Prepare v0.6.0 (#648)

* Bump version to 0.6.0

* Write v0.6.0 release notes

* Fix bug with plot_diagram on empty diagrams

Author: ulupo

CODE_AUTHORS.rst

@@ -7,7 +7,7 @@ Where component authors are known, add them here.
 | Lewis Tunstall, [email protected]
 | Matteo Caorsi, [email protected]
 | Philippe Nguyen, [email protected]
-| Julian Burella Pérez, [email protected]
+| Julián Burella Pérez, [email protected]
 | Alessio Ghiraldello, [email protected]
 | Adélie Garin, [email protected]
 | Anibal Medina-Mardones, [email protected]

doc/library.rst

@@ -124,5 +124,5 @@ What's new
 
 .. include::
    release.rst
-   :start-after: Release 0.5.1
-   :end-before: Release 0.5.0
+   :start-after: Release 0.6.0
+   :end-before: Release 0.5.1

doc/release.rst

@@ -4,6 +4,41 @@ Release Notes
 
 .. _stable:
 
+*************
+Release 0.6.0
+*************
+
+This is a major release including a new local homology subpackage, a new backend for computing Vietoris–Rips barcodes, wheels for Python 3.10 and Apple Silicon systems, and end of support for Python 3.6.
+
+Major Features and Improvements
+===============================
+
+- A new ``local_homology`` subpackage containing ``scikit-learn``–compatible transformers for the extraction of local homology features has been added (`#602 <https://github.com/giotto-ai/giotto-tda/pull/602>`_). A `tutorial <https://giotto-ai.github.io/gtda-docs/0.6.0/notebooks/local_homology.html>`_ and an `example <https://giotto-ai.github.io/gtda-docs/0.6.0/notebooks/local_hom_NLP_disambiguation.html>`_ notebooks explain it.
+- Wheels for Python 3.10 are now available (`#644 <https://github.com/giotto-ai/giotto-tda/pull/644>`_ and `#646 <https://github.com/giotto-ai/giotto-tda/pull/646>`_).
+- Wheels for Apple Silicon systems are now available for Python versions 3.8, 3.9 and 3.10 (`#646 <https://github.com/giotto-ai/giotto-tda/pull/646>`_).
+- ``giotto-ph`` is now the backend for the computation of Vietoris–Rips barcodes, replacing ``ripser.py`` (`#614 <https://github.com/giotto-ai/giotto-tda/pull/614>`_).
+- The documentation has been improved (`#609 <https://github.com/giotto-ai/giotto-tda/pull/609>`_).
+
+Bug Fixes
+=========
+
+- A bug involving tests for the ``mapper`` subpackage has been fixed (`#638 <https://github.com/giotto-ai/giotto-tda/pull/638>`_).
+
+Backwards-Incompatible Changes
+==============================
+
+- Python 3.6 is no longer supported, and the manylinux standard has been bumped from ``manylinux2010`` to ``manylinux2014`` (`#644 <https://github.com/giotto-ai/giotto-tda/pull/644>`_ and `#646 <https://github.com/giotto-ai/giotto-tda/pull/646>`_).
+- The ``python-igraph`` requirement has been replaced with ``igraph >= 0.9.8`` (`#616 <https://github.com/giotto-ai/giotto-tda/pull/616>`_).
+
+Thanks to our Contributors
+==========================
+
+This release contains contributions from:
+
+Umberto Lupo, Jacob Bamberger, Wojciech Reise, Julián Burella Pérez, and Anibal Medina-Mardones
+
+We are also grateful to all who filed issues or helped resolve them, asked and answered questions, and were part of inspiring discussions.
+
 *************
 Release 0.5.1
 *************

doc/versions

@@ -6,4 +6,5 @@
 ./0.4.0
 ./0.5.0
 ./0.5.1
+./0.6.0
 ./latest

gtda/_version.py

@@ -19,4 +19,4 @@
 # 'X.Y.dev0' is the canonical version of 'X.Y.dev'
 #
 
-__version__ = "0.5.1"
+__version__ = "0.6.0"

gtda/plotting/persistence_diagrams.py

@@ -40,8 +40,13 @@ def plot_diagram(diagram, homology_dimensions=None, plotly_params=None):
     diagram_no_dims = diagram[:, :2]
     posinfinite_mask = np.isposinf(diagram_no_dims)
     neginfinite_mask = np.isneginf(diagram_no_dims)
-    max_val = np.max(np.where(posinfinite_mask, -np.inf, diagram_no_dims))
-    min_val = np.min(np.where(neginfinite_mask, np.inf, diagram_no_dims))
+    if diagram_no_dims.size:
+        max_val = np.max(np.where(posinfinite_mask, -np.inf, diagram_no_dims))
+        min_val = np.min(np.where(neginfinite_mask, np.inf, diagram_no_dims))
+    else:
+        # Dummy values if diagram is empty
+        max_val = 1
+        min_val = 0
     parameter_range = max_val - min_val
     extra_space_factor = 0.02
     has_posinfinite_death = np.any(posinfinite_mask[:, 1])

gtda/plotting/tests/test_persistence_diagrams.py

@@ -0,0 +1,13 @@
+"""Testing for plot_diagram."""
+# License: GNU AGPLv3
+
+import numpy as np
+
+from gtda.plotting import plot_diagram
+
+
+def test_plot_diagram_empty():
+    """Test that plot_diagram does not crash on a diagram with no non-trivial
+    points."""
+    plot_diagram(np.array([[0., 0., 0.],
+                           [0., 0., 1.]]))