diff --git a/docs/_templates/globaltoc.html b/docs/_templates/globaltoc.html
index 5ac0abbd..07028351 100644
--- a/docs/_templates/globaltoc.html
+++ b/docs/_templates/globaltoc.html
@@ -7,5 +7,5 @@
:copyright: Copyright 2007-2021 by the Sphinx team, see AUTHORS.
:license: BSD, see LICENSE for details.
#}
-
+
{{ toctree(includehidden=theme_globaltoc_includehidden, collapse=theme_globaltoc_collapse, maxdepth=theme_globaltoc_maxdepth) }}
diff --git a/docs/citations.txt b/docs/citations.txt
new file mode 100644
index 00000000..b8c45fd4
--- /dev/null
+++ b/docs/citations.txt
@@ -0,0 +1,55 @@
+Citations
+---------
+
+To credit KeplerMapper in your work, please cite both the `JOSS paper`_
+and the `Zenodo archive`_. The former provides a high level description
+of the package, and the latter points to a permanent record of all KeplerMapper versions
+(we encourage you to cite the specific version you used).
+
+.. _JOSS paper: https://doi.org/10.21105/joss.01315
+.. _Zenodo archive: https://doi.org/10.5281/zenodo.1002377
+
+Example citations (for KeplerMapper 1.4.1):
+
+ van Veen et al., (2019). Kepler Mapper: A flexible Python implementation of the Mapper algorithm.
+ Journal of Open Source Software, 4(42), 1315, https://doi.org/10.21105/joss.01315
+
+ Hendrik Jacob van Veen, Nathaniel Saul, David Eargle, & Sam W. Mangham.
+ (2019, October 14). Kepler Mapper: A flexible Python implementation of the Mapper algorithm (Version 1.4.1).
+ Zenodo. http://doi.org/10.5281/zenodo.4077395
+
+Bibtex entry for JOSS article:
+
+::
+
+ @article{KeplerMapper_JOSS,
+ doi = {10.21105/joss.01315},
+ url = {https://doi.org/10.21105/joss.01315},
+ year = {2019},
+ publisher = {The Open Journal},
+ volume = {4},
+ number = {42},
+ pages = {1315},
+ author = {Hendrik Jacob van Veen and Nathaniel Saul and David Eargle and Sam W. Mangham},
+ title = {Kepler Mapper: A flexible Python implementation of the Mapper algorithm.},
+ journal = {Journal of Open Source Software}
+ }
+
+Bibtex entry for the Zenodo archive, version 1.4.1:
+
+::
+
+ @software{KeplerMapper_v1.4.1-Zenodo,
+ author = {Hendrik Jacob van Veen and
+ Nathaniel Saul and
+ Eargle, David and
+ Sam W. Mangham},
+ title = {{Kepler Mapper: A flexible Python implementation of
+ the Mapper algorithm}},
+ month = oct,
+ year = 2020,
+ publisher = {Zenodo},
+ version = {1.4.1},
+ doi = {10.5281/zenodo.4077395},
+ url = {https://doi.org/10.5281/zenodo.4077395}
+ }
diff --git a/docs/conf.py b/docs/conf.py
index c6b6659d..7631cda1 100644
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -21,7 +21,7 @@
html_static_path = ["../examples/output", "_static", "notebooks/output"]
html_sidebars = {
- 'index': [ 'searchbox.html', 'githubbox.html', 'localtoc.html' ],
+ # 'index': [ 'searchbox.html', 'githubbox.html', 'localtoc.html' ],
'**': [ 'searchbox.html', 'githubbox.html', 'globaltoc.html' ],
}
diff --git a/docs/contributions.txt b/docs/contributions.txt
new file mode 100644
index 00000000..eb0b6e46
--- /dev/null
+++ b/docs/contributions.txt
@@ -0,0 +1,12 @@
+Contributions
+-------------
+
+We welcome contributions of all shapes and sizes. There are lots of
+opportunities for potential projects, so please get in touch if you would like
+to help out. Everything from an implementation of your favorite distance,
+notebooks, examples, and documentation are all equally valuable so please don’t
+feel you can’t contribute.
+
+See `the contributing page in the code repository`__ for more details.
+
+__ https://github.com/scikit-tda/kepler-mapper/blob/master/CONTRIBUTING.md
diff --git a/docs/index.rst b/docs/index.rst
index d5f4f7ec..65ed278c 100644
--- a/docs/index.rst
+++ b/docs/index.rst
@@ -9,8 +9,11 @@
Kepler Mapper
=============
+.. epigraph::
- Nature uses as little as possible of anything. - Johannes Kepler
+ Nature uses as little as possible of anything.
+
+ -- Johannes Kepler
This is a library implementing the Mapper algorithm in Python. KeplerMapper can
be used for visualization of high-dimensional data and 3D point cloud data.
@@ -25,13 +28,17 @@ first described in the paper "Topological Methods for the Analysis of High
Dimensional Data Sets and 3D Object Recognition".
-User's Guide
-------------
+.. User's Guide
+.. ------------
+..
+.. These pages explain what KeplerMapper is, illustrate how to use it, and discuss
+.. and demonstrate applications of it.
+
+
-These pages explain what KeplerMapper is, illustrate how to use it, and discuss
-and demonstrate applications of it.
.. toctree::
+ :caption: User's Guide
:maxdepth: 2
theory
@@ -42,87 +49,21 @@ and demonstrate applications of it.
case_studies
-API Reference
--------------
-
-These pages link to documentation for specific KeplerMapper classes and functions.
+.. API Reference
+.. -------------
+..
+.. These pages link to documentation for specific KeplerMapper classes and functions.
.. toctree::
- :maxdepth: 3
+ :caption: API Reference
+ :maxdepth: 2
reference/index
-Citations
----------
-
-To credit KeplerMapper in your work, please cite both the `JOSS paper`_
-and the `Zenodo archive`_. The former provides a high level description
-of the package, and the latter points to a permanent record of all KeplerMapper versions
-(we encourage you to cite the specific version you used).
-
-.. _JOSS paper: https://doi.org/10.21105/joss.01315
-.. _Zenodo archive: https://doi.org/10.5281/zenodo.1002377
-
-Example citations (for KeplerMapper 1.4.1):
-
- van Veen et al., (2019). Kepler Mapper: A flexible Python implementation of the Mapper algorithm.
- Journal of Open Source Software, 4(42), 1315, https://doi.org/10.21105/joss.01315
-
- Hendrik Jacob van Veen, Nathaniel Saul, David Eargle, & Sam W. Mangham.
- (2019, October 14). Kepler Mapper: A flexible Python implementation of the Mapper algorithm (Version 1.4.1).
- Zenodo. http://doi.org/10.5281/zenodo.4077395
-
-Bibtex entry for JOSS article:
-
-::
-
- @article{KeplerMapper_JOSS,
- doi = {10.21105/joss.01315},
- url = {https://doi.org/10.21105/joss.01315},
- year = {2019},
- publisher = {The Open Journal},
- volume = {4},
- number = {42},
- pages = {1315},
- author = {Hendrik Jacob van Veen and Nathaniel Saul and David Eargle and Sam W. Mangham},
- title = {Kepler Mapper: A flexible Python implementation of the Mapper algorithm.},
- journal = {Journal of Open Source Software}
- }
-
-Bibtex entry for the Zenodo archive, version 1.4.1:
-
-::
-
- @software{KeplerMapper_v1.4.1-Zenodo,
- author = {Hendrik Jacob van Veen and
- Nathaniel Saul and
- Eargle, David and
- Sam W. Mangham},
- title = {{Kepler Mapper: A flexible Python implementation of
- the Mapper algorithm}},
- month = oct,
- year = 2020,
- publisher = {Zenodo},
- version = {1.4.1},
- doi = {10.5281/zenodo.4077395},
- url = {https://doi.org/10.5281/zenodo.4077395}
- }
-
-
-
-Contributions
--------------
-
-We welcome contributions of all shapes and sizes. There are lots of
-opportunities for potential projects, so please get in touch if you would like
-to help out. Everything from an implementation of your favorite distance,
-notebooks, examples, and documentation are all equally valuable so please don’t
-feel you can’t contribute.
-
-See `the contribution guideline page in the source code repository`__ for more details.
+.. include:: citations.txt
+.. include:: contributions.txt
-__ https://github.com/scikit-tda/kepler-mapper/blob/master/CONTRIBUTING.md
.. |Downloads| image:: https://img.shields.io/pypi/dm/kmapper
diff --git a/docs/reference/index.rst b/docs/reference/index.rst
index db172d9b..1a70a6ae 100644
--- a/docs/reference/index.rst
+++ b/docs/reference/index.rst
@@ -1,6 +1,6 @@
-API Reference
----------------
+API
+---
.. currentmodule:: kmapper