Hyppo

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

<a href="https://github.com/sampan501">
<img src="https://github.com/sampan501.png" width="50">
</a>
<a href="https://github.com/j1c">
<img src="https://github.com/j1c.png" width="50">
</a>
<a href="https://github.com/transpersonify">
<img src="https://github.com/transpersonify.png" width="50">
</a>
<a href="https://github.com/saivythik">
<img src="https://github.com/saivythik.png" width="50">
</a>
<a href="https://github.com/victoris93">
<img src="https://github.com/victoris93.png" width="50">
</a>
<a href="https://github.com/prabhatkgupta">
<img src="https://github.com/prabhatkgupta.png" width="50">
</a>
<a href="https://github.com/harsh204016">
<img src="https://github.com/harsh204016.png" width="50">
</a>
<a href="https://github.com/oakla">
<img src="https://github.com/oakla.png" width="50">
</a>
<a href="https://github.com/TacticalFallacy">
<img src="https://github.com/TacticalFallacy.png" width="50">
</a>
<a href="https://github.com/zdbzdb123123">
<img src="https://github.com/zdbzdb123123.png" width="50">
</a>
<a href="https://github.com/MatthewZhao26">
<img src="https://github.com/MatthewZhao26.png" width="50">
</a>
<a href="https://github.com/darsh-patel">
<img src="https://github.com/darsh-patel.png" width="50">
</a>

Issues Closed

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

PRs Merged

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

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

Authors

<a href="https://github.com/sampan501">
<img src="https://github.com/sampan501.png" width="50">
</a>

Issues Closed

N/A

PRs Merged

N/A

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

Authors

<a href="https://github.com/sampan501">
<img src="https://github.com/sampan501.png" width="50">
</a>

Issues Closed

N/A

PRs Merged

N/A

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

<a href="https://github.com/bdpedigo">
<img src="https://github.com/bdpedigo.png" width="50">
</a>
<a href="https://github.com/darsh-patel">
<img src="https://github.com/darsh-patel.png" width="50">
</a>
<a href="https://github.com/dlee0156">
<img src="https://github.com/dlee0156.png" width="50">
</a>
<a href="https://github.com/MatthewZhao26">
<img src="https://github.com/MatthewZhao26.png" width="50">
</a>
<a href="https://github.com/najmieh">
<img src="https://github.com/najmieh.png" width="50">
</a>
<a href="https://github.com/rflperry">
<img src="https://github.com/rflperry.png" width="50">
</a>
<a href="https://github.com/sampan501">
<img src="https://github.com/sampan501.png" width="50">
</a>
<a href="https://github.com/TacticalFallacy">
<img src="https://github.com/TacticalFallacy.png" width="50">
</a>
<a href="https://github.com/zdbzdb123123">
<img src="https://github.com/zdbzdb123123.png" width="50">
</a>

Issues Closed

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

PRs Merged

* [232](https://github.com/neurodata/hyppo/pull/232): Creating a goodness-of-fit module in hyppo
* [233](https://github.com/neurodata/hyppo/pull/233): Adding dHSIC
* [234](https://github.com/neurodata/hyppo/pull/234): Fast tstest
* [238](https://github.com/neurodata/hyppo/pull/238): Fast HHG Test
* [239](https://github.com/neurodata/hyppo/pull/239): Friedman Rafsky PR
* [242](https://github.com/neurodata/hyppo/pull/242): add permutation test example to docs
* [244](https://github.com/neurodata/hyppo/pull/244): Edited the types in the documentation section.
* [299](https://github.com/neurodata/hyppo/pull/299): Bump ipython from 7.19.0 to 7.31.1 in /docs
* [304](https://github.com/neurodata/hyppo/pull/304): Copy SciPy private _contains_nan function

**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 +

**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