change mgc to hyppo (#56)

* fix black formatting * upgrade to joblib and add default permutation test (#52) (#54) * upgrade to joblib and add default permutation test * fix assertion errors * fix block_size error * fix black formatting * remove random state and local dcorr tests * Update independence.ipynb * reformat to black code * match notebooks to figures in paper * updated algorith speed code * just run HHG on this test * Update indep_alg_speed.ipynb * updated benchmark code * remove random forest module * update figure 1 of paper * update mgc references to hyppo * Fix bold letters in index.rst * correct code coverage calculation * make header longer in contributing * change references from mgc to hyppo
neurodata · Feb 17, 2020 · 5b9cbf4 · 5b9cbf4
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diff --git a/.coveragerc b/.coveragerc
@@ -10,4 +10,4 @@ show_missing = True
 omit =
     *tests*
     *__init__.py
-    *mgc/_utils.py
+    *hyppo/_utils.py
diff --git a/.github/ISSUE_TEMPLATE/bug_report.md b/.github/ISSUE_TEMPLATE/bug_report.md
@@ -1,6 +1,6 @@
 ---
 name: Bug Report
-about: Create a report to help us improve mgc
+about: Create a report to help us improve hyppo
 label: bug
 
 ---

diff --git a/.github/ISSUE_TEMPLATE/documentation_fix.md b/.github/ISSUE_TEMPLATE/documentation_fix.md
@@ -1,6 +1,6 @@
 ---
 name: Documentation Fix
-about: Create a report to help us improve the documentation of mgc
+about: Create a report to help us improve the documentation of hyppo
 label: documentation
 
 ---

diff --git a/.github/ISSUE_TEMPLATE/feature_request.md b/.github/ISSUE_TEMPLATE/feature_request.md
@@ -1,6 +1,6 @@
 ---
 name: Feature Request
-about: Suggest an idea for mgc
+about: Suggest an idea for hyppo
 label: enhancement
 
 ---

diff --git a/.travis.yml b/.travis.yml
@@ -27,8 +27,8 @@ install:
 - if [[ $TRAVIS_PYTHON_VERSION != '3.5' ]]; then travis_retry pip install black; fi
 
 script:
-- pytest mgc/
-- if [[ $TRAVIS_PYTHON_VERSION != '3.5' ]]; then black --check --diff ./mgc; fi
+- pytest hyppo/
+- if [[ $TRAVIS_PYTHON_VERSION != '3.5' ]]; then black --check --diff ./hyppo; fi
 
 after_success:
 - codecov

diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
@@ -1,22 +1,22 @@
-Contributing to mgc
-===================
+Contributing to hyppo
+=====================
 
 (adopted from scikit-learn)
 
 The latest contributing guide is available in the repository at
 `docs/contributing.rst`, or online at:
 
-[https://mgc.neurodata.io/contributing.html](https://mgc.neurodata.io/contributing.html)
+[https://hyppo.neurodata.io/contributing.html](https://hyppo.neurodata.io/contributing.html)
 
-There are many ways to contribute to mgc, with the most common ones
+There are many ways to contribute to `hyppo`, with the most common ones
 being contribution of code or documentation to the project. Improving the
 documentation is no less important than improving the library itself. If you
 find a typo in the documentation, or have made improvements,do not hesitate to
 submit a GitHub pull request. Documentation can be found under the
-[docs/](https://github.com/neurodata/mgc/tree/master/docs) directory.
+[docs/](https://github.com/neurodata/hyppo/tree/master/docs) directory.
 
 But there are many other ways to help. In particular answering queries on the
-[issue tracker](https://github.com/neurodata/mgc/issues), and
+[issue tracker](https://github.com/neurodata/hyppo/issues), and
 investigating bugs are very valuable contributions that decrease the burden on
 the project maintainers.
 
@@ -28,9 +28,9 @@ link to it from your website, or simply star it in GitHub to say "I use it".
 Quick links
 -----------
 
-* [Submitting a bug report or feature request](http://mgc.neurodata.io/contributing.html#submitting-a-bug-report-or-a-feature-request)
-* [Contributing code](http://mgc.neurodata.io/contributing.html#contributing-code)
-* [Coding guidelines](http://mgc.neurodata.io/contributing.html#coding-guidelines)
+* [Submitting a bug report or feature request](http://hyppo.neurodata.io/contributing.html#submitting-a-bug-report-or-a-feature-request)
+* [Contributing code](http://hyppo.neurodata.io/contributing.html#contributing-code)
+* [Coding guidelines](http://hyppo.neurodata.io/contributing.html#coding-guidelines)
 
 Code of Conduct
 ---------------

diff --git a/LICENSE b/LICENSE
@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2019 Sambit Panda
+Copyright (c) 2019 Neurodata
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

diff --git a/README.md b/README.md
@@ -1,12 +1,12 @@
-# mgc
+# hyppo
 
 [![Build Status](https://travis-ci.org/neurodata/mgc.svg?branch=master)](https://travis-ci.org/neurodata/mgc)
 [![codecov](https://codecov.io/gh/neurodata/mgc/branch/master/graph/badge.svg)](https://codecov.io/gh/neurodata/mgc)
 [![PyPI version](https://img.shields.io/pypi/v/mgc.svg)](https://pypi.org/project/mgc/)
 [![License](https://img.shields.io/github/license/neurodata/mgc)](https://mgc.neurodata.io/license.html)
 [![arXiv shield](https://img.shields.io/badge/arXiv-1907.02088-red.svg?style=flat)](https://arxiv.org/abs/1907.02088)
 
-`mgc` (pronounced "Magic") is an open-source software package for independence and k-sample testing.
+`hyppo` (**HYP**othesis Testing in **P**yth**O**n, pronounced "Hippo") is an open-source software package for independence and k-sample testing.
 
 - **Installation Guide:** [https://mgc.neurodata.io/install.html](https://mgc.neurodata.io/install.html)
 - **Documentation:** [https://mgc.neurodata.io/](https://mgc.neurodata.io/)
@@ -15,4 +15,4 @@
 - **Issues:** [https://github.com/neurodata/mgc/issues](https://github.com/neurodata/mgc/issues)
 - **Contribution Guide:** [https://mgc.neurodata.io/contributing.html](https://mgc.neurodata.io/contributing.html)
 
-`mgc` intends to be a comprehensive independence and k-sample testing package and runs on all major versions of operating systems. It also includes novel tests not found in other packages that operate on multivariate data. It is quick to install and free of charge. If you need to use high dimensional independence or k-sample testing, be sure to give `mgc` a try!
+`hyppo` intends to be a comprehensive independence and k-sample testing package and runs on all major versions of operating systems. It also includes novel tests not found in other packages that operate on multivariate data. 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
@@ -12,14 +12,14 @@
     "import sys, os\n",
     "sys.path.append(os.path.realpath('..'))\n",
     "\n",
-    "from mgc.ksample import KSample\n",
-    "from mgc.independence import *\n",
-    "from mgc.sims import linear"
+    "from hyppo.ksample import KSample\n",
+    "from hyppo.independence import *\n",
+    "from hyppo.sims import linear"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 11,
+   "execution_count": 2,
    "metadata": {},
    "outputs": [],
    "source": [

diff --git a/benchmarks/2samp_power_angle.ipynb b/benchmarks/2samp_power_angle.ipynb
@@ -28,8 +28,8 @@
     "import matplotlib.pyplot as plt\n",
     "\n",
     "from benchmarks import power_2samp_angle\n",
-    "from mgc.independence import CCA, Dcorr, HHG, Hsic, RV, MGC\n",
-    "from mgc.sims import *\n",
+    "from hyppo.independence import CCA, Dcorr, HHG, Hsic, RV, MGC\n",
+    "from hyppo.sims import *\n",
     "\n",
     "sys.path.append(os.path.realpath('..'))"
    ]

diff --git a/benchmarks/2samp_power_dimension.ipynb b/benchmarks/2samp_power_dimension.ipynb
@@ -28,8 +28,8 @@
     "import matplotlib.pyplot as plt\n",
     "\n",
     "from benchmarks import power_2samp_dimension\n",
-    "from mgc.independence import CCA, Dcorr, HHG, Hsic, RV, MGC\n",
-    "from mgc.sims import *\n",
+    "from hyppo.independence import CCA, Dcorr, HHG, Hsic, RV, MGC\n",
+    "from hyppo.sims import *\n",
     "\n",
     "sys.path.append(os.path.realpath('..'))"
    ]

diff --git a/benchmarks/2samp_power_sampsize.ipynb b/benchmarks/2samp_power_sampsize.ipynb
@@ -28,8 +28,8 @@
     "import matplotlib.pyplot as plt\n",
     "\n",
     "from benchmarks import power_2samp_sample\n",
-    "from mgc.independence import CCA, Dcorr, HHG, Hsic, RV, MGC\n",
-    "from mgc.sims import *\n",
+    "from hyppo.independence import CCA, Dcorr, HHG, Hsic, RV, MGC\n",
+    "from hyppo.sims import *\n",
     "\n",
     "sys.path.append(os.path.realpath('..'))"
    ]

diff --git a/benchmarks/2samp_simulations.ipynb b/benchmarks/2samp_simulations.ipynb
@@ -24,7 +24,7 @@
     "import matplotlib.pyplot as plt\n",
     "from tqdm.notebook import tqdm\n",
     "\n",
-    "from mgc.sims import *"
+    "from hyppo.sims import *"
    ]
   },
   {

diff --git a/benchmarks/3samp_power_epsilon.ipynb b/benchmarks/3samp_power_epsilon.ipynb
@@ -16,7 +16,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": 1,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -28,8 +28,8 @@
     "from matplotlib.legend import Legend\n",
     "\n",
     "from benchmarks import power_3samp_epsweight\n",
-    "from mgc.independence import Dcorr, Hsic, MGC\n",
-    "from mgc.sims import gaussian_3samp\n",
+    "from hyppo.independence import Dcorr, Hsic, MGC\n",
+    "from hyppo.sims import gaussian_3samp\n",
     "\n",
     "sys.path.append(os.path.realpath('..'))"
    ]

diff --git a/benchmarks/figs/indep_wall_times.pdf b/benchmarks/figs/indep_wall_times.pdf
diff --git a/benchmarks/figs/same_stat.pdf b/benchmarks/figs/same_stat.pdf
diff --git a/benchmarks/indep_alg_speed.R b/benchmarks/indep_alg_speed.R
@@ -1,19 +1,26 @@
 require("energy")
 require("kernlab")
 require("mgc")
+require("HHG")
 require("microbenchmark")
 
-num_samples_range = c(20, 50, 100, 200, 500, 1000, 2000, 5000, 10000)
+num_samples_range = c(50, 100, 200, 500, 1000, 2000, 5000, 10000)
 linear_data <- list()
 i <- 1
 for (num_samples in num_samples_range){
-  data <- mgc.sims.linear(num_samples, 1, eps=0.1)
+  data <- mgc.sims.linear(num_samples, 1)
+  x <- data$X
+  y <- data$Y
   times = seq(1, 3, by=1)
   executions <- list()
   for (t in times){
-    func <- kmmd
-    #func <- dcov.test
-    time_taken <- microbenchmark(func(data$X, data$Y), times=1, unit="secs") # best of 5 executions
+    #x <- as.matrix(dist((x), diag = TRUE, upper = TRUE))
+    #y <- as.matrix(dist((y), diag = TRUE, upper = TRUE))
+    #time_taken <- microbenchmark(kmmd(x, y, ntimes=1000), times=1, unit="secs") # best of 5 executions
+    #time_taken <- microbenchmark(dcor.test(x, y, R=1000), times=1, unit="secs") # best of 5 executions
+    #time_taken <- microbenchmark(dcor.test(x, y, R=1000), times=1, unit="secs") # best of 5 executions
+    time_taken <- microbenchmark(dcor2d(x, y), times=1, unit="secs") # best of 5 executions
+    #time_taken <- microbenchmark(hhg.test(x, y, nr.perm = 1000), times=1, unit="secs") # best of 5 executions
     executions <- c(executions, list(time_taken[1, 2]/(10^9)))
   }
   linear_data <- c(linear_data, list(sapply(executions, mean)))
@@ -22,4 +29,5 @@ for (num_samples in num_samples_range){
   i <- i + 1
 }
 
-print(linear_data)
+df <- data.frame(matrix(unlist(linear_data), nrow=length(linear_data), byrow=T), stringsAsFactors=FALSE)
+write.csv(df, row.names=FALSE)