TransformerResamplerMixin notebook, make Labeller.transform return 1D arrays #475
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lewtun
reviewed
Sep 2, 2020
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This is a great notebook @ulupo! I just made some small grammatical suggestions / typo fixing |
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@lewtun thanks for the review! Note to self: Use graphical printed representations of pipelines as per scikit-learn 0.23. Use slicing notation to show intermediate steps. |
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Overall LGTM! Good note to self :) |
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wreise
reviewed
Sep 6, 2020
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Sep 10, 2020
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Oct 9, 2020
* Make path to giotto-tda logo absolute for display on PyPI (#415) * Fix formatting in CONTRIBUTING.rst (#416) * Fix typo in Mapper docs for n_sig_figs (#417) * Adds FlagserPersistence (#339) * Add pyflagser >= 0.4.0 to requirements, GH pages installation instructions, and README.rst * Add FlagserPersistence * Add tests for FlagserPersistence * Add FlagserPersistence to doc index * Add See Also entries in simplicial * Linting in ripser_interface * Update See also for Cubical * Fix max_edge_length docs in other simplicial transformers * Add tests to check max_edge and infinity_values * Fix low infinity value bug and put dimension padding in _utils * Add test for low infinity values * Simplify code in homology/_utils.py Signed-off-by: Guillaume Tauzin <guillaumetauzin.ut@gmail.com> Co-authored-by: Umberto <umberto.lupo@gmail.com> Co-authored-by: Wojciech Reise <reisewojtus@gmail.com> * Introduce `nightly_release` variable in azure-pipelines.yml (#421) * Link Giotto-tda logo to raw.githubusercontent.com * Add FlagserPersistence to the documentation (#425) * Refactor GraphGeodesicDistance (#422) * Refactor GraphGeodesicDistance - Change return type to list for compatibility with homology transformers - Use scipy's shortest_path instead of sklearn's graph_shortest_path - Make clearer rules on the role of zero entries, infinity entries, and non-stored values - Add parameters directed, unweighted, and method - Support masked arrays - Rewrite docstring * Fix See Also in KNeighborsGraph and TransitionGraph * Prevent using FW algorithms when some edges are zero - Work around scipy/scipy#12424 - Introduce user warnings when algorithm cannot be chosen automatically or set to FW - Fix test ground truth - Improves array conversion in GraphGeodesicDistance.transform * Add GraphGeodesicDistance unit tests on sparse/masked array input and more dtypes * Fix Azure CI for nightly releases (#429) * Add *.pyo and *.pyd to .gitignore (#430) Extend list of ignored extensions to other Python bytecode-type files * Modify check_point_clouds to allow for sparse input (#424) * Modify check_point_cloud to allow for sparse input - Allow for sparse input in VietorisRipsPersistence and FlagserPersistence when metric is precomputed. - Fix docstrings to reflect the changes. - Fix some typos and wording issues. * Make docstrings more consistent across simplicial transformers * Fix reference for FlagserPersistence * Remove warning for different point cloud embedding dimensions * Eliminate tests for different embedding dimension warnings * Convert list input to 3D ndarray when possible * Update my email address * Accept sparse inputs even in non-precomputed case for VietorisRips and SparseRips * Cover sparse cases and more metrics in simplicial unit tests Co-authored-by: Umberto <u.lupo@l2f.ch> * Update collaborator email addresses (#435) * Update @lewtun's and @ulupo's emails in CODE_AUTHORS.rst * Update @lewtun's and @ulupo's emails in GOVERNANCE.rst * Refactor _subdiagrams to take all homology dimensions into account (#439) * Fix mmap settings used by joblib.Parallel (#428) * Fix mmap settings used by joblib.Parallel in HeatKernel and PersistenceImage * Add tests * Slice X first inside parallel calls to _subdiagrams * Minor simplifications in plot_diagram * Add @NickSale to CODE_AUTHORS.rst Co-authored-by: Umberto Lupo <umberto.lupo@gmail.com> * Fix axis ranges in `plot_diagram` (#437) * Remove **input_layout kwargs, refactor layouts in plot_diagram - Fix #409 - Fix calculation of the maximum filtration parameter which incorrectly included the homology dimensions - Simplify code * Transpose the output of PairwiseDistance to match scikit-learn convention (#420) * Transpose output shape in PairwiseDistance.transform * Update tests * Simplify _parallel_pairwise Co-authored-by: Umberto Lupo <46537483+ulupo@users.noreply.github.com> * Replace pip install with python -m pip install in docs and Readme (#440) * Remove incorrect assumptions in Filtering (#436) * Remove `_sort` and refactor `filter` in gtda/diagrams/_utils.py Arrays are no longer sorted by lifetime before filtering. * Fix test for Filtering * Improve documentation, begin addressing #233 * Small improvement to `_subdiagrams` * Return figures instead of showing them (#441) * Refactor of plotting API - Make all functions in gtda/plotting return figures (or tuples of figures for betti_surfaces) instead of showing them - `plot` class methods also return figures instead of showing them - `transform_plot` and `fit_transform_plot` still show figures and only return transformed data - Add `plot_params` kwarg throughout to allow user customisability of output figures (subtlety: one of the key can be either "trace" when the output figure only has one trace, or "traces" when it has several) * Suppress user warnings on graph geodesic distance algorithms in tests * Resolve overflow warnings in mapper filter tests * Resolve numpy DeprecationWarning in test_validation * [DOCS] Clarify expected diagram properties to fix #233 (#443) * Allow plot_heatmap to take boolean arguments (#444) * Add pullback cover set labels and partial cluster labels to Mapper hovertext, improve docs (#445) * Add pullback set ID to mapper hovertext * Add partial cluster label to Mapper hovertext * Improve docs for plot_static_mapper_graph and plot_interactive_mapper_graph * Fix tests after changes * Slight wording improvement * Further wording clarification * Make wording on edges even clearer * Refactor igraph.Graph output of Nerve, modify `fit` behaviour of Nerve, add `store_edge_elements` kwarg to Nerve and make_mapper_pipeline, add Nerve and ParallelClustering to docs (#447) * Refactor igraph.Graph output, add Nerve and ParallelClustering to docs, add store_edge_elements kwarg to Nerve and make_mapper_pipeline - Store node metadata not as a graph-level dictionary, but as vertex attributes accessible by graph.vs[attr_name][node_id] or graph.vs[node_id][attr_name] for attr_name in ["pullback_set_label", "partial_cluster_label", "node_elements"] - Remove "node_id" from node attributes as it always coincided with the igraph.Graph node number anyway. - Automatically store sizes of intersections as edge weights, accessible by graph.es["weight"]. - Add "store_intersections" kwarg to Nerve and make_mapper_pipeline to allow storing indices of node intersections as edge attributes, accessible via graph.es["edge_elements"]. - Simplify logic of Nerve.fit_transform code - Change the attributes stored by Nerve.fit. Now the entire graph is stored as graph_ instead. - Improve documentation of make_mapper_pipeline - Expose ParallelClustering and Nerve in __init__ and docs. - Adapt tests, mapper quickstart notebook, and mapper plotting functions. * Add two tests for the behaviour of store_edge_elements and min_intersection * Remove check for shape of `layout` in _calculate_graph_data `layout` can only be a string or a callable, not an ndarray * Improve test coverage of mapper visualization modules * Create tests for plot_betti_surfaces and plot_betti_curves * Add plotly_params to remaining plot methods in diagrams/representations, missed out in #441 * Fix some linting and docstrings * Minor improvements * Avoid shadowing range function in plot_diagram * Fix minimum birth bug in `plot_diagram` (#449) * Fix bug introduced in 4bc90b2 np.max should have been np.min in plot_diagram for minimum birth and death calculation * Clean/simplify plot_diagram further to be more ready for extended persistence and better behave under plotly HTML autoscaling * Make `store_edge_elements` work with MapperPipeline.get_mapper_params and MapperPipeline.set_params, missed out in 4bc90b2 * Remove displayed SegmentLocal from gif hyperlink in classifying_shapes example notebook (#448) * Remove displayed SegmentLocal from classifying_shapes example notebook * Fix doc typos * Pybind11 quick fix (#451) * Fix pybind11 broken master pybind11 checkout version v2.5.0, some issues are observed on master Signed-off-by: julian <julian.burellaperez@heig-vd.ch> * Fix bug in use of homology_dimension_ix with samplings_, rename homology_dimension_ix (#452) * Rename homology_dimension_ix to homology_dimension_idx, fix bug * Add normalization of persistence entropy (#450) * Add normalization of persistence entropy via `normalize` kwarg in gtda.diagrams.PersistenceEntropy * Use entropy from scipy.stats in gtda.diagrams.PersistenceEntropy, gtda.time_series.PermutationEntropy and gtda.mapper.Entropy * Rename _entropy hidden method in gtda.diagrams.PersistenceEntropy * Add tests for normalize=True * Add `fill_nan_value` kwarg to gtda.diagrams.PersistenceEntropy - See #450 (comment) - Adapt pipeline tests to use this kwarg Co-authored-by: Umberto Lupo <umberto.lupo@gmail.com> * Fix y-axis in HeatKernel plots, add default titles to plot methods (#453) * Fix y-axis in HeatKernel.plot * Add titles to figures generated via plot_heatmap in plot class methods * PEP8 E133 improvements * Refactor gtda/diagrams (#454) * First attempt at fix of #438 * Fix y-axis in `PersistenceImage` plots, extending #453 * Represent multiplicity of persistence pairs in hovertext in `plot_diagram` * Change reflect mode of `gaussian_filter` to "constant" from "reflect" Affects `HeatKernel` and `PersistenceImage` * Fix `PersistenceLandscape` plot method - Only the figure corresponding to the first seen homology dimension was returned - Output is now a figure with subplots, a main title, and one subtitle per plot (homology dimension) * Improve tests for plot methods in gtda.diagrams.representations Cover use of `plotly_params` * Minor docstring linting * Miscellaneous docstring improvements in gtda/diagrams * Fix validation dictionary for `metric_params` in the case of `PersistenceImage` * Change default value of `order` in Amplitude, from 2. to None (vector features) * Change meaning of default None for `weight_function` in `PersistenceImage` - ``None`` corresponding the identity means that there really is a non-trivial weighting in that case. Semantically, this does not seem correct ("None" should mean no weighting at all) * Improve code style and clarity in plot methods in gtda.diagrams.representations * Refactor gtda/diagrams/_metrics.py to fix several bugs - Change computation of heat/persistence image distances and amplitudes to yield the continuum limit when `n_bins` tends to infinity. - Make `sigma` in persistence-image-- and heat-kernel--based representations/distances/amplitudes measured in the same units as the filtration parameter (not in pixels), thus decoupling its effect from the effect of `n_bins`. Also change the default value in PairwiseDistance, Amplitude, HeatKernel and PersistenceImage from 1. to 0.1. - Remove trivial points from diagrams before creating a sampled image in `heats` and `persistence_images`. This ensures in particular that the trivial points really give no contribution regardless of the weight function used for persistence images. - Finish fixing #438 and similar issues with PairwiseDistance when the metric is persistence-image--based. - Ensure `silhouettes` does not create NaNs when a subdiagram is trivial. - Change default value of `power` in `silhouette_amplitudes` and `silhouette_distances` to 1., to agree with Amplitude and PairwiseDistance docs. - Fix use of np.array_equal in `persistence_image_distances` and `heat_distances` -- so far the boolean check for equal inputs always failed due to the in-place modifications of `diagrams_1`. - No longer store weights in `effective_metric_params_` attribute of PairwiseDistance and Amplitude when the metric is persistence-image--based. - Remove _heat from gtda.diagrams._metrics. - Remove identity from gtda.diagrams._utils and make default `weight_function` kwargs equal to np.ones_like everywhere to agree with default in `PersistenceImage`. - Other style improvements (variable names, linting) * Fix trace name when homology dimension is np.inf in `BettiCurve` and `Silhouette` * Adapt `test_all_pts_the_same` to new behaviour of `heats_` in gtda.diagrams._metrics * Improve test coverage of `Amplitude` and `PairwiseDistance` - Make sure silhouettes and persistence images are covered throughout - Cover `order` parameter throughout * Add test of zero `weight_function` for `PersistenceImage` * Make behaviour of `Scaler.fit` when the metric is persistence image the same as `Amplitude` Accordingly add more combinations of metrics and metric_params in tests for Scaler * Delete never-used `_matrix_wrapper` and `_arrays_wrapper` functions * Remove `_pad` from gtda.diagrams._utils as it is never used * Make `copy=True` in calls to check_diagrams in Scaler.transform and Scaler.inverse_transform * Make `homology_dimensions_` attributes tuples instead of lists, with integers when possible * Improve code style * Hard-code zero array outputs by `heats` and `persistence_images` when step sizes are zero * Add `homology_dimensions` kwarg to `_bin` Achieves beautification of self._samplings and self.samplings_ (ints shown instead of floats) in several transformers (and saves some computation) * Adapt choices of `min_values`, `max_values` and `sigma` in hypothesis-based tests New meaning of sigma led to overflow issues in existing tests. * Make all homology dimensions equal in `test_hk_big_sigma` Also extend this test to `PersistenceImage`, and rename it accordingly * Cover use of `plotly_params` kwarg in diagram preprocessing classes plot methods * Extract some common logic from plot methods in gtda.diagrams.representations * Silence expected warnings from image transformers in test_common * Implement @wreise's suggestion to abstract away sorting and integer conversion of fit hom dims * Add tests for `Amplitude` and `PairwiseDistance` to check that a zero weight function yields identically zero amplitudes/distances. * Refactor `_subdiagrams` to throw informative errors on unfulfilled input properties * Bump package dependencies to latest available in conda (#457) * Bump dependencies to latest available in conda (or PyPI if conda unavailable) * [CI] Bump pip version in .azure-ci/docker_scripts.sh * Plot infinite deaths in plot_diagrams (#461) * Plot infinite deaths in plot_diagrams - Dynamically establish a certain value greater than the maximum observed death as the y-coordinate of infinity - Plot points with infinite death as having this death value - Plot a horizontal dashed line to show the position of infinity * Add first draft of FlagserPersistence notebook * Fix errors with use of homology_dimensions kwarg in FlagserPersistence - Implementation was incorrect in cases where minimum in homology_dimensions is greater than 1 - Implementation would crash whenever `flagser_weighted` does not return a list of size self._max_homology_dimension + 1 - self._min_homology_dimension, as can happen with small graphs * Fix #92 Document removal of one infinite bar in simplicial transformers * Polish up classifying_shapes notebook * Remove null cell from vietoris_rips_quickstart * Upload clique complex filtration images * Crop image * Crop and colour images * New versions of clique complex * New notebook version * Test a small version of a png * Update notebook and pngs * Remove plotly code * Add SVGs for directed flag complex illustration * Correct one SVG * Add color fill * Fix color fill * Reorient one triangle * Finish up notebook * Remove some PNGs * Delete legacy image * More "correct" name for a PNG * Reflect name change on notebook * LaTeX formatting * Add reference to ripser.py tutorials * Fix handling of COO matrices by ripser mirroring scikit-tda/ripser.py#104 (#465) * Update gudhi bindings to latest changes on August 2020 (#468) * Pull latest changes on Gudhi-devel:giotto * Add Eigen as a submodule Eigen is now required for latest Gudhi version * Add Eigen for gudhi modules that require it * Update get_filtration and get_skeleton with the new Gudhi API * Update ccache in CI * Fix type issue for get_persistence in simplex_tree * Fix persistence in periodic cubical complex * Fix simplex tree * Fix cubical complex * Beautify setup.py * Move towards fixing #307 in azure_pipelines.yml (still not addressing docker_scripts.sh) Signed-off-by: julian <julian.burellaperez@heig-vd.ch> Co-authored-by: Umberto Lupo <umberto.lupo@gmail.com> * Change DISTNAME back form "giotto-tda" to 'giotto-tda' in setup.py (#470) Avoids uploading nightly distributions accidentally to PyPI from CI as happened on 28.08.2020 * Change title as suggested by @lewtun, fix GitHub capitalization in all notebooks * Unify postprocessing of diagrams between simplicial and cubical, remove one H0 inf bar in cubical * Fix imports, reinstate reshape * Fix slicing and tests * Document removal of infinite bar in 0D * Improve readability * Place _replace_infinity_values and _pad_diagram in scope of _postprocess_diagrams * Forfeit use of n_jobs in _postprocess_diagrams Favour use of purely in-place operations by a logic replacing _pad_diagram * Linting * Remove unused joblib imports from homology/_utils.py * Ignore SparseRipsPersistence in code cells as suggested by @lewtun * LaTeXify indices as suggested by @lewtun * Fix typos * Fix typo * Convert pycairo note from inline comments to markdown text * Implement some of @lewtun's suggestions for classifying shapes notebook * Migrate general persistence diagram discussion to vr notebook, create "General API" section In partial fulfillment of @lewtun's review suggestions * Fix VR notebook and add explanation of homology_dimensions parameter * Make PyPI nightly uploads more robust to changes in quote types (#471) * Make PyPI nightly uploads more robust to changes in quote types Look for both single and double quotes when modifying DISTNAME in setup.py * Reinstate double quotes in setup.py * Change sed -i to sed -i.bak in macOS Azure jobs (#472) * Adds WeakAlphaPersistence (#464) * Add WeakAlphaPersistence (gtda.homology.simplicial) * Change relative order of simplicial transformers * Add tests of correctness of VietorisRipsPersistence and WeakAlphaPersistence (circle PH) * Adapt to sklearn 0.23 API in test_common Silences warnings * Improve docstrings in gtda.homogy (type of X in fit and transform, and type of Xt in plot) * Avoid dtype search and always make a float array * Adapt WeakAlphaPersistence to changes * Some style consistency * Fix small bug with plot_diagrams Trivial points were not excluded from computation of plot ranges * Bump pyflagser version in requirements * Improve docs for VietorisRipsPersistence by explaining how precomputed input is handled * Improve writing following @lewtun's comments, fix hyperlinks in preparation for merge * Add a regression test for FlagserPersistence * Introduce a `reduced_homology` kwarg to toggle or not removal of infinite H0 bar * Change default value of nan_fill_value in PersistenceEntropy to -1 (#474) * Change default value of nan_fill_value in PersistenceEntropy to -1. * Remove false URL in README (#476) * Fix read-only error analogous to #427 in Amplitude and PairwiseDistance (#481) * Improve naming of parallelism tests for PersistenceImage and HeatKernel * Extend #428 to Amplitude and PairwiseDistance, add regression test, improve edge case handling in _metrics.py * Cover n_jobs > 1 in test_features_representations.py * Fix formatting issues in notebooks (#482) * Add persistent homology of graphs notebook to docs * Add Vietoris-Rips gif to examples/images and use it instead of Medium links notebooks * Change single backticks for monospace to double backticks, recommended for Markdown * Fix a parenthesis in classifying_shapes.ipynb * Add bindings for collapser, refactor ripser_interface (#469) * Add bindings for collapser * Add collapse_edges kwarg to ripser to enable edge collapser * Add tests for the collapser bindings * Add tests for ripser with edge collapse * Add regression test for #465 * Refactor ripser_interface to simplify code, improve lexsort logic, and improve detection of sparse matrix shape * Disable computation of cocycles by default Signed-off-by: julian <julian.burellaperez@heig-vd.ch> Co-authored-by: Umberto Lupo <umberto.lupo@gmail.com> * Enable edge collapse in VietorisRipsPersistence (#483) * Enable edge collapse in VietorisRipsPersistence Also cover coefficient different from 2 in tests of collapser * Cover collapse_edges kwarg in simple VietorisRipsPersistence tests * Rename TakensEmbedding to SingleTakensEmbedding, introduce new TakensEmbeding transformer on collections and a function for time-delay embedding parameter optimization, replace "width" parameter with "size" in Labeller and SlidingWindow, fix bug with Labeller.resampler when n_steps_future >= size - 1 (#460) * Extract time delay embedding logic into a _time_delay_embedding function in the new file gtda.time_series._utils * Rename TakensEmbedding to SingleTakensEmbedding * Extract and expose code for finding optimal Takens embedding parameters, as a new takens_embedding_optimal_parameters function * Simplify logic of resample method of SingleTakensEmbedding and SlidingWindow * Improve tests for Stationarizer * Fix bug in Labeller.resample when n_steps_future >= width, add test to cover this scenario * Allow zero width (meaning 1 point) in SlidingWindow and Labeller * Add simple test for invalid width in Labeller * Faster implementation of _slice_windows in SlidingWindow and of SlidingWindow.transform * Make SlidingWindow.slice_windows public, add test * Rename "width" parameter of Labeller to "size", addressing #94 * Rename "width" parameter of SlidingWindow to "size", addressing #94 * Create new TakensEmbedding function to deal with collections of univariate or multivariate time series * Support list of time series input in gtda.time_series.embedding by means of a new check_collection function in gtda.utils.validation * Fix typos in glossary.tex * Remove plot method from SlidingWindow and place it in new TakensEmbedding * Refactor Lorenz attractor notebook following API changes involving TakensEmbedding and SlidingWindow * Use check_collection in CubicalPersistence * TransformerResamplerMixin notebook, make Labeller.transform return 1D arrays (#475) * Add notebook on TransformerResamplerMixins and time series forecasting with sliding windows + topology * Change return shape or Labeller.transform to 1D * Fix Labeller docstring following change in #475 * Modify `PlotterMixin.transform_plot` to give a dictionary to the call to `plot` (#484) * Fix sample numbers in automatically-generated plot titles when using `transform_plot` * Add test for Takens to use fit_transform_plot * Remove papermill version from azure-pipelines Co-authored-by: wreise <wojciech.reise@epfl.ch> * removed check_collection from docs * Fix references in takens and simplicial * Change todo in weak alpha filtration reference to the section name, remove empty line from release * Add `mode` kwarg to KNeighborsGraph, refactor input-output formats in gtda.graphs, turn outputs of KNeighborsGraph and TransitionGraph into asymmetric adjacency matrices (#478) * Add mode kwarg to KNeighborsGraph, allow for list input in gtda.graphs, return lists instead of ragged arrays * Turn output of TransitionGraph into a directed 0-1 adjacency matrix * Docstring improvements in gtda.graphs * Add check_collection again * Reference ripser [1] * Move the references before the full stops * Replace missing glossry entries with TODOs, following Umberto's comment * Docstring improvements following @gtauzin's review * Tiny wording fix * Improve docstring following @gtauzin's comment * Add missing references * Flag weak_alpha_complex as missing entry * Reference in the documentation * Add a target for testing notebooks in the docs * Make html does not fail on missing versions * Capitalize "Euclidean" in glossary.tex * Remove spaces after references, check that publication names are in italic * Add check_collection to gtda/utils/__init__.py (#491) * Add check_collection to gtda/utils/__init__.py * Improve paths in some tests * Add option to contract Mapper vertices when pairs are in a subset relation, change layout in interactive mode (#456) * Add contract_nodes kwarg to Nerve - When True, igraph.Graph's contract_vertices is employed together with the limit flow by a mapping with fixed points to execute the contraction - Add a test for this option * Filter out nodes from same pullback set when checking intersections, to increase performance * Ensure that setting min_intersection < 1 does not lead to fully connected graphs * Remove unused variable name in ParallelClustering * Make nerve parameters interactive in plot_interactive_mapper_graph, refactor get_widgets_per_params, change layouts * Improve method_to_transform code and docstring * Small improvements to transformer_from_callable_on_rows * Linting throughout gtda.mapper * Remove effective_metric_params_ from Eccentricity * Remove unused import and sort the remaining ones * Provide an explicit name for the substituition * Copy images from examples to notebooks * Remove the use of imgonverter, change the logo back to svg and add supported image types list * Name for substitution did not work * Wording improvements in persistent_homology_graphs.ipynb * Typo fix in notebook * Fix variable name error in GraphGeodesicDistance.transform * Extend Padder and Inverter to greyscale images (#489) * Extend Padder to greyscale images * Extend Inverter to greyscale images Signed-off-by: Guillaume Tauzin <guillaumetauzin.ut@gmail.com> Co-authored-by: wreise <wojciech.reise@epfl.ch> * Add notebook for topological time series classification to examples (#458) * Add notebook for topological time series classification example * Add Takens embedding GIF to images directory * Add gravitational wave dataset Co-authored-by: Umberto Lupo <umberto.lupo@gmail.com> * Fix links to time series classification notebook by @lewtun * Move datasets.py and gravitational-wave-signals.npy to new data subfolder, and rename them * Fix errors in check_point_clouds docstrings * Try easier paths in See also Test for @wreise * Create captions across all notebooks * Small wording improvement in persistent_homology_graphs.ipynb * Change the path (sub)package in the index * Implement double backticks consistently * Simplify some captions * Slightly reduce size of plots by plot_point_cloud * Fix some errors in make_mapper_pipeline docs * Fix typo in Nerve docs * Change citation style for consistency * Remove new lines in array printouts in docs * Make citation style more consistent throughout * Reorder notebooks, modularize Makefile * Reformat the references * More link and backtick fixes in mapper_quickstart * More RST fixes in notebooks * Fix linting * Fix an error in WeakAlphaPersistence Notes * Fix URLs for GUDHI * Fix TakensEmbedding docstrings * Linting * Try changing some SVG attributes for better display * Further SVG improvements * Update CODE_AUTHORS.rst (#497) * More Mapper tests, small change to `max_fraction` in FirstSimpleGap and FirstHistogramGap (#412) * Add first tests for plot_interactive_mapper_graph * Change deprecated 'overflow_y' to 'overflow' property in_logging, and remove unnecessary warning catching * Avoid name clashes with Python built-ins throughout mapper/tests * Slightly change meaning of `max_fraction` in FirstSimpleGap and FirstHistogramGap Make the default 1. instead of None, and give it a simpler interpretation: (the floor of) max_fraction * n_samples is the maximum number of clusters the algorithm can return * Implement a looser criterion for the hk_pi_big_sigma test Co-authored-by: Umberto Lupo <umberto.lupo@gmail.com> * Fix some warnings seen in tests (#498) - `continuous_updates` is deprecated from ToggleButton - `np.stack` should not take generators - should explicitly pass dtype=object for ragged arrays * Add the giotto-tda icon in the browser tab (#500) (favicon) * Add NumberOfPoints (#496) * Add NumberOfPoints * Make See alsos more consistent throughout diagrams.features Sined-off-by: Guillaume Tauzin <guillaumetauzin.ut@gmail.com> Co-authored-by: wreise <wojciech.reise@epfl.ch> Co-authored-by: Umberto Lupo <umberto.lupo@gmail.com> * Fix and improve validate_params (#502) * Fix validate_params bug and improve behaviour when both numeric and list-like types are allowed * Add a test * Fix mistake in validate_params docs * Pybind11 as a git submodule (#459) * Add MODULE keyword in CMakeLists.txt to explicitly show expectation * Update collapser to latest standard in the CMake file * Add pybind11 as a submodule * Remove downloading pybind11 from setup.py Signed-off-by: julian <julian.burellaperez@heig-vd.ch> Co-authored-by: Umberto Lupo <umberto.lupo@gmail.com> * Fix metric_params documentation in KNeighborsGraph * Improve ripser bindings performance (#501) * Update ripser & collapser bindings to allow pass by reference with numpy * Update making the distance matrix triangular more memory friendly * Remove unnecessary dict inherited from ripser.py cython Signed-off-by: julian <julian.burellaperez@heig-vd.ch> * Add MNIST image classification example notebook (#477) * Add MNIST image classification/full blown ML example notebook Signed-off-by: Guillaume Tauzin <guillaumetauzin.ut@gmail.com> Co-authored-by: Lewis Tunstall <lewis.c.tunstall@gmail.com> Co-authored-by: Umberto Lupo <umberto.lupo@gmail.com> * Add ComplexPolynomial (#479) * Add ComplexPolynomial Signed-off-by: Guillaume Tauzin <guillaume.tauzin@inait.ai> Co-authored-by: Umberto Lupo <umberto.lupo@gmail.com> Co-authored-by: wreise <wojciech.reise@epfl.ch> * Fix precomputed behaviour in KNeighborsGraph (#506) * Fix precomputed behaviour in KNeighborsGraph - Avoid warnings when metric is passed as 'precomputed' - Fix errors in docstrings and improve wording - Improve tests * Fix #499 by covering case of list input in CubicalPersistence.fit (#503) * Improve memory use in ripser_interface (#507) Implement suggestions in #501 (comment) - Use scipy's squareform function for fast extraction of the upper diagonal part of dm * Add DensityFiltration (#473) Signed-off-by: Guillaume Tauzin <guillaumetauzin.ut@gmail.com> Co-authored-by: Umberto Lupo <umberto.lupo@gmail.com> * Add metaestimators subpackage with CollectionTransformer meta-estimator (#495) * Add gtda/metaestimators with CollectionTransformer meta-estimator * Fix docstring for make_mapper_pipeline * Cchange parallel_backend_prefer default to None in ParallelClustering and make_mapper_pipeline * Cross-reference two time series notebooks with See also * Improve time series classification notebook by making use of CollectionTransformer * Temp fix for macOS CI failures by preventing automatic brew cleanup (#513) Also make mapper tests more lenient to reduce number of flaky tests Co-authored-by: ulupo <umberto.lupo@googlemail.com> * Add a curves subpackage and a StandardFeatures transformer to extract features from them (#480) * Add curves subpackage with StandardFeatures * Reshape output of PersistenceLandscape so that it's a multi channel curve * Add curves to main init and to rst docs * Add Feature extraction subtitle in curves.rst * Split simplicial homology into undirected and directed subsections * Fix typo in validate_params * Raise deadlines for some mapper tests * Remove notebook tests even in macOS jobs Signed-off-by: Guillaume Tauzin <guillaume.tauzin@inait.ai> Co-authored-by: Umberto Lupo <umberto.lupo@gmail.com> * Add curves.Derivative (#492) * Add curves.Derivative * Fix curves.StandardFeatures docs Signed-off-by: Guillaume Tauzin <guillaume.tauzin@inait.ai> Co-authored-by: Umberto Lupo <umberto.lupo@gmail.com> Co-authored-by: wreise <wojciech.reise@epfl.ch> * Raise test coverage and make ParallelClustering clusterer parameter required (#508) * Improve test coverage of mapper visualization tools * Make pandas part of test requirements in setup.py * Add pandas installation in Linux Azure jobs * Avoid notebooks checks even in macOS unless notebooks_checks is true * Make clusterer a required parameter in ParallelClustering, add ParallelClustering tests * Change kind of error for bad transformers in CollectionTransformer * Improve check_diagrams and its tests * Use validate_params in plot_point_cloud * Cover plotting of diagrams with infinite deaths in simplicial tests * Prepare for v0.3.0 release (#516) * Bump version to 0.3.0 * Add release notes * Minor corrections in notebooks Co-authored-by: wreise <wojciech.reise@epfl.ch> Co-authored-by: Guillaume Tauzin <guillaumetauzin.ut@gmail.com> Co-authored-by: Wojciech Reise <reisewojtus@gmail.com> Co-authored-by: Wojciech Reise <32167173+wreise@users.noreply.github.com> Co-authored-by: Umberto <u.lupo@l2f.ch> Co-authored-by: Nicholas Sale <nicholas.j.sale@gmail.com> Co-authored-by: MonkeyBreaker <julian.burellaperez@heig-vd.ch> Co-authored-by: REDS institute <reds-heig@users.noreply.github.com> Co-authored-by: lewtun <lewis.c.tunstall@gmail.com> Co-authored-by: wreise <wojciech.reise@epfl.ch> Co-authored-by: ulupo <umberto.lupo@googlemail.com>
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Adds a notebook explaining about the TransformerResamplerMixin and giotto pipeline API in the context of doing time series forecasting.
Also introduces a breaking change by making the output of
Labeller.transforma 1D array instead of a column array.