release 0.5.0

neurodata · Sep 13, 2024 · e50b28e · e50b28e
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diff --git a/README.md b/README.md
@@ -9,7 +9,6 @@
 [![PyPI - Python Version](https://img.shields.io/pypi/pyversions/hyppo?style=flat)](https://pypi.org/project/hyppo/)
 [![PyPI](https://img.shields.io/pypi/v/hyppo?style=flat)](https://pypi.org/project/hyppo/)
 [![arXivshield](https://img.shields.io/badge/arXiv-1907.02088-red.svg?style=flat)](https://arxiv.org/abs/1907.02088)
-[![All Contributors][all-contrib]](#contributors)
 
 hyppo (**HYP**othesis Testing in **P**yth**O**n, pronounced "Hippo") is an open-source software package for multivariate hypothesis testing. We decided to develop hyppo for the following reasons:
 
@@ -26,7 +25,7 @@ Website: [https://hyppo.neurodata.io/](https://hyppo.neurodata.io/)
 
 hyppo requires the following:
 
-* [python](https://www.python.org/) (>= 3.6)
+* [python](https://www.python.org/) (>= 3.8)
 * [numba](https://numba.pydata.org/) (>= 0.46)
 * [numpy](https://numpy.org/)  (>= 1.17)
 * [scipy](https://docs.scipy.org/doc/scipy/reference/) (>= 1.4.0)
@@ -71,74 +70,16 @@ has detailed information about contributing code, documentation, and tests.
 
 ## Contributors
 
-Thanks goes to these wonderful people ([emoji key](https://allcontributors.org/docs/en/emoji-key)):
-
-<!-- ALL-CONTRIBUTORS-LIST:START - Do not remove or modify this section -->
-<!-- prettier-ignore-start -->
-<!-- markdownlint-disable -->
-<table>
-  <tbody>
-    <tr>
-      <td align="center" valign="top" width="14.28%"><a href="http://sampan.me"><img src="https://avatars.githubusercontent.com/u/36676569?v=4?s=100" width="100px;" alt="Sambit Panda"/><br /><sub><b>Sambit Panda</b></sub></a><br /><a href="https://github.com/neurodata/hyppo/issues?q=author%3Asampan501" title="Bug reports">🐛</a> <a href="https://github.com/neurodata/hyppo/commits?author=sampan501" title="Code">💻</a> <a href="https://github.com/neurodata/hyppo/commits?author=sampan501" title="Documentation">📖</a> <a href="#ideas-sampan501" title="Ideas, Planning, & Feedback">🤔</a> <a href="#maintenance-sampan501" title="Maintenance">🚧</a> <a href="https://github.com/neurodata/hyppo/pulls?q=is%3Apr+reviewed-by%3Asampan501" title="Reviewed Pull Requests">👀</a></td>
-      <td align="center" valign="top" width="14.28%"><a href="https://github.com/cshen6"><img src="https://avatars.githubusercontent.com/u/11924683?v=4?s=100" width="100px;" alt="cshen6"/><br /><sub><b>cshen6</b></sub></a><br /><a href="#ideas-cshen6" title="Ideas, Planning, & Feedback">🤔</a></td>
-      <td align="center" valign="top" width="14.28%"><a href="http://neurodata.io"><img src="https://avatars.githubusercontent.com/u/41842?v=4?s=100" width="100px;" alt="joshua vogelstein"/><br /><sub><b>joshua vogelstein</b></sub></a><br /><a href="#fundingFinding-jovo" title="Funding Finding">🔍</a> <a href="#mentoring-jovo" title="Mentoring">🧑‍🏫</a> <a href="#ideas-jovo" title="Ideas, Planning, & Feedback">🤔</a></td>
-      <td align="center" valign="top" width="14.28%"><a href="https://in.linkedin.com/in/satishpalaniappan/en"><img src="https://avatars.githubusercontent.com/u/10278507?v=4?s=100" width="100px;" alt="Satish Palaniappan"/><br /><sub><b>Satish Palaniappan</b></sub></a><br /><a href="https://github.com/neurodata/hyppo/commits?author=tpsatish95" title="Code">💻</a> <a href="#ideas-tpsatish95" title="Ideas, Planning, & Feedback">🤔</a></td>
-      <td align="center" valign="top" width="14.28%"><a href="https://github.com/junhaobearxiong"><img src="https://avatars.githubusercontent.com/u/30681308?v=4?s=100" width="100px;" alt="Junhao Xiong"/><br /><sub><b>Junhao Xiong</b></sub></a><br /><a href="https://github.com/neurodata/hyppo/commits?author=junhaobearxiong" title="Code">💻</a> <a href="#ideas-junhaobearxiong" title="Ideas, Planning, & Feedback">🤔</a></td>
-      <td align="center" valign="top" width="14.28%"><a href="http://ericwb.me"><img src="https://avatars.githubusercontent.com/u/8883547?v=4?s=100" width="100px;" alt="Eric Bridgeford"/><br /><sub><b>Eric Bridgeford</b></sub></a><br /><a href="https://github.com/neurodata/hyppo/issues?q=author%3Aebridge2" title="Bug reports">🐛</a> <a href="#ideas-ebridge2" title="Ideas, Planning, & Feedback">🤔</a></td>
-      <td align="center" valign="top" width="14.28%"><a href="https://github.com/ronakdm"><img src="https://avatars.githubusercontent.com/u/72722942?v=4?s=100" width="100px;" alt="Ronak D. Mehta"/><br /><sub><b>Ronak D. Mehta</b></sub></a><br /><a href="https://github.com/neurodata/hyppo/commits?author=ronakdm" title="Code">💻</a> <a href="#ideas-ronakdm" title="Ideas, Planning, & Feedback">🤔</a></td>
-    </tr>
-    <tr>
-      <td align="center" valign="top" width="14.28%"><a href="https://github.com/j1c"><img src="https://avatars.githubusercontent.com/u/5142539?v=4?s=100" width="100px;" alt="Jaewon Chung"/><br /><sub><b>Jaewon Chung</b></sub></a><br /><a href="https://github.com/neurodata/hyppo/issues?q=author%3Aj1c" title="Bug reports">🐛</a> <a href="https://github.com/neurodata/hyppo/commits?author=j1c" title="Code">💻</a> <a href="https://github.com/neurodata/hyppo/commits?author=j1c" title="Documentation">📖</a></td>
-      <td align="center" valign="top" width="14.28%"><a href="https://github.com/jdey4"><img src="https://avatars.githubusercontent.com/u/52499217?v=4?s=100" width="100px;" alt="Jayanta Dey"/><br /><sub><b>Jayanta Dey</b></sub></a><br /><a href="https://github.com/neurodata/hyppo/commits?author=jdey4" title="Code">💻</a></td>
-      <td align="center" valign="top" width="14.28%"><a href="https://github.com/bvarjavand"><img src="https://avatars.githubusercontent.com/u/8294669?v=4?s=100" width="100px;" alt="Bijan Varjavand"/><br /><sub><b>Bijan Varjavand</b></sub></a><br /><a href="https://github.com/neurodata/hyppo/commits?author=bvarjavand" title="Code">💻</a></td>
-      <td align="center" valign="top" width="14.28%"><a href="https://bdpedigo.github.io/"><img src="https://avatars.githubusercontent.com/u/25714207?v=4?s=100" width="100px;" alt="Benjamin Pedigo"/><br /><sub><b>Benjamin Pedigo</b></sub></a><br /><a href="https://github.com/neurodata/hyppo/issues?q=author%3Abdpedigo" title="Bug reports">🐛</a> <a href="https://github.com/neurodata/hyppo/commits?author=bdpedigo" title="Code">💻</a></td>
-      <td align="center" valign="top" width="14.28%"><a href="http://alyakin314.github.io"><img src="https://avatars.githubusercontent.com/u/25692376?v=4?s=100" width="100px;" alt="alyakin314"/><br /><sub><b>alyakin314</b></sub></a><br /><a href="https://github.com/neurodata/hyppo/commits?author=alyakin314" title="Code">💻</a> <a href="#ideas-alyakin314" title="Ideas, Planning, & Feedback">🤔</a></td>
-      <td align="center" valign="top" width="14.28%"><a href="https://vivekg.dev"><img src="https://avatars.githubusercontent.com/u/29757116?v=4?s=100" width="100px;" alt="Vivek Gopalakrishnan"/><br /><sub><b>Vivek Gopalakrishnan</b></sub></a><br /><a href="https://github.com/neurodata/hyppo/commits?author=v715" title="Code">💻</a></td>
-      <td align="center" valign="top" width="14.28%"><a href="https://rflperry.github.io/"><img src="https://avatars.githubusercontent.com/u/13107341?v=4?s=100" width="100px;" alt="Ronan Perry"/><br /><sub><b>Ronan Perry</b></sub></a><br /><a href="https://github.com/neurodata/hyppo/issues?q=author%3Arflperry" title="Bug reports">🐛</a> <a href="https://github.com/neurodata/hyppo/commits?author=rflperry" title="Code">💻</a> <a href="#ideas-rflperry" title="Ideas, Planning, & Feedback">🤔</a> <a href="https://github.com/neurodata/hyppo/pulls?q=is%3Apr+reviewed-by%3Arflperry" title="Reviewed Pull Requests">👀</a> <a href="https://github.com/neurodata/hyppo/commits?author=rflperry" title="Documentation">📖</a></td>
-    </tr>
-    <tr>
-      <td align="center" valign="top" width="14.28%"><a href="https://github.com/PSSF23"><img src="https://avatars.githubusercontent.com/u/20309845?v=4?s=100" width="100px;" alt="Haoyin Xu"/><br /><sub><b>Haoyin Xu</b></sub></a><br /><a href="https://github.com/neurodata/hyppo/commits?author=PSSF23" title="Code">💻</a> <a href="https://github.com/neurodata/hyppo/commits?author=PSSF23" title="Documentation">📖</a> <a href="https://github.com/neurodata/hyppo/pulls?q=is%3Apr+reviewed-by%3APSSF23" title="Reviewed Pull Requests">👀</a></td>
-      <td align="center" valign="top" width="14.28%"><a href="https://github.com/hadasarik"><img src="https://avatars.githubusercontent.com/u/39025628?v=4?s=100" width="100px;" alt="Hadas Arik"/><br /><sub><b>Hadas Arik</b></sub></a><br /><a href="https://github.com/neurodata/hyppo/commits?author=hadasarik" title="Code">💻</a></td>
-      <td align="center" valign="top" width="14.28%"><a href="https://github.com/kareef928"><img src="https://avatars.githubusercontent.com/u/51966539?v=4?s=100" width="100px;" alt="kareef928"/><br /><sub><b>kareef928</b></sub></a><br /><a href="https://github.com/neurodata/hyppo/commits?author=kareef928" title="Code">💻</a></td>
-      <td align="center" valign="top" width="14.28%"><a href="https://github.com/Verathagnus"><img src="https://avatars.githubusercontent.com/u/59093644?v=4?s=100" width="100px;" alt="Verathagnus"/><br /><sub><b>Verathagnus</b></sub></a><br /><a href="https://github.com/neurodata/hyppo/commits?author=Verathagnus" title="Code">💻</a></td>
-      <td align="center" valign="top" width="14.28%"><a href="https://github.com/dlee0156"><img src="https://avatars.githubusercontent.com/u/47963020?v=4?s=100" width="100px;" alt="dlee0156"/><br /><sub><b>dlee0156</b></sub></a><br /><a href="https://github.com/neurodata/hyppo/commits?author=dlee0156" title="Code">💻</a></td>
-      <td align="center" valign="top" width="14.28%"><a href="https://github.com/najmieh"><img src="https://avatars.githubusercontent.com/u/31998054?v=4?s=100" width="100px;" alt="Najmieh Sadat Safarabadi"/><br /><sub><b>Najmieh Sadat Safarabadi</b></sub></a><br /><a href="https://github.com/neurodata/hyppo/commits?author=najmieh" title="Documentation">📖</a></td>
-      <td align="center" valign="top" width="14.28%"><a href="https://github.com/TacticalFallacy"><img src="https://avatars.githubusercontent.com/u/56208921?v=4?s=100" width="100px;" alt="TacticalFallacy"/><br /><sub><b>TacticalFallacy</b></sub></a><br /><a href="https://github.com/neurodata/hyppo/commits?author=TacticalFallacy" title="Code">💻</a></td>
-    </tr>
-    <tr>
-      <td align="center" valign="top" width="14.28%"><a href="https://github.com/darsh-patel"><img src="https://avatars.githubusercontent.com/u/70541374?v=4?s=100" width="100px;" alt="darsh-patel"/><br /><sub><b>darsh-patel</b></sub></a><br /><a href="https://github.com/neurodata/hyppo/commits?author=darsh-patel" title="Code">💻</a></td>
-      <td align="center" valign="top" width="14.28%"><a href="https://github.com/zdbzdb123123"><img src="https://avatars.githubusercontent.com/u/95720890?v=4?s=100" width="100px;" alt="zdbzdb123123"/><br /><sub><b>zdbzdb123123</b></sub></a><br /><a href="https://github.com/neurodata/hyppo/commits?author=zdbzdb123123" title="Code">💻</a></td>
-      <td align="center" valign="top" width="14.28%"><a href="https://github.com/MatthewZhao26"><img src="https://avatars.githubusercontent.com/u/52184663?v=4?s=100" width="100px;" alt="MatthewZhao26"/><br /><sub><b>MatthewZhao26</b></sub></a><br /><a href="https://github.com/neurodata/hyppo/commits?author=MatthewZhao26" title="Code">💻</a></td>
-      <td align="center" valign="top" width="14.28%"><a href="https://github.com/oakla"><img src="https://avatars.githubusercontent.com/u/2579439?v=4?s=100" width="100px;" alt="Alexander Oakley"/><br /><sub><b>Alexander Oakley</b></sub></a><br /><a href="https://github.com/neurodata/hyppo/commits?author=oakla" title="Documentation">📖</a></td>
-      <td align="center" valign="top" width="14.28%"><a href="https://www.linkedin.com/in/harsh-gupta-/"><img src="https://avatars.githubusercontent.com/u/37452506?v=4?s=100" width="100px;" alt="Harsh Gupta"/><br /><sub><b>Harsh Gupta</b></sub></a><br /><a href="https://github.com/neurodata/hyppo/commits?author=harsh204016" title="Documentation">📖</a></td>
-      <td align="center" valign="top" width="14.28%"><a href="https://github.com/prabhatkgupta"><img src="https://avatars.githubusercontent.com/u/42283586?v=4?s=100" width="100px;" alt="Prabhat Kr. Gupta"/><br /><sub><b>Prabhat Kr. Gupta</b></sub></a><br /><a href="https://github.com/neurodata/hyppo/issues?q=author%3Aprabhatkgupta" title="Bug reports">🐛</a></td>
-      <td align="center" valign="top" width="14.28%"><a href="https://github.com/victoris93"><img src="https://avatars.githubusercontent.com/u/49495286?v=4?s=100" width="100px;" alt="Victoria Shevchenko"/><br /><sub><b>Victoria Shevchenko</b></sub></a><br /><a href="https://github.com/neurodata/hyppo/commits?author=victoris93" title="Code">💻</a></td>
-    </tr>
-    <tr>
-      <td align="center" valign="top" width="14.28%"><a href="https://github.com/saivythik"><img src="https://avatars.githubusercontent.com/u/60150574?v=4?s=100" width="100px;" alt="saivythik"/><br /><sub><b>saivythik</b></sub></a><br /><a href="https://github.com/neurodata/hyppo/commits?author=saivythik" title="Documentation">📖</a> <a href="https://github.com/neurodata/hyppo/issues?q=author%3Asaivythik" title="Bug reports">🐛</a></td>
-      <td align="center" valign="top" width="14.28%"><a href="https://github.com/transpersonify"><img src="https://avatars.githubusercontent.com/u/8897933?v=4?s=100" width="100px;" alt="Shruti Naik"/><br /><sub><b>Shruti Naik</b></sub></a><br /><a href="https://github.com/neurodata/hyppo/commits?author=transpersonify" title="Documentation">📖</a></td>
-      <td align="center" valign="top" width="14.28%"><a href="https://github.com/ohpraveenprasad"><img src="https://avatars.githubusercontent.com/u/119914283?v=4?s=100" width="100px;" alt="Praveen Prasad "/><br /><sub><b>Praveen Prasad </b></sub></a><br /><a href="https://github.com/neurodata/hyppo/commits?author=ohpraveenprasad" title="Documentation">📖</a></td>
-      <td align="center" valign="top" width="14.28%"><a href="https://github.com/JenniferWTam"><img src="https://avatars.githubusercontent.com/u/80274896?v=4?s=100" width="100px;" alt="Jennifer Tam"/><br /><sub><b>Jennifer Tam</b></sub></a><br /><a href="https://github.com/neurodata/hyppo/commits?author=JenniferWTam" title="Documentation">📖</a></td>
-      <td align="center" valign="top" width="14.28%"><a href="https://github.com/PoojaMandal"><img src="https://avatars.githubusercontent.com/u/63387928?v=4?s=100" width="100px;" alt="PoojaMandal"/><br /><sub><b>PoojaMandal</b></sub></a><br /><a href="https://github.com/neurodata/hyppo/commits?author=PoojaMandal" title="Documentation">📖</a></td>
-      <td align="center" valign="top" width="14.28%"><a href="http://sciencestatia.in"><img src="https://avatars.githubusercontent.com/u/84276219?v=4?s=100" width="100px;" alt="Satarupa Deb"/><br /><sub><b>Satarupa Deb</b></sub></a><br /><a href="https://github.com/neurodata/hyppo/commits?author=Satarupa22-SD" title="Documentation">📖</a></td>
-      <td align="center" valign="top" width="14.28%"><a href="https://github.com/Alex1-ai"><img src="https://avatars.githubusercontent.com/u/78540958?v=4?s=100" width="100px;" alt="Alex1-ai"/><br /><sub><b>Alex1-ai</b></sub></a><br /><a href="https://github.com/neurodata/hyppo/commits?author=Alex1-ai" title="Documentation">📖</a></td>
-    </tr>
-    <tr>
-      <td align="center" valign="top" width="14.28%"><a href="https://github.com/vatsalya-vyas"><img src="https://avatars.githubusercontent.com/u/140804211?v=4?s=100" width="100px;" alt="Vatsalya Vyas"/><br /><sub><b>Vatsalya Vyas</b></sub></a><br /><a href="https://github.com/neurodata/hyppo/commits?author=vatsalya-vyas" title="Documentation">📖</a></td>
-    </tr>
-  </tbody>
-</table>
-
-<!-- markdownlint-restore -->
-<!-- prettier-ignore-end -->
-
-<!-- ALL-CONTRIBUTORS-LIST:END -->
-
-This project follows the [all-contributors](https://allcontributors.org) specification.
-Contributions of any kind are welcome!
+Thanks goes to these wonderful people:
+
+<a href="https://github.com/neurodata/hyppo/graphs/contributors">
+  <img src="https://contrib.rocks/image?repo=neurodata/hyppo" />
+</a>
+
+Made with [contrib.rocks](https://contrib.rocks).
 
 ## Project History
 
 hyppo is a rebranding of mgcpy, which was founded in November 2018.
-mgcpy was designed and written by @tpsatish95, @sampan501, @junhaobearxiong, @sundaysundya, @ananyas713, and @ronakdm. hyppo
-was designed and written by Sambit Panda and first released in February 2020.
+mgcpy was designed and written by [@tpsatish95](https://github.com/tpsatish95), [@sampan501](https://github.com/sampan501), [@junhaobearxiong](https://github.com/junhaobearxiong), [@sundaysundya](https://github.com/sundaysundya), [@ananyas713](https://github.com/ananyas713), and [@ronakdm](https://github.com/ronakdm). hyppo
+was designed and written by [@sampan501](https://github.com/sampan501) and first released in February 2020.
diff --git a/docs/changelog/index.rst b/docs/changelog/index.rst
@@ -6,6 +6,7 @@ This is the list of changes to hyppo between each release. For full details, see
 .. toctree::
    :maxdepth: 1
 
+   v0.5.0.md
    v0.4.0.md
    v0.3.2.md
    v0.3.1.md

diff --git a/docs/changelog/v0.4.0.md b/docs/changelog/v0.4.0.md
@@ -1,7 +1,5 @@
 # hyppo v0.4.0
 
-> **Note:** hyppo v0.4.0 has not been released yet!
-
 ## Highlights of this release
 
 hyppo v0.4.0 is the culmination of 12 months of hard work. It contains
@@ -10,7 +8,7 @@ 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+.
+This release requires Python 3.8+.
 
 ## New features
 

diff --git a/docs/changelog/v0.5.0.md b/docs/changelog/v0.5.0.md
@@ -0,0 +1,39 @@
+# 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](https://github.com/neurodata/hyppo/compare/v0.4.0...v0.5.0)
+
diff --git a/hyppo/__init__.py b/hyppo/__init__.py
@@ -7,4 +7,4 @@
 import hyppo.d_variate
 import hyppo.conditional
 
-__version__ = "0.4.0"
+__version__ = "0.5.0"
diff --git a/setup.py b/setup.py
@@ -75,19 +75,18 @@ def run(self):
     author_email=AUTHOR_EMAIL,
     install_requires=REQUIRED_PACKAGES,
     url=URL,
-    license="MIT",
+    license="PolyForm Noncommercial License 1.0.0",
     classifiers=[
         "Development Status :: 3 - Alpha",
         "Intended Audience :: Science/Research",
         "Topic :: Scientific/Engineering :: Mathematics",
         "License :: OSI Approved :: MIT License",
         "Programming Language :: Python :: 3",
-        "Programming Language :: Python :: 3.6",
-        "Programming Language :: Python :: 3.7",
         "Programming Language :: Python :: 3.8",
         "Programming Language :: Python :: 3.9",
         "Programming Language :: Python :: 3.10",
         "Programming Language :: Python :: 3.11",
+        "Programming Language :: Python :: 3.12",
     ],
     packages=find_packages(),
     include_package_data=True,