+        )
+        ndim = vertex_df.shape[1]
+        vertex_df.columns = _make_layout_columns(ndim)
+
+        # Vertices are ordered integers, no gaps
+
+        # Vertex labels
+        # Recast vertex_labels=False as vertex_labels=None
+        if np.isscalar(vertex_labels) and (not vertex_labels):
+            vertex_labels = None
+        if vertex_labels is not None:
+            if np.isscalar(vertex_labels):
+                vertex_df["label"] = vertex_df.index.astype(str)
+            elif len(vertex_labels) != len(vertex_df):
+                raise ValueError("Vertex labels must be the same length as the number of vertices.")
+            else:
+                vertex_df["label"] = vertex_labels
+
+        # Edges are a list of tuples, because of multiedges
+        tmp = []
+        for edge in self.network.edges():
+            row = {"_ipx_source": edge.source(), "_ipx_target": edge.target()}
+            # TODO: add graph-tool edge attributes
+            # row.update(edge.attributes())
+            tmp.append(row)
+        if len(tmp):
+            edge_df = pd.DataFrame(tmp)
+        else:
+            edge_df = pd.DataFrame(columns=["_ipx_source", "_ipx_target"])
+        del tmp
+
+        # Edge labels
+        if edge_labels is not None:
+            if len(edge_labels) != len(edge_df):
+                raise ValueError("Edge labels must be the same length as the number of edges.")
+            edge_df["label"] = edge_labels
+
+        network_data = {
+            "vertex_df": vertex_df,
+            "edge_df": edge_df,
+            "directed": self.is_directed(),
+            "ndim": ndim,
+        }
+        return network_data
+
+    @staticmethod
+    def check_dependencies() -> bool:
+        return importlib.util.find_spec("graph_tool") is not None
+
+    @staticmethod
+    def graph_type():
+        import graph_tool.all as gt
+
+        return gt.Graph
+
+    def is_directed(self):
+        """Whether the network is directed."""
+        return self.network.is_directed()
+
+    def number_of_vertices(self):
+        """The number of vertices/nodes in the network."""
+        return self.network.num_vertices()

{iplotx-1.0.0 → iplotx-1.1.0}/iplotx/layout.py

@@ -2,7 +2,10 @@
 Layout functions, currently limited to trees.
 """
 
-from typing import Any
+from typing import (
+    Any,
+    Optional,
+)
 from collections.abc import (
     Hashable,
     Callable,
@@ -99,6 +102,8 @@ def _horizontal_tree_layout_right(
 
 def _horizontal_tree_layout(
     orientation="right",
+    start: tuple[float, float] = (0, 0),
+    span: Optional[float] = None,
     **kwargs,
 ) -> dict[Hashable, list[float]]:
     """Horizontal tree layout."""
@@ -110,11 +115,24 @@ def _horizontal_tree_layout(
     if orientation == "left":
         for key in layout:
             layout[key][0] *= -1
+
+    if span is not None:
+        cur_span = len(layout) - 1
+        for key in layout:
+            layout[key][1] = float(layout[key][1]) * span / cur_span
+
+    if start != (0, 0):
+        for key in layout:
+            layout[key][0] += start[0]
+            layout[key][1] += start[1]
+
     return layout
 
 
 def _vertical_tree_layout(
     orientation="descending",
+    start: tuple[float, float] = (0, 0),
+    span: Optional[float] = None,
     **kwargs,
 ) -> dict[Hashable, list[float]]:
     """Vertical tree layout."""
@@ -125,6 +143,17 @@ def _vertical_tree_layout(
         layout[key] = value[::-1]
         # Orient vertically
         layout[key][1] *= sign
+
+    if span is not None:
+        cur_span = len(layout) - 1
+        for key in layout:
+            layout[key][0] = float(layout[key][0]) * span / cur_span
+
+    if start != (0, 0):
+        for key in layout:
+            layout[key][0] += start[0]
+            layout[key][1] += start[1]
+
     return layout
 
 

{iplotx-1.0.0 → iplotx-1.1.0}/iplotx/tree/__init__.py

@@ -669,6 +669,7 @@ class TreeArtist(mpl.artist.Artist):
     def scalebar(
         self,
         loc: str = "upper left",
+        label_format: str = ".2f",
         **kwargs,
     ):
         """Create scalebar for the tree.
@@ -689,6 +690,8 @@ class TreeArtist(mpl.artist.Artist):
             self,
             layout=self.get_layout_name(),
             loc=loc,
+            label_format=label_format,
+            **kwargs,
         )
 
         # Remove previous scalebars if any

{iplotx-1.0.0 → iplotx-1.1.0}/iplotx/tree/scalebar.py

@@ -37,13 +37,15 @@ class TreeScalebarArtist(Legend):
         self,
         treeartist,
         layout: str = "horizontal",
-        frameon=False,
+        frameon: bool = False,
+        label_format: str = ".2f",
         **kwargs,
     ):
         handles = [treeartist.get_edges()]
         labels = [""]
         self._layout = layout
         self._treeartist = treeartist
+        self._label_format = label_format
 
         if layout == "vertical":
             handler_kwargs = dict(xerr_size=0, yerr_size=1)
@@ -191,13 +193,12 @@ class TreeScalebarArtist(Legend):
 
         bar_trans = bar_handle.get_transform()
         data_trans = self.parent.transData
-        # FIXME: this is off, probably because of some Packer anchor additional transform
         composite_trans = data_trans.inverted() + bar_trans
 
         p0_data = composite_trans.transform(p0)
         p1_data = composite_trans.transform(p1)
         distance = np.linalg.norm(p1_data - p0_data)
-        label = f"{distance:.2f}"
+        label = format(distance, self._label_format)
         return label
 
     def draw(self, renderer):

{iplotx-1.0.0 → iplotx-1.1.0}/iplotx/version.py

@@ -2,4 +2,4 @@
 iplotx version information module.
 """
 
-__version__ = "1.0.0"
+__version__ = "1.1.0"

iplotx-1.1.0/tests/baseline_images/test_graph_tool/graph_basic.png

@@ -0,0 +1 @@
+../test_igraph/graph_basic.png

iplotx-1.1.0/tests/baseline_images/test_graph_tool/graph_directed.png

@@ -0,0 +1 @@
+../test_igraph/graph_directed.png

iplotx-1.1.0/tests/test_graph_tool.py

@@ -0,0 +1,44 @@
+import pytest
+import matplotlib as mpl
+
+mpl.use("agg")
+import matplotlib.pyplot as plt
+import iplotx as ipx
+
+from utils import image_comparison
+
+gt = pytest.importorskip("graph_tool")
+
+
+@pytest.fixture
+def layout_small_ring():
+    coords = [
+        [1.015318095035966, 0.03435580194714975],
+        [0.29010409851547664, 1.0184451153265959],
+        [-0.8699239050738742, 0.6328259400443561],
+        [-0.8616466426732888, -0.5895891303732176],
+        [0.30349699041342515, -0.9594640169691343],
+    ]
+    return coords
+
+
+@image_comparison(baseline_images=["graph_basic"], remove_text=True)
+def test_basic(layout_small_ring):
+    g = gt.Graph(directed=False)
+    vertices = list(g.add_vertex(5))
+    for i in range(5):
+        g.add_edge(vertices[i], vertices[(i + 1) % 5])
+
+    fig, ax = plt.subplots(figsize=(3, 3))
+    ipx.graph(g, ax=ax, layout=layout_small_ring)
+
+
+@image_comparison(baseline_images=["graph_directed"], remove_text=True)
+def test_directed(layout_small_ring):
+    g = gt.Graph(directed=True)
+    vertices = list(g.add_vertex(5))
+    for i in range(5):
+        g.add_edge(vertices[i], vertices[(i + 1) % 5])
+
+    fig, ax = plt.subplots(figsize=(3, 3))
+    ipx.graph(g, ax=ax, layout=layout_small_ring)

iplotx-1.0.0/.github/workflows/test.yml

@@ -1,43 +0,0 @@
-# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
-# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
-
-name: Python package
-
-on:
-  [push, pull_request]
-
-jobs:
-  build:
-
-    runs-on: ubuntu-latest
-    strategy:
-      fail-fast: false
-      matrix:
-        python-version: ["3.11", "3.12", "3.13"]
-
-    steps:
-    - uses: actions/checkout@v4
-
-    - name: Install uv
-      uses: astral-sh/setup-uv@v5
-      with:
-        python-version: ${{ matrix.python-version }}
-
-    - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v5
-      with:
-        python-version: ${{ matrix.python-version }}
-
-    - name: Install the project
-      run: uv sync --all-extras --group test
-
-    - name: Run pytest
-      run: uv run pytest --cov-report term-missing --cov=iplotx tests
-
-    - name: Coveralls
-      uses: coverallsapp/github-action@v2
-      with:
-        fail-on-error: false
-
-    - name: Run flake8
-      run: uv run flake8 iplotx --count --exit-zero --max-complexity=20 --max-line-length=127 --statistics