Fix documentation (#74)

* Update readthedocs yml to new style

* Update index.rst for landscape paths

* Update notebook

* Add all variable, remove unnec docstring

* Revert index.rst change

* Update conf.py settings for toc overlap

* Update notebook

* Update badges

The travis CI build status badge wasn't working, so it was removed. Used new badge for downloads

* Run ruff on landscape code, fix typo

* Update notebook code, add new userguide notebook, add to ToC

* Update notebook

* Formatting tweaks to notebooks

* Return axes, figure objects with landscape viz code. Update notebooks

* More notebook tweaking

* Add basic viz end-to-end test

---------

Co-authored-by: Michael Catanzaro <[email protected]>

Author: catanzaromj

README.md

@@ -1,8 +1,7 @@
 [![PyPI version](https://badge.fury.io/py/persim.svg)](https://badge.fury.io/py/persim)
-[![Downloads](https://pypip.in/download/persim/badge.svg)](https://pypi.python.org/pypi/persim/) 
+![PyPI - Downloads](https://img.shields.io/pypi/dm/persim)
 [![Conda Version](https://img.shields.io/conda/vn/conda-forge/persim.svg)](https://anaconda.org/conda-forge/persim)
 [![Conda Downloads](https://img.shields.io/conda/dn/conda-forge/persim.svg)](https://anaconda.org/conda-forge/persim)
-[![Build Status](https://travis-ci.org/scikit-tda/persim.svg?branch=master)](https://travis-ci.org/scikit-tda/persim)
 [![codecov](https://codecov.io/gh/scikit-tda/persim/branch/master/graph/badge.svg)](https://codecov.io/gh/scikit-tda/persim)
 [![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
 

docs/conf.py

@@ -1,29 +1,34 @@
 # -*- coding: utf-8 -*-
 import os
 import sys
-sys.path.insert(0, os.path.abspath('.'))
-from persim import __version__
+
+sys.path.insert(0, os.path.abspath("."))
 from sktda_docs_config import *
 
-project = u'Persim'
-copyright = u'2019, Nathaniel Saul'
-author = u'Nathaniel Saul'
+from persim import __version__
+
+project = "Persim"
+copyright = "2019, Nathaniel Saul"
+author = "Nathaniel Saul"
 
 version = __version__
 release = __version__
 
-html_theme_options.update({
-  # Google Analytics info
-  'ga_ua': 'UA-124965309-3',
-  'ga_domain': '',
-  'gh_url': 'scikit-tda/persim'
-})
+language = "en"
+
+html_theme_options.update(
+    {
+        "collapse_naviation": False,
+        # Google Analytics info
+        "ga_ua": "UA-124965309-3",
+        "ga_domain": "",
+        "gh_url": "scikit-tda/persim",
+    }
+)
 
 html_short_title = project
-htmlhelp_basename = 'Persimdoc'
+htmlhelp_basename = "Persimdoc"
 
-autodoc_default_options = {
-    'members': True
-}
+autodoc_default_options = {"members": False, "maxdepth": 1}
 
-autodoc_member_order = 'groupwise'
+autodoc_member_order = "groupwise"

docs/index.rst

@@ -36,6 +36,7 @@ Documentation
 
     notebooks/Persistence images
     notebooks/distances
+    notebooks/Persistence landscapes
     reference/index
 
 

docs/notebooks/Differentiation with Persistence Landscapes.ipynb

@@ -18,6 +18,7 @@
     "The experiment is to determine if persistent homology can distinguish between spheres of different dimensions. Here we restrict to differentiating $S^2$ from $S^3$. We will further restrict ourselves to persistent homology in degree one (but one can use all relevant homological degrees as well). A priori, we would not expect this to be an effective discriminator, since the ordinary first homology of both spheres is trivial. Note that this is a simplified version of the experiment from Bubenik and Dlotko's *A persistence landscapes toolbox for topological statistics* [1]. \n",
     "\n",
     "In detail: \n",
+    "\n",
     "- Repeat the following `num_runs = 100` times:\n",
     "  - Sample `num_pts = 100` points from the 2-sphere and the 3-sphere. We rescale the spheres so the average distance between the points on each sphere is approximately 1.\n",
     "  - Compute the VR persistent homology (using `ripser`) and compute the associated landscapes. Store each of these landscapes.\n",
@@ -356,7 +357,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -370,7 +371,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.1"
+   "version": "3.12.0"
   }
  },
  "nbformat": 4,

docs/notebooks/Persistence Landscapes and Machine Learning.ipynb

@@ -494,9 +494,9 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "persimenv",
+   "display_name": "Python 3",
    "language": "python",
-   "name": "persimenv"
+   "name": "python3"
   },
   "language_info": {
    "codemirror_mode": {
@@ -508,7 +508,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.9"
+   "version": "3.9.1"
   }
  },
  "nbformat": 4,

docs/notebooks/Persistence images.ipynb

@@ -1,9 +1,13 @@
-from .images import *
-from .sliced_wasserstein import *
+from ._version import __version__
 from .bottleneck import *
-from .wasserstein import *
-from .heat import *
 from .gromov_hausdorff import *
+from .heat import *
+from .images import *
+from .landscapes.approximate import PersLandscapeApprox
+from .landscapes.exact import PersLandscapeExact
+from .landscapes.transformer import PersistenceLandscaper
+from .sliced_wasserstein import *
 from .visuals import *
+from .wasserstein import *
 
-from ._version import __version__
+__all__ = ["PersLandscapeApprox", "PersistenceLandscaper", "PersLandscapeExact"]

docs/notebooks/Persistence landscapes.ipynb

@@ -87,8 +87,8 @@ class are much faster compared to `PersLandscapeExact` in general.
 
         ValueError: Start values of grids do not coincide
 
-        >>> from persim import snap_PL
-        >>> [snapped_pla, snapped_wide_pl] = snap_PL([pla,wide_pl])
+        >>> from persim import snap_pl
+        >>> [snapped_pla, snapped_wide_pl] = snap_pl([pla,wide_pl])
         >>> print(snapped_pla, snapped_wide_pl)
 
         Approximate persistence landscape in homological degree 0 on grid from -1 to 4 with 1000 steps Approximate persistence landscape in homological degree 0 on grid from -1 to 4 with 1000 steps
@@ -128,7 +128,6 @@ def __init__(
         values=np.array([]),
         compute: bool = True,
     ) -> None:
-
         super().__init__(dgms=dgms, hom_deg=hom_deg)
         if not dgms and values.size == 0:
             raise ValueError("dgms and values cannot both be emtpy")

persim/__init__.py

@@ -44,7 +44,10 @@ def union_crit_pairs(A, B):
         else:
             result_pairs.append(
                 slope_to_pos_interp(
-                    sum_slopes(pos_to_slope_interp(a), pos_to_slope_interp(b),)
+                    sum_slopes(
+                        pos_to_slope_interp(a),
+                        pos_to_slope_interp(b),
+                    )
                 )
             )
     return result_pairs
@@ -141,7 +144,7 @@ def ndsnap_regular(points, *grid_axes):
 
 def _p_norm(p: float, critical_pairs: list = []):
     """
-    Compute `p` norm of interpolated piecewise linear function defined from list of 
+    Compute `p` norm of interpolated piecewise linear function defined from list of
     critical pairs.
     """
     result = 0.0