Merge branch 'main' of github.com:lucasimi/tda-mapper-python into add-type-hints

Author: lucasimi

.github/workflows/test-bench.yml

@@ -13,10 +13,8 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12", "3.13"]
+        python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
         include:
-          - python-version: 3.8
-            allow-failure: false
           - python-version: 3.9
             allow-failure: false
           - python-version: 3.10
@@ -49,7 +47,7 @@ jobs:
 
       - name: Install dependencies
         run: | 
-          python -m pip install -e .[dev,app]
+          python -m pip install -e .[dev]
 
       - name: Run benchmarks
         run: | 

.github/workflows/test-unit.yml

@@ -10,13 +10,11 @@ on:
 
 jobs:
   test-unit-matrix-job:
-    runs-on: ubuntu-22.04
+    runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12", "3.13"]
+        python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
         include:
-          - python-version: 3.8
-            allow-failure: false
           - python-version: 3.9
             allow-failure: false
           - python-version: 3.10
@@ -49,7 +47,7 @@ jobs:
 
       - name: Install dependencies
         run: | 
-          python -m pip install -e .[dev,app]
+          python -m pip install -e .[dev]
 
       - name: Run tests and code coverage
         run: | 

README.md

@@ -1,5 +1,7 @@
 ![Logo](https://github.com/lucasimi/tda-mapper-python/raw/main/docs/source/logos/tda-mapper-logo-horizontal.png)
 
+[![Project Status: Active – The project has reached a stable, usable state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active)
+
 [![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)
 [![codecov](https://img.shields.io/codecov/c/github/lucasimi/tda-mapper-python?logo=codecov&logoColor=silver)](https://codecov.io/github/lucasimi/tda-mapper-python)
@@ -64,16 +66,6 @@ mathematical foundations and practical applications, read
 | ![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) |
 | Choose lens | Cover image | Run clustering | Build graph |
 
-## Citations
-
-If you use **tda-mapper** in your work, please consider citing both the
-[library](https://doi.org/10.5281/zenodo.10642381), archived in a permanent
-Zenodo record, and the [paper](https://openreview.net/pdf?id=lTX4bYREAZ),
-which provides a broader methodological overview. We recommend citing the
-specific version of the library used in your research, along with the paper.
-For citation examples, please refer to the
-[documentation](https://tda-mapper.readthedocs.io/en/main/#citations).
-
 ## Quick Start
 
 ### Installation
@@ -158,3 +150,13 @@ To run it locally:
     ```
 
 ![tda-mapper-app](https://github.com/lucasimi/tda-mapper-python/raw/main/resources/tda-mapper-app.png)
+
+## Citations
+
+If you use **tda-mapper** in your work, please consider citing both the
+[library](https://doi.org/10.5281/zenodo.10642381), archived in a permanent
+Zenodo record, and the [paper](https://openreview.net/pdf?id=lTX4bYREAZ),
+which provides a broader methodological overview. We recommend citing the
+specific version of the library used in your research, along with the paper.
+For citation examples, please refer to the
+[documentation](https://tda-mapper.readthedocs.io/en/main/#citations).

docs/source/citations.rst

@@ -0,0 +1,38 @@
+Citations
+=========
+
+If you use **tda-mapper** in your work, please consider citing both the
+`library <https://doi.org/10.5281/zenodo.10642381>`__,
+archived in a permanent Zenodo record, and the
+`paper <https://openreview.net/pdf?id=lTX4bYREAZ>`__,
+which provides a broader methodological overview. We recommend citing the
+specific version of the library used in your research, along with the paper.
+
+- **tda-mapper**: For example to cite version 0.8.0 you can use:
+
+  .. code:: bibtex
+
+      @software{simi_2024_14194667,
+         author       = {Simi, Luca},
+         title        = {tda-mapper},
+         month        = nov,
+         year         = 2024,
+         publisher    = {Zenodo},
+         version      = {v0.8.0},
+         doi          = {10.5281/zenodo.14194667},
+         url          = {https://doi.org/10.5281/zenodo.14194667}
+      }
+
+- **Methodology**: For the paper, you can use:
+
+  .. code:: bibtex
+
+      @article{simi2025a,
+         title    = {A Scalable Approach for Mapper via Efficient Spatial Search},
+         author   = {Luca Simi},
+         journal  = {Transactions on Machine Learning Research},
+         issn     = {2835-8856},
+         year     = {2025},
+         url      = {https://openreview.net/forum?id=lTX4bYREAZ},
+         note     = {}
+      }

docs/source/conf.py

@@ -46,6 +46,7 @@ def convert_py_to_ipynb():
 
 extensions = [
     "sphinx.ext.autodoc",
+    "sphinx.ext.doctest",
     "sphinx.ext.viewcode",
     "sphinx_rtd_theme",
     "nbsphinx",

docs/source/examples.rst

@@ -6,4 +6,5 @@ Examples
 
    notebooks/circles
    notebooks/digits
+   notebooks/cover
 

docs/source/index.rst

@@ -1,3 +1,6 @@
+.. |Repo Status| image:: https://www.repostatus.org/badges/latest/active.svg
+   :alt: Project Status: Active – The project has reached a stable, usable state and is being actively developed.
+   :target: https://www.repostatus.org/#active
 .. |Source Code| image:: https://img.shields.io/badge/lucasimi-tda--mapper--python-blue?logo=github&logoColor=silver
    :target: https://github.com/lucasimi/tda-mapper-python
 .. |PyPI version| image:: https://img.shields.io/pypi/v/tda-mapper?logo=python&logoColor=silver
@@ -23,9 +26,10 @@
    https://github.com/lucasimi/tda-mapper-python/raw/main/docs/source/logos/tda-mapper-logo-horizontal.png
    :alt: Logo
 
+|Repo Status| |Source Code|
+
 |PyPI version| |downloads| |codecov| |test| |publish| |docs|  |DOI|
 
-|Source Code|
 
 tda-mapper
 ==========
@@ -90,52 +94,13 @@ mathematical foundations and practical applications, read
 | Choose lens     | Cover image     | Run clustering  | Build graph     |
 +-----------------+-----------------+-----------------+-----------------+
 
-Citations
----------
-
-If you use **tda-mapper** in your work, please consider citing both the
-`library <https://doi.org/10.5281/zenodo.10642381>`__,
-archived in a permanent Zenodo record, and the
-`paper <https://openreview.net/pdf?id=lTX4bYREAZ>`__,
-which provides a broader methodological overview. We recommend citing the
-specific version of the library used in your research, along with the paper.
-
-- **tda-mapper**: For example to cite version 0.8.0 you can use:
-
-  .. code:: bibtex
-
-      @software{simi_2024_14194667,
-         author       = {Simi, Luca},
-         title        = {tda-mapper},
-         month        = nov,
-         year         = 2024,
-         publisher    = {Zenodo},
-         version      = {v0.8.0},
-         doi          = {10.5281/zenodo.14194667},
-         url          = {https://doi.org/10.5281/zenodo.14194667}
-      }
-
-- **Methodology**: For the paper, you can use:
-
-  .. code:: bibtex
-
-      @article{simi2025a,
-         title    = {A Scalable Approach for Mapper via Efficient Spatial Search},
-         author   = {Luca Simi},
-         journal  = {Transactions on Machine Learning Research},
-         issn     = {2835-8856},
-         year     = {2025},
-         url      = {https://openreview.net/forum?id=lTX4bYREAZ},
-         note     = {}
-      }
-
-
 .. toctree::
    :caption: User's Guide
    :maxdepth: 1
 
    quickstart
    examples 
+   citations
 
 
 .. toctree::