hyppo - hyppo v0.5.2

What's Changed

• Update cca.py by @ricor07 in https://github.com/neurodata/hyppo/pull/425
• fix of negative unbiased dcov for chi-square test by @LaggyMan in https://github.com/neurodata/hyppo/pull/430
• Causal Treatment Effect Testing by @ebridge2 in https://github.com/neurodata/hyppo/pull/431
• Bump ipython from 7.19.0 to 8.10.0 in /docs by @dependabot in https://github.com/neurodata/hyppo/pull/433
• Remove autograd fallback in DifferentiableKernel and enforce manual gradients (Issue 322) by @tjoab in https://github.com/neurodata/hyppo/pull/432
• fix future bug that is affecting package installs by @sampan501 in https://github.com/neurodata/hyppo/pull/435

New Contributors

• @ricor07 made their first contribution in https://github.com/neurodata/hyppo/pull/425
• @LaggyMan made their first contribution in https://github.com/neurodata/hyppo/pull/430
• @ebridge2 made their first contribution in https://github.com/neurodata/hyppo/pull/431
• @tjoab made their first contribution in https://github.com/neurodata/hyppo/pull/432

Full Changelog: https://github.com/neurodata/hyppo/compare/v0.5.1...v0.5.2

- Python
Published by sampan501 about 1 year ago

hyppo - hyppo v0.5.1

Highlights of this release

This release fixes the future version.

What's Changed

• fix future dependency by @sampan501 in https://github.com/neurodata/hyppo/pull/421

Full Changelog: https://github.com/neurodata/hyppo/compare/v0.5.0...v0.5.1

- Python
Published by sampan501 over 1 year ago

hyppo - hyppo v0.5.0

Highlights of this release

hyppo v0.5.0 is the culmination of 16 months of hard work. It contains many new features, numerous bug-fixes, improved test coverage and better documentation. All users are encouraged to upgrade to this release, as there are a large number of bug-fixes and optimizations.

This release requires Python 3.8+.

New features

• Add Conditional Dcorr
• Add Partial Dcorr
• Add Partial Correlation

Bug fixes

• Fixed fast KMERF stat/pvalue so not always significant
• Biased Dcorr test statistic has been corrected

Documentation

• Fixed documentation rendering issues
• Fixed typos in various docstrings
• Added new license
• Improved contributing guidelines
• Added code of conduct

Maintenance

• Move Friedman Rafsky from hyppo.ksample to hyppo.independence

Full Changelog

v0.4.0...v0.5.0

- Python
Published by sampan501 over 1 year ago

hyppo - hyppo v0.4.0

Highlights of this release

hyppo v0.4.0 is the culmination of 12 months of hard work. It contains many new features, numerous bug-fixes, improved test coverage and better documentation. All users are encouraged to upgrade to this release, as there are a large number of bug-fixes and optimizations.

This release requires Python 3.6+.

New features

• Add Ljung-Box test
• Add fast chi-square approximation to KMERF
• Add null distribution to DiscrimOneSample
• Add Fast HHG 2-sample test
• Add KCI test
• Add FCIT test

Bug fixes

• Fixed energy statistic computation
• Fix type checking for permutation groups

Documentation

• Incorrect inference in the overview doc file
• Fixed documentation rendering issues
• Fixed typos in various docstrings
• Make clear statistic issues in FR test

Maintenance

• Make Circle CI faster
• Removed numpy >1.25 because of numba issues
• Migrate Netlify from Xenial to Focal
• Refactor kgof module
• Temporarily skip two-sample discrinability tets

Authors

Issues Closed

• #333: FIX migrate Netlify image from Xenial to Focal
• #330: The statistic returned by the test method is different to the statistic returned by the statistic method
• #328: Two typos
• #325: Locator files?
• #344: [BUG] Possible issue with numba and numpy 1.24 compatibilitiy
• #350: Lots missing from API reference
• #348: jupyter notebooks are no longer rendering in docs
• #359: About Module 'hyppo.conditional'
• #363: Incorrect Inference in Overview of Workflow using MGC?
• #341: Energy statistic is wrong

PRs Merged

• #310: run pytest in parallel
• #321: add skip decorator for two sample circleci tests
• #319: update sphinx to fix jinja error
• #318: Refactor kgof module
• #315: FCIT
• #317: KCI Dev Pull Request
• #314: Fast HHG 2-Sample Test
• #327: fix typos
• #331: Stat ranges to docs
• #335: DOC remove extra comma in dcorr docstring
• #336: make docs clear about FR corrected stat
• #337: fix two typos in docs
• #340: Fix typo in distance covariance equation
• #345: bugfix: reduce maximum dependency of numpy to 1.23.5
• #346: Add null distribution to DiscrimOneSampleTestOutput
• #352: v0.4.0
• #351: Bump ipython from 7.31.1 to 8.10.0 in /docs
• #356: Bump ipython from 7.31.1 to 8.10.0 in /docs
• #357: Fix type checking
• #361: Parameter noise for function squaredimond
• #364: Fixes typo/ wrong inference in overview.py
• #366: Addition of Ljung-Box test and a simulation
• #368: fix energy statistic bug
• #369: Add Fast kmerf
• #371: docs: add transpersonify as a contributor for doc
• #372: docs: add saivythik as a contributor for doc, and bug
• #373: docs: add victoris93 as a contributor for code
• #374: docs: add j1c as a contributor for code
• #375: docs: add prabhatkgupta as a contributor for bug
• #376: docs: add harsh204016 as a contributor for doc
• #377: docs: add oakla as a contributor for doc
• #378: docs: add MatthewZhao26 as a contributor for code

- Python
Published by sampan501 about 3 years ago

hyppo - hyppo v0.3.2

This release just fixes the bug of using emojis in the long description so the package can build on Windows.

Authors

Issues Closed

N/A

PRs Merged

N/A

- Python
Published by sampan501 over 4 years ago

hyppo - hyppo v0.3.1

This release just fixes the bug of not adding autograd as a dependency.

Authors

Issues Closed

N/A

PRs Merged

N/A

- Python
Published by sampan501 over 4 years ago

hyppo - hyppo v0.3.0

hyppo v0.3.0 is the culmination of 12 months of hard work. It contains many new features, numerous bug-fixes, improved test coverage and better documentation. All users are encouraged to upgrade to this release, as there are a large number of bug-fixes and optimizations.

This release requires Python 3.6+.

Highlights of this release

New features

• Added goodness of fit module with FSSD
• Added d-variate independence testing module with dHsic
• Added fast HHG
• Added Friedman Rafsky test
• Added Smooth CF Test
• Added Mean Embedding Test

Bug fixes

• Copy _contains_nan function from SciPy since it is gone

Documentation

• Made documentation more accessible with a new theme
• Added example for block permutation
• Mentioned types of inputs of ndarrays

Maintenance

• Drafted PR to include Dcorr in SciPy
• Bumped iPython for security reasons

Authors

Issues Closed

• #103: Create a goodness of fit module in hyppo
• #104: Add dHsic to hyppo
• #106: Add fast HHG
• #140: Discriminability y should allow arbitrary type or make docs more clear
• #187: potential k-sample tests to add
• #211: Fast Two-Sample Testing with Analytic Representations of Probability Measures
• #235: Add existing permutation tree simulation notebook to docs
• #245: Add more description about types of ndarray in all methods in documentation
• #249: Add contributors to README
• #303: [BUG] scipy 1.8 breaks hyppo import

PRs Merged

• #232: Creating a goodness-of-fit module in hyppo
• #233: Adding dHSIC
• #234: Fast tstest
• #238: Fast HHG Test
• #239: Friedman Rafsky PR
• #242: add permutation test example to docs
• #244: Edited the types in the documentation section.
• #299: Bump ipython from 7.19.0 to 7.31.1 in /docs
• #304: Copy SciPy private containsnan function

- Python
Published by sampan501 over 4 years ago

hyppo - hyppo v0.2.2

Note: People with a "+" by their names contributed a patch for the first time.

Release date: 7 December 2021 Supports: Python 3.6+.

New features

• Functions now can be reproducible using a random_state parameter
• Add warning for redundant rows when running :class:hyppo.independence.MGC
• Tests now also retun a namedtuple

Bug Fixes

• Change from L1 to L2 distance for the median heuristic
• Make median heuristic default for RBF and Gaussian kernels

Documentation

• Update license in setup.py
• Change reference style and store reference in a refs.bib file
• Updated papers in documentation from preprint to published versions
• Rename badges in README

Maintenance

• Added support for Python 3.9
• Update pytest orbs version
• Make repository citeable with the new GitHub feature

Authors

• @sampan501
• @kareef928 +
• @rflperry
• @Verathagnus +
• @PSSF23 +
• @hadasarik +

- Python
Published by sampan501 over 4 years ago

hyppo - hyppo v0.2.1

Note: People with a "+" by their names contributed a patch for the first time.

Release date: 25 February 2021 Supports: Python 3.6+.

Bug Fixes

• hyppo.independence.Dcorr and hyppo.independence.Hsic when auto=True had low finite power, fixed.
• Fast exact statistic for hyppo.independence.Dcorr was incorrect, fixed

Documentation

• Fix PyPi description rendering issues
• Add more descriptive contributing guidelines
• Add ROLES.md for specification about maintainers
• Added power computation for independence increasing sample size and dimension
• Add benchmark section and move relevant examples there
• Add base classes

Maintenance

• Fix gaussian kernel to prevent division by 0
• Add checks for Type I error

Authors

• Sambit Panda

- Python
Published by sampan501 over 5 years ago

hyppo - hyppo v0.2.0

Note: People with a "+" by their names contributed a patch for the first time.

Release date: 08 February 2021 Supports: Python 3.6+.

New features

• Added restricted permutation functionality for Dcorr
• Kernel functions now wrap scikit-learn and support keyword arguments
• hyppo.ksample.Energy
• hyppo.ksample.DISCO
• hyppo.ksample.MMD
• Fast 1D exact Dcorr O(n log n)
• hyppo.ksample.Hotelling
• hyppo.ksample.MANOVA
• hyppo.independence.MaxMargin

Bug Fixes

• Fixed error check for k-sample tests to be between samples instead of within
• Time series doesn't clip negative values
• Fix docs not building on netlify
• Fix p-value calculations for permutation tests to be more in line with the literature
• Fix hyppo.independence.Dcorr and hyppo.independence.Hsic incorrect stats

Documentation

• Update badges and README to FIRM guidelines
• Incorrect equation in :meth:hyppo.tools.circle docstring
• Update README to be in line with scikit-learn
• Remove literature reference section in docstrings, add links to papers
• Add docstrings for :mod:hyppo.tools functions
• Add overview.py file for an overview of the package
• Add tutorials folder, rewrite so it is more user-friendly (port independence, k-sample, time series)
• Add examples folder with more information about unique features
• Move to sphinx-gallery instead of nbconvert
• Use automodule instead of autoclass
• Make clear about the package requirements and docs requirements
• Make changelog into a single file
• Add external links to neurodata and code of conduct
• Add citing page to cite the package papers
• Make index page a clone of README
• Update MakeFile for more options
• Add intersphinx mapping with links externally (numpy, scipy, etc.) and internally
• Add docs for statistic function
• Add discriminability tutorial

Maintenance

• Fix typos in warning commits
• Updated tests to precalculate distance matrix
• Moved from Travis CI to Circle CI
• Raise base requirements.txt to fix failing tests on CircleCI
• Add code coverage config files
• Add documentation folders and files to .gitignore
• Remove reps warning test
• Cache numba after first call to speed up runs
• Fix netlify config to new doc build structure

Authors

• Sambit Panda
• Vivek Gopalakrishnan +
• Ronak Mehta
• Ronan Perry +

- Python
Published by sampan501 over 5 years ago

hyppo - hyppo v0.1.3

hyppo 0.1.3 does not include any new features, just fixes. This release requires Python 3.6+.

Fixes

k-sample testing

Prevent division by zero when calculating using default gaussian median kernel.

Other

Used chi2.sf instead of 1 - chi2.cdf

Authors

This release contains work by the following people (contributed at least one patch to this release, names in alphabetical order by last name):

• Benjamin Pedigo +
• Anton Alayakin +

People with a "+" by their names contributed a patch for the first time.

- Python
Published by sampan501 almost 6 years ago

hyppo - hyppo v0.1.2

hyppo 0.1.2 does not include any new features, just fixes. This release requires Python 3.6+.

Fixes

k-sample testing

Fixed MMD/k-samp;e Hsic not running bug.

Authors

This release contains work by the following people (contributed at least one patch to this release, names in alphabetical order by last name):

• Sambit Panda

A total of 1 person contributed to this release. People with a "+" by their names contributed a patch for the first time.

- Python
Published by sampan501 about 6 years ago

hyppo - hyppo v0.1.1

hyppo 0.1.1 does not include any new features, just removal of extraneous features.

Release highlights:

• Kernel matrices calculated once before calculating p-values
• Pearson, Kendall, and Spearman are no longer tests

This release requires Python 3.6+.

Improvements

Independence testing

Null distribution added as a class atribute. Calculate kernel once before calculating p-value.

k-sample testing

Null distribution added as a class atribute. Calculate kernel once before calculating p-value. Upper and lower-case inputs are available for indep_test.

Time series

Reference docs and tutorials added to Time Series module.

Other changes

OS/Software requirements and license changes updated in ReadME. pairwise_distances from sklearn used instead of cdist from scipy.

Removed features

Pearson, Spearman, and Kendall are no longer tests within the package. arXiv badge added to docs. Python 3.5 no longer supported.

Authors

This release contains work by the following people (contributed at least one patch to this release, names in alphabetical order by last name):

• Ronak Mehta +
• Sambit Panda
• Bijan Varjavand +

A total of 3 people contributed to this release. People with a "+" by their names contributed a patch for the first time.

- Python
Published by sampan501 about 6 years ago

hyppo - hyppo v0.1.0

hyppo 0.1.0 is the culmination of 8 months of hard work. It contains many new features, numerous bug-fixes, improved test coverage and better documentation. All users are encouraged to use this release instead of the mgcpy, which this package is replacing, are a large number of bug-fixes and optimizations. Moreover, our development attention will now shift to bug-fix releases on this branch, and on adding new features on the development master branch.

Release highlights (as compared to mgcpy):

• New time series and discriminability modules
• More user-friendly implementation of k-Sample Testing

This release requires Python 3.5+.

New features

Independence testing

Tests have been given a unique class as compared to mgcpy. Parallelization in this module makes tests faster and Hsic has been added as a standalone test within this package (uses exact equivalence implementation).

k-sample testing

k-Sample testing is now organized within a class that is modeled similarly to how independence tests are run. More information about the specifics of how this works can be found in the docs.

Time series

Time series based independence tests have been included as a separate module from independence tests.

Simulations

Simulations have been included as a separate module and hyppo.sims now includes k-sample simulations and time series simulations.

Discriminability

Discriminability has been included from the r-mgc package and has been changed so it conforms to the hyppo API.

Benchmarks

A benchmarks folder as been added that contains notebooks comparing statistical power, algorithm wall times, and test statistics comparisons between the algorithms and sometimes between the respective R implementations. Many of those notebooks have been condensed into tutorials in the documentation.

Other changes

API has been changed as compared to mgcpy and is modeled after scikit-learn with the inclusion of the base.py containing an abstract class within each module and energy with a .test method calculating test statistic in p-value.

Authors

This release contains work by the following people (contributed at least one patch to this release, names in alphabetical order by last name):

• Jayanta Dey +
• Sambit Panda +

A total of 2 people contributed to this release. People with a "+" by their names contributed a patch for the first time.

- Python
Published by sampan501 over 6 years ago