Hyppo

Latest version: v0.4.0

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0.2.0

Not secure
**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 +

0.1.3

Not secure
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.

0.1.2

Not secure
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.

0.1.1

Not secure
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.

0.1.0

Not secure
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.

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