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<!DOCTYPE html>
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<title>Release Notes — giotto-tda 0.3.1 documentation</title>
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<li class="toctree-l2"><a class="reference internal" href="modules/mapper.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">gtda.mapper</span></code>: Mapper</a><ul>
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</ul>
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<li class="toctree-l3"><a class="reference internal" href="modules/mapper.html#clustering">Clustering</a><ul>
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<li class="toctree-l4"><a class="reference internal" href="modules/generated/mapper/clustering/gtda.mapper.FirstHistogramGap.html">FirstHistogramGap</a></li>
<li class="toctree-l4"><a class="reference internal" href="modules/generated/mapper/clustering/gtda.mapper.ParallelClustering.html">ParallelClustering</a></li>
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<li class="toctree-l2"><a class="reference internal" href="modules/homology.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">gtda.homology</span></code>: Persistent homology</a><ul>
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<li class="toctree-l4"><a class="reference internal" href="modules/generated/homology/gtda.homology.VietorisRipsPersistence.html">VietorisRipsPersistence</a></li>
<li class="toctree-l4"><a class="reference internal" href="modules/generated/homology/gtda.homology.SparseRipsPersistence.html">SparseRipsPersistence</a></li>
<li class="toctree-l4"><a class="reference internal" href="modules/generated/homology/gtda.homology.WeakAlphaPersistence.html">WeakAlphaPersistence</a></li>
<li class="toctree-l4"><a class="reference internal" href="modules/generated/homology/gtda.homology.EuclideanCechPersistence.html">EuclideanCechPersistence</a></li>
</ul>
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<li class="toctree-l3"><a class="reference internal" href="modules/homology.html#directed-simplicial-homology">Directed simplicial homology</a><ul>
<li class="toctree-l4"><a class="reference internal" href="modules/generated/homology/gtda.homology.FlagserPersistence.html">FlagserPersistence</a></li>
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<li class="toctree-l3"><a class="reference internal" href="modules/homology.html#cubical-homology">Cubical homology</a><ul>
<li class="toctree-l4"><a class="reference internal" href="modules/generated/homology/gtda.homology.CubicalPersistence.html">CubicalPersistence</a></li>
</ul>
</li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="modules/diagrams.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">gtda.diagrams</span></code>: Persistence diagrams</a><ul>
<li class="toctree-l3"><a class="reference internal" href="modules/diagrams.html#preprocessing">Preprocessing</a><ul>
<li class="toctree-l4"><a class="reference internal" href="modules/generated/diagrams/preprocessing/gtda.diagrams.ForgetDimension.html">ForgetDimension</a></li>
<li class="toctree-l4"><a class="reference internal" href="modules/generated/diagrams/preprocessing/gtda.diagrams.Scaler.html">Scaler</a></li>
<li class="toctree-l4"><a class="reference internal" href="modules/generated/diagrams/preprocessing/gtda.diagrams.Filtering.html">Filtering</a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="modules/diagrams.html#distances">Distances</a><ul>
<li class="toctree-l4"><a class="reference internal" href="modules/generated/diagrams/distances/gtda.diagrams.PairwiseDistance.html">PairwiseDistance</a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="modules/diagrams.html#representations">Representations</a><ul>
<li class="toctree-l4"><a class="reference internal" href="modules/generated/diagrams/representations/gtda.diagrams.PersistenceLandscape.html">PersistenceLandscape</a></li>
<li class="toctree-l4"><a class="reference internal" href="modules/generated/diagrams/representations/gtda.diagrams.BettiCurve.html">BettiCurve</a></li>
<li class="toctree-l4"><a class="reference internal" href="modules/generated/diagrams/representations/gtda.diagrams.HeatKernel.html">HeatKernel</a></li>
<li class="toctree-l4"><a class="reference internal" href="modules/generated/diagrams/representations/gtda.diagrams.PersistenceImage.html">PersistenceImage</a></li>
<li class="toctree-l4"><a class="reference internal" href="modules/generated/diagrams/representations/gtda.diagrams.Silhouette.html">Silhouette</a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="modules/diagrams.html#features">Features</a><ul>
<li class="toctree-l4"><a class="reference internal" href="modules/generated/diagrams/features/gtda.diagrams.Amplitude.html">Amplitude</a></li>
<li class="toctree-l4"><a class="reference internal" href="modules/generated/diagrams/features/gtda.diagrams.PersistenceEntropy.html">PersistenceEntropy</a></li>
<li class="toctree-l4"><a class="reference internal" href="modules/generated/diagrams/features/gtda.diagrams.NumberOfPoints.html">NumberOfPoints</a></li>
<li class="toctree-l4"><a class="reference internal" href="modules/generated/diagrams/features/gtda.diagrams.ComplexPolynomial.html">ComplexPolynomial</a></li>
</ul>
</li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="modules/curves.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">gtda.curves</span></code>: Curves</a><ul>
<li class="toctree-l3"><a class="reference internal" href="modules/curves.html#preprocessing">Preprocessing</a><ul>
<li class="toctree-l4"><a class="reference internal" href="modules/generated/curves/preprocessing/gtda.curves.Derivative.html">Derivative</a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="modules/curves.html#feature-extraction">Feature extraction</a><ul>
<li class="toctree-l4"><a class="reference internal" href="modules/generated/curves/gtda.curves.StandardFeatures.html">StandardFeatures</a></li>
</ul>
</li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="modules/point_clouds.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">gtda.point_clouds</span></code>: Point clouds</a><ul>
<li class="toctree-l3"><a class="reference internal" href="modules/generated/gtda.point_clouds.ConsistentRescaling.html">ConsistentRescaling</a></li>
<li class="toctree-l3"><a class="reference internal" href="modules/generated/gtda.point_clouds.ConsecutiveRescaling.html">ConsecutiveRescaling</a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="modules/time_series.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">gtda.time_series</span></code>: Time series</a><ul>
<li class="toctree-l3"><a class="reference internal" href="modules/time_series.html#preprocessing">Preprocessing</a><ul>
<li class="toctree-l4"><a class="reference internal" href="modules/generated/time_series/preprocessing/gtda.time_series.SlidingWindow.html">SlidingWindow</a></li>
<li class="toctree-l4"><a class="reference internal" href="modules/generated/time_series/preprocessing/gtda.time_series.Resampler.html">Resampler</a></li>
<li class="toctree-l4"><a class="reference internal" href="modules/generated/time_series/preprocessing/gtda.time_series.Stationarizer.html">Stationarizer</a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="modules/time_series.html#time-delay-embedding">Time-delay embedding</a><ul>
<li class="toctree-l4"><a class="reference internal" href="modules/generated/time_series/embedding/gtda.time_series.TakensEmbedding.html">TakensEmbedding</a></li>
<li class="toctree-l4"><a class="reference internal" href="modules/generated/time_series/embedding/gtda.time_series.SingleTakensEmbedding.html">SingleTakensEmbedding</a></li>
<li class="toctree-l4"><a class="reference internal" href="modules/generated/time_series/embedding/gtda.time_series.takens_embedding_optimal_parameters.html">takens_embedding_optimal_parameters</a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="modules/time_series.html#target-preparation">Target preparation</a><ul>
<li class="toctree-l4"><a class="reference internal" href="modules/generated/time_series/target_preparation/gtda.time_series.Labeller.html">Labeller</a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="modules/time_series.html#dynamical-systems">Dynamical systems</a><ul>
<li class="toctree-l4"><a class="reference internal" href="modules/generated/time_series/dynamical_system/gtda.time_series.PermutationEntropy.html">PermutationEntropy</a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="modules/time_series.html#multivariate">Multivariate</a><ul>
<li class="toctree-l4"><a class="reference internal" href="modules/generated/time_series/multivariate/gtda.time_series.PearsonDissimilarity.html">PearsonDissimilarity</a></li>
</ul>
</li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="modules/graphs.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">gtda.graphs</span></code>: Graphs</a><ul>
<li class="toctree-l3"><a class="reference internal" href="modules/graphs.html#graph-creation">Graph creation</a><ul>
<li class="toctree-l4"><a class="reference internal" href="modules/generated/graphs/creation/gtda.graphs.TransitionGraph.html">TransitionGraph</a></li>
<li class="toctree-l4"><a class="reference internal" href="modules/generated/graphs/creation/gtda.graphs.KNeighborsGraph.html">KNeighborsGraph</a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="modules/graphs.html#graph-processing">Graph processing</a><ul>
<li class="toctree-l4"><a class="reference internal" href="modules/generated/graphs/processing/gtda.graphs.GraphGeodesicDistance.html">GraphGeodesicDistance</a></li>
</ul>
</li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="modules/images.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">gtda.images</span></code>: Images</a><ul>
<li class="toctree-l3"><a class="reference internal" href="modules/images.html#preprocessing">Preprocessing</a><ul>
<li class="toctree-l4"><a class="reference internal" href="modules/generated/images/gtda.images.Binarizer.html">Binarizer</a></li>
<li class="toctree-l4"><a class="reference internal" href="modules/generated/images/gtda.images.Inverter.html">Inverter</a></li>
<li class="toctree-l4"><a class="reference internal" href="modules/generated/images/gtda.images.Padder.html">Padder</a></li>
<li class="toctree-l4"><a class="reference internal" href="modules/generated/images/gtda.images.ImageToPointCloud.html">ImageToPointCloud</a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="modules/images.html#filtrations">Filtrations</a><ul>
<li class="toctree-l4"><a class="reference internal" href="modules/generated/images/gtda.images.HeightFiltration.html">HeightFiltration</a></li>
<li class="toctree-l4"><a class="reference internal" href="modules/generated/images/gtda.images.RadialFiltration.html">RadialFiltration</a></li>
<li class="toctree-l4"><a class="reference internal" href="modules/generated/images/gtda.images.DilationFiltration.html">DilationFiltration</a></li>
<li class="toctree-l4"><a class="reference internal" href="modules/generated/images/gtda.images.ErosionFiltration.html">ErosionFiltration</a></li>
<li class="toctree-l4"><a class="reference internal" href="modules/generated/images/gtda.images.SignedDistanceFiltration.html">SignedDistanceFiltration</a></li>
<li class="toctree-l4"><a class="reference internal" href="modules/generated/images/gtda.images.DensityFiltration.html">DensityFiltration</a></li>
</ul>
</li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="modules/plotting.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">gtda.plotting</span></code>: Plotting functions</a><ul>
<li class="toctree-l3"><a class="reference internal" href="modules/generated/plotting/gtda.plotting.plot_point_cloud.html">plot_point_cloud</a></li>
<li class="toctree-l3"><a class="reference internal" href="modules/generated/plotting/gtda.plotting.plot_heatmap.html">plot_heatmap</a></li>
<li class="toctree-l3"><a class="reference internal" href="modules/generated/plotting/gtda.plotting.plot_diagram.html">plot_diagram</a></li>
<li class="toctree-l3"><a class="reference internal" href="modules/generated/plotting/gtda.plotting.plot_betti_curves.html">plot_betti_curves</a></li>
<li class="toctree-l3"><a class="reference internal" href="modules/generated/plotting/gtda.plotting.plot_betti_surfaces.html">plot_betti_surfaces</a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="modules/base.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">gtda.base</span></code>: Base</a><ul>
<li class="toctree-l3"><a class="reference internal" href="modules/generated/base/gtda.base.TransformerResamplerMixin.html">TransformerResamplerMixin</a></li>
<li class="toctree-l3"><a class="reference internal" href="modules/generated/base/gtda.base.PlotterMixin.html">PlotterMixin</a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="modules/pipeline.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">gtda.pipeline</span></code>: Pipeline</a><ul>
<li class="toctree-l3"><a class="reference internal" href="modules/generated/base/gtda.pipeline.Pipeline.html">Pipeline</a></li>
<li class="toctree-l3"><a class="reference internal" href="modules/generated/gtda.pipeline.make_pipeline.html">make_pipeline</a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="modules/metaestimators.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">gtda.metaestimators</span></code>: Meta-estimators</a><ul>
<li class="toctree-l3"><a class="reference internal" href="modules/generated/base/gtda.metaestimators.CollectionTransformer.html">CollectionTransformer</a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="modules/utils.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">gtda.utils</span></code>: Utilities</a><ul>
<li class="toctree-l3"><a class="reference internal" href="modules/generated/utils/gtda.utils.check_collection.html">check_collection</a></li>
<li class="toctree-l3"><a class="reference internal" href="modules/generated/utils/gtda.utils.check_point_clouds.html">check_point_clouds</a></li>
<li class="toctree-l3"><a class="reference internal" href="modules/generated/utils/gtda.utils.check_diagrams.html">check_diagrams</a></li>
<li class="toctree-l3"><a class="reference internal" href="modules/generated/utils/gtda.utils.validate_params.html">validate_params</a></li>
</ul>
</li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="notebooks/index.html">Tutorials and examples</a><ul>
<li class="toctree-l2"><a class="reference internal" href="notebooks/tutorials.html">Tutorials</a><ul>
<li class="toctree-l3"><a class="reference internal" href="notebooks/vietoris_rips_quickstart.html">Topological feature extraction using <code class="docutils literal notranslate"><span class="pre">VietorisRipsPersistence</span></code> and <code class="docutils literal notranslate"><span class="pre">PersistenceEntropy</span></code></a><ul>
<li class="toctree-l4"><a class="reference internal" href="notebooks/vietoris_rips_quickstart.html#generate-data">Generate data</a></li>
<li class="toctree-l4"><a class="reference internal" href="notebooks/vietoris_rips_quickstart.html#calculate-persistent-homology">Calculate persistent homology</a></li>
<li class="toctree-l4"><a class="reference internal" href="notebooks/vietoris_rips_quickstart.html#extract-features">Extract features</a></li>
<li class="toctree-l4"><a class="reference internal" href="notebooks/vietoris_rips_quickstart.html#use-the-new-features-in-a-standard-classifier">Use the new features in a standard classifier</a></li>
<li class="toctree-l4"><a class="reference internal" href="notebooks/vietoris_rips_quickstart.html#encapsulate-the-steps-above-in-a-pipeline">Encapsulate the steps above in a pipeline</a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="notebooks/plotting_api.html">Plotting in <code class="docutils literal notranslate"><span class="pre">giotto-tda</span></code></a><ul>
<li class="toctree-l4"><a class="reference internal" href="notebooks/plotting_api.html#basic-philosophy-and-plot-methods">1. Basic philosophy and <code class="docutils literal notranslate"><span class="pre">plot</span></code> methods</a></li>
<li class="toctree-l4"><a class="reference internal" href="notebooks/plotting_api.html#derived-convenience-methods-transform-plot-and-fit-transform-plot">2 Derived convenience methods: <code class="docutils literal notranslate"><span class="pre">transform_plot</span></code> and <code class="docutils literal notranslate"><span class="pre">fit_transform_plot</span></code></a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="notebooks/mapper_quickstart.html">Getting started with Mapper</a><ul>
<li class="toctree-l4"><a class="reference internal" href="notebooks/mapper_quickstart.html#useful-references">Useful references</a></li>
<li class="toctree-l4"><a class="reference internal" href="notebooks/mapper_quickstart.html#import-libraries">Import libraries</a></li>
<li class="toctree-l4"><a class="reference internal" href="notebooks/mapper_quickstart.html#generate-and-visualise-data">Generate and visualise data</a></li>
<li class="toctree-l4"><a class="reference internal" href="notebooks/mapper_quickstart.html#configure-the-mapper-pipeline">Configure the Mapper pipeline</a></li>
<li class="toctree-l4"><a class="reference internal" href="notebooks/mapper_quickstart.html#visualise-the-mapper-graph">Visualise the Mapper graph</a></li>
<li class="toctree-l4"><a class="reference internal" href="notebooks/mapper_quickstart.html#run-the-mapper-pipeline">Run the Mapper pipeline</a></li>
<li class="toctree-l4"><a class="reference internal" href="notebooks/mapper_quickstart.html#creating-custom-filter-functions">Creating custom filter functions</a></li>
<li class="toctree-l4"><a class="reference internal" href="notebooks/mapper_quickstart.html#visualise-the-2d-mapper-graph-interactively-live-jupyter-session-needed">Visualise the 2D Mapper graph interactively (Live Jupyter session needed)</a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="notebooks/topology_time_series.html">Topology of time series</a><ul>
<li class="toctree-l4"><a class="reference internal" href="notebooks/topology_time_series.html#useful-references">Useful references</a></li>
<li class="toctree-l4"><a class="reference internal" href="notebooks/topology_time_series.html#see-also">See also</a></li>
<li class="toctree-l4"><a class="reference internal" href="notebooks/topology_time_series.html#from-time-series-to-time-delay-embeddings">From time series to time delay embeddings</a></li>
<li class="toctree-l4"><a class="reference internal" href="notebooks/topology_time_series.html#a-periodic-example">A periodic example</a></li>
<li class="toctree-l4"><a class="reference internal" href="notebooks/topology_time_series.html#a-non-periodic-example">A non-periodic example</a></li>
<li class="toctree-l4"><a class="reference internal" href="notebooks/topology_time_series.html#from-time-delay-embeddings-to-persistence-diagrams">From time delay embeddings to persistence diagrams</a></li>
<li class="toctree-l4"><a class="reference internal" href="notebooks/topology_time_series.html#picking-the-embedding-dimension-and-time-delay">Picking the embedding dimension and time delay</a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="notebooks/time_series_forecasting.html">Topology in time series forecasting</a><ul>
<li class="toctree-l4"><a class="reference internal" href="notebooks/time_series_forecasting.html#see-also">See also</a></li>
<li class="toctree-l4"><a class="reference internal" href="notebooks/time_series_forecasting.html#slidingwindow"><code class="docutils literal notranslate"><span class="pre">SlidingWindow</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="notebooks/time_series_forecasting.html#multivariate-time-series-example-sliding-window-topology-pipeline">Multivariate time series example: Sliding window + topology <code class="docutils literal notranslate"><span class="pre">Pipeline</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="notebooks/time_series_forecasting.html#univariate-time-series-takensembedding-and-singletakensembedding">Univariate time series – <code class="docutils literal notranslate"><span class="pre">TakensEmbedding</span></code> and <code class="docutils literal notranslate"><span class="pre">SingleTakensEmbedding</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="notebooks/time_series_forecasting.html#endogeneous-target-preparation-with-labeller">Endogeneous target preparation with <code class="docutils literal notranslate"><span class="pre">Labeller</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="notebooks/time_series_forecasting.html#where-to-next">Where to next?</a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="notebooks/persistent_homology_graphs.html">Topological feature extraction from graphs</a><ul>
<li class="toctree-l4"><a class="reference internal" href="notebooks/persistent_homology_graphs.html#see-also">See also</a></li>
<li class="toctree-l4"><a class="reference internal" href="notebooks/persistent_homology_graphs.html#import-libraries">Import libraries</a></li>
<li class="toctree-l4"><a class="reference internal" href="notebooks/persistent_homology_graphs.html#undirected-graphs-vietorisripspersistence-and-sparseripspersistence">Undirected graphs – <code class="docutils literal notranslate"><span class="pre">VietorisRipsPersistence</span></code> and <code class="docutils literal notranslate"><span class="pre">SparseRipsPersistence</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="notebooks/persistent_homology_graphs.html#directed-graphs-flagserpersistence">Directed graphs – <code class="docutils literal notranslate"><span class="pre">FlagserPersistence</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="notebooks/persistent_homology_graphs.html#where-to-next">Where to next?</a></li>
</ul>
</li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="notebooks/examples.html">Examples</a><ul>
<li class="toctree-l3"><a class="reference internal" href="notebooks/gravitational_waves_detection.html">Gravitational wave detection</a><ul>
<li class="toctree-l4"><a class="reference internal" href="notebooks/gravitational_waves_detection.html#useful-references">Useful references</a></li>
<li class="toctree-l4"><a class="reference internal" href="notebooks/gravitational_waves_detection.html#see-also">See also</a></li>
<li class="toctree-l4"><a class="reference internal" href="notebooks/gravitational_waves_detection.html#motivation">Motivation</a></li>
<li class="toctree-l4"><a class="reference internal" href="notebooks/gravitational_waves_detection.html#generate-the-data">Generate the data</a></li>
<li class="toctree-l4"><a class="reference internal" href="notebooks/gravitational_waves_detection.html#constant-signal-to-noise-ratio">Constant signal-to-noise ratio</a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="notebooks/classifying_shapes.html">Classifying 3D shapes</a><ul>
<li class="toctree-l4"><a class="reference internal" href="notebooks/classifying_shapes.html#generate-simple-shapes">Generate simple shapes</a></li>
<li class="toctree-l4"><a class="reference internal" href="notebooks/classifying_shapes.html#from-data-to-persistence-diagrams">From data to persistence diagrams</a></li>
<li class="toctree-l4"><a class="reference internal" href="notebooks/classifying_shapes.html#train-a-classifier">Train a classifier</a></li>
<li class="toctree-l4"><a class="reference internal" href="notebooks/classifying_shapes.html#putting-it-all-together">Putting it all together</a></li>
<li class="toctree-l4"><a class="reference internal" href="notebooks/classifying_shapes.html#a-more-realistic-example">A more realistic example</a></li>
<li class="toctree-l4"><a class="reference internal" href="notebooks/classifying_shapes.html#improving-our-model">Improving our model</a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="notebooks/lorenz_attractor.html">The Lorenz attractor</a><ul>
<li class="toctree-l4"><a class="reference internal" href="notebooks/lorenz_attractor.html#see-also">See also</a></li>
<li class="toctree-l4"><a class="reference internal" href="notebooks/lorenz_attractor.html#import-libraries">Import libraries</a></li>
<li class="toctree-l4"><a class="reference internal" href="notebooks/lorenz_attractor.html#setting-up-the-lorenz-attractor-simulation">Setting up the Lorenz attractor simulation</a></li>
<li class="toctree-l4"><a class="reference internal" href="notebooks/lorenz_attractor.html#resampling-the-time-series">Resampling the time series</a></li>
<li class="toctree-l4"><a class="reference internal" href="notebooks/lorenz_attractor.html#takens-embedding">Takens Embedding</a></li>
<li class="toctree-l4"><a class="reference internal" href="notebooks/lorenz_attractor.html#persistence-diagram">Persistence diagram</a></li>
<li class="toctree-l4"><a class="reference internal" href="notebooks/lorenz_attractor.html#scikit-learnstyle-pipeline">Scikit-learn–style pipeline</a></li>
<li class="toctree-l4"><a class="reference internal" href="notebooks/lorenz_attractor.html#rescaling-the-diagram">Rescaling the diagram</a></li>
<li class="toctree-l4"><a class="reference internal" href="notebooks/lorenz_attractor.html#filtering-diagrams">Filtering diagrams</a></li>
<li class="toctree-l4"><a class="reference internal" href="notebooks/lorenz_attractor.html#persistence-entropy">Persistence entropy</a></li>
<li class="toctree-l4"><a class="reference internal" href="notebooks/lorenz_attractor.html#betti-curves">Betti Curves</a></li>
<li class="toctree-l4"><a class="reference internal" href="notebooks/lorenz_attractor.html#distances-among-diagrams">Distances among diagrams</a></li>
<li class="toctree-l4"><a class="reference internal" href="notebooks/lorenz_attractor.html#new-distances-in-the-embedding-space-knn-graphs-and-geodesic-distances">New distances in the embedding space: kNN graphs and geodesic distances</a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="notebooks/MNIST_classification.html">Classifying handwritten digits</a><ul>
<li class="toctree-l4"><a class="reference internal" href="notebooks/MNIST_classification.html#useful-references">Useful references</a></li>
<li class="toctree-l4"><a class="reference internal" href="notebooks/MNIST_classification.html#load-the-mnist-dataset">Load the MNIST dataset</a></li>
<li class="toctree-l4"><a class="reference internal" href="notebooks/MNIST_classification.html#from-pixels-to-topological-features">From pixels to topological features</a></li>
<li class="toctree-l4"><a class="reference internal" href="notebooks/MNIST_classification.html#building-a-full-blown-feature-extraction-pipeline">Building a full-blown feature extraction pipeline</a></li>
<li class="toctree-l4"><a class="reference internal" href="notebooks/MNIST_classification.html#training-a-classifier">Training a classifier</a></li>
<li class="toctree-l4"><a class="reference internal" href="notebooks/MNIST_classification.html#using-hyperparameter-search-with-topological-pipelines">Using hyperparameter search with topological pipelines</a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="notebooks/voids_on_the_plane.html">Can two-dimensional topological voids exist in two dimensions?</a><ul>
<li class="toctree-l4"><a class="reference internal" href="notebooks/voids_on_the_plane.html#import-libraries">Import libraries</a></li>
</ul>
</li>
</ul>
</li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="theory/glossary.html">Theory Glossary</a><ul>
<li class="toctree-l2"><a class="reference internal" href="theory/glossary.html#symbols">Symbols</a></li>
<li class="toctree-l2"><a class="reference internal" href="theory/glossary.html#analysis">Analysis</a><ul>
<li class="toctree-l3"><a class="reference internal" href="theory/glossary.html#metric-space">Metric space</a></li>
<li class="toctree-l3"><a class="reference internal" href="theory/glossary.html#normed-space">Normed space</a></li>
<li class="toctree-l3"><a class="reference internal" href="theory/glossary.html#inner-product-space">Inner product space</a></li>
<li class="toctree-l3"><a class="reference internal" href="theory/glossary.html#vectorization-amplitude-and-kernel">Vectorization, amplitude and kernel</a></li>
<li class="toctree-l3"><a class="reference internal" href="theory/glossary.html#euclidean-distance-and-l-p-norms">Euclidean distance and <span class="math notranslate nohighlight">\(l^p\)</span>-norms</a></li>
<li class="toctree-l3"><a class="reference internal" href="theory/glossary.html#distance-matrices-and-point-clouds">Distance matrices and point clouds</a></li>
<li class="toctree-l3"><a class="reference internal" href="theory/glossary.html#l-p-norms"><span class="math notranslate nohighlight">\(L^p\)</span>-norms</a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="theory/glossary.html#homology">Homology</a><ul>
<li class="toctree-l3"><a class="reference internal" href="theory/glossary.html#cubical-complex">Cubical complex</a><ul>
<li class="toctree-l4"><a class="reference internal" href="theory/glossary.html#reference">Reference:</a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="theory/glossary.html#simplicial-complex">Simplicial complex</a></li>
<li class="toctree-l3"><a class="reference internal" href="theory/glossary.html#abstract-simplicial-complex">Abstract simplicial complex</a></li>
<li class="toctree-l3"><a class="reference internal" href="theory/glossary.html#ordered-simplicial-complex">Ordered simplicial complex</a></li>
<li class="toctree-l3"><a class="reference internal" href="theory/glossary.html#directed-simplicial-complex">Directed simplicial complex</a></li>
<li class="toctree-l3"><a class="reference internal" href="theory/glossary.html#chain-complex">Chain complex</a></li>
<li class="toctree-l3"><a class="reference internal" href="theory/glossary.html#homology-and-cohomology">Homology and cohomology</a></li>
<li class="toctree-l3"><a class="reference internal" href="theory/glossary.html#simplicial-chains-and-simplicial-homology">Simplicial chains and simplicial homology</a></li>
<li class="toctree-l3"><a class="reference internal" href="theory/glossary.html#cubical-chains-and-cubical-homology">Cubical chains and cubical homology</a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="theory/glossary.html#persistence">Persistence</a><ul>
<li class="toctree-l3"><a class="reference internal" href="theory/glossary.html#filtered-complex">Filtered complex</a></li>
<li class="toctree-l3"><a class="reference internal" href="theory/glossary.html#cellwise-filtration">Cellwise filtration</a></li>
<li class="toctree-l3"><a class="reference internal" href="theory/glossary.html#clique-and-flag-complexes">Clique and flag complexes</a></li>
<li class="toctree-l3"><a class="reference internal" href="theory/glossary.html#persistence-module">Persistence module</a></li>
<li class="toctree-l3"><a class="reference internal" href="theory/glossary.html#persistent-simplicial-co-homology">Persistent simplicial (co)homology</a></li>
<li class="toctree-l3"><a class="reference internal" href="theory/glossary.html#vietoris-rips-complex-and-vietoris-rips-persistence">Vietoris-Rips complex and Vietoris-Rips persistence</a></li>
<li class="toctree-l3"><a class="reference internal" href="theory/glossary.html#cech-complex-and-cech-persistence">Čech complex and Čech persistence</a></li>
<li class="toctree-l3"><a class="reference internal" href="theory/glossary.html#multiset">Multiset</a></li>
<li class="toctree-l3"><a class="reference internal" href="theory/glossary.html#persistence-diagram">Persistence diagram</a></li>
<li class="toctree-l3"><a class="reference internal" href="theory/glossary.html#wasserstein-and-bottleneck-distance">Wasserstein and bottleneck distance</a><ul>
<li class="toctree-l4"><a class="reference internal" href="theory/glossary.html#reference-1">Reference:</a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="theory/glossary.html#persistence-landscape">Persistence landscape</a><ul>
<li class="toctree-l4"><a class="reference internal" href="theory/glossary.html#references">References:</a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="theory/glossary.html#weighted-silhouette">Weighted silhouette</a><ul>
<li class="toctree-l4"><a class="reference internal" href="theory/glossary.html#references-1">References:</a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="theory/glossary.html#heat-vectorizations">Heat vectorizations</a><ul>
<li class="toctree-l4"><a class="reference internal" href="theory/glossary.html#references-2">References:</a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="theory/glossary.html#persistence-entropy">Persistence entropy</a><ul>
<li class="toctree-l4"><a class="reference internal" href="theory/glossary.html#references-3">References:</a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="theory/glossary.html#betti-curve">Betti curve</a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="theory/glossary.html#time-series">Time series</a><ul>
<li class="toctree-l3"><a class="reference internal" href="theory/glossary.html#id31">Time series</a></li>
<li class="toctree-l3"><a class="reference internal" href="theory/glossary.html#takens-embedding">Takens embedding</a><ul>
<li class="toctree-l4"><a class="reference internal" href="theory/glossary.html#reference-2">Reference:</a></li>
</ul>
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<li class="toctree-l3"><a class="reference internal" href="theory/glossary.html#manifold">Manifold</a><ul>
<li class="toctree-l4"><a class="reference internal" href="theory/glossary.html#references-4">References:</a></li>
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<li class="toctree-l3"><a class="reference internal" href="theory/glossary.html#compact-subset">Compact subset</a></li>
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<li class="toctree-l2"><a class="reference internal" href="theory/glossary.html#bibliography">Bibliography</a></li>
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<li class="toctree-l4"><a class="reference internal" href="contributing/index.html#running-unit-tests">Running unit tests</a></li>
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<li class="toctree-l1 current"><a class="current reference internal" href="#">Release Notes</a><ul>
<li class="toctree-l2"><a class="reference internal" href="#release-0-3-1">Release 0.3.1</a><ul>
<li class="toctree-l3"><a class="reference internal" href="#major-features-and-improvements">Major Features and Improvements</a></li>
<li class="toctree-l3"><a class="reference internal" href="#bug-fixes">Bug Fixes</a></li>
<li class="toctree-l3"><a class="reference internal" href="#backwards-incompatible-changes">Backwards-Incompatible Changes</a></li>
<li class="toctree-l3"><a class="reference internal" href="#thanks-to-our-contributors">Thanks to our Contributors</a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="#release-0-3-0">Release 0.3.0</a><ul>
<li class="toctree-l3"><a class="reference internal" href="#id8">Major Features and Improvements</a><ul>
<li class="toctree-l4"><a class="reference internal" href="#persistent-homology-of-directed-flag-complexes-via-pyflagser">Persistent homology of directed flag complexes via <code class="docutils literal notranslate"><span class="pre">pyflagser</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="#edge-collapsing-and-performance-improvements-for-persistent-homology">Edge collapsing and performance improvements for persistent homology</a></li>
<li class="toctree-l4"><a class="reference internal" href="#new-transformers-and-functionality-in-gtda-homology">New transformers and functionality in <code class="docutils literal notranslate"><span class="pre">gtda.homology</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="#persistence-diagrams">Persistence diagrams</a></li>
<li class="toctree-l4"><a class="reference internal" href="#new-curves-subpackage">New <code class="docutils literal notranslate"><span class="pre">curves</span></code> subpackage</a></li>
<li class="toctree-l4"><a class="reference internal" href="#new-metaestimators-subpackage">New <code class="docutils literal notranslate"><span class="pre">metaestimators</span></code> subpackage</a></li>
<li class="toctree-l4"><a class="reference internal" href="#images">Images</a></li>
<li class="toctree-l4"><a class="reference internal" href="#time-series">Time series</a></li>
<li class="toctree-l4"><a class="reference internal" href="#graphs">Graphs</a></li>
<li class="toctree-l4"><a class="reference internal" href="#mapper">Mapper</a></li>
<li class="toctree-l4"><a class="reference internal" href="#plotting">Plotting</a></li>
<li class="toctree-l4"><a class="reference internal" href="#new-tutorials-and-examples">New tutorials and examples</a></li>
<li class="toctree-l4"><a class="reference internal" href="#utils">Utils</a></li>
<li class="toctree-l4"><a class="reference internal" href="#installation-improvements">Installation improvements</a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="#id49">Bug Fixes</a></li>
<li class="toctree-l3"><a class="reference internal" href="#id68">Backwards-Incompatible Changes</a></li>
<li class="toctree-l3"><a class="reference internal" href="#id89">Thanks to our Contributors</a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="#release-0-2-2">Release 0.2.2</a><ul>
<li class="toctree-l3"><a class="reference internal" href="#id90">Major Features and Improvements</a></li>
<li class="toctree-l3"><a class="reference internal" href="#id91">Bug Fixes</a></li>
<li class="toctree-l3"><a class="reference internal" href="#id92">Backwards-Incompatible Changes</a></li>
<li class="toctree-l3"><a class="reference internal" href="#id93">Thanks to our Contributors</a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="#release-0-2-1">Release 0.2.1</a><ul>
<li class="toctree-l3"><a class="reference internal" href="#id94">Major Features and Improvements</a></li>
<li class="toctree-l3"><a class="reference internal" href="#id95">Bug Fixes</a></li>
<li class="toctree-l3"><a class="reference internal" href="#id96">Backwards-Incompatible Changes</a></li>
<li class="toctree-l3"><a class="reference internal" href="#id97">Thanks to our Contributors</a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="#release-0-2-0">Release 0.2.0</a><ul>
<li class="toctree-l3"><a class="reference internal" href="#id98">Major Features and Improvements</a><ul>
<li class="toctree-l4"><a class="reference internal" href="#plotting-functions-and-plotting-api">Plotting functions and plotting API</a></li>
<li class="toctree-l4"><a class="reference internal" href="#changes-and-additions-to-gtda-homology">Changes and additions to <code class="docutils literal notranslate"><span class="pre">gtda.homology</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="#new-images-subpackage">New <code class="docutils literal notranslate"><span class="pre">images</span></code> subpackage</a></li>
<li class="toctree-l4"><a class="reference internal" href="#new-point-clouds-subpackage">New <code class="docutils literal notranslate"><span class="pre">point_clouds</span></code> subpackage</a></li>
<li class="toctree-l4"><a class="reference internal" href="#list-of-point-cloud-input">List of point cloud input</a></li>
<li class="toctree-l4"><a class="reference internal" href="#changes-and-additions-to-gtda-diagrams">Changes and additions to <code class="docutils literal notranslate"><span class="pre">gtda.diagrams</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="#changes-and-additions-to-gtda-utils">Changes and additions to <code class="docutils literal notranslate"><span class="pre">gtda.utils</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="#external-modules-and-hpc-improvements">External modules and HPC improvements</a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="#id99">Bug Fixes</a></li>
<li class="toctree-l3"><a class="reference internal" href="#id100">Backwards-Incompatible Changes</a></li>
<li class="toctree-l3"><a class="reference internal" href="#id101">Thanks to our Contributors</a></li>
</ul>
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<li class="toctree-l2"><a class="reference internal" href="#release-0-1-4">Release 0.1.4</a><ul>
<li class="toctree-l3"><a class="reference internal" href="#library-name-change">Library name change</a></li>
<li class="toctree-l3"><a class="reference internal" href="#change-of-license">Change of license</a></li>
<li class="toctree-l3"><a class="reference internal" href="#id102">Major Features and Improvements</a></li>
<li class="toctree-l3"><a class="reference internal" href="#id103">Bug Fixes</a></li>
<li class="toctree-l3"><a class="reference internal" href="#id104">Backwards-Incompatible Changes</a></li>
<li class="toctree-l3"><a class="reference internal" href="#id105">Thanks to our Contributors</a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="#release-0-1-3">Release 0.1.3</a><ul>
<li class="toctree-l3"><a class="reference internal" href="#id106">Major Features and Improvements</a></li>
<li class="toctree-l3"><a class="reference internal" href="#id107">Bug Fixes</a></li>
<li class="toctree-l3"><a class="reference internal" href="#id108">Backwards-Incompatible Changes</a></li>
<li class="toctree-l3"><a class="reference internal" href="#id109">Thanks to our Contributors</a></li>
<li class="toctree-l3"><a class="reference internal" href="#id110">Major Features and Improvements</a></li>
<li class="toctree-l3"><a class="reference internal" href="#id111">Bug Fixes</a></li>
<li class="toctree-l3"><a class="reference internal" href="#id112">Backwards-Incompatible Changes</a></li>
<li class="toctree-l3"><a class="reference internal" href="#id113">Thanks to our Contributors</a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="#release-0-1-1">Release 0.1.1</a><ul>
<li class="toctree-l3"><a class="reference internal" href="#id114">Major Features and Improvements</a></li>
<li class="toctree-l3"><a class="reference internal" href="#id115">Bug Fixes</a></li>
<li class="toctree-l3"><a class="reference internal" href="#id116">Backwards-Incompatible Changes</a></li>
<li class="toctree-l3"><a class="reference internal" href="#id117">Thanks to our Contributors</a></li>
</ul>
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<li class="toctree-l2"><a class="reference internal" href="#release-0-1-0">Release 0.1.0</a><ul>
<li class="toctree-l3"><a class="reference internal" href="#id118">Major Features and Improvements</a></li>
<li class="toctree-l3"><a class="reference internal" href="#id119">Bug Fixes</a></li>
<li class="toctree-l3"><a class="reference internal" href="#id120">Backwards-Incompatible Changes</a></li>
<li class="toctree-l3"><a class="reference internal" href="#id121">Thanks to our Contributors</a></li>
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<li class="toctree-l2"><a class="reference internal" href="#release-0-1a-0">Release 0.1a.0</a></li>
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<div class="section" id="release-notes">
<h1>Release Notes<a class="headerlink" href="#release-notes" title="Permalink to this headline">¶</a></h1>
<div class="section" id="release-0-3-1">
<span id="stable"></span><h2>Release 0.3.1<a class="headerlink" href="#release-0-3-1" title="Permalink to this headline">¶</a></h2>
<div class="section" id="major-features-and-improvements">
<h3>Major Features and Improvements<a class="headerlink" href="#major-features-and-improvements" title="Permalink to this headline">¶</a></h3>
<ul class="simple">
<li><p>The latest changes made to the <code class="docutils literal notranslate"><span class="pre">ripser.py</span></code> submodule have been pulled (<a class="reference external" href="https://github.com/giotto-ai/giotto-tda/pull/530">#530</a>, see also <a class="reference external" href="https://github.com/giotto-ai/giotto-tda/pull/532">#532</a>). This includes in particular the performance improvements to the C++ backend submitted by Julian Burella Pérez via <a class="reference external" href="https://github.com/scikit-tda/ripser.py/pull/106">scikit-tda/ripser.py#106</a>. The developer installation now includes a new dependency in <a class="reference external" href="https://github.com/martinus/robin-hood-hashing">robinhood hashmap</a>. These changes do not affect functionality.</p></li>
<li><p>The example notebook <a class="reference external" href="https://github.com/giotto-ai/giotto-tda/blob/46b18a48205e5611f3c2e0eaa21072a93ada5bcb/examples/classifying_shapes.ipynb">classifying_shapes.ipynb</a> has been modified and improved (<a class="reference external" href="https://github.com/giotto-ai/giotto-tda/pull/523">#523</a>).</p></li>
<li><p>The tutorial previously called <code class="docutils literal notranslate"><span class="pre">time_series_classification.ipynb</span></code> has been split into an introductory tutorial on the Takens embedding ideas (<a class="reference external" href="https://github.com/wreise/giotto-tda/blob/b5321f5858eb12103a5f08126ad68d597b41aca9/examples/topology_time_series.ipynb">topology_time_series.ipynb</a>) and an example notebook on gravitational wave detection (<a class="reference external" href="https://github.com/wreise/giotto-tda/blob/b5321f5858eb12103a5f08126ad68d597b41aca9/examples/gravitational_waves_detection.ipynb">gravitational_waves_detection.ipynb</a>) which presents a time series classification task (<a class="reference external" href="https://github.com/giotto-ai/giotto-tda/pull/529">#529</a>).</p></li>
<li><p>The documentation for <code class="docutils literal notranslate"><span class="pre">PairwiseDistance</span></code> has been improved (<a class="reference external" href="https://github.com/giotto-ai/giotto-tda/pull/525">#525</a>).</p></li>
</ul>
</div>
<div class="section" id="bug-fixes">
<h3>Bug Fixes<a class="headerlink" href="#bug-fixes" title="Permalink to this headline">¶</a></h3>
<ul class="simple">
<li><p>Timeout deadlines for some of the <code class="docutils literal notranslate"><span class="pre">hypothesis</span></code> tests have been increased to make them less flaky (<a class="reference external" href="https://github.com/giotto-ai/giotto-tda/pull/531">#531</a>).</p></li>
</ul>
</div>
<div class="section" id="backwards-incompatible-changes">
<h3>Backwards-Incompatible Changes<a class="headerlink" href="#backwards-incompatible-changes" title="Permalink to this headline">¶</a></h3>
<ul class="simple">
<li><p>Due to poor support for <code class="docutils literal notranslate"><span class="pre">brew</span></code> in the macOS 10.14 virtual machines by Azure, the CI for macOS systems is now run on 10.15 virtual machines and 10.14 is no longer supported by the wheels (<a class="reference external" href="https://github.com/giotto-ai/giotto-tda/pull/527">#527</a>)</p></li>
</ul>
</div>
<div class="section" id="thanks-to-our-contributors">
<h3>Thanks to our Contributors<a class="headerlink" href="#thanks-to-our-contributors" title="Permalink to this headline">¶</a></h3>
<p>This release contains contributions from many people:</p>
<p>Julian Burella Pérez, Umberto Lupo, Lewis Tunstall, Wojciech Reise, and Rayna Andreeva.</p>
<p>We are also grateful to all who filed issues or helped resolve them, asked and answered questions, and were part of inspiring discussions.</p>
</div>
</div>
<div class="section" id="release-0-3-0">
<h2>Release 0.3.0<a class="headerlink" href="#release-0-3-0" title="Permalink to this headline">¶</a></h2>
<div class="section" id="id8">
<h3>Major Features and Improvements<a class="headerlink" href="#id8" title="Permalink to this headline">¶</a></h3>
<p>This is a major release which adds substantial new functionality and introduces several improvements.</p>
<div class="section" id="persistent-homology-of-directed-flag-complexes-via-pyflagser">
<h4>Persistent homology of directed flag complexes via <code class="docutils literal notranslate"><span class="pre">pyflagser</span></code><a class="headerlink" href="#persistent-homology-of-directed-flag-complexes-via-pyflagser" title="Permalink to this headline">¶</a></h4>
<ul class="simple">
<li><p>The <code class="docutils literal notranslate"><span class="pre">pyflagser</span></code> package (<a class="reference external" href="https://github.com/giotto-ai/pyflagser">source</a>, <a class="reference external" href="https://docs-pyflagser.giotto.ai/">docs</a>) is now an official dependency of <code class="docutils literal notranslate"><span class="pre">giotto-tda</span></code>.</p></li>
<li><p>The <code class="docutils literal notranslate"><span class="pre">FlagserPersistence</span></code> transformer has been added to <code class="docutils literal notranslate"><span class="pre">gtda.homology</span></code> (<a class="reference external" href="https://github.com/giotto-ai/giotto-tda/pull/339">#339</a>). It wraps <code class="docutils literal notranslate"><span class="pre">pyflagser.flagser_weighted</span></code> to allow for computations of persistence diagrams from directed or undirected weighted graphs. A <a class="reference external" href="https://giotto-ai.github.io/gtda-docs/0.3.0/notebooks/persistent_homology_graphs.html">new notebook</a> demonstrates its use.</p></li>
</ul>
</div>
<div class="section" id="edge-collapsing-and-performance-improvements-for-persistent-homology">
<h4>Edge collapsing and performance improvements for persistent homology<a class="headerlink" href="#edge-collapsing-and-performance-improvements-for-persistent-homology" title="Permalink to this headline">¶</a></h4>
<ul class="simple">
<li><p>GUDHI C++ components have been updated to the state of GUDHI v3.3.0, yielding performance improvements in <code class="docutils literal notranslate"><span class="pre">SparseRipsPersistence</span></code>, <code class="docutils literal notranslate"><span class="pre">EuclideanCechPersistence</span></code> and <code class="docutils literal notranslate"><span class="pre">CubicalPersistence</span></code> (<a class="reference external" href="https://github.com/giotto-ai/giotto-tda/pull/468">#468</a>).</p></li>
<li><p>Bindings for GUDHI’s <a class="reference external" href="https://hal.inria.fr/hal-02395227">edge collapser</a> have been created and can now be used as an optional preprocessing step via the optional keyword argument <code class="docutils literal notranslate"><span class="pre">collapse_edges</span></code> in <code class="docutils literal notranslate"><span class="pre">VietorisRipsPersistence</span></code> and in <code class="docutils literal notranslate"><span class="pre">gtda.externals.ripser</span></code> (<a class="reference external" href="https://github.com/giotto-ai/giotto-tda/pull/469">#469</a> and <a class="reference external" href="https://github.com/giotto-ai/giotto-tda/pull/483">#483</a>). When <code class="docutils literal notranslate"><span class="pre">collapse_edges=True</span></code>, and the input data and/or number of required homology dimensions is sufficiently large, the resulting runtimes for Vietoris–Rips persistent homology are state of the art.</p></li>
<li><p>The performance of the Ripser bindings has otherwise been improved by avoiding unnecessary data copies, better managing the memory, and using more efficient matrix routines (<a class="reference external" href="https://github.com/giotto-ai/giotto-tda/pull/501">#501</a> and <a class="reference external" href="https://github.com/giotto-ai/giotto-tda/pull/507">#507</a>).</p></li>
</ul>
</div>
<div class="section" id="new-transformers-and-functionality-in-gtda-homology">
<h4>New transformers and functionality in <code class="docutils literal notranslate"><span class="pre">gtda.homology</span></code><a class="headerlink" href="#new-transformers-and-functionality-in-gtda-homology" title="Permalink to this headline">¶</a></h4>
<ul class="simple">
<li><p>The <code class="docutils literal notranslate"><span class="pre">WeakAlphaPersistence</span></code> transformer has been added to <code class="docutils literal notranslate"><span class="pre">gtda.homology</span></code> (<a class="reference external" href="https://github.com/giotto-ai/giotto-tda/pull/464">#464</a>). Like <code class="docutils literal notranslate"><span class="pre">VietorisRipsPersistence</span></code>, <code class="docutils literal notranslate"><span class="pre">SparseRipsPersistence</span></code> and <code class="docutils literal notranslate"><span class="pre">EuclideanCechPersistence</span></code>, it computes persistent homology from point clouds, but its runtime can scale much better with size in low dimensions.</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">VietorisRipsPersistence</span></code> now accepts sparse input when <code class="docutils literal notranslate"><span class="pre">metric="precomputed"</span></code> (<a class="reference external" href="https://github.com/giotto-ai/giotto-tda/pull/424">#424</a>).</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">CubicalPersistence</span></code> now accepts lists of 2D arrays (<a class="reference external" href="https://github.com/giotto-ai/giotto-tda/pull/503">#503</a>).</p></li>
<li><p>A <code class="docutils literal notranslate"><span class="pre">reduced_homology</span></code> parameter has been added to all persistent homology transformers. When <code class="docutils literal notranslate"><span class="pre">True</span></code>, one infinite bar in the H0 barcode is removed for the user automatically. Previously, it was not possible to <em>keep</em> these bars in the simplicial homology transformers. The default is always <code class="docutils literal notranslate"><span class="pre">True</span></code>, which implies a breaking change in the case of <code class="docutils literal notranslate"><span class="pre">CubicalPersistence</span></code> (<a class="reference external" href="https://github.com/giotto-ai/giotto-tda/pull/467">#467</a>).</p></li>
</ul>
</div>
<div class="section" id="persistence-diagrams">
<h4>Persistence diagrams<a class="headerlink" href="#persistence-diagrams" title="Permalink to this headline">¶</a></h4>
<ul class="simple">
<li><p>A <code class="docutils literal notranslate"><span class="pre">ComplexPolynomial</span></code> feature extraction transformer has been added (<a class="reference external" href="https://github.com/giotto-ai/giotto-tda/pull/479">#479</a>).</p></li>
<li><p>A <code class="docutils literal notranslate"><span class="pre">NumberOfPoints</span></code> feature extraction transformer has been added (<a class="reference external" href="https://github.com/giotto-ai/giotto-tda/pull/496">#496</a>).</p></li>
<li><p>An option to normalize the entropy in <code class="docutils literal notranslate"><span class="pre">PersistenceEntropy</span></code> according to a heuristic has been added, and a <code class="docutils literal notranslate"><span class="pre">nan_fill_value</span></code> parameter allows to replace any NaN produced by the entropy calculation with a fixed constant (<a class="reference external" href="https://github.com/giotto-ai/giotto-tda/pull/450">#450</a>).</p></li>
<li><p>The computations in <code class="docutils literal notranslate"><span class="pre">HeatKernel</span></code>, <code class="docutils literal notranslate"><span class="pre">PersistenceImage</span></code> and in the pairwise distances and amplitudes related to them has been changed to yield the continuum limit when <code class="docutils literal notranslate"><span class="pre">n_bins</span></code> tends to infinity; <code class="docutils literal notranslate"><span class="pre">sigma</span></code> is now measured in the same units as the filtration parameter and defaults to 0.1 (<a class="reference external" href="https://github.com/giotto-ai/giotto-tda/pull/454">#454</a>).</p></li>
</ul>
</div>
<div class="section" id="new-curves-subpackage">
<h4>New <code class="docutils literal notranslate"><span class="pre">curves</span></code> subpackage<a class="headerlink" href="#new-curves-subpackage" title="Permalink to this headline">¶</a></h4>
<p>A new <code class="docutils literal notranslate"><span class="pre">curves</span></code> subpackage has been added to preprocess, and extract features from, collections of multi-channel curves such as returned by <code class="docutils literal notranslate"><span class="pre">BettiCurve</span></code>, <code class="docutils literal notranslate"><span class="pre">PersistenceLandscape</span></code> and <code class="docutils literal notranslate"><span class="pre">Silhouette</span></code> (<a class="reference external" href="https://github.com/giotto-ai/giotto-tda/pull/480">#480</a>). It contains:</p>
<ul class="simple">
<li><p>A <code class="docutils literal notranslate"><span class="pre">StandardFeatures</span></code> transformer that can extract features channel-wise in a generic way.</p></li>
<li><p>A <code class="docutils literal notranslate"><span class="pre">Derivative</span></code> transformer that computes channel-wise derivatives of any order by discrete differences (<a class="reference external" href="https://github.com/giotto-ai/giotto-tda/pull/492">#492</a>).</p></li>
</ul>
</div>
<div class="section" id="new-metaestimators-subpackage">
<h4>New <code class="docutils literal notranslate"><span class="pre">metaestimators</span></code> subpackage<a class="headerlink" href="#new-metaestimators-subpackage" title="Permalink to this headline">¶</a></h4>
<p>A new <code class="docutils literal notranslate"><span class="pre">metaestimator</span></code> subpackage has been added with a <code class="docutils literal notranslate"><span class="pre">CollectionTransformer</span></code> meta-estimator which converts any transformer instance into a fit-transformer acting on collections (<a class="reference external" href="https://github.com/giotto-ai/giotto-tda/pull/495">#495</a>).</p>
</div>
<div class="section" id="images">
<h4>Images<a class="headerlink" href="#images" title="Permalink to this headline">¶</a></h4>
<ul class="simple">
<li><p>A <code class="docutils literal notranslate"><span class="pre">DensityFiltration</span></code> for collections of binary images has been added (<a class="reference external" href="https://github.com/giotto-ai/giotto-tda/pull/473">#473</a>).</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">Padder</span></code> and <code class="docutils literal notranslate"><span class="pre">Inverter</span></code> have been extended to greyscale images (<a class="reference external" href="https://github.com/giotto-ai/giotto-tda/pull/489">#489</a>).</p></li>
</ul>
</div>
<div class="section" id="time-series">
<h4>Time series<a class="headerlink" href="#time-series" title="Permalink to this headline">¶</a></h4>
<ul class="simple">
<li><p><code class="docutils literal notranslate"><span class="pre">TakensEmbedding</span></code> is now a new transformer acting on collections of time series (<a class="reference external" href="https://github.com/giotto-ai/giotto-tda/pull/460">#460</a>).</p></li>
<li><p>The former <code class="docutils literal notranslate"><span class="pre">TakensEmbedding</span></code> acting on a single time series has been renamed to <code class="docutils literal notranslate"><span class="pre">SingleTakensEmbedding</span></code> transformer, and the internal logic employed in its <code class="docutils literal notranslate"><span class="pre">fit</span></code> for computing optimal hyperparameters is now available via a <code class="docutils literal notranslate"><span class="pre">takens_embedding_optimal_parameters</span></code> convenience function (<a class="reference external" href="https://github.com/giotto-ai/giotto-tda/pull/460">#460</a>).</p></li>
<li><p>The <code class="docutils literal notranslate"><span class="pre">_slice_windows</span></code> method of <code class="docutils literal notranslate"><span class="pre">SlidingWindow</span></code> has been made public and renamed into <code class="docutils literal notranslate"><span class="pre">slice_windows</span></code> (<a class="reference external" href="https://github.com/giotto-ai/giotto-tda/pull/460">#460</a>).</p></li>
</ul>
</div>
<div class="section" id="graphs">
<h4>Graphs<a class="headerlink" href="#graphs" title="Permalink to this headline">¶</a></h4>
<ul class="simple">
<li><p><code class="docutils literal notranslate"><span class="pre">GraphGeodesicDistance</span></code> has been improved as follows (<a class="reference external" href="https://github.com/giotto-ai/giotto-tda/pull/422">#422</a>):</p>
<ul>
<li><p>The new parameters <code class="docutils literal notranslate"><span class="pre">directed</span></code>, <code class="docutils literal notranslate"><span class="pre">unweighted</span></code> and <code class="docutils literal notranslate"><span class="pre">method</span></code> have been added.</p></li>
<li><p>The rules on the role of zero entries, infinity entries, and non-stored values have been made clearer.</p></li>
<li><p>Masked arrays are now supported.</p></li>
</ul>
</li>
<li><p>A <code class="docutils literal notranslate"><span class="pre">mode</span></code> parameter has been added to <code class="docutils literal notranslate"><span class="pre">KNeighborsGraph</span></code>; as in <code class="docutils literal notranslate"><span class="pre">scikit-learn</span></code>, it can be set to either <code class="docutils literal notranslate"><span class="pre">"distance"</span></code> or <code class="docutils literal notranslate"><span class="pre">"connectivity"</span></code> (<a class="reference external" href="https://github.com/giotto-ai/giotto-tda/pull/478">#478</a>).</p></li>
<li><p>List input is now accepted by all transformers in <code class="docutils literal notranslate"><span class="pre">gtda.graphs</span></code>, and outputs are consistently either lists or 3D arrays (<a class="reference external" href="https://github.com/giotto-ai/giotto-tda/pull/478">#478</a>).</p></li>
<li><p>Sparse matrices returned by <code class="docutils literal notranslate"><span class="pre">KNeighborsGraph</span></code> and <code class="docutils literal notranslate"><span class="pre">TransitionGraph</span></code> now have int dtype (0-1 adjacency matrices), and are not necessarily symmetric (<a class="reference external" href="https://github.com/giotto-ai/giotto-tda/pull/478">#478</a>).</p></li>
</ul>
</div>
<div class="section" id="mapper">
<h4>Mapper<a class="headerlink" href="#mapper" title="Permalink to this headline">¶</a></h4>
<ul class="simple">
<li><p>Pullback cover set labels and partial cluster labels have been added to Mapper node hovertexts (<a class="reference external" href="https://github.com/giotto-ai/giotto-tda/pull/445">#445</a>).</p></li>
<li><p>The functionality of <code class="docutils literal notranslate"><span class="pre">Nerve</span></code> and <code class="docutils literal notranslate"><span class="pre">make_mapper_pipeline</span></code> has been greatly extended (<a class="reference external" href="https://github.com/giotto-ai/giotto-tda/pull/447">#447</a> and <a class="reference external" href="https://github.com/giotto-ai/giotto-tda/pull/456">#456</a>):</p>
<ul>
<li><p>Node and edge metadata are now accessible in output <code class="docutils literal notranslate"><span class="pre">igraph.Graph</span></code> objects by means of the <code class="docutils literal notranslate"><span class="pre">VertexSeq</span></code> and <code class="docutils literal notranslate"><span class="pre">EdgeSeq</span></code> attributes <code class="docutils literal notranslate"><span class="pre">vs</span></code> and <code class="docutils literal notranslate"><span class="pre">es</span></code> (respectively). Graph-level dictionaries are no longer used.</p></li>
<li><p>Available node metadata can be accessed by <code class="docutils literal notranslate"><span class="pre">graph.vs[attr_name]</span></code> where for <code class="docutils literal notranslate"><span class="pre">attr_name</span></code> is one of <code class="docutils literal notranslate"><span class="pre">"pullback_set_label"</span></code>, <code class="docutils literal notranslate"><span class="pre">"partial_cluster_label"</span></code>, or <code class="docutils literal notranslate"><span class="pre">"node_elements"</span></code>.</p></li>
<li><p>Sizes of intersections are automatically stored as edge weights, accessible by <code class="docutils literal notranslate"><span class="pre">graph.es["weight"]</span></code>.</p></li>
<li><p>A <code class="docutils literal notranslate"><span class="pre">"store_intersections"</span></code> keyword argument has been added to <code class="docutils literal notranslate"><span class="pre">Nerve</span></code> and <code class="docutils literal notranslate"><span class="pre">make_mapper_pipeline</span></code> to allow to store the indices defining node intersections as edge attributes, accessible via <code class="docutils literal notranslate"><span class="pre">graph.es["edge_elements"]</span></code>.</p></li>
<li><p>A <code class="docutils literal notranslate"><span class="pre">contract_nodes</span></code> optional parameter has been added to both <code class="docutils literal notranslate"><span class="pre">Nerve</span></code> and <code class="docutils literal notranslate"><span class="pre">make_mapper_pipeline</span></code>; nodes which are subsets of other nodes are thrown away from the graph when this parameter is set to <code class="docutils literal notranslate"><span class="pre">True</span></code>.</p></li>
<li><p>A <code class="docutils literal notranslate"><span class="pre">graph_</span></code> attribute is stored during <code class="docutils literal notranslate"><span class="pre">Nerve.fit</span></code>.</p></li>
</ul>
</li>
<li><p>Two of the <code class="docutils literal notranslate"><span class="pre">Nerve</span></code> parameters (<code class="docutils literal notranslate"><span class="pre">min_intersection</span></code> and the new <code class="docutils literal notranslate"><span class="pre">contract_nodes</span></code>) are now available in the widgets generated by <code class="docutils literal notranslate"><span class="pre">plot_interactive_mapper_graph</span></code>, and the layout of these widgets has been improved (<a class="reference external" href="https://github.com/giotto-ai/giotto-tda/pull/456">#456</a>).</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">ParallelClustering</span></code> and <code class="docutils literal notranslate"><span class="pre">Nerve</span></code> have been exposed in the documentation and in <code class="docutils literal notranslate"><span class="pre">gtda.mapper</span></code>’s <code class="docutils literal notranslate"><span class="pre">__init__</span></code> (<a class="reference external" href="https://github.com/giotto-ai/giotto-tda/pull/447">#447</a>).</p></li>
</ul>
</div>
<div class="section" id="plotting">
<h4>Plotting<a class="headerlink" href="#plotting" title="Permalink to this headline">¶</a></h4>
<ul class="simple">
<li><p>A <code class="docutils literal notranslate"><span class="pre">plot_params</span></code> kwarg is available in plotting functions and methods throughout to allow user customisability of output figures. The user must pass a dictionary with keys <code class="docutils literal notranslate"><span class="pre">"layout"</span></code> and/or <code class="docutils literal notranslate"><span class="pre">"trace"</span></code> (or <code class="docutils literal notranslate"><span class="pre">"traces"</span></code> in some cases) (<a class="reference external" href="https://github.com/giotto-ai/giotto-tda/pull/441">#441</a>).</p></li>
<li><p>Several plots produced by <code class="docutils literal notranslate"><span class="pre">plot</span></code> class methods now have default titles (<a class="reference external" href="https://github.com/giotto-ai/giotto-tda/pull/453">#453</a>).</p></li>
<li><p>Infinite deaths are now plotted by <code class="docutils literal notranslate"><span class="pre">plot_diagrams</span></code> (<a class="reference external" href="https://github.com/giotto-ai/giotto-tda/pull/461">#461</a>).</p></li>
<li><p>Possible multiplicities of persistence pairs in persistence diagram plots are now indicated in the hovertext (<a class="reference external" href="https://github.com/giotto-ai/giotto-tda/pull/454">#454</a>).</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">plot_heatmap</span></code> now accepts boolean array input (<a class="reference external" href="https://github.com/giotto-ai/giotto-tda/pull/444">#444</a>).</p></li>
</ul>
</div>
<div class="section" id="new-tutorials-and-examples">
<h4>New tutorials and examples<a class="headerlink" href="#new-tutorials-and-examples" title="Permalink to this headline">¶</a></h4>
<p>The following new tutorials have been added:</p>
<ul class="simple">
<li><p><a class="reference external" href="https://giotto-ai.github.io/gtda-docs/0.3.0/notebooks/time_series_classification.html">Topology of time series</a>, which explains the theory of the Takens time-delay embedding and its use with persistent homology, demonstrates the new <code class="docutils literal notranslate"><span class="pre">API</span></code> of several components in <code class="docutils literal notranslate"><span class="pre">gtda.time_series</span></code>, and shows how to construct time series <em>classification</em> pipelines in <code class="docutils literal notranslate"><span class="pre">giotto-tda</span></code> by partially reproducing <a class="reference external" href="https://arxiv.org/abs/1910.08245">arXiv:1910:08245</a>.</p></li>
<li><p><a class="reference external" href="https://giotto-ai.github.io/gtda-docs/0.3.0/notebooks/time_series_forecasting.html">Topology in time series forecasting</a>, which explains how to set up time series <em>forecasting</em> pipelines in <code class="docutils literal notranslate"><span class="pre">giotto-tda</span></code> via <code class="docutils literal notranslate"><span class="pre">TransformerResamplerMixin``s</span> <span class="pre">and</span> <span class="pre">the</span> <span class="pre">``giotto-tda</span></code> <code class="docutils literal notranslate"><span class="pre">Pipeline</span></code> class.</p></li>
<li><p><a class="reference external" href="https://giotto-ai.github.io/gtda-docs/0.3.0/notebooks/persistent_homology_graphs.html">Topological feature extraction from graphs</a>, which explains what the features extracted from directed or undirected graphs by <code class="docutils literal notranslate"><span class="pre">VietorisRipsPersistence</span></code>, <code class="docutils literal notranslate"><span class="pre">SparseRipsPersistence</span></code> and <code class="docutils literal notranslate"><span class="pre">FlagserPersistence</span></code> are.</p></li>
<li><p><a class="reference external" href="https://giotto-ai.github.io/gtda-docs/0.3.0/notebooks/MNIST_classification.html">Classifying handwritten digits</a>, which presents a fully-fledged machine learning pipeline in which cubical persistent homology is applied to the classification of handwritten images from he MNIST dataset, partially reproducing <a class="reference external" href="https://arxiv.org/abs/1910.08345">arXiv:1910.08345</a>.</p></li>
</ul>
</div>
<div class="section" id="utils">
<h4>Utils<a class="headerlink" href="#utils" title="Permalink to this headline">¶</a></h4>
<ul class="simple">
<li><p>A <code class="docutils literal notranslate"><span class="pre">check_collection</span></code> input validation function has been added (<a class="reference external" href="https://github.com/giotto-ai/giotto-tda/pull/491">#491</a>).</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">validate_params</span></code> now accepts <code class="docutils literal notranslate"><span class="pre">"in"</span></code> and <code class="docutils literal notranslate"><span class="pre">"of"</span></code> keys simultaneously in the <code class="docutils literal notranslate"><span class="pre">references</span></code> dictionaries, with <code class="docutils literal notranslate"><span class="pre">"in"</span></code> used for non-list-like types and <code class="docutils literal notranslate"><span class="pre">"of"</span></code> otherwise (<a class="reference external" href="https://github.com/giotto-ai/giotto-tda/pull/502">#502</a>).</p></li>
</ul>
</div>
<div class="section" id="installation-improvements">
<h4>Installation improvements<a class="headerlink" href="#installation-improvements" title="Permalink to this headline">¶</a></h4>
<ul class="simple">
<li><p><code class="docutils literal notranslate"><span class="pre">pybind11</span></code> is now treated as a standard git submodule in the developer installation (<a class="reference external" href="https://github.com/giotto-ai/giotto-tda/pull/459">#459</a>).</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">pandas</span></code> is now part of the testing requirements when intalling from source (<a class="reference external" href="https://github.com/giotto-ai/giotto-tda/pull/508">#508</a>).</p></li>
</ul>
</div>
</div>
<div class="section" id="id49">
<h3>Bug Fixes<a class="headerlink" href="#id49" title="Permalink to this headline">¶</a></h3>
<ul class="simple">
<li><p>A bug has been fixed which could lead to features with negative lifetime in persistent homology transformers when <code class="docutils literal notranslate"><span class="pre">infinity_values</span></code> was set too low (<a class="reference external" href="https://github.com/giotto-ai/giotto-tda/pull/339">#339</a>).</p></li>
<li><p>By relying on <code class="docutils literal notranslate"><span class="pre">scipy</span></code>’s <code class="docutils literal notranslate"><span class="pre">shortest_path</span></code> instead of <code class="docutils literal notranslate"><span class="pre">scikit-learn</span></code>’s <code class="docutils literal notranslate"><span class="pre">graph_shortest_path</span></code>, some errors in computing <code class="docutils literal notranslate"><span class="pre">GraphGeodesicDistance</span></code> (e.g. when som edges are zero) have been fixed (<a class="reference external" href="https://github.com/giotto-ai/giotto-tda/pull/422">#422</a>).</p></li>
<li><p>A bug in the handling of COO matrices by the <code class="docutils literal notranslate"><span class="pre">ripser</span></code> interface has been fixed (<a class="reference external" href="https://github.com/giotto-ai/giotto-tda/pull/465">#465</a>).</p></li>
<li><p>A bug which led to the incorrect handling of the <code class="docutils literal notranslate"><span class="pre">homology_dimensions</span></code> parameter in <code class="docutils literal notranslate"><span class="pre">Filtering</span></code> has been fixed (<a class="reference external" href="https://github.com/giotto-ai/giotto-tda/pull/439">#439</a>).</p></li>
<li><p>An issue with the use of <code class="docutils literal notranslate"><span class="pre">joblib.Parallel</span></code>, which led to errors when attempting to run <code class="docutils literal notranslate"><span class="pre">HeatKernel</span></code>, <code class="docutils literal notranslate"><span class="pre">PersistenceImage</span></code>, and the corresponding amplitudes and distances on large datasets, has been fixed (<a class="reference external" href="https://github.com/giotto-ai/giotto-tda/pull/428">#428</a> and <a class="reference external" href="https://github.com/giotto-ai/giotto-tda/pull/481">#481</a>).</p></li>
<li><p>A bug leading to plots of persistence diagrams not showing points with negative births or deaths has been fixed, as has a bug with the computation of the range to be shown in the plot (<a class="reference external" href="https://github.com/giotto-ai/giotto-tda/pull/437">#437</a>).</p></li>
<li><p>A bug in the handling of persistence pairs with negative death values by <code class="docutils literal notranslate"><span class="pre">Filtering</span></code> has been fixed (<a class="reference external" href="https://github.com/giotto-ai/giotto-tda/pull/436">#436</a>).</p></li>
<li><p>A bug in the handling of <code class="docutils literal notranslate"><span class="pre">homology_dimension_ix</span></code> (now renamed to <code class="docutils literal notranslate"><span class="pre">homology_dimension_idx</span></code>) in the <code class="docutils literal notranslate"><span class="pre">plot</span></code> methods of <code class="docutils literal notranslate"><span class="pre">HeatKernel</span></code> and <code class="docutils literal notranslate"><span class="pre">PersistenceImage</span></code> has been fixed (<a class="reference external" href="https://github.com/giotto-ai/giotto-tda/pull/452">#452</a>).</p></li>
<li><p>A bug in the labelling of axes in <code class="docutils literal notranslate"><span class="pre">HeatKernel</span></code> and <code class="docutils literal notranslate"><span class="pre">PersistenceImage</span></code> plots has ben fixed (<a class="reference external" href="https://github.com/giotto-ai/giotto-tda/pull/453">#453</a> and <a class="reference external" href="https://github.com/giotto-ai/giotto-tda/pull/454">#454</a>).</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">PersistenceLandscape</span></code> plots now show all homology dimensions, instead of just the first (<a class="reference external" href="https://github.com/giotto-ai/giotto-tda/pull/454">#454</a>).</p></li>
<li><p>A bug in the computation of amplitudes and pairwise distances based on persistence images has been fixed (<a class="reference external" href="https://github.com/giotto-ai/giotto-tda/pull/454">#454</a>).</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">Silhouette</span></code> now does not create NaNs when a subdiagram is trivial (<a class="reference external" href="https://github.com/giotto-ai/giotto-tda/pull/454">#454</a>).</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">CubicalPersistence</span></code> now does not create pairs with negative persistence when <code class="docutils literal notranslate"><span class="pre">infinity_values</span></code> is set too low (<a class="reference external" href="https://github.com/giotto-ai/giotto-tda/pull/467">#467</a>).</p></li>
<li><p>Warnings are no longer thrown by <code class="docutils literal notranslate"><span class="pre">KNeighborsGraph</span></code> when <code class="docutils literal notranslate"><span class="pre">metric="precomputed"</span></code> (<a class="reference external" href="https://github.com/giotto-ai/giotto-tda/pull/506">#506</a>).</p></li>
<li><p>A bug in <code class="docutils literal notranslate"><span class="pre">Labeller.resample</span></code> affecting cases in which <code class="docutils literal notranslate"><span class="pre">n_steps_future</span> <span class="pre">>=</span> <span class="pre">size</span> <span class="pre">-</span> <span class="pre">1</span></code>, has been fixed (<a class="reference external" href="https://github.com/giotto-ai/giotto-tda/pull/460">#460</a>).</p></li>
<li><p>A bug in <code class="docutils literal notranslate"><span class="pre">validate_params</span></code>, affecting the case of tuples of allowed types, has been fixed (<a class="reference external" href="https://github.com/giotto-ai/giotto-tda/pull/502">#502</a>).</p></li>
</ul>
</div>
<div class="section" id="id68">
<h3>Backwards-Incompatible Changes<a class="headerlink" href="#id68" title="Permalink to this headline">¶</a></h3>
<ul class="simple">
<li><p>The minimum required versions from most of the dependencies have been bumped. The updated dependencies are <code class="docutils literal notranslate"><span class="pre">numpy</span> <span class="pre">>=</span> <span class="pre">1.19.1</span></code>, <code class="docutils literal notranslate"><span class="pre">scipy</span> <span class="pre">>=</span> <span class="pre">1.5.0</span></code>, <code class="docutils literal notranslate"><span class="pre">joblib</span> <span class="pre">>=</span> <span class="pre">0.16.0</span></code>, <code class="docutils literal notranslate"><span class="pre">scikit-learn</span> <span class="pre">>=</span> <span class="pre">0.23.1</span></code>, <code class="docutils literal notranslate"><span class="pre">python-igraph</span> <span class="pre">>=</span> <span class="pre">0.8.2</span></code>, <code class="docutils literal notranslate"><span class="pre">plotly</span> <span class="pre">>=</span> <span class="pre">4.8.2</span></code>, and <code class="docutils literal notranslate"><span class="pre">pyflagser</span> <span class="pre">>=</span> <span class="pre">0.4.1</span></code> (<a class="reference external" href="https://github.com/giotto-ai/giotto-tda/pull/457">#457</a>).</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">GraphGeodesicDistance</span></code> now returns either lists or 3D dense ndarrays for compatibility with the homology transformers - By relying on <code class="docutils literal notranslate"><span class="pre">scipy</span></code>’s <code class="docutils literal notranslate"><span class="pre">shortest_path</span></code> instead of <code class="docutils literal notranslate"><span class="pre">scikit-learn</span></code>’s <code class="docutils literal notranslate"><span class="pre">graph_shortest_path</span></code>, some errors in computing <code class="docutils literal notranslate"><span class="pre">GraphGeodesicDistance</span></code> (e.g. when som edges are zero) have been fixed (<a class="reference external" href="https://github.com/giotto-ai/giotto-tda/pull/422">#422</a>).</p></li>
<li><p>The output of <code class="docutils literal notranslate"><span class="pre">PairwiseDistance</span></code> has been transposed to match <code class="docutils literal notranslate"><span class="pre">scikit-learn</span></code> convention <code class="docutils literal notranslate"><span class="pre">(n_samples_transform,</span> <span class="pre">n_samples_fit)</span></code> (<a class="reference external" href="https://github.com/giotto-ai/giotto-tda/pull/420">#420</a>).</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">plot</span></code> class methods now return figures instead of showing them (<a class="reference external" href="https://github.com/giotto-ai/giotto-tda/pull/441">#441</a>).</p></li>
<li><p>Mapper node and edge attributes are no longer stored as graph-level dictionaries, <code class="docutils literal notranslate"><span class="pre">"node_id"</span></code> is no longer an available node attribute, and the attributes <code class="docutils literal notranslate"><span class="pre">nodes_</span></code> and <code class="docutils literal notranslate"><span class="pre">edges_</span></code> previously stored by <code class="docutils literal notranslate"><span class="pre">Nerve.fit</span></code> have been removed in favour of a <code class="docutils literal notranslate"><span class="pre">graph_</span></code> attribute (<a class="reference external" href="https://github.com/giotto-ai/giotto-tda/pull/447">#447</a>).</p></li>
<li><p>The <code class="docutils literal notranslate"><span class="pre">homology_dimension_ix</span></code> parameter available in some transformers in <code class="docutils literal notranslate"><span class="pre">gtda.diagrams</span></code> has been renamed to <code class="docutils literal notranslate"><span class="pre">homology_dimensions_idx</span></code> (<a class="reference external" href="https://github.com/giotto-ai/giotto-tda/pull/452">#452</a>).</p></li>
<li><p>The base of the logarithm used by <code class="docutils literal notranslate"><span class="pre">PersistenceEntropy</span></code> is now 2 instead of <em>e</em>, and NaN values are replaced with -1 instead of 0 by default (<a class="reference external" href="https://github.com/giotto-ai/giotto-tda/pull/450">#450</a> and <a class="reference external" href="https://github.com/giotto-ai/giotto-tda/pull/474">#474</a>).</p></li>
<li><p>The outputs of <code class="docutils literal notranslate"><span class="pre">PersistenceImage</span></code>, <code class="docutils literal notranslate"><span class="pre">HeatKernel</span></code> and of the pairwise distances and amplitudes based on them is now different due to the improvements described above.</p></li>
<li><p>Weights are no longer stored in the <code class="docutils literal notranslate"><span class="pre">effective_metric_params_</span></code> attribute of <code class="docutils literal notranslate"><span class="pre">PairwiseDistance</span></code>, <code class="docutils literal notranslate"><span class="pre">Amplitude</span></code> and <code class="docutils literal notranslate"><span class="pre">Scaler</span></code> objects when the metric is persistence-image–based; only the weight function is (<a class="reference external" href="https://github.com/giotto-ai/giotto-tda/pull/454">#454</a>).</p></li>
<li><p>The <code class="docutils literal notranslate"><span class="pre">homology_dimensions_</span></code> attributes of several transformers have been converted from lists to tuples. When possible, homology dimensions stored as parts of attributes are now presented as ints (<a class="reference external" href="https://github.com/giotto-ai/giotto-tda/pull/454">#454</a>).</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">gaussian_filter</span></code> (used to make heat– and persistence-image–based representations/pairwise distances/amplitudes) is now called with <code class="docutils literal notranslate"><span class="pre">mode="constant"</span></code> instead of <code class="docutils literal notranslate"><span class="pre">"reflect"</span></code> (<a class="reference external" href="https://github.com/giotto-ai/giotto-tda/pull/454">#454</a>).</p></li>
<li><p>The default value of <code class="docutils literal notranslate"><span class="pre">order</span></code> in <code class="docutils literal notranslate"><span class="pre">Amplitude</span></code> has been changed from <code class="docutils literal notranslate"><span class="pre">2.</span></code> to <code class="docutils literal notranslate"><span class="pre">None</span></code>, giving vector instead of scalar features (<a class="reference external" href="https://github.com/giotto-ai/giotto-tda/pull/454">#454</a>).</p></li>
<li><p>The meaning of the default <code class="docutils literal notranslate"><span class="pre">None</span></code> for <code class="docutils literal notranslate"><span class="pre">weight_function</span></code> in <code class="docutils literal notranslate"><span class="pre">PersistenceImage</span></code> (and in <code class="docutils literal notranslate"><span class="pre">Amplitude</span></code> and <code class="docutils literal notranslate"><span class="pre">PairwiseDistance</span></code> when <code class="docutils literal notranslate"><span class="pre">metric="persistence_image"</span></code>) has been changed from the identity function to the function returning a vector of ones (<a class="reference external" href="https://github.com/giotto-ai/giotto-tda/pull/454">#454</a>).</p></li>
<li><p>Due to the updates in the GUDHI components, some of the bindings and Python interfaces to the GUDHI C++ components in <code class="docutils literal notranslate"><span class="pre">gtda.externals</span></code> have changed (<a class="reference external" href="https://github.com/giotto-ai/giotto-tda/pull/468">#468</a>).</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">Labeller.transform</span></code> now returns a 1D array instead of a column array (<a class="reference external" href="https://github.com/giotto-ai/giotto-tda/pull/475">#475</a>).</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">PersistenceLandscape</span></code> now returns 3D arrays instead of 4D ones, for compatibility with the new <code class="docutils literal notranslate"><span class="pre">curves</span></code> subpackage (<a class="reference external" href="https://github.com/giotto-ai/giotto-tda/pull/480">#480</a>).</p></li>
<li><p>By default, <code class="docutils literal notranslate"><span class="pre">CubicalPersistence</span></code> now removes one infinite bar in H0 (<a class="reference external" href="https://github.com/giotto-ai/giotto-tda/pull/467">#467</a>, and see above).</p></li>
<li><p>The former <code class="docutils literal notranslate"><span class="pre">width</span></code> parameter in <code class="docutils literal notranslate"><span class="pre">SlidingWindow</span></code> and <code class="docutils literal notranslate"><span class="pre">Labeller</span></code> has been replaced with a more intuitive <code class="docutils literal notranslate"><span class="pre">size</span></code> parameter. The relation between the two is: <code class="docutils literal notranslate"><span class="pre">size</span> <span class="pre">=</span> <span class="pre">width</span> <span class="pre">+</span> <span class="pre">1</span></code> (<a class="reference external" href="https://github.com/giotto-ai/giotto-tda/pull/460">#460</a>).</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">clusterer</span></code> is now a required parameter in <code class="docutils literal notranslate"><span class="pre">ParallelClustering</span></code> (<a class="reference external" href="https://github.com/giotto-ai/giotto-tda/pull/508">#508</a>).</p></li>
<li><p>The <code class="docutils literal notranslate"><span class="pre">max_fraction</span></code> parameter in <code class="docutils literal notranslate"><span class="pre">FirstSimpleGap</span></code> and <code class="docutils literal notranslate"><span class="pre">FirstHistogramGap</span></code> now indicates the floor of <code class="docutils literal notranslate"><span class="pre">max_fraction</span> <span class="pre">*</span> <span class="pre">n_samples</span></code>; its default value has been changed from <code class="docutils literal notranslate"><span class="pre">None</span></code> to <code class="docutils literal notranslate"><span class="pre">1</span></code> (<a class="reference external" href="https://github.com/giotto-ai/giotto-tda/pull/412">#412</a>).</p></li>
</ul>
</div>
<div class="section" id="id89">
<h3>Thanks to our Contributors<a class="headerlink" href="#id89" title="Permalink to this headline">¶</a></h3>
<p>This release contains contributions from many people:</p>
<p>Umberto Lupo, Guillaume Tauzin, Julian Burella Pérez, Wojciech Reise, Lewis Tunstall, Nick Sale, and Anibal Medina-Mardones.</p>
<p>We are also grateful to all who filed issues or helped resolve them, asked and answered questions, and were part of inspiring discussions.</p>
</div>
</div>
<div class="section" id="release-0-2-2">
<h2>Release 0.2.2<a class="headerlink" href="#release-0-2-2" title="Permalink to this headline">¶</a></h2>
<div class="section" id="id90">
<h3>Major Features and Improvements<a class="headerlink" href="#id90" title="Permalink to this headline">¶</a></h3>
<ul>
<li><p>The documentation for <code class="docutils literal notranslate"><span class="pre">gtda.mapper.utils.decorators.method_to_transform</span></code> has been improved.</p></li>
<li><p>A table of contents has been added to the theory glossary.</p></li>
<li><p>The theory glossary has been restructured by including a section titled “Analysis”. Entries for l^p norms, L^p norms and heat vectorization have been added.</p></li>
<li><p>The project’s Azure CI for Windows versions has been sped-up by ensuring that the locally installed boost version is detected.</p></li>
<li><p>Several python bindings to external code from GUDHI, ripser.py and Hera have been made public: specifically, <code class="docutils literal notranslate"><span class="pre">from</span> <span class="pre">gtda.externals</span> <span class="pre">import</span> <span class="pre">*</span></code> now gives power users access to:</p>
<ul class="simple">
<li><p><code class="docutils literal notranslate"><span class="pre">bottleneck_distance</span></code>,</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">wasserstein_distance</span></code>,</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">ripser</span></code>,</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">SparseRipsComplex</span></code>,</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">CechComplex</span></code>,</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">CubicalComplex</span></code>,</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">PeriodicCubicalComplex</span></code>,</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">SimplexTree</span></code>,</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">WitnessComplex</span></code>,</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">StrongWitnessComplex</span></code>.</p></li>
</ul>
<p>However, these functionalities are still undocumented.</p>
</li>
<li><p>The <code class="docutils literal notranslate"><span class="pre">gtda.mapper.visualisation</span></code> and <code class="docutils literal notranslate"><span class="pre">gtda.mapper.utils._visualisation</span></code> modules have been thoroughly refactored to improve code clarity, add functionality, change behaviour and fix bugs. Specifically, in figures generated by both <code class="docutils literal notranslate"><span class="pre">plot_static_mapper_graph</span></code> and <code class="docutils literal notranslate"><span class="pre">plot_interactive_mapper_graph</span></code>:</p>
<ul class="simple">
<li><p>The colorbar no longer shows values rescaled to the interval [0, 1]. Instead, it always shows the true range of node summary statistics.</p></li>
<li><p>The values of the node summary statistics are now displayed in the hovertext boxes. A a new keyword argument <code class="docutils literal notranslate"><span class="pre">n_sig_figs</span></code> controls their rounding (3 is the default).</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">plotly_kwargs</span></code> has been renamed to <code class="docutils literal notranslate"><span class="pre">plotly_params</span></code> (see “Backwards-Incompatible Changes” below).</p></li>
<li><p>The dependency on <code class="docutils literal notranslate"><span class="pre">matplotlib</span></code>’s <code class="docutils literal notranslate"><span class="pre">rgb2hex</span></code> and <code class="docutils literal notranslate"><span class="pre">get_cmap</span></code> functions has been removed. As no other component in <code class="docutils literal notranslate"><span class="pre">giotto-tda</span></code> required <code class="docutils literal notranslate"><span class="pre">matplotlib</span></code>, the dependency on this library has been removed completely.</p></li>
<li><p>A <code class="docutils literal notranslate"><span class="pre">node_scale</span></code> keyword argument has been added which can be used to controls the size of nodes (see “Backwards-Incompatible Changes” below).</p></li>
<li><p>The overall look of Mapper graphs has been improved by increasing the opacity of node colors so that edges do not hide them, and by reducing the thickness of marker lines.</p></li>
</ul>
<p>Furthermore, a <code class="docutils literal notranslate"><span class="pre">clone_pipeline</span></code> keyword argument has been added to <code class="docutils literal notranslate"><span class="pre">plot_interactive_mapper_graph</span></code>, which when set to <code class="docutils literal notranslate"><span class="pre">False</span></code> allows the user to mutate the input pipeline via the interactive widget.</p>
</li>
<li><p>The docstrings of <code class="docutils literal notranslate"><span class="pre">plot_static_mapper_graph</span></code>, <code class="docutils literal notranslate"><span class="pre">plot_interactive_mapper_graph</span></code> and <code class="docutils literal notranslate"><span class="pre">make_mapper_pipeline</span></code> have been improved.</p></li>
</ul>
</div>
<div class="section" id="id91">
<h3>Bug Fixes<a class="headerlink" href="#id91" title="Permalink to this headline">¶</a></h3>
<ul class="simple">
<li><p>A CI bug introduced by an update to the XCode compiler installed on the Azure Mac machines has been fixed.</p></li>
<li><p>A bug afflicting Mapper colors, which was due to an incorrect rescaling to [0, 1], has been fixed.</p></li>
</ul>
</div>
<div class="section" id="id92">
<h3>Backwards-Incompatible Changes<a class="headerlink" href="#id92" title="Permalink to this headline">¶</a></h3>
<ul class="simple">
<li><p>The keyword parameter <code class="docutils literal notranslate"><span class="pre">plotly_kwargs</span></code> in <code class="docutils literal notranslate"><span class="pre">plot_static_mapper_graph</span></code> and <code class="docutils literal notranslate"><span class="pre">plot_interactive_mapper_graph</span></code> has been renamed to <code class="docutils literal notranslate"><span class="pre">plotly_params</span></code> and has now slightly different specifications. A new logic controls how the information contained in <code class="docutils literal notranslate"><span class="pre">plotly_params</span></code> is used to update plotly figures.</p></li>
<li><p>The function <code class="docutils literal notranslate"><span class="pre">get_node_sizeref</span></code> in <code class="docutils literal notranslate"><span class="pre">gtda.mapper.utils.visualization</span></code> has been hidden by renaming it to <code class="docutils literal notranslate"><span class="pre">_get_node_sizeref</span></code>. Its main intended use is subsumed by the new <code class="docutils literal notranslate"><span class="pre">node_scale</span></code> parameter of <code class="docutils literal notranslate"><span class="pre">plot_static_mapper_graph</span></code> and <code class="docutils literal notranslate"><span class="pre">plot_interactive_mapper_graph</span></code>.</p></li>
</ul>
</div>
<div class="section" id="id93">
<h3>Thanks to our Contributors<a class="headerlink" href="#id93" title="Permalink to this headline">¶</a></h3>
<p>This release contains contributions from many people:</p>
<p>Umberto Lupo, Julian Burella Pérez, Anibal Medina-Mardones, Wojciech Reise and Guillaume Tauzin.</p>
<p>We are also grateful to all who filed issues or helped resolve them, asked and answered questions, and were part of inspiring discussions.</p>
</div>
</div>
<div class="section" id="release-0-2-1">
<h2>Release 0.2.1<a class="headerlink" href="#release-0-2-1" title="Permalink to this headline">¶</a></h2>
<div class="section" id="id94">
<h3>Major Features and Improvements<a class="headerlink" href="#id94" title="Permalink to this headline">¶</a></h3>
<ul class="simple">
<li><p>The theory glossary has been improved to include the notions of vectorization, kernel and amplitude for persistence diagrams.</p></li>
<li><p>The <code class="docutils literal notranslate"><span class="pre">ripser</span></code> function in <code class="docutils literal notranslate"><span class="pre">gtda.externals.python.ripser_interface</span></code> no longer uses scikit-learn’s <code class="docutils literal notranslate"><span class="pre">pairwise_distances</span></code> when
<code class="docutils literal notranslate"><span class="pre">metric</span></code> is <code class="docutils literal notranslate"><span class="pre">'precomputed'</span></code>, thus allowing square arrays with negative entries or infinities to be passed.</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">check_point_clouds</span></code> in <code class="docutils literal notranslate"><span class="pre">gtda.utils.validation</span></code> now checks for square array input when the input should be a collection of
distance-type matrices. Warnings guide the user to correctly setting the <code class="docutils literal notranslate"><span class="pre">distance_matrices</span></code> parameter. <code class="docutils literal notranslate"><span class="pre">force_all_finite=False</span></code>
no longer means accepting NaN input (only infinite input is accepted).</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">VietorisRipsPersistence</span></code> in <code class="docutils literal notranslate"><span class="pre">gtda.homology.simplicial</span></code> no longer masks out infinite entries in the input to be fed to
<code class="docutils literal notranslate"><span class="pre">ripser</span></code>.</p></li>
<li><p>The docstrings for <code class="docutils literal notranslate"><span class="pre">check_point_clouds</span></code> and <code class="docutils literal notranslate"><span class="pre">VietorisRipsPersistence</span></code> have been improved to reflect these changes and the
extra level of generality for <code class="docutils literal notranslate"><span class="pre">ripser</span></code>.</p></li>
</ul>
</div>
<div class="section" id="id95">
<h3>Bug Fixes<a class="headerlink" href="#id95" title="Permalink to this headline">¶</a></h3>
<ul class="simple">
<li><p>The variable used to indicate the location of Boost headers has been renamed from <code class="docutils literal notranslate"><span class="pre">Boost_INCLUDE_DIR</span></code> to <code class="docutils literal notranslate"><span class="pre">Boost_INCLUDE_DIRS</span></code>
to address developer installation issues in some Linux systems.</p></li>
</ul>