scikit-network 0.32.1__cp311-cp311-win_amd64.whl → 0.33.1__cp311-cp311-win_amd64.whl

sknetwork/utils/__init__.py

@@ -1,5 +1,5 @@
 """utils module"""
-from sknetwork.data import Bunch
+from sknetwork.data import *
 from sknetwork.utils.check import is_symmetric
 from sknetwork.utils.format import *
 from sknetwork.utils.membership import get_membership, from_membership

sknetwork/utils/values.py

@@ -10,9 +10,11 @@ from typing import Optional, Union
 import numpy as np
 
 
-def get_values(shape: tuple, values: Union[np.ndarray, dict], default_value: float = -1) -> np.ndarray:
+def get_values(shape: tuple, values: Union[np.ndarray, list, dict], default_value: float = -1) -> np.ndarray:
     """Get values as array."""
     n = shape[0]
+    if isinstance(values, list):
+        values = np.array(values)
     if isinstance(values, np.ndarray):
         if len(values) != n:
             raise ValueError('Dimensions mismatch between adjacency and values.')
@@ -29,8 +31,8 @@ def get_values(shape: tuple, values: Union[np.ndarray, dict], default_value: flo
     return values
 
 
-def stack_values(shape: tuple, values_row: Optional[Union[np.ndarray, dict]],
-                 values_col: Optional[Union[np.ndarray, dict]] = None, default_value: float = -1) -> np.ndarray:
+def stack_values(shape: tuple, values_row: Optional[Union[np.ndarray, list, dict]],
+                 values_col: Optional[Union[np.ndarray, list, dict]] = None, default_value: float = -1) -> np.ndarray:
     """Process values for rows and columns and stack the results into a single vector."""
     n_row, n_col = shape
     if values_row is None and values_col is None:

sknetwork/visualization/graphs.py

@@ -368,7 +368,7 @@ def visualize_graph(adjacency: Optional[sparse.csr_matrix] = None, position: Opt
                     node_width: float = 1, node_width_max: float = 3, node_color: str = 'gray',
                     display_edges: bool = True, edge_labels: Optional[list] = None,
                     edge_width: float = 1, edge_width_min: float = 0.5,
-                    edge_width_max: float = 20, display_edge_weight: bool = True,
+                    edge_width_max: float = 20, display_edge_weight: bool = False,
                     edge_color: Optional[str] = None, label_colors: Optional[Iterable] = None,
                     font_size: int = 12, directed: Optional[bool] = None, filename: Optional[str] = None) -> str:
     """Return the image of a graph in SVG format.

scikit_network-0.32.1.dist-info/METADATA

@@ -1,511 +0,0 @@
-Metadata-Version: 2.1
-Name: scikit-network
-Version: 0.32.1
-Summary: Graph algorithms
-Home-page: https://github.com/sknetwork-team/scikit-network
-Author: Scikit-network team
-Author-email: bonald@enst.fr
-License: BSD license
-Keywords: sknetwork
-Classifier: Development Status :: 3 - Alpha
-Classifier: Intended Audience :: Developers
-Classifier: Intended Audience :: Information Technology
-Classifier: Intended Audience :: Education
-Classifier: Intended Audience :: Science/Research
-Classifier: License :: OSI Approved :: BSD License
-Classifier: Natural Language :: English
-Classifier: Programming Language :: Cython
-Classifier: Programming Language :: Python :: 3.8
-Classifier: Programming Language :: Python :: 3.9
-Classifier: Programming Language :: Python :: 3.10
-Classifier: Programming Language :: Python :: 3.11
-Requires-Python: >=3.8
-Description-Content-Type: text/x-rst
-License-File: LICENSE
-License-File: AUTHORS.rst
-Requires-Dist: numpy >=1.22.4
-Requires-Dist: scipy >=1.7.3
-
-.. image:: https://perso.telecom-paristech.fr/bonald/logo_sknetwork.png
-    :align: right
-    :width: 150px
-    :alt: logo sknetwork
-
-
-
-.. image:: https://img.shields.io/pypi/v/scikit-network.svg
-        :target: https://pypi.python.org/pypi/scikit-network
-
-.. image:: https://github.com/sknetwork-team/scikit-network/actions/workflows/ci_checks.yml/badge.svg
-        :target: https://github.com/sknetwork-team/scikit-network/actions/workflows/ci_checks.yml
-
-.. image:: https://readthedocs.org/projects/scikit-network/badge/?version=latest
-        :target: https://scikit-network.readthedocs.io/en/latest/?badge=latest
-        :alt: Documentation Status
-
-.. image:: https://codecov.io/gh/sknetwork-team/scikit-network/branch/master/graph/badge.svg
-        :target: https://codecov.io/gh/sknetwork-team/scikit-network
-
-.. image:: https://img.shields.io/pypi/pyversions/scikit-network.svg
-        :target: https://pypi.python.org/pypi/scikit-network
-
-Free software library in Python for machine learning on graphs:
-
-* Memory-efficient representation of graphs as sparse matrices in scipy_ format
-* Fast algorithms
-* Simple API inspired by scikit-learn_
-
-.. _scipy: https://www.scipy.org
-.. _scikit-learn: https://scikit-learn.org/
-
-Resources
----------
-
-* Free software: BSD license
-* GitHub: https://github.com/sknetwork-team/scikit-network
-* Documentation: https://scikit-network.readthedocs.io
-
-Quick start
------------
-
-Install scikit-network:
-
-.. code-block:: console
-
-    $ pip install scikit-network
-
-Import scikit-network::
-
-    import sknetwork
-
-Overview
---------
-
-An overview of the package is presented in this `notebook <https://scikit-network.readthedocs.io/en/latest/tutorials/overview/index.html>`_.
-
-Documentation
--------------
-
-The documentation is structured as follows:
-
-* `Getting started <https://scikit-network.readthedocs.io/en/latest/first_steps.html>`_: First steps to install, import and use scikit-network.
-* `User manual <https://scikit-network.readthedocs.io/en/latest/reference/data.html>`_: Description of each function and object of scikit-network.
-* `Tutorials <https://scikit-network.readthedocs.io/en/latest/tutorials/data/index.html>`_: Application of the main tools to toy examples.
-* `Examples <https://scikit-network.readthedocs.io/en/latest/use_cases/text.html>`_: Examples combining several tools on specific use cases.
-* `About <https://scikit-network.readthedocs.io/en/latest/authors.html>`_: Authors, history of the library, how to contribute, index of functions and objects.
-
-Citing
-------
-
-If you want to cite scikit-network, please refer to the publication in
-the `Journal of Machine Learning Research <https://jmlr.org>`_:
-
-.. code::
-
-    @article{JMLR:v21:20-412,
-      author  = {Thomas Bonald and Nathan de Lara and Quentin Lutz and Bertrand Charpentier},
-      title   = {Scikit-network: Graph Analysis in Python},
-      journal = {Journal of Machine Learning Research},
-      year    = {2020},
-      volume  = {21},
-      number  = {185},
-      pages   = {1-6},
-      url     = {http://jmlr.org/papers/v21/20-412.html}
-    }
-
-
-=======
-History
-=======
-
-0.32.1 (2024-04-02)
--------------------
-
-* Fix documentation
-* Fix wheel upload
-
-0.32.0 (2024-03-29)
--------------------
-
-* Add Leiden clustering algorithm
-* Add k-center clustering algorithm
-* Add functions to detect and break cycles
-* Add damping factor in diffusion
-* Fix F1 scores
-* Remove hierarchical Louvain embedding
-* Get clustering coefficient for directed graphs
-
-0.31.0 (2023-05-22)
--------------------
-
-* Add Python 3.11
-* Add set_param / get_param to algorithms, suggested by Franz Kiraly (#557)
-* Compute shortest paths by matrix-vector multiplications
-* Make tools on topology (cliques, code-decomposition, etc.) as functions
-* Rename parameter membership -> probs for soft classification / clustering
-* Add softmax to classification by diffusion
-
-0.30.0 (2023-04-12)
--------------------
-
-* Add overview
-* Add predict_proba method to classification and clustering
-
-0.29.0 (2023-03-30)
--------------------
-
-* Change API for clustering (predict / transform)
-* Change API for classification (seeds -> labels)
-* Change API for ranking (seeds -> weights)
-* Change API for GNN (same as classifiers)
-* Remove first order methods for link prediction
-* Add nearest neighbor methods for link prediction
-* Add KNN classifier without embedding
-* Add TF-IDF
-* Solve security issues by upgrade of wheels and ipython
-
-0.28.3 (2023-01-06)
--------------------
-
-* Drop Python 3.7
-* Update Numpy requirement
-
-0.28.2 (2022-11-30)
--------------------
-
-* Allow Python 3.7, by Thomas Bonald
-* Fix input format for KMeans, issue #548 raised by @sgerbe
-
-0.28.1 (2022-11-22)
--------------------
-
-* Fix sampling for GraphSage, by Simon Delarue
-* Fix leakage on GNNs, by Thomas Bonald and Simon Delarue
-* Update tutorial on GNNs with node inference, by Thomas Bonald and Simon Delarue
-
-0.28.0 (2022-11-16)
--------------------
-
-* Update Graph neural networks (e.g., add GraphSAGE), by Simon Delarue
-* Clean data home folder (set one folder per dataset collection, NetSet, Konect, ...), by Thomas Bonald
-* Improve classification by diffusion, setting -1 to unreached nodes, by Thomas Bonald
-* Fix bug on modularity, raised by Alessandro (#543)
-* Clean up source distribution, by Nicholas Bollweg (#544)
-* Safe file extraction, by TrellixVulnTeam
-* Fix bug on dendrogram cut, raised by Nina Sachdev (#546)
-* Add a function to aggregate a graph per label, by Thomas Bonald
-
-0.27.1 (2022-07-29)
--------------------
-
-* Fix documentation
-
-0.27.0 (2022-07-29)
--------------------
-
-* Drop Python 3.7
-* Update NumPy and SciPy requirements
-* Add graph neural networks, by Simon Delarue (#533)
-* Add fit_predict / fit_transform where appropriate, by Thomas Bonald
-* Add Louvain hierarchical clustering (bottom-up), by Thomas Bonald
-* Improve classification by diffusion (vectorial), by Thomas Bonald
-* Add F1 scores for classification, by Thomas Bonald
-* Add cosine similarity metric for embeddings, by Thomas Bonald
-* Add acyclic test for undirected graphs, by Thomas Bonald
-* Update algorithms to accept all sparse matrix formats of scipy, by Thomas Bonald
-
-0.26.0 (2022-05-03)
--------------------
-
-* Add module on regression, by Thomas Bonald
-* Add connected components for bipartite graphs, by Thomas Bonald
-* Update functions for loading graphs, by Thomas Bonald
-* Fix shuffling nodes in Louvain (issue #521), by Thomas Bonald
-* Add radius and eccentricity metrics, by Henry Carscadden (#522)
-* Add new use case (recommendation), by Thomas Bonald
-
-0.25.0 (2022-03-15)
--------------------
-
-* Add use cases as notebooks, by Thomas Bonald
-* Add list/dict of neighbors for building graphs, by Thomas Bonald
-* Update Spectral embedding, by Thomas Bonald
-* Update Block models, by Thomas Bonald (#507)
-* Fix Tree sampling divergence, by Thomas Bonald (#505)
-* Allow parsers to return weighted graphs, by Thomas Bonald
-* Add Apple Silicon and Python 3.10 wheels, by Quentin Lutz (#503)
-
-0.24.0 (2021-07-27)
--------------------
-
-* Merge Bi* algorithms (e.g., BiLouvain -> Louvain) by Thomas Bonald (#490)
-* Transition from Travis to Github actions by Quentin Lutz (#488)
-* Added sdist build for conda recipes
-* Added name position for graph visualization
-* Removed randomized algorithms
-
-0.23.1 (2021-04-24)
--------------------
-
-* Updated NumPy and SciPy requirements
-
-0.23.0 (2021-04-23)
--------------------
-
-* New push-based implementation of PageRank by Wenzhuo Zhao (#475)
-* Fixed cut_balanced in hierarchy
-* Dropped Python 3.6, wheels for Python 3.9 (switched to manylinux2014)
-
-0.22.0 (2021-02-09)
--------------------
-
-* Added hierarchical Louvain embedding by Quentin Lutz (#468)
-* Doc fixes and updates
-* Requirements update
-
-0.21.0 (2021-01-29)
--------------------
-
-* Added random projection embedding by Thomas Bonald (#461)
-* Added PCA-based embedding by Thomas Bonald (#461)
-* Added 64-bit support for Louvain by Flávio Juvenal (#450)
-* Added verbosity options for dataset loaders
-* Fixed Louvain embedding
-* Various doc and tutorial updates
-
-0.20.0 (2020-10-20)
--------------------
-
-* Added betweenness algorithm by Tiphaine Viard (#444)
-
-0.19.3 (2020-09-17)
--------------------
-
-* Added Louvain-based embedding
-* Fix documentation with new dataset website URLs
-
-0.19.2 (2020-09-14)
--------------------
-
-* Fix documentation with new dataset website URLs.
-
-0.19.1 (2020-09-09)
--------------------
-
-* Fix visualization features
-* Fix documentation
-
-0.19.0 (2020-09-02)
--------------------
-
-* Added link prediction module
-* Added pie-node visualization of memberships
-* Added Weisfeiler-Lehman graph coloring by Pierre Pebereau and Alexis Barreaux (#394)
-* Added Force Atlas 2 graph layout by Victor Manach and Rémi Jaylet (#396)
-* Added triangle listing algorithm for directed and undirected graph by Julien Simonnet and Yohann Robert (#376)
-* Added k-core decomposition algorithm by Julien Simonnet and Yohann Robert (#377)
-* Added k-clique listing algorithm by Julien Simonnet and Yohann Robert (#377)
-* Added color map option in visualization module
-* Updated NetSet URL
-
-0.18.0 (2020-06-08)
--------------------
-
-* Added Katz centrality
-* Refactor connectivity module into paths and topology
-* Refactor Diffusion into Dirichlet
-* Added parsers for adjacency list TSV and GraphML
-* Added shortest paths and distances
-
-0.17.0 (2020-05-07)
--------------------
-
-* Add clustering by label propagation
-* Add models
-* Add function to build graph from edge list
-* Change a parameter in SVG visualization functions
-* Minor corrections
-
-0.16.0 (2020-04-30)
--------------------
-
-* Refactor basics module into connectivity
-* Cython version for label propagation
-* Minor corrections
-
-0.15.2 (2020-04-24)
--------------------
-
-* Clarified requirements
-* Minor corrections
-
-0.15.1 (2020-04-21)
--------------------
-
-* Added OpenMP support for all platforms
-
-0.15.0 (2020-04-20)
--------------------
-
-* Updated ranking module : new pagerank solver, new HITS params, post-processing
-* Polynomes in linear algebra
-* Added meta.name attribute for Bunch
-* Minor corrections
-
-0.14.0 (2020-04-17)
--------------------
-
-* Added spring layout in embedding
-* Added label propagation in classification
-* Added save / load functions in data
-* Added display edges parameter in svg graph exports
-* Corrected typos in documentation
-
-0.13.3 (2020-04-13)
--------------------
-
-* Minor bug
-
-0.13.2 (2020-04-13)
--------------------
-
-* Added wheels for multiple platforms (OSX, Windows (32 & 64 bits) and many Linux) and Python version (3.6/3.7/3.8)
-* Documentation update (SVG dendrograms, tutorial updates)
-
-0.13.1a (2020-04-09)
---------------------
-
-* Minor bug
-
-0.13.0a (2020-04-09)
---------------------
-
-* Changed from Numba to Cython for better performance
-* Added visualization module
-* Added k-nearest neighbors classifier
-* Added Louvain hierarchy
-* Added predict method in embedding
-* Added soft clustering to clustering algorithms
-* Added soft classification to classification algorithms
-* Added graphs in data module
-* Various API change
-
-0.12.1 (2020-01-20)
--------------------
-
-* Added heat kernel based node classifier
-* Updated loaders for WikiLinks
-* Fixed file-related issues for Windows
-
-0.12.0 (2019-12-10)
--------------------
-
-* Added VerboseMixin for verbosity features
-* Added Loaders for WikiLinks & Konect databases
-
-0.11.0 (2019-11-28)
--------------------
-
-* sknetwork: new API for bipartite graphs
-* new module: Soft node classification
-* new module: Node classification
-* new module: data (merge toy graphs + loader)
-* clustering: Spectral Clustering
-* ranking: new algorithms
-* utils: K-neighbors
-* hierarchy: Spectral WardDense
-* data: loader (Vital Wikipedia)
-
-0.10.1 (2019-08-26)
--------------------
-
-* Minor bug
-
-0.10.0 (2019-08-26)
--------------------
-
-* Clustering (and related metrics) for directed and bipartite graphs
-* Hierarchical clustering (and related metrics) for directed and bipartite graphs
-* Fix bugs on embedding algorithms
-
-
-0.9.0 (2019-07-24)
-------------------
-
-* Change parser output
-* Fix bugs in ranking algorithms (zero-degree nodes)
-* Add notebooks
-* Import algorithms from scipy (shortest path, connected components, bfs/dfs)
-* Change SVD embedding (now in decreasing order of singular values)
-
-0.8.2 (2019-07-19)
-------------------
-
-* Minor bug
-
-0.8.1 (2019-07-18)
-------------------
-
-* Added diffusion ranking
-* Minor fixes
-* Minor doc tweaking
-
-0.8.0 (2019-07-17)
-------------------
-
-* Changed Louvain, BiLouvain, Paris and PageRank APIs
-* Changed PageRank method
-* Documentation overhaul
-* Improved Jupyter tutorials
-
-0.7.1 (2019-07-04)
-------------------
-
-* Added Algorithm class for nicer repr of some classes
-* Added Jupyter notebooks as tutorials in the docs
-* Minor fixes
-
-0.7.0 (2019-06-24)
-------------------
-
-* Updated PageRank
-* Added tests for Numba versioning
-
-0.6.1 (2019-06-19)
-------------------
-
-* Minor bug
-
-0.6.0 (2019-06-19)
-------------------
-
-* Largest connected component
-* Simplex projection
-* Sparse Low Rank Decomposition
-* Numba support for Paris
-* Various fixes and updates
-
-0.5.0 (2019-04-18)
-------------------
-
-* Unified Louvain.
-
-0.4.0 (2019-04-03)
-------------------
-
-* Added Louvain for directed graphs and ComboLouvain for bipartite graphs.
-
-0.3.0 (2019-03-29)
-------------------
-
-* Updated clustering module and documentation.
-
-0.2.0 (2019-03-21)
-------------------
-
-* First real release on PyPI.
-
-0.1.1 (2018-05-29)
-------------------
-
-* First release on PyPI.