Merge pull request #189 from lucasimi/develop

Develop

Author: lucasimi

.github/workflows/publish.yml .github/workflows/publish-pypi.yml

@@ -1,16 +1,15 @@
-name: publish
+name: publish-pypi
 
 on:
   workflow_run:
-    workflows: ["publish-test"]
+    workflows: ["publish-testpypi"]
     types:
       - completed
     status: success
-  workflow_dispatch:
 
 jobs:
   publish:
-    name: Publish
+    name: Publish [PyPI]
     runs-on: ubuntu-latest
     environment: pypi
     permissions:

.github/workflows/publish-test.yml .github/workflows/publish-testpypi.yml

@@ -1,14 +1,13 @@
-name: publish-test
+name: publish-testpypi
 
 on:
   push:
     tags:
       - 'v[0-9]+.[0-9]+.[0-9]+'
-  workflow_dispatch:
 
 jobs:
-  publish-test:
-    name: Publish
+  publish:
+    name: Publish [TestPyPI]
     runs-on: ubuntu-latest
     environment: pypi
     permissions:

.github/workflows/bench.yml .github/workflows/test-bench.yml

@@ -1,4 +1,4 @@
-name: bench
+name: test-bench
 
 on: 
   push:
@@ -7,7 +7,7 @@ on:
       - main      
 
 jobs:
-  test-job:
+  test-bench-job:
     runs-on: ubuntu-latest
     steps:
       - name: Check out repository code

.github/workflows/test.yml .github/workflows/test-unit.yml

@@ -1,4 +1,4 @@
-name: test
+name: test-unit
 
 on: 
   push:
@@ -7,7 +7,7 @@ on:
       - main      
 
 jobs:
-  test-job:
+  test-unit-job:
     runs-on: ubuntu-latest
     steps:
       - name: Check out repository code

README.md

@@ -3,8 +3,8 @@
 [![Source Code](https://img.shields.io/badge/lucasimi-tda--mapper--python-blue?logo=github&logoColor=silver)](https://github.com/lucasimi/tda-mapper-python)
 [![PyPI version](https://img.shields.io/pypi/v/tda-mapper?logo=python&logoColor=silver)](https://pypi.python.org/pypi/tda-mapper)
 [![downloads](https://img.shields.io/pypi/dm/tda-mapper?logo=python&logoColor=silver)](https://pypi.python.org/pypi/tda-mapper)
-[![test](https://img.shields.io/github/actions/workflow/status/lucasimi/tda-mapper-python/test.yml?logo=github&logoColor=silver&branch=main&label=test)](https://github.com/lucasimi/tda-mapper-python/actions/workflows/test.yml)
-[![publish](https://img.shields.io/github/actions/workflow/status/lucasimi/tda-mapper-python/publish.yml?logo=github&logoColor=silver&label=publish)](https://github.com/lucasimi/tda-mapper-python/actions/workflows/publish.yml)
+[![test](https://img.shields.io/github/actions/workflow/status/lucasimi/tda-mapper-python/test-unit.yml?logo=github&logoColor=silver&branch=main&label=test)](https://github.com/lucasimi/tda-mapper-python/actions/workflows/test-unit.yml)
+[![publish](https://img.shields.io/github/actions/workflow/status/lucasimi/tda-mapper-python/publish-pypi.yml?logo=github&logoColor=silver&label=publish)](https://github.com/lucasimi/tda-mapper-python/actions/workflows/publish-pypi.yml)
 [![docs](https://img.shields.io/readthedocs/tda-mapper/main?logo=readthedocs&logoColor=silver)](https://tda-mapper.readthedocs.io/en/main/)
 [![codecov](https://img.shields.io/codecov/c/github/lucasimi/tda-mapper-python?logo=codecov&logoColor=silver)](https://codecov.io/github/lucasimi/tda-mapper-python)
 [![DOI](https://img.shields.io/badge/DOI-10.5281/zenodo.10642381-blue?logo=doi&logoColor=silver)](https://doi.org/10.5281/zenodo.10642381)

docs/source/index.rst

@@ -4,10 +4,10 @@
    :target: https://pypi.python.org/pypi/tda-mapper
 .. |downloads| image:: https://img.shields.io/pypi/dm/tda-mapper?logo=python&logoColor=silver
    :target: https://pypi.python.org/pypi/tda-mapper
-.. |test| image:: https://img.shields.io/github/actions/workflow/status/lucasimi/tda-mapper-python/test.yml?logo=github&logoColor=silver&branch=main&label=test
-   :target: https://github.com/lucasimi/tda-mapper-python/actions/workflows/test.yml
-.. |publish| image:: https://img.shields.io/github/actions/workflow/status/lucasimi/tda-mapper-python/publish.yml?logo=github&logoColor=silver&label=publish
-   :target: https://github.com/lucasimi/tda-mapper-python/actions/workflows/publish.yml
+.. |test| image:: https://img.shields.io/github/actions/workflow/status/lucasimi/tda-mapper-python/test-unit.yml?logo=github&logoColor=silver&branch=main&label=test
+   :target: https://github.com/lucasimi/tda-mapper-python/actions/workflows/test-unit.yml
+.. |publish| image:: https://img.shields.io/github/actions/workflow/status/lucasimi/tda-mapper-python/publish-pypi.yml?logo=github&logoColor=silver&label=publish
+   :target: https://github.com/lucasimi/tda-mapper-python/actions/workflows/publish-pypi.yml
 .. |docs| image:: https://img.shields.io/readthedocs/tda-mapper/main?logo=readthedocs&logoColor=silver
    :target: https://tda-mapper.readthedocs.io/en/main/
 .. |codecov| image:: https://img.shields.io/codecov/c/github/lucasimi/tda-mapper-python?logo=codecov&logoColor=silver

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "tda-mapper"
-version = "0.8.1"
+version = "0.9.0"
 description = "A simple and efficient Python implementation of Mapper algorithm for Topological Data Analysis"
 readme = "README.md"
 authors = [{ name = "Luca Simi", email = "lucasimi90@gmail.com" }]
@@ -19,6 +19,7 @@ keywords = ["tda", "mapper", "topology", "topological data analysis"]
 dependencies = [
     "matplotlib>=3.3.4",
     "networkx>=2.5",
+    "igraph>=0.11.8",
     "numba>=0.54",
     "numpy>=1.20.1, <2.0.0",
     "plotly>=4.14.3",

src/tdamapper/clustering.py

@@ -42,7 +42,7 @@ def __init__(self, *args, **kwargs):
 
 class _MapperClustering(EstimatorMixin, ParamsMixin):
 
-    def __init__(self, cover=None, clustering=None, n_jobs=1):
+    def __init__(self, cover=None, clustering=None, n_jobs=-1):
         self.cover = cover
         self.clustering = clustering
         self.n_jobs = n_jobs

src/tdamapper/core.py

@@ -58,7 +58,7 @@
 )
 
 
-def mapper_labels(X, y, cover, clustering, n_jobs=1):
+def mapper_labels(X, y, cover, clustering, n_jobs=-1):
     """
     Identify the nodes of the Mapper graph.
 
@@ -87,7 +87,7 @@ def mapper_labels(X, y, cover, clustering, n_jobs=1):
         interface, typically from :mod:`sklearn.cluster`.
     :param n_jobs: The maximum number of parallel clustering jobs. This
         parameter is passed to the constructor of :class:`joblib.Parallel`.
-        Defaults to 1.
+        Defaults to -1.
     :type n_jobs: int
     :return: A list of node labels for each point in the dataset.
     :rtype: list[list[int]]
@@ -112,7 +112,7 @@ def _run_clustering(local_ids):
     return itm_lbls
 
 
-def mapper_connected_components(X, y, cover, clustering, n_jobs=1):
+def mapper_connected_components(X, y, cover, clustering, n_jobs=-1):
     """
     Identify the connected components of the Mapper graph.
 
@@ -139,7 +139,7 @@ def mapper_connected_components(X, y, cover, clustering, n_jobs=1):
         interface, typically from :mod:`sklearn.cluster`.
     :param n_jobs: The maximum number of parallel clustering jobs. This
         parameter is passed to the constructor of :class:`joblib.Parallel`.
-        Defaults to 1.
+        Defaults to -1.
     :type n_jobs: int
     :return: A list of labels. The label at position i identifies the connected
         component of the point at position i in the dataset.
@@ -162,7 +162,7 @@ def mapper_connected_components(X, y, cover, clustering, n_jobs=1):
     return labels
 
 
-def mapper_graph(X, y, cover, clustering, n_jobs=1):
+def mapper_graph(X, y, cover, clustering, n_jobs=-1):
     """
     Create the Mapper graph.
 
@@ -189,7 +189,7 @@ def mapper_graph(X, y, cover, clustering, n_jobs=1):
         interface, typically from :mod:`sklearn.cluster`.
     :param n_jobs: The maximum number of parallel clustering jobs. This
         parameter is passed to the constructor of :class:`joblib.Parallel`.
-        Defaults to 1.
+        Defaults to -1.
     :type n_jobs: int
     :return: The Mapper graph.
     :rtype: :class:`networkx.Graph`
@@ -378,7 +378,7 @@ def __init__(
         clustering=None,
         failsafe=True,
         verbose=True,
-        n_jobs=1,
+        n_jobs=-1,
     ):
         self.cover = cover
         self.clustering = clustering

src/tdamapper/learn.py

@@ -35,15 +35,15 @@ class MapperClustering(_MapperClustering):
         :mod:`sklearn.cluster`
     :param n_jobs: The maximum number of parallel clustering jobs. This
         parameter is passed to the constructor of :class:`joblib.Parallel`.
-        Defaults to 1.
+        Defaults to -1.
     :type n_jobs: int
     """
 
     def __init__(
         self,
         cover=None,
         clustering=None,
-        n_jobs=1,
+        n_jobs=-1,
     ):
         super().__init__(
             cover=cover,
@@ -99,7 +99,7 @@ class MapperAlgorithm(_MapperAlgorithm):
     :type verbose: bool, optional
     :param n_jobs: The maximum number of parallel clustering jobs. This
         parameter is passed to the constructor of :class:`joblib.Parallel`.
-        Defaults to 1.
+        Defaults to -1.
     :type n_jobs: int
     """
 
@@ -109,7 +109,7 @@ def __init__(
         clustering=None,
         failsafe=True,
         verbose=True,
-        n_jobs=1,
+        n_jobs=-1,
     ):
         super().__init__(
             cover=cover,

src/tdamapper/plot.py

@@ -2,6 +2,7 @@
 This module provides functionalities to visualize the Mapper graph.
 """
 import networkx as nx
+import igraph as ig
 
 import numpy as np
 
@@ -31,20 +32,68 @@ class MapperPlot:
     :param seed: The random seed used to construct the graph embedding.
         Defaults to None.
     :type seed: int, optional
+    :param layout_engine: The engine used to compute the graph layout in the
+        specified dimensions. Possible values are 'igraph' and 'networkx'.
+        Defaults to 'igraph'.
+    :type layout_engine: str, optional
     """
 
-    def __init__(self, graph, dim, iterations=50, seed=None):
+    def __init__(
+        self,
+        graph,
+        dim,
+        iterations=50,
+        seed=None,
+        layout_engine='igraph',
+    ):
         self.graph = graph
         self.dim = dim
         self.iterations = iterations
         self.seed = seed
-        self.positions = nx.spring_layout(
+        self.layout_engine = layout_engine
+        self.positions = self._compute_pos()
+
+    def _compute_pos(self):
+        if self.layout_engine == 'igraph':
+            return self._compute_pos_ig()
+        elif self.layout_engine == 'networkx':
+            return self._compute_pos_nx()
+        else:
+            raise ValueError(
+                f'Unknown engine {self.layout_engine}. '
+                "Only possible values are 'igraph' and 'networkx'"
+            )
+
+    def _compute_pos_nx(self):
+        return nx.spring_layout(
             self.graph,
             dim=self.dim,
             seed=self.seed,
             iterations=self.iterations,
         )
 
+    def _compute_pos_ig(self):
+        if self.graph.number_of_nodes() == 0:
+            return {}
+        rng = np.random.default_rng(self.seed)
+        random_pos = rng.random((len(self.graph.nodes()), self.dim))
+        graph_ig = ig.Graph.from_networkx(self.graph)
+        if self.dim == 2:
+            layout = graph_ig.layout_fruchterman_reingold(
+                niter=self.iterations,
+                seed=random_pos,
+            )
+            pos = {node: (layout[i][0], layout[i][1]) for i, node in
+                   enumerate(self.graph.nodes())}
+        elif self.dim == 3:
+            layout = graph_ig.layout_fruchterman_reingold_3d(
+                niter=self.iterations,
+                seed=random_pos,
+            )
+            pos = {node: (layout[i][0], layout[i][1], layout[i][2])
+                   for i, node in enumerate(self.graph.nodes())}
+        return pos
+
     def plot_matplotlib(
         self,
         colors,