Prepare for v0.3.0 release

doc/library.rst

@@ -114,5 +114,5 @@ What's new
 
 .. include::
    release.rst
-   :start-after: Release 0.2.2
-   :end-before: Release 0.2.1
+   :start-after: Release 0.3.0
+   :end-before: Release 0.2.2

doc/modules/homology.rst

@@ -20,6 +20,12 @@ Undirected simplicial homology
 
 Directed simplicial homology
 ----------------------------
+.. currentmodule:: gtda
+
+.. autosummary::
+   :toctree: generated/homology/
+   :template: class.rst
+
    homology.FlagserPersistence
 
 Cubical homology

examples/MNIST_classification.ipynb

@@ -90,7 +90,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "## Create train and test sets"
+    "### Create train and test sets"
    ]
   },
   {
@@ -149,7 +149,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "# Binarize the image"
+    "### Binarize the image"
    ]
   },
   {
@@ -491,7 +491,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "### Training a classifier"
+    "## Training a classifier"
    ]
   },
   {

examples/vietoris_rips_quickstart.ipynb

@@ -62,7 +62,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "**Important note**: ``VietorisRipsPersistence``, and all other \"persistence homology\" transformers in ``gtda.homology``, expect input in the form of a 3D array or, in some cases, a list of 2D arrays. For each entry in the input (here, for each point cloud in ``point_clouds``) they compute a topological summary which is also a 2D array, and then stack all these summaries into a single output 3D array. So, in our case, ``diagrams[i]`` represents the topology of ``point_clouds[i]``. ``diagrams[i]`` is interpreted as follows:\n",
+    "**Important note**: ``VietorisRipsPersistence``, and all other \"persistent homology\" transformers in ``gtda.homology``, expect input in the form of a 3D array or, in some cases, a list of 2D arrays. For each entry in the input (here, for each point cloud in ``point_clouds``) they compute a topological summary which is also a 2D array, and then stack all these summaries into a single output 3D array. So, in our case, ``diagrams[i]`` represents the topology of ``point_clouds[i]``. ``diagrams[i]`` is interpreted as follows:\n",
     "- Each row is a triplet describing a single topological feature found in ``point_clouds[i]``.\n",
     "- The first and second entries (respectively) in the triplet denote the values of the \"filtration parameter\" at which the feature appears or disappears respectively. They are referred to as the \"birth\" and \"death\" values of the feature (respectively). The meaning of \"filtration parameter\" depends on the specific transformer, but in the case of ``VietorisRipsPersistence`` on point clouds it has the interpretation of a length scale.\n",
     "- A topological feature can be a connected component, 1D hole/loop, 2D cavity, or more generally $d$-dimensional \"void\" which exists in the data at scales between its birth and death values. The integer $d$ is the *homology dimension* (or degree) of the feature and is stored as the third entry in the triplet. In this example, the shapes should have 2D cavities so we explicitly tell ``VietorisRipsPersistence`` to look for these by using the ``homology_dimensions`` parameter!\n",

gtda/_version.py

@@ -19,4 +19,4 @@
 # 'X.Y.dev0' is the canonical version of 'X.Y.dev'
 #
 
-__version__ = '0.2.2'
+__version__ = "0.3.0"

gtda/diagrams/features.py

@@ -697,7 +697,7 @@ def transform(self, X, y=None):
         Returns
         -------
         Xt : ndarray of shape (n_samples, n_homology_dimensions * 2 \
-            * n_coefficients_)
+            * n_coefficients)
             Polynomial coefficients: real and imaginary parts of the complex
             polynomials obtained in each homology dimension from each diagram
             in `X`.

gtda/diagrams/preprocessing.py

@@ -471,7 +471,7 @@ def transform(self, X, y=None):
         Xt : ndarray of shape (n_samples, n_features_filtered, 3)
             Filtered persistence diagrams. Only the subdiagrams corresponding
             to dimensions in :attr:`homology_dimensions_` are filtered.
-            ``n_features_filtered`` is less than or equal to ``n_features`.
+            ``n_features_filtered`` is less than or equal to ``n_features``.
 
         """
         check_is_fitted(self)

setup.py

@@ -29,7 +29,7 @@
 MAINTAINER_EMAIL = "maintainers@giotto.ai"
 URL = "https://github.com/giotto-ai/giotto-tda"
 LICENSE = "GNU AGPLv3"
-DOWNLOAD_URL = "https://github.com/giotto-ai/giotto-tda/tarball/v0.2.2"
+DOWNLOAD_URL = "https://github.com/giotto-ai/giotto-tda/tarball/v0.3.0"
 VERSION = __version__  # noqa
 CLASSIFIERS = ["Intended Audience :: Science/Research",
                "Intended Audience :: Developers",