Tests for plotting functions and methods, other increases in test coverage #384

ulupo · 2020-03-30T07:35:52Z

Reference issues/PRs
Addresses several remaining gaps in coverage (but still not the ones indicated in #182).

Types of changes

Bug fix (non-breaking change which fixes an issue)
New feature (non-breaking change which adds functionality)
Breaking change (fix or feature that would cause existing functionality to change)

Description

Adds tests for all PlotterMixins or other classes containing plot methods. These are just dummy tests implementing trivial calls to fit_transform_plot or plot.
Updates .coveragerc file so that gtda.images is included in coverage reports, gtda.utils._docs and gtda.utils.intervals are excluded, and all test directories are excluded.
Adds simple tests for Filtering.
Adds simple shape tests for BettiCurve and PersistenceLandscape.
Minor typo fixes and other code style improvements.

Checklist

I have read the guidelines for contributing.
My code follows the code style of this project. I used flake8 to check my Python changes.
My change requires a change to the documentation.
~~I have updated the documentation accordingly.~~
I have added tests to cover my changes.
All new and existing tests passed. I used pytest to check this on Python tests.

- Rename test_features -> test_features_representations - Create parametrized dummy tests for fit_transform_plot method of transformers in representations.py - Improve structure and range of tests in test_preprocessing in a similar way - Create dummy tests of shape for BettiCurve and PersistenceLandscape - Linting and code style changes elsewhere

ulupo · 2020-03-30T07:46:38Z

@wreise @gtauzin one downside of having plot methods which not only create figures but also show them is that locally running tests causes one tab per plot to be automatically opened by my browser. Have you encountered/resolved this?

ulupo · 2020-03-30T08:49:03Z

The failures in the manylinux builds seem to be related to a problem with the boost website. I wouldn't worry too much about it yet, hopefully it will be up and running soon.

gtda/diagrams/representations.py

gtda/diagrams/tests/test_features_representations.py

wreise · 2020-03-30T08:04:44Z

gtda/diagrams/tests/test_features_representations.py

+
+
+@pytest.mark.parametrize('hom_dim_ix', [0, 1])
+def test_fit_transform_plot_1(hom_dim_ix):


Would you mind giving a more descriptive name, or a comment for future selves?
If i understand correctly, we plot a single homology dimension.

Some classes have the homology_dimension_ix parameter, others homology_dimensions. I could not find a short convincing name, but test_fit_transform_plot_one_hom_dim for this one, and test_fit_transform_plot_single_many_hom_dims for the next, could work with me.

gtda/diagrams/tests/test_features_representations.py

ulupo · 2020-03-30T08:59:13Z

gtda/diagrams/representations.py

-                        f'All homology dimensions must be in '
-                        f'self.homology_dimensions_ which is '
-                        f'{self.homology_dimensions_}. {dim} is not.')
+                        f"All homology dimensions must be in "


I'm starting to use these quotation marks consistently in sentence-like strings as they are safe when apostrophes have to be used inside as well.

- Rename some test functions - Implement a solution to the automatic tab opening problem, based on setting the default value of plotly.io.renderers in test files

ulupo · 2020-03-30T09:36:52Z

@gtauzin this is ready to merge and the new coverage percentage is between 93% and 94%. Due to issues at the boost website's end (Forbidden errors when following the tar.gz download link), we are delaying merging until the latter works as expected again.

* Add twine check to CI, attempt fix in README (#379) * Tests for plotting functions and methods, other increases in test coverage (#384) * Vectorization2 (#378) * Fix azure on windows (#388) * Allow more general input to ripser when metric='precomputed', improve/refactor check_point_clouds and add tests (#386) * Add citing entry to README.rst and doc/faq.rst (#389) * Fix markdown subsection formatting (#390) * Prepare release 0.2.1 (#391) Co-authored-by: Anibal M. Medina-Mardones <ammedmar@gmail.com> Co-authored-by: REDS institute <reds-heig@users.noreply.github.com> Co-authored-by: Guillaume Tauzin <guillaumetauzin.ut@gmail.com>

@wreise

* Add temporary patch to azure-pipelines.yml (#369) Get around Azure DevOps issues by following a suggestion by Sean Law: https://twitter.com/seanmylaw/status/1239332444865773568 * Remove metatransformers (#368) Signed-off-by: Guillaume Tauzin <guillaumetauzin.ut@gmail.com> * Extend plotting functionalities to more transformers and other modules (#362) * start plotting for images * Add the image plotting file * Add an imagePlotMixin subclassing the ImagePlot for theimage submodule, add persistenceImage plots * Add plot_persistence_image to the package * Add plotting functionalities to filtrations in the image module and forbetticurves * Preprocessing covered by plots * Add basic plotting functions for different vectorisation methods * Incorporate plotting for diagram representations and images/preprocessing * Change the docstring for ImagePlotterMixin and add fail on 3d images * Correct the samplingsin features, and titles * Small wording fix * Change dosctrings for plot in diagrams/features * Fix typo in variable name * Change plotting of heatkernel to the same as persistenceimage, use samplings * Cast images to floats, so as they can be always plotted * Add a Homology and PointCloud Mixin * Use the new PlotMixins * Add todo in Forgetdimensions, in relation to plotting * Add plotting to point_cloudsrescaling, correctimports * Wording changes * Correct n_values to n_bins and add 's' to n_homologydimensionS * Correct spelling mistakes * Change the name of ...PlotterMixin to ...Plotter * Make SlidingWindowEmbedding a PointCloudPlotter * Fix typoin import * Fix linting * Correct the way the distance matrices are displayed, and add the SlidingWindow.plot method * Change behaviour of transform_plot to return the 0-th sample * Docstring fixes * Create diagrams/representations.py, and migrate amplitude to features.py This change reflects the new documentation structure and the difference now drawn there between feature creation for diagrams (scalars) and vector representations/vectorizations. These changes are mostly invisible to the user. * Remove unused identity function * Rename HomologyPlotter as DiagramPlotter * Add homology_dimensions kwarg to DiagramPlotter, revise docstring * Small docstring fixes * Try adding triggers in the yaml * Remove excessive blank line * Revert "Change behaviour of transform_plot to return the 0-th sample" This reverts commit 2fa0209. * Fix docstring for PlotterMixin * Further docstring refinements in `PlotterMixin` * Remove `DiagramPlotter`, differentiate between implementations of `plot` Also make plot methods static in classes in `gtda.homology` and in ForgetDimensino * Correctly import PlotterMixin * Correct the plotting in the lorentz notebook * Remove PointCloudPlotter and refine plot methods for point clouds * Thorough refactoring of plotting API - Eliminate some top-level functions for diagram representations, leave only betti_curves and betti_surfaces - Remove ImagePlotter mixin and plotting/_plot.py, create top-level plot_heatmap function - Rename plotting/diagrams.py to plotting/diagrams_representations.py - Rename plotting/image.py to plotting/images.py - Rename plotting/homology.py to plotting/persistence_digrams.py - Fix problem with Binarizer coming from now-removed normalize parameter - Refactor notebooks to use plotting API - MIscellaneous small changes elsewhere The philosophy behind the file changes in gtda/plotting is that file names now reflect data structures and do not try to follow the names of subpackages like diagrams, image, etc. * Grammar * Fix default parameter for homology_dimension_ix in HeatKernel * Change plot_diagrams to allow ForgetDimension to work * Allow _subdiagrams to better handle infs of different kind * Add inline comment for future selves * Write check_diagrams docstring and make it convert to float, revert previous changes to _subdiagrams * Pass copy=False to astype in check_diagrams Co-authored-by: Guillaume Tauzin <guillaume.tauzin@epfl.ch> Co-authored-by: Guillaume Tauzin <guillaumetauzin.ut@gmail.com> Co-authored-by: Umberto Lupo <46537483+ulupo@users.noreply.github.com> Co-authored-by: Umberto <u.lupo@l2f.ch> * Glossary entry: distance, inner products & kernels (#370) * Update P landscapes * Add distances, inner products and kernels glossary entry * Update after W's comments Signed-off-by: ammedmar <ammedmar@gmail.com> Co-authored-by: ammedmar <anibal@medina-mardones.com> * Add reference for images submodules (#372) * Add reference for images submodules Signed-off-by: Guillaume Tauzin <guillaumetauzin.ut@gmail.com> * Move hera to submodule (#371) * delete hera repository * Add hera as submodule * Remove unnecessary branch for submodule * Add parameter max_bids_per_round when computing wasserstein * Fix an inconsistency with wasserstein implementation In Wasserstein, by default epsilon_common_ratio is equal 5, and it can be equal 0, which our bindings did not allow * Add test for python bindings of wasserstein Add method to retrieve what wasserstein consider to be infinity as an input * Add test for python bindings of bottleneck * Add fixes done by author after I contact him Signed-off-by: julian <julian.burellaperez@heig-vd.ch> * Miscellaneous refinements to GitHub pages (#363) * Remove code fetching logo as it is now stored in doc/images * Fix logo in examples directory * Partial rewriting of contributing page * Remove instructions for building documentation * Simplify path in Makefile * Remove documentation job in azure-pipelines.yml * Add @wreise to authors in doc/conf.py * Remove paper citation from FAQ * Rename Glossary to Theory Glossary * Linting in images subpackage * Add PlotterMixin to base.rst * Update FAQ * Improve README with pointers to GH pages * Implement @wreise's review suggestions * Fix links to svgs * Remove remaining mentions of plotting.py * Rename basic to tutorials and advanced to examples * Fixes in jupyter notebooks in examples folder * Add plotting in docs * Fixes in glossary * Correct the VBox display * Add TODO instead of empty reference in Cech docstring * Fix references in docstrings * Reintroduce scrollZoom in mapper_quickstart * Improve landing page and move Lewis' blog post to notebooks/tutorials.rst Co-authored-by: Wojciech Reise <reisewojtus@gmail.com> * Pcs different sizes (#318) * Add a check_point_clouds fct in utils/validation, and apply it throughout classes in ``homology/simplicial.py`` * Adapt and add tests * Make the output of ImageToPointCloud variable in size, and adjust the tests (modify the expected values) * Add mapper and utils to global __init__ * Revise use of check_array throughout * Linting and code clarity improvements throughout * Fix some incorrect links to GH pages * Revert to trivial slicing in transform_plot method of PlotterMixin, to cover case of list input Co-authored-by: Umberto <u.lupo@l2f.ch> * Release of v0.2.0 (#375) * Bump version to 0.2.0, add release notes * Improve LaTeX rendering in mapper_quickstart.ipynb * Add @rth as a contributor and code author for v0.2.0 (#376) * Add @rth to code authors and list of contributors for v0.2.0 * [WIP] Add twine check to CI, attempt fix in README (#379) * Add twine check to azure-pipelines.yml * Fix formatting and duplicate issues in README.rst * Tests for plotting functions and methods, other increases in test coverage (#384) * Remove images subpackage from code omitted from coverage * Add tests for Filtering class * Add tests in diagrams subpackage, linting - Rename test_features -> test_features_representations - Create parametrized dummy tests for fit_transform_plot method of transformers in representations.py - Improve structure and range of tests in test_preprocessing in a similar way - Create dummy tests of shape for BettiCurve and PersistenceLandscape - Linting and code style changes elsewhere * Add fit_transform_plot test for GraphGeodesicDistance * Add fit_transform_plot tests in gtda.homology * Fix typo in voids_on_the_plane notebook * Add fit_transform_plot tests for images subpackage * Add fit_transform_plot tests for point_clouds subpackage * Add test for SlidingWindow.plot * Linting * Exclude gtda.utils._doc and gtda.utils.intervals from coveragerc * Implement @wreise's suggestions - Rename some test functions - Implement a solution to the automatic tab opening problem, based on setting the default value of plotly.io.renderers in test files * Upload coverage report only from Azure macOS job * Exclude test folders from coverage reports * Vectorization2 (#378) * Update P landscapes * Add distances, inner products and kernels glossary entry Signed-off-by: ammedmar <anibal@medina-mardones.com> * Fix azure on windows (#388) * Update ccache * Update variable used to indicate boost headers location Official answer from boost devs: https://discourse.cmake.org/t/findboost-difference-between-boost-include-dir-and-boost-include-dirs/855 * Add install boost step in Azure CI, which downloads boost Signed-off-by: julian <julian.burellaperez@heig-vd.ch> * Allow more general input to ripser when metric='precomputed', improve/refactor check_point_clouds and add tests (#386) * Remove boolean mask on infinite values in VietorisRipsPersistence * Refactoring of check_point_clouds - Rename distance_matrix kwarg to distance_matrices - Add checks for square input when distance_matrices is set to True - More comprehensive/friendly error messages and warnings * Increase generality of ripser function when metric == 'precomputed' Sklearn's pairwise_distances is no longer called when metric='precomputed'. This is because pairwise_distances checks for positivity and finite input in that case, but this is unnecessarily restrictive for ripser. pairwise_distances also checks for square input so this is no longer checked in the case metric='precomputed'. But the ripser function is not meant for use in isolation. It is meant to be called by a VietorisRipsPersistence instance, and input validation can be offloaded to that class. In particular, 9bab872 introduces checks for square input. * Add tests for check_point_clouds * Refresh docstrings for VietorisRipsPersistence - Mention "adjacency matrices of weighted undirected graphs" as well as distance matrices - Mention compatibility with filtration in docstrings for fit and transform * Add citing entry to README.rst and doc/faq.rst (#389) * Add citation section in README * Add citation info to FAQ page in docs Signed-off-by: Guillaume Tauzin <guillaumetauzin.ut@gmail.com> Co-authored-by: Umberto Lupo <46537483+ulupo@users.noreply.github.com> * Fix markdown subsection formatting (#390) * Fix citing giotto-tda section * Fix Important link section * Prepare release 0.2.1 (#391) * Make the docs and push to a test branch in gtda-docs * Fix indentation Co-authored-by: Umberto Lupo <46537483+ulupo@users.noreply.github.com> Co-authored-by: Guillaume Tauzin <guillaumetauzin.ut@gmail.com> Co-authored-by: Guillaume Tauzin <guillaume.tauzin@epfl.ch> Co-authored-by: Umberto <u.lupo@l2f.ch> Co-authored-by: Anibal M. Medina-Mardones <ammedmar@gmail.com> Co-authored-by: ammedmar <anibal@medina-mardones.com> Co-authored-by: REDS institute <reds-heig@users.noreply.github.com>

Umberto added 30 commits March 23, 2020 12:46

Bump version to 0.2.0, add release notes

877dad3

Add Adelie as contributor

6bc28c0

Add Mapper color bug

a13f5e6

Update ccache

fb79a4d

Add @ammermar as a contributor in release notes

50b372a

List all classes in images subpackage

804a161

Add @ammedmar as a contributor in release notes

5aa2723

List all classes in images subpackage

86be78f

Merge remote-tracking branch 'origin/master'

93747b6

Add new lines before bullet lists in rst

02cb3b9

Add forgotten line break

0da531d

Attempt at improving LaTeX rendering in mapper_quickstart

79c5d4a

Fix broken URL in release notes

396d6b3

Merge branch 'master' of https://github.com/giotto-ai/giotto-tda

97ebebb

Add @rth to code authors and list of contributors for v0.2.0

a11e75b

Add twine check to azure-pipelines.yml, attempt at fix to README

439e49b

Merge branch 'master' of https://github.com/giotto-ai/giotto-tda

9045d95

Fix duplicate link, not accepted by twine

89a5d63

Fix typo and remove another duplicate

57eac94

Merge branch 'master' of https://github.com/giotto-ai/giotto-tda

44d76cb

Remove images subpackage from code omitted from coverage

96f8caa

Add tests for Filtering class

fc85d35

Add fit_transform_plot test for GraphGeodesicDistance

0ce028c

Add fit_transform_plot tests in gtda.homology

0be4ada

Fix typo in voids_on_the_plane notebook

03b5afa

Add fit_transform_plot tests for images subpackage

0bc60e0

Add fit_transform_plot tests for point_clouds subpackage

9acbb28

Add test for SlidingWindow.plot

550ba59

Linting

62f9aa0

ulupo requested a review from wreise March 30, 2020 07:35

Fix flake8 issues

25f7b9b

Exclude gtda.utils._doc and gtda.utils.intervals from coveragerc

612f35c

wreise reviewed Mar 30, 2020

View reviewed changes

ulupo commented Mar 30, 2020

View reviewed changes

Implement @wreise's suggestions

b0d66c3

- Rename some test functions - Implement a solution to the automatic tab opening problem, based on setting the default value of plotly.io.renderers in test files

wreise approved these changes Mar 30, 2020

View reviewed changes

Umberto added 3 commits March 30, 2020 11:42

Upload coverage report only from macOS job

8b69bb4

Fix typo

6e5b4fc

Exclude test folders from coverage reports

21f38b1

ulupo merged commit c78de1e into giotto-ai:master Mar 30, 2020

ulupo deleted the simple_plotting_tests branch March 30, 2020 12:26

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Tests for plotting functions and methods, other increases in test coverage #384

Tests for plotting functions and methods, other increases in test coverage #384

ulupo commented Mar 30, 2020 •

edited

ulupo commented Mar 30, 2020

ulupo commented Mar 30, 2020

wreise Mar 30, 2020

ulupo Mar 30, 2020 •

edited

wreise Mar 30, 2020

ulupo Mar 30, 2020 •

edited

ulupo commented Mar 30, 2020 •

edited



		@pytest.mark.parametrize('hom_dim_ix', [0, 1])
		def test_fit_transform_plot_1(hom_dim_ix):

Tests for plotting functions and methods, other increases in test coverage #384

Tests for plotting functions and methods, other increases in test coverage #384

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