refactor package and add utilities documentation (#156)

* add additional depth to docs * add utils to a tools module * add kernel and distance matrix docs * rework weird if return with kwargs * fix doctest assertion issues * remove random_forest module and add kmerf to independence * remove benchmarks folder (ref new repo) * fix black formatting * add ksample kmerf * add kmerf docstrings * add time series sim reference * rename k-sample heading * add time series reference * speed up doctest times * flake8 warning fixes * simplify __all__ for modules * simplify title ksample * add permutation docstrings * link to p-value computation methods * add updates for ksample paper * skip discrim doctests (slow)
neurodata · Jan 12, 2021 · 4cd7844 · 4cd7844
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diff --git a/README.md b/README.md
@@ -17,11 +17,7 @@
 - **Issues:** [https://github.com/neurodata/hyppo/issues](https://github.com/neurodata/hyppo/issues)
 - **Contribution Guide:** [https://hyppo.neurodata.io/contributing.html](https://hyppo.neurodata.io/contributing.html)
 
-Some system/package requirements:
-
-- **Python**: 3.6+
-- **OS**: All major platforms (Linux, macOS, Windows)
-- **Dependencies**: `numpy`, `scipy`, `numba`, `scikit-learn`
+**Note: We have recently moved our `benchmarks` (with relevant figure replication code for our papers) folder to a new [repo](https://github.com/neurodata/hyppo-papers)!** We aim to add test development code and paper figure replication code there, and will add relevant tests (with tutorials) to ``hyppo``.
 
 `hyppo` intends to be a comprehensive multivariate hypothesis testing package and runs on all major versions of operating systems. It also includes novel tests not found in other packages. It is quick to install and free of charge. If you need to use multivariate hypothesis testing, be sure to give `hyppo` a try!
 

diff --git a/benchmarks/2samp_alg_speed.ipynb b/benchmarks/2samp_alg_speed.ipynb
diff --git a/benchmarks/2samp_power_angle.ipynb b/benchmarks/2samp_power_angle.ipynb
diff --git a/benchmarks/2samp_power_dimension.ipynb b/benchmarks/2samp_power_dimension.ipynb
diff --git a/benchmarks/2samp_power_sampsize.ipynb b/benchmarks/2samp_power_sampsize.ipynb
diff --git a/benchmarks/2samp_simulations.ipynb b/benchmarks/2samp_simulations.ipynb
diff --git a/benchmarks/2samp_vs_angle/circle_CCA.csv b/benchmarks/2samp_vs_angle/circle_CCA.csv
diff --git a/benchmarks/2samp_vs_angle/circle_Dcorr.csv b/benchmarks/2samp_vs_angle/circle_Dcorr.csv
diff --git a/benchmarks/2samp_vs_angle/circle_HHG.csv b/benchmarks/2samp_vs_angle/circle_HHG.csv
diff --git a/benchmarks/2samp_vs_angle/circle_Hsic.csv b/benchmarks/2samp_vs_angle/circle_Hsic.csv
diff --git a/benchmarks/2samp_vs_angle/circle_MGC.csv b/benchmarks/2samp_vs_angle/circle_MGC.csv
diff --git a/benchmarks/2samp_vs_angle/circle_Manova.csv b/benchmarks/2samp_vs_angle/circle_Manova.csv
diff --git a/benchmarks/2samp_vs_angle/circle_RManova.csv b/benchmarks/2samp_vs_angle/circle_RManova.csv
diff --git a/benchmarks/2samp_vs_angle/circle_RV.csv b/benchmarks/2samp_vs_angle/circle_RV.csv
diff --git a/benchmarks/2samp_vs_angle/cubic_CCA.csv b/benchmarks/2samp_vs_angle/cubic_CCA.csv
diff --git a/benchmarks/2samp_vs_angle/cubic_Dcorr.csv b/benchmarks/2samp_vs_angle/cubic_Dcorr.csv
diff --git a/benchmarks/2samp_vs_angle/cubic_HHG.csv b/benchmarks/2samp_vs_angle/cubic_HHG.csv
diff --git a/benchmarks/2samp_vs_angle/cubic_Hsic.csv b/benchmarks/2samp_vs_angle/cubic_Hsic.csv
diff --git a/benchmarks/2samp_vs_angle/cubic_MGC.csv b/benchmarks/2samp_vs_angle/cubic_MGC.csv
diff --git a/benchmarks/2samp_vs_angle/cubic_Manova.csv b/benchmarks/2samp_vs_angle/cubic_Manova.csv
diff --git a/benchmarks/2samp_vs_angle/cubic_RManova.csv b/benchmarks/2samp_vs_angle/cubic_RManova.csv
diff --git a/benchmarks/2samp_vs_angle/cubic_RV.csv b/benchmarks/2samp_vs_angle/cubic_RV.csv
diff --git a/benchmarks/2samp_vs_angle/diamond_CCA.csv b/benchmarks/2samp_vs_angle/diamond_CCA.csv
diff --git a/benchmarks/2samp_vs_angle/diamond_Dcorr.csv b/benchmarks/2samp_vs_angle/diamond_Dcorr.csv
diff --git a/benchmarks/2samp_vs_angle/diamond_HHG.csv b/benchmarks/2samp_vs_angle/diamond_HHG.csv