iplotx 0.4.0__tar.gz → 0.5.1__tar.gz

{iplotx-0.4.0 → iplotx-0.5.1}/.github/workflows/test.yml

@@ -35,7 +35,10 @@ jobs:
       run: uv sync --all-extras --group test
 
     - name: Run pytest
-      run: uv run pytest tests
+      run: uv run pytest --cov-report term-missing --cov=iplotx tests
+
+    - name: Coveralls
+      uses: coverallsapp/github-action@v2
 
     - name: Run flake8
-      run: uv run flake8 iplotx --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+      run: uv run flake8 iplotx --count --exit-zero --max-complexity=20 --max-line-length=127 --statistics

iplotx-0.5.1/.pre-commit-config.yaml

@@ -0,0 +1,54 @@
+# See https://pre-commit.com for more information
+# See https://pre-commit.com/hooks.html for more hooks
+repos:
+- repo: https://github.com/pre-commit/pre-commit-hooks
+  rev: v5.0.0
+  hooks:
+  -   id: trailing-whitespace
+  -   id: end-of-file-fixer
+  -   id: check-yaml
+  -   id: check-added-large-files
+
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  # Ruff version.
+  rev: v0.12.3
+  hooks:
+    # Run the linter.
+    - id: ruff-check
+      types_or: [ python, pyi ]
+      args: [ --fix ]
+    # Run the formatter.
+    - id: ruff-format
+      types_or: [ python, pyi ]
+
+#- repo: https://github.com/psf/black
+#  rev: 25.1.0
+#  hooks:
+#  -   id: black
+#      args: [--check,--target-version,py311]
+- repo: https://github.com/PyCQA/flake8
+  rev: 7.3.0
+  hooks:
+  -   id: flake8
+      args: [
+          --count,
+          --max-complexity=20,
+          --max-line-length=127,
+          --statistics,
+          --extend-ignore=RST399,
+          --exit-zero,
+      ]
+      additional_dependencies: [
+          'flake8-rst-docstrings>=0.2.3',
+      ]
+#-   repo: https://github.com/pre-commit/mirrors-mypy
+#    rev: v1.16.1
+#    hooks:
+#    -   id: mypy
+#        files: '^(iplotx)/'
+
+- repo: https://github.com/astral-sh/uv-pre-commit
+  # uv version.
+  rev: 0.7.20
+  hooks:
+    - id: uv-lock

{iplotx-0.4.0 → iplotx-0.5.1}/MANIFEST.in

@@ -10,4 +10,3 @@ prune doc/html
 prune doc/source/tutorials
 
 global-exclude .dockerignore .DS_Store .gitattributes .gitignore .gitmodules
-

{iplotx-0.4.0 → iplotx-0.5.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: iplotx
-Version: 0.4.0
+Version: 0.5.1
 Summary: Plot networkx from igraph and networkx.
 Project-URL: Homepage, https://github.com/fabilab/iplotx
 Project-URL: Documentation, https://readthedocs.org/iplotx
@@ -39,12 +39,29 @@ 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)
+[![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)
 
 # iplotx
-Plotting networks from igraph and networkx.
+[![Banner](docs/source/_static/banner.png)](https://iplotx.readthedocs.io/en/latest/gallery/index.html).
 
-**NOTE**: This is currently beta quality software. The API and functionality are settling in and might break occasionally.
+Visualise networks and trees in Python, with style.
+
+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) (for educational purposes)
+- **trees**:
+  - [ETE4](https://etetoolkit.github.io/ete/)
+  - [cogent3](https://cogent3.org/)
+  - [Biopython](https://biopython.org/)
+  - [scikit-bio](https://scikit.bio)
+  - [minimal tree data structure](https://iplotx.readthedocs.io/en/latest/gallery/tree/plot_simpletreedataprovider.html#sphx-glr-gallery-tree-plot-simpletreedataprovider-py) (for educational purposes)
+
+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.
+
+**NOTE**: This is currently late beta quality software. The API and functionality might break rarely.
 
 ## Installation
 ```bash
@@ -71,19 +88,20 @@ See [readthedocs](https://iplotx.readthedocs.io/en/latest/) for the full documen
 ## Gallery
 See [gallery](https://iplotx.readthedocs.io/en/latest/gallery/index.html).
 
-## Roadmap
-- Plot networks from igraph and networkx interchangeably, using matplotlib as a backend. ✅
-- Support interactive plotting, e.g. zooming and panning after the plot is created. ✅
-- Support storing the plot to disk thanks to the many matplotlib backends (SVG, PNG, PDF, etc.). ✅
-- Support flexible yet easy styling. ✅
+## Features
+- Plot networks from multiple libraries including networkx and igraph, using matplotlib as a backend. ✅
+- Plot trees from multiple libraries such as cogent3, ETE4, skbio, and biopython. ✅
+- 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.). ✅
 - Efficient plotting of large graphs using matplotlib's collection functionality. ✅
-- Support editing plotting elements after the plot is created, e.g. changing node colors, labels, etc. ✅
-- Support animations, e.g. showing the evolution of a network over time. ✅
-- Support mouse interaction, e.g. hovering over or clicking on nodes and edges to get information about them. ✅
-- Support trees from special libraries such as ete3, biopython, etc. This will need a dedicated function and layouting. ✅
-- Support uni- and bi-directional communication between graph object and plot object.🏗️
-
-**NOTE:** The last item can probably be achieved already by using `matplotlib`'s existing callback functionality. It is currently untested, but if you manage to get it to work on your graph let me know and I'll add it to the examples (with credit).
+- Edit plotting elements after the plot is created, e.g. changing node colors, labels, etc. ✅
+- Animations, e.g. showing the evolution of a network over time. ✅
+- Mouse and keyboard interaction, e.g. hovering over nodes/edges to get information about them. ✅
+- Node clustering and covers, e.g. showing communities in a network. ✅
+- Choice of tree layouts and orientations. ✅
+- Tree-specific options: cascades, subtree styling, split edges, etc. ✅
+- (WIP) Support uni- and bi-directional communication between graph object and plot object.🏗️
 
 ## Authors
 Fabio Zanini (https://fabilab.org)

iplotx-0.5.1/README.md

@@ -0,0 +1,69 @@
+![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)
+[![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)
+
+# iplotx
+[![Banner](docs/source/_static/banner.png)](https://iplotx.readthedocs.io/en/latest/gallery/index.html).
+
+Visualise networks and trees in Python, with style.
+
+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) (for educational purposes)
+- **trees**:
+  - [ETE4](https://etetoolkit.github.io/ete/)
+  - [cogent3](https://cogent3.org/)
+  - [Biopython](https://biopython.org/)
+  - [scikit-bio](https://scikit.bio)
+  - [minimal tree data structure](https://iplotx.readthedocs.io/en/latest/gallery/tree/plot_simpletreedataprovider.html#sphx-glr-gallery-tree-plot-simpletreedataprovider-py) (for educational purposes)
+
+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.
+
+**NOTE**: This is currently late beta quality software. The API and functionality might break rarely.
+
+## Installation
+```bash
+pip install iplotx
+```
+
+## Quick Start
+```python
+import networkx as nx
+import matplotlib.pyplot as plt
+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)
+```
+
+![Quick start image](docs/source/_static/graph_basic.png)
+
+## Documentation
+See [readthedocs](https://iplotx.readthedocs.io/en/latest/) for the full documentation.
+
+## Gallery
+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 trees from multiple libraries such as cogent3, ETE4, skbio, and biopython. ✅
+- 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.). ✅
+- Efficient plotting of large graphs using matplotlib's collection functionality. ✅
+- Edit plotting elements after the plot is created, e.g. changing node colors, labels, etc. ✅
+- Animations, e.g. showing the evolution of a network over time. ✅
+- Mouse and keyboard interaction, e.g. hovering over nodes/edges to get information about them. ✅
+- Node clustering and covers, e.g. showing communities in a network. ✅
+- Choice of tree layouts and orientations. ✅
+- Tree-specific options: cascades, subtree styling, split edges, etc. ✅
+- (WIP) Support uni- and bi-directional communication between graph object and plot object.🏗️
+
+## Authors
+Fabio Zanini (https://fabilab.org)

{iplotx-0.4.0 → iplotx-0.5.1}/docs/source/api/artists.md

@@ -22,4 +22,3 @@ In turn, a `VertexCollection` or `EdgeCollection` instance **may** contain a `La
 .. autoclass:: iplotx.edge.arrow.EdgeArrowCollection
     :members:
 ```
-

{iplotx-0.4.0 → iplotx-0.5.1}/docs/source/api/complete_style_specification.md

@@ -16,7 +16,7 @@
 
         # Marker style. Currently supported markers:
         # o, c, circle: circle
-    f   # s, square, r, rectangle: rectangle (square if only one size specified)
+        # s, square, r, rectangle: rectangle (square if only one size specified)
         # ^, triangle: upward triangle
         # v, triangle_down: downward triangle
         # <, triangle_left: leftward triangle
@@ -28,7 +28,7 @@
         # 8, octagon: octagon
         # *, star: 5-point star, upright
         "marker": str,
-        
+
         "facecolor": str | Any,  # Color of the vertex face (e.g. 'red', '#FF0000')
         "edgecolor": str | Any,  # Color of the vertex edge (e.g. 'black', '#000000')
         "alpha": float,  # Opacity of the vertex (0.0 for fully transparent, 1.0 for fully opaque)

{iplotx-0.4.0 → iplotx-0.5.1}/docs/source/api/providers.md

@@ -14,4 +14,3 @@
     :members:
 
 ```
-

{iplotx-0.4.0 → iplotx-0.5.1}/docs/source/conf.py

@@ -49,7 +49,6 @@ myst_enable_extensions = ["colon_fence"]
 sphinx_gallery_conf = {
     "examples_dirs": "../../gallery",  # path to your example scripts
     "gallery_dirs": "./gallery",  # path to where to save gallery generated output
-    #'matplotlib_animations': (True, 'mp4'),
     "matplotlib_animations": True,
 }
 
@@ -135,7 +134,7 @@ if link_github:
 
         version = parse_version(iplotx.__version__)
         tag = "main" if version.is_devrelease else f"v{version.public}"
-        return "https://github.com/fabilab/iplotx/blob" f"/{tag}/{fn}{linespec}"
+        return f"https://github.com/fabilab/iplotx/blob/{tag}/{fn}{linespec}"
 
 else:
     extensions.append("sphinx.ext.viewcode")

{iplotx-0.4.0 → iplotx-0.5.1}/docs/source/sg_execution_times.rst

@@ -6,7 +6,7 @@
 
 Computation times
 =================
-**00:01.295** total execution time for 47 files **from all galleries**:
+**00:01.263** total execution time for 51 files **from all galleries**:
 
 .. container::
 
@@ -32,8 +32,8 @@ Computation times
    * - Example
      - Time
      - Mem (MB)
-   * - :ref:`sphx_glr_gallery_tree_plot_support.py` (``../../gallery/tree/plot_support.py``)
-     - 00:01.295
+   * - :ref:`sphx_glr_gallery_tree_plot_split_edges.py` (``../../gallery/tree/plot_split_edges.py``)
+     - 00:01.263
      - 0.0
    * - :ref:`sphx_glr_gallery_plot_animation.py` (``../../gallery/plot_animation.py``)
      - 00:00.000
@@ -122,7 +122,7 @@ Computation times
    * - :ref:`sphx_glr_gallery_plot_simple_path.py` (``../../gallery/plot_simple_path.py``)
      - 00:00.000
      - 0.0
-   * - :ref:`sphx_glr_gallery_plot_simpledataprovider.py` (``../../gallery/plot_simpledataprovider.py``)
+   * - :ref:`sphx_glr_gallery_plot_simplenetworkdataprovider.py` (``../../gallery/plot_simplenetworkdataprovider.py``)
      - 00:00.000
      - 0.0
    * - :ref:`sphx_glr_gallery_plot_style.py` (``../../gallery/plot_style.py``)
@@ -143,9 +143,15 @@ Computation times
    * - :ref:`sphx_glr_gallery_plot_with_colorbar.py` (``../../gallery/plot_with_colorbar.py``)
      - 00:00.000
      - 0.0
+   * - :ref:`sphx_glr_gallery_tree_plot_angular_waypoints.py` (``../../gallery/tree/plot_angular_waypoints.py``)
+     - 00:00.000
+     - 0.0
    * - :ref:`sphx_glr_gallery_tree_plot_biopython_tree.py` (``../../gallery/tree/plot_biopython_tree.py``)
      - 00:00.000
      - 0.0
+   * - :ref:`sphx_glr_gallery_tree_plot_cladeedges.py` (``../../gallery/tree/plot_cladeedges.py``)
+     - 00:00.000
+     - 0.0
    * - :ref:`sphx_glr_gallery_tree_plot_cogent3_layouts.py` (``../../gallery/tree/plot_cogent3_layouts.py``)
      - 00:00.000
      - 0.0
@@ -161,9 +167,15 @@ 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_simpletreedataprovider.py` (``../../gallery/tree/plot_simpletreedataprovider.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
+   * - :ref:`sphx_glr_gallery_tree_plot_support.py` (``../../gallery/tree/plot_support.py``)
+     - 00:00.000
+     - 0.0
    * - :ref:`sphx_glr_gallery_tree_plot_tree_node_background.py` (``../../gallery/tree/plot_tree_node_background.py``)
      - 00:00.000
      - 0.0

{iplotx-0.4.0 → iplotx-0.5.1}/gallery/plot_animation.py

@@ -2,9 +2,12 @@
 Animations
 ==========
 
-This tutorial shows how to animate `iplotx` visualizations using `matplotlib.animation.FuncAnimation`.
+This tutorial shows how to animate `iplotx` visualizations using
+`matplotlib.animation.FuncAnimation`.
 
-For illustration purposes, we will animate a simple directed graph, rotating it around its center. We also modify the opacity of the vertices and edges, just for fun.
+For illustration purposes, we will animate a simple directed graph,
+rotating it around its center. We also modify the opacity of the
+vertices and edges, just for fun.
 """
 
 import matplotlib.pyplot as plt

{iplotx-0.4.0 → iplotx-0.5.1}/gallery/plot_chess_masters.py

@@ -2,10 +2,17 @@
 Chess masters
 =============
 
-This example from networkx shows the relatinoships between chess masters. The example has a lot of network analysis code that is somewhat irrelevant for `iplotx` and is kept to demonstrate functional parity.
+This example from networkx shows the relatinoships between chess masters.
+The example has a lot of network analysis code that is somewhat irrelevant
+for `iplotx` and is kept to demonstrate functional parity.
 
 .. note::
-  The layout of this graph is computed with the Kamada-Kawai algorithm. In networkx, that requires the `scipy` package to be installed. Here, we also demonstrate the alternative, which is to convert the network to `igraph`, which has an internal implementation of the algorithm. While the exact layout is not identical, it is equally accurate and visually similar.
+  The layout of this graph is computed with the Kamada-Kawai algorithm. In
+  networkx, that requires the `scipy` package to be installed. Here, we
+  also demonstrate the alternative, which is to convert the network to
+  `igraph`, which has an internal implementation of the algorithm. While
+  the exact layout is not identical, it is equally accurate and visually
+  similar.
 """
 
 import numpy as np
@@ -52,9 +59,7 @@ def chess_pgn_graph(pgn_file="data/chess_masters_WCC.pgn.bz2"):
 
 G = chess_pgn_graph()
 
-print(
-    f"Loaded {G.number_of_edges()} chess games between {G.number_of_nodes()} players\n"
-)
+print(f"Loaded {G.number_of_edges()} chess games between {G.number_of_nodes()} players\n")
 
 # identify connected components of the undirected version
 H = G.to_undirected()

{iplotx-0.4.0 → iplotx-0.5.1}/gallery/plot_dag.py

@@ -7,7 +7,6 @@ This example demonstrates how to create a random directed acyclic graph (DAG) an
 
 import random
 import igraph as ig
-import matplotlib.pyplot as plt
 import iplotx as ipx
 
 

{iplotx-0.4.0 → iplotx-0.5.1}/gallery/plot_edit_artists.py

@@ -2,17 +2,17 @@
 Editing artists after plotting
 ==============================
 
-One of the strengths of `iplotx` is the support for editing artists after they have been plotted the first time without making a whole new figure.
+One of the strengths of `iplotx` is the support for editing artists after
+they have been plotted the first time without making a whole new figure.
 
-In this example, we will change vertices, edges, arrows, etc. and check out how they look like.
+In this example, we will change vertices, edges, arrows, etc. and check
+out how they look like.
 """
 
 # %%
 # This is the vanilla version, taken from the "Ports" gallery example:
 
 import igraph as ig
-import numpy as np
-import matplotlib.pyplot as plt
 import iplotx as ipx
 
 g = ig.Graph.Ring(3, directed=True)

{iplotx-0.4.0 → iplotx-0.5.1}/gallery/plot_grouping.py

@@ -2,9 +2,11 @@
 Grouping
 ========
 
-This example shows how to use the `grouping` argument to visualise vertex covers or clustering, including singletons (i.e. groups of one vertex).
+This example shows how to use the `grouping` argument to visualise vertex
+covers or clustering, including singletons (i.e. groups of one vertex).
 
-The function takes a few different formats for the groups, but the easiest is a dictionary of sets, in which each key is the name of the group and
+The function takes a few different formats for the groups, but the easiest
+is a dictionary of sets, in which each key is the name of the group and
 each value is the set of vertices in that group.
 
 """
@@ -15,7 +17,7 @@ import iplotx as ipx
 
 g = ig.Graph.Ring(8)
 
-ipx.plot(
+ipx.network(
     network=g,
     layout="circle",
     grouping={
@@ -28,11 +30,13 @@ plt.gca().set_aspect(1.0)
 
 # %%
 # .. note::
-#   Group layouts are computed as rounded convex hulls around each group of vertices. If you are interested in contributing an algorithm that computes concave group layouts, please reach out on GitHub!
+#   Group layouts are computed as rounded convex hulls around each group of vertices.
+#   If you are interested in contributing an algorithm that computes concave group
+#   layouts, please reach out on GitHub!
 #
 # Groups can be styles in a similar way as all other elements in `iplotx`:
 
-ipx.plot(
+ipx.network(
     network=g,
     layout="circle",
     grouping={
@@ -61,7 +65,7 @@ plt.gca().set_aspect(1.0)
 
 layout = g.layout("circle")
 fig, ax = plt.subplots(figsize=(5, 5))
-ipx.plot(
+ipx.network(
     network=g,
     layout=layout,
     ax=ax,
@@ -70,7 +74,7 @@ ipx.plot(
     vertex_label_color="white",
     zorder=2,
 )
-ipx.plot(
+ipx.network(
     grouping={
         "singleton": {0},
         "doublet": {1, 2},
@@ -87,6 +91,7 @@ ipx.plot(
 
 # %%
 # .. note::
-#   The argument `zorder` is applied to both network and grouping style, however since only one of them is plotted each
-#   time this is equivalent to setting `network_zorder` and `grouping_zorder`. If both are specified, `zorder` takes
+#   The argument `zorder` is applied to both network and grouping style, however
+#   since only one of them is plotted each time this is equivalent to setting
+#   `network_zorder` and `grouping_zorder`. If both are specified, `zorder` takes
 #   priority over its more specific cousins.

{iplotx-0.4.0 → iplotx-0.5.1}/gallery/plot_house.py

@@ -11,9 +11,7 @@ import iplotx as ipx
 
 G = nx.house_graph()
 fig, ax = plt.subplots()
-nx.set_node_attributes(
-    G, {0: (0, 0), 1: (1, 0), 2: (0, 1), 3: (1, 1), 4: (0.5, 2.0)}, "pos"
-)
+nx.set_node_attributes(G, {0: (0, 0), 1: (1, 0), 2: (0, 1), 3: (1, 1), 4: (0.5, 2.0)}, "pos")
 nx.set_node_attributes(
     G,
     {

{iplotx-0.4.0 → iplotx-0.5.1}/gallery/plot_knuth_miles.py

@@ -8,7 +8,6 @@ This example from newtorkx shows an undirected graph of 128 US cities.
 import gzip
 import re
 
-import numpy as np
 import matplotlib.pyplot as plt
 import networkx as nx
 import iplotx as ipx

{iplotx-0.4.0 → iplotx-0.5.1}/gallery/plot_loops.py

@@ -6,7 +6,6 @@ This minimal example shows how to style a plot in a few different ways.
 """
 
 import networkx as nx
-import matplotlib.pyplot as plt
 import iplotx as ipx
 
 # Create a graph and add a self-loop to node 0
@@ -22,7 +21,7 @@ G.add_edges_from(edgelist)
 # Style the edge lines
 linestyle = {e: "-" if e not in edgelist else "--" for e in G.edges()}
 
-ipx.plot(
+ipx.network(
     G,
     layout=pos,
     vertex_labels=True,
@@ -47,11 +46,11 @@ ipx.plot(
 )
 
 # %%
-# In addition to fully structured styles in the form of nested dictionaries, `iplotx`
-# also accepts flat or semi-flat styles, with levels separated by underscores ("_").
-# The above is equivalent to:
+# In addition to fully structured styles in the form of nested dictionaries,
+# `iplotx` also accepts flat or semi-flat styles, with levels separated by
+# underscores ("_"). The above is equivalent to:
 
-ipx.plot(
+ipx.network(
     G,
     layout=pos,
     vertex_labels=True,
@@ -71,7 +70,7 @@ ipx.plot(
 # The `**kwargs` flexible argument of `ipx.plotting` can be used for this purpose as well,
 # for increased readability:
 
-ipx.plot(
+ipx.network(
     G,
     layout=pos,
     vertex_labels=True,
@@ -98,7 +97,7 @@ with ipx.style.context(
     edge_looptension=3.5,
     edge_arrow_marker="|>",
 ):
-    ipx.plot(
+    ipx.network(
         G,
         layout=pos,
         vertex_labels=True,

{iplotx-0.4.0 → iplotx-0.5.1}/gallery/plot_max_bipartite_matching.py

@@ -2,12 +2,12 @@
 Maximum Bipartite Matching by Maximum Flow
 ==========================================
 
-This example from `igraph` presents how to visualise bipartite matching using maximum flow, with edge linewidth and vertex facecolor styling.
+This example from `igraph` presents how to visualise bipartite matching
+using maximum flow, with edge linewidth and vertex facecolor styling.
 
 """
 
 import igraph as ig
-import matplotlib.pyplot as plt
 import iplotx as ipx
 
 # We start by creating the bipartite directed graph.
@@ -37,7 +37,7 @@ layout = g.layout_bipartite()
 layout[9] = (2, -1)
 layout[10] = (2, 2)
 
-ipx.plot(
+ipx.network(
     g,
     layout=layout,
     vertex_labels=True,
@@ -57,7 +57,7 @@ ipx.plot(
 # vertex style accordingly, perhaps with pronounced vertex borders to
 # increase constrast:
 #
-ipx.plot(
+ipx.network(
     g,
     layout=layout,
     vertex_labels=True,

{iplotx-0.4.0 → iplotx-0.5.1}/gallery/plot_minimum_spanning_trees.py

@@ -7,7 +7,6 @@ This example from igraph shows how to work with edge labels and linewidths.
 
 import random
 import igraph as ig
-import matplotlib.pyplot as plt
 import iplotx as ipx
 
 
@@ -24,7 +23,7 @@ g.es[mst_edges]["width"] = 3.0
 
 layout = g.layout("grid")
 
-ipx.plot(
+ipx.network(
     g,
     layout=layout,
     edge_labels=g.es["weight"],
@@ -48,10 +47,11 @@ ipx.plot(
 )
 
 # %%
-# If you want to avoid rotating the labels vertically and let them follow the edge directions instead,
-# just set the "rotate" parameter to False (or skip it in the default style):
+# If you want to avoid rotating the labels vertically and let them follow the
+# edge directions instead, just set the "rotate" parameter to False (or skip
+# it in the default style):
 
-ipx.plot(
+ipx.network(
     g,
     layout=layout,
     edge_labels=g.es["weight"],

{iplotx-0.4.0 → iplotx-0.5.1}/gallery/plot_mouse_hover.py

@@ -12,7 +12,6 @@ This example shows how to interact with mouse events (e.g. hovering) in `iplotx`
 """
 
 import matplotlib.pyplot as plt
-import numpy as np
 import igraph as ig
 import iplotx as ipx
 
@@ -48,7 +47,7 @@ def hover_callback(event):
         if cont:
             i = ind["ind"][0]
             annot.xy = vc.get_offsets()[i]
-            annot.set_text(f"{i+1}")
+            annot.set_text(f"{i + 1}")
             annot.set_visible(True)
         # Otherwise, hide the bubble
         elif annot.get_visible():