Merge branch 'develop' of github.com:lucasimi/tda-mapper-python into feature/add-streamlit-app

Author: lucasimi

README.md

@@ -1,10 +1,13 @@
+![Logo](https://github.com/lucasimi/tda-mapper-python/raw/main/docs/source/logos/tda-mapper-logo-horizontal.png)
+
 [![PyPI version](https://badge.fury.io/py/tda-mapper.svg)](https://badge.fury.io/py/tda-mapper)
 [![downloads](https://img.shields.io/pypi/dm/tda-mapper)](https://pypi.python.org/pypi/tda-mapper/)
 [![test](https://github.com/lucasimi/tda-mapper-python/actions/workflows/test.yml/badge.svg)](https://github.com/lucasimi/tda-mapper-python/actions/workflows/test.yml)
 [![deploy](https://github.com/lucasimi/tda-mapper-python/actions/workflows/deploy.yml/badge.svg)](https://github.com/lucasimi/tda-mapper-python/actions/workflows/deploy.yml)
 [![docs](https://readthedocs.org/projects/tda-mapper/badge/?version=main)](https://tda-mapper.readthedocs.io/en/main/?badge=main)
 [![codecov](https://codecov.io/github/lucasimi/tda-mapper-python/graph/badge.svg?token=FWSD8JUG6R)](https://codecov.io/github/lucasimi/tda-mapper-python)
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.10642381.svg)](https://doi.org/10.5281/zenodo.10642381)
+[![Streamlit App](https://static.streamlit.io/badges/streamlit_badge_black_white.svg)](https://tda-mapper-app.streamlit.app/)
 
 # tda-mapper
 
@@ -14,12 +17,14 @@ A simple and efficient Python implementation of Mapper algorithm for Topological
 
 * **Documentation**: https://tda-mapper.readthedocs.io/en/main/
 
+* **Demo App**: https://tda-mapper-app.streamlit.app/
+
 The Mapper algorithm is a well-known technique in the field of topological data analysis that allows data to be represented as a graph.
 Mapper is used in various fields such as machine learning, data mining, and social sciences, due to its ability to preserve topological features of the underlying space, providing a visual representation that facilitates exploration and interpretation.
 For an in-depth coverage of Mapper you can read [the original paper](https://research.math.osu.edu/tgda/mapperPBG.pdf).
 
 | Step 1 | Step 2 | Step 3 | Step 4 |
-|--------|--------|--------|--------|
+| ------ | ------ | ------ | ------ |
 | ![Step 1](https://github.com/lucasimi/tda-mapper-python/raw/main/resources/mapper_1.png) | ![Step 2](https://github.com/lucasimi/tda-mapper-python/raw/main/resources/mapper_2.png) | ![Step 3](https://github.com/lucasimi/tda-mapper-python/raw/main/resources/mapper_3.png) | ![Step 2](https://github.com/lucasimi/tda-mapper-python/raw/main/resources/mapper_4.png) |
 | Chose lens | Cover image | Run clustering | Build graph |
 
@@ -78,8 +83,8 @@ fig_std = mapper_plot.plot()
 fig_std.show(config={'scrollZoom': True})
 ```
 
-| Dataset                                                                                          | Mapper graph (average)                                                                                       | Mapper graph (deviation)                                                                                               |
-|--------------------------------------------------------------------------------------------------|--------------------------------------------------------------------------------------------------------------|------------------------------------------------------------------------------------------------------------------------|
+| Dataset | Mapper graph (average) | Mapper graph (deviation) |
+| ------- | ---------------------- | ------------------------ |
 | ![Dataset](https://github.com/lucasimi/tda-mapper-python/raw/main/resources/circles_dataset.png) | ![Mapper graph (average)](https://github.com/lucasimi/tda-mapper-python/raw/main/resources/circles_mean.png) | ![Mapper graph (standard deviation)](https://github.com/lucasimi/tda-mapper-python/raw/main/resources/circles_std.png) |
 
 More examples can be found in the documentation https://tda-mapper.readthedocs.io/en/main/.

docs/source/citations.rst

@@ -0,0 +1,25 @@
+Citations
+=========
+
+If you want to use **tda-mapper** in your research please use one of the following citation.
+For the methodology you can use:
+
+    Simi, L. (2024). A Scalable Implementation of Mapper for Topological Data Analysis via Vantage Point Trees. Zenodo. https://doi.org/10.5281/zenodo.10659652
+
+BibTeX entry:
+
+.. code:: RST
+
+    @misc{simi_2024_10659652,
+        author       = {Simi, Luca},
+        title        = {A Scalable Implementation of Mapper for Topological Data Analysis via Vantage Point Trees},
+        month        = feb,
+        year         = 2024,
+        publisher    = {Zenodo},
+        doi          = {10.5281/zenodo.10659652},
+        url          = {https://doi.org/10.5281/zenodo.10659652}
+    }
+
+If you want to refer to the actual library instead, you can reference the Zenodo 
+archive `https://doi.org/10.5281/zenodo.10642381 <https://doi.org/10.5281/zenodo.10642381>`__.
+In the archive you can find a permanent reference to the exact version used in your work. 

docs/source/conf.py

@@ -24,6 +24,7 @@
 
 html_theme = 'sphinx_rtd_theme'
 html_static_path = ['_static']
+html_logo = 'logos/tda-mapper-logo-horizontal.png'
 
 html_theme_options = {
     'sticky_navigation': True,

docs/source/examples.rst

@@ -0,0 +1,12 @@
+Examples
+========
+
+.. toctree::
+   :maxdepth: 2
+
+   notebooks/circles_online
+   notebooks/digits_online
+
+.. |Dataset| image:: https://github.com/lucasimi/tda-mapper-python/raw/main/resources/circles_dataset.png
+.. |Mapper graph (average)| image:: https://github.com/lucasimi/tda-mapper-python/raw/main/resources/circles_mean.png
+.. |Mapper graph (standard deviation)| image:: https://github.com/lucasimi/tda-mapper-python/raw/main/resources/circles_std.png

docs/source/index.rst

@@ -3,73 +3,28 @@
    You can adapt this file completely to your liking, but it should at least
    contain the root `toctree` directive.
 
-|PyPI version| |downloads| |test| |deploy| |docs| |codecov| |DOI|
-
-tda-mapper
-==========
-
-A simple and efficient implementation of Mapper algorithm for
-Topological Data Analysis.
-
--  **Installation**: ``pip install tda-mapper``
+########################
+tda-mapper documentation
+########################
 
--  **Documentation**: https://tda-mapper.readthedocs.io/en/main/
-
-The Mapper algorithm is a well-known technique in the field of
-topological data analysis that allows data to be represented as a graph.
-Mapper is used in various fields such as machine learning, data mining,
-and social sciences, due to its ability to preserve topological features
-of the underlying space, providing a visual representation that
-facilitates exploration and interpretation. For an in-depth coverage of
-Mapper you can read `the original
-paper <https://research.math.osu.edu/tgda/mapperPBG.pdf>`__.
-
-+-----------------+-----------------+-----------------+-----------------+
-| Step 1          | Step 2          | Step 3          | Step 4          |
-+=================+=================+=================+=================+
-| |Step 1|        | |Step 2|        | |Step 3|        | |image1|        |
-+-----------------+-----------------+-----------------+-----------------+
-
-.. toctree::
-   :maxdepth: 2
-   :caption: Examples
+|Logo|
 
-   notebooks/circles_online
-   notebooks/digits_online
-
-Citations
-^^^^^^^^^
-
-To cite **tda-mapper** in your work you can use the Zenodo archive
-`https://doi.org/10.5281/zenodo.10642381 <https://doi.org/10.5281/zenodo.10642381>`__.
-In the archive you can find a permanent reference to the exact version
-you used in your work. For example, to cite version ``v0.4.0`` you can use:
-
-::
-
-   Simi, L. (2024). tda-mapper (v0.4.0). Zenodo. https://doi.org/10.5281/zenodo.10655755
-
-BibTeX entry:
-
-::
+|PyPI version| |downloads| |test| |deploy| |docs| |codecov| |DOI|
 
-   @software{tda-mapper_v0.4.0,
-     author       = {Simi, Luca},
-     title        = {tda-mapper},
-     month        = feb,
-     year         = 2024,
-     publisher    = {Zenodo},
-     version      = {v0.4.0},
-     doi          = {10.5281/zenodo.10655755},
-     url          = {https://doi.org/10.5281/zenodo.10655755}
-   }
+Contents
+========
 
 .. toctree::
-   :maxdepth: 2
-   :caption: API Reference
+   :maxdepth: 1
 
-   tdamapper
+   overview
+   examples 
+   citations
+   modules
 
+.. |Logo| image:: logos/tda-mapper-logo-horizontal.png
+   :alt: tda-mapper
+   :target: https://github.com/lucasimi/tda-mapper-python
 .. |PyPI version| image:: https://badge.fury.io/py/tda-mapper.svg
    :target: https://badge.fury.io/py/tda-mapper
 .. |downloads| image:: https://img.shields.io/pypi/dm/tda-mapper
@@ -83,11 +38,4 @@ BibTeX entry:
 .. |codecov| image:: https://codecov.io/github/lucasimi/tda-mapper-python/graph/badge.svg?token=FWSD8JUG6R
    :target: https://codecov.io/github/lucasimi/tda-mapper-python
 .. |DOI| image:: https://zenodo.org/badge/DOI/10.5281/zenodo.10642381.svg
-   :target: https://doi.org/10.5281/zenodo.10642381
-.. |Step 1| image:: https://github.com/lucasimi/tda-mapper-python/raw/main/resources/mapper_1.png
-.. |Step 2| image:: https://github.com/lucasimi/tda-mapper-python/raw/main/resources/mapper_2.png
-.. |Step 3| image:: https://github.com/lucasimi/tda-mapper-python/raw/main/resources/mapper_3.png
-.. |image1| image:: https://github.com/lucasimi/tda-mapper-python/raw/main/resources/mapper_4.png
-.. |Dataset| image:: https://github.com/lucasimi/tda-mapper-python/raw/main/resources/circles_dataset.png
-.. |Mapper graph (average)| image:: https://github.com/lucasimi/tda-mapper-python/raw/main/resources/circles_mean.png
-.. |Mapper graph (standard deviation)| image:: https://github.com/lucasimi/tda-mapper-python/raw/main/resources/circles_std.png
+   :target: https://doi.org/10.5281/zenodo.10642381