Conditional Correlation Tests #349
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* perm tree docs * base docstrings
* sort imports * fix docs error short underline * add energy source code * fix tutorials not rendering * add more detail to compute distance and kernel
* Add .circleci/config.yml * remove travis config and lower parallel * use new circleci config file * fix setup.py init * add codecov package * fix circle ci build issues * remove build from yaml * remove build * fix ci build errors * rerun circle ci * set docker image for deployment * parralelize circleci config * Update config.yml * fix cache issues * don't cache test suite * see if cimg to circleci fixes build * back to cimg * fix cache issues * remove test dependence on build * change cache among python versions * maintain order for build * change cache * run on lowest environment packages * use min python versions * don't test 3.8 * add joblib as a dependency * add joblib * set llvm version * update llvm before numba * workers default should be 1 * fix python 3.7 failings * raise base sklearn package * remove smoke test
* speed up circleci builds * add module definition * change name from build * change required branch * set workflows * change parameter names * name parameter preserved * name param reserved * numpy conditional on python version * forgot equal sign * fix python version issues * fix 3.6 dependency issues * fix requirements.txt * fix duplicate requirements error * upgrade pip fix double requirement * upload code coverage correctly * add pytest-cov * change location of coverage reports * Updated config.yml * default file * use coveralls instead * add codecov orb * fix coverage not uploading * Update config.yml * add proper path for coverage reports * fix codecov reports * limit coverage per module
* use xml for coverage reports * change to project root * fix name of file * use terminal command instead of orb * use codecov orb for faster report merges * use orb to merge reports faster
* update readme badges * update readme badges
* sort imports * fix docs error short underline * add energy source code * fix tutorials not rendering * add more detail to compute distance and kernel * add tutorials folder with overview * add folder to gitignore * add contributing guidelines to github repo * make docs look nicer * change reference to use automodule * add changelog to single file * remove reference folder * make clear the package reqs needs to be installed * simplify autosummary table * remove old changelog files * add file with all automodules * change docs layout * add gallery and misc docs changes * change order of sidebar * make install docs more clear * update makefile with autogen and more options * update docs package requirements * remove github_links file * remove old tutorial folder * remove tutorials and gallery folders from docs * add discriminability * add statistic to the docs * fix dcorr and hsic incorrect stats * add citation page * add internal links within docs * use readme in index.rst * add links for dependencies * use meth and class * update doc requirements * remove docs tutorial page * update README to rst * Update setup.py * fix reference docs formatting * remove figure from package overview * add example folder * add mgc map example * add independence simulations example * add feature importance example * install package pip netlify * Update netlify.toml * add recommonmark * add matplotlib and seaborn * add tutorials and mmd * add disco * update doctest errors * Update mmd.py * fix intersphinx mapping * move gaussian sim to new example * remove reps warning * add fast 1D Dcorr * add helper functions reference * add manova and hotelling * fix documentation weird renderings * remove unused import indep_sims * add max margin test * fix doctest assertion errors * cache numba * add k-sample tutorial * move general example to overview py file * add time-series tutorial * add time series tutorial * add time series sims * fix tutorials * add v to tag name * change order of independence test * add discriminability tutorial * change name of time series sim file * [skip ci] clean netlify directory * [skip ci] rebuild docs * [skip ci] update netlify runtime version * change netlify build command to fix intersphinx
* fix overview rendering issue * increment version * update changelog * fix changelog release date * remove make clean in netlify toml * README codecov typo
* incorporate changes from other branches to master (#175) * update changelog rendering * expose independence tests dictionary * add same statistic example * expose time series dict * add max margin test * remove warning js button * add anton kernel fix * update same statistic * add performance comparison example * rename common test file * add dictionary for k-sample tests * add docs dependencies to README * remove perf file rename 1d * add information about base classes * improve test coverage * reformat black * reformat with upgraded black * improve coverage * [skip-ci] add discrim error check * add question template * Update CONTRIBUTING.md * add power * update misc docs * add independence power curves * Type i error checks (#178) * add benchmarks folder to gitignore * sum used to prevent deprecation warning * fix fast 1D dcorr invalid implementation * add power unit tests * add base classes to documentation * fix doctest assertion errors * rename codecov so yml shows up * fix pytest assertions * update version to 0.2.1 * add changelog for new version
* Delete cubic_Hsic.csv * Delete cubic_KMERF.csv * Delete cubic_MGC.csv * Delete cubic_RV.csv * Delete diamond_CCA.csv * Delete diamond_Dcorr.csv * Delete diamond_HHG.csv * Delete diamond_Hsic.csv * Delete diamond_KMERF.csv * Delete diamond_MGC.csv * Delete diamond_RV.csv * Delete ellipse_CCA.csv * Delete ellipse_Dcorr.csv * Delete ellipse_HHG.csv * Delete ellipse_Hsic.csv * Delete ellipse_KMERF.csv * Delete ellipse_MGC.csv * Delete ellipse_RV.csv * Delete w_shaped_CCA.csv * Delete w_shaped_Dcorr.csv * Delete w_shaped_HHG.csv * Delete w_shaped_Hsic.csv * Delete w_shaped_KMERF.csv * Delete w_shaped_MGC.csv * Delete w_shaped_RV.csv * Delete uncorrelated_bernoulli_CCA.csv * Delete uncorrelated_bernoulli_Dcorr.csv * Delete uncorrelated_bernoulli_HHG.csv * Delete uncorrelated_bernoulli_Hsic.csv * Delete uncorrelated_bernoulli_KMERF.csv * Delete uncorrelated_bernoulli_MGC.csv * Delete uncorrelated_bernoulli_RV.csv * Delete two_parabolas_CCA.csv * Delete two_parabolas_Dcorr.csv * Delete two_parabolas_HHG.csv * Delete two_parabolas_Hsic.csv * Delete two_parabolas_KMERF.csv * Delete two_parabolas_MGC.csv * Delete two_parabolas_RV.csv * Delete step_CCA.csv * Delete step_Dcorr.csv * Delete step_HHG.csv * Delete step_Hsic.csv * Delete step_KMERF.csv * Delete step_MGC.csv * Delete step_RV.csv * Delete exponential_CCA.csv * Delete exponential_Dcorr.csv * Delete exponential_HHG.csv * Delete exponential_Hsic.csv * Delete exponential_KMERF.csv * Delete exponential_MGC.csv * Delete exponential_RV.csv * Delete square_CCA.csv * Delete square_Dcorr.csv * Delete square_HHG.csv * Delete square_Hsic.csv * Delete square_KMERF.csv * Delete square_MGC.csv * Delete square_RV.csv * Delete spiral_CCA.csv * Delete spiral_Dcorr.csv * Delete spiral_HHG.csv * Delete spiral_Hsic.csv * Delete spiral_KMERF.csv * Delete spiral_MGC.csv * Delete spiral_RV.csv * Delete sin_sixteen_pi_CCA.csv * Delete sin_sixteen_pi_Dcorr.csv * Delete sin_sixteen_pi_HHG.csv * Delete sin_sixteen_pi_Hsic.csv * Delete sin_sixteen_pi_KMERF.csv * Delete sin_sixteen_pi_MGC.csv * Delete sin_sixteen_pi_RV.csv * Delete fourth_root_CCA.csv * Delete fourth_root_Dcorr.csv * Delete fourth_root_HHG.csv * Delete fourth_root_Hsic.csv * Delete fourth_root_KMERF.csv * Delete fourth_root_MGC.csv * Delete fourth_root_RV.csv * Delete joint_normal_CCA.csv * Delete joint_normal_Dcorr.csv * Delete joint_normal_HHG.csv * Delete joint_normal_Hsic.csv * Delete joint_normal_KMERF.csv * Delete joint_normal_MGC.csv * Delete joint_normal_RV.csv * Delete sin_four_pi_CCA.csv * Delete sin_four_pi_Dcorr.csv * Delete sin_four_pi_HHG.csv * Delete sin_four_pi_Hsic.csv * Delete sin_four_pi_KMERF.csv * Delete sin_four_pi_MGC.csv * Delete sin_four_pi_RV.csv * Delete quadratic_CCA.csv * Delete quadratic_Dcorr.csv * Delete quadratic_HHG.csv * Delete quadratic_Hsic.csv * Delete quadratic_KMERF.csv * Delete quadratic_MGC.csv * Delete quadratic_RV.csv * Delete multiplicative_noise_CCA.csv * Delete multiplicative_noise_Dcorr.csv * Delete multiplicative_noise_HHG.csv * Delete multiplicative_noise_Hsic.csv * Delete multiplicative_noise_KMERF.csv * Delete multiplicative_noise_MGC.csv * Delete multiplicative_noise_RV.csv * Delete multimodal_independence_CCA.csv * Delete multimodal_independence_Dcorr.csv * Delete multimodal_independence_HHG.csv * Delete multimodal_independence_Hsic.csv * Delete multimodal_independence_KMERF.csv * Delete multimodal_independence_MGC.csv * Delete multimodal_independence_RV.csv * Delete logarithmic_CCA.csv * Delete logarithmic_Dcorr.csv * Delete logarithmic_HHG.csv * Delete logarithmic_Hsic.csv * Delete logarithmic_KMERF.csv * Delete logarithmic_MGC.csv * Delete logarithmic_RV.csv * Delete linear_CCA.csv * Delete linear_Dcorr.csv * Delete linear_HHG.csv * Delete linear_Hsic.csv * Delete linear_KMERF.csv * Delete linear_MGC.csv * Delete linear_RV.csv * Delete circle_CCA.csv * Delete circle_Dcorr.csv * Delete circle_HHG.csv * Delete circle_Hsic.csv * Delete circle_MGC.csv * Delete circle_RV.csv * Delete cubic_CCA.csv * Delete cubic_Dcorr.csv * Delete cubic_HHG.csv * Delete cubic_MGC.csv * Delete cubic_Hsic.csv * Delete cubic_RV.csv * Delete diamond_CCA.csv * Delete diamond_Dcorr.csv * Delete diamond_HHG.csv * Delete diamond_Hsic.csv * Delete diamond_MGC.csv * Delete diamond_RV.csv * Delete ellipse_CCA.csv * Delete ellipse_Dcorr.csv * Delete ellipse_HHG.csv * Delete ellipse_Hsic.csv * Delete ellipse_MGC.csv * Delete ellipse_RV.csv * Delete exponential_CCA.csv * Delete exponential_Dcorr.csv * Delete exponential_HHG.csv * Delete exponential_Hsic.csv * Delete exponential_MGC.csv * Delete exponential_RV.csv * Delete fourth_root_CCA.csv * Delete fourth_root_Dcorr.csv * Delete fourth_root_HHG.csv * Delete fourth_root_Hsic.csv * Delete fourth_root_MGC.csv * Delete fourth_root_RV.csv * Delete joint_normal_CCA.csv * Delete joint_normal_Dcorr.csv * Delete joint_normal_HHG.csv * Delete joint_normal_Hsic.csv * Delete joint_normal_MGC.csv * Delete joint_normal_RV.csv * Delete linear_CCA.csv * Delete linear_Dcorr.csv * Delete linear_HHG.csv * Delete linear_Hsic.csv * Delete linear_MGC.csv * Delete linear_RV.csv * Delete logarithmic_CCA.csv * Delete logarithmic_Dcorr.csv * Delete logarithmic_HHG.csv * Delete logarithmic_Hsic.csv * Delete logarithmic_MGC.csv * Delete logarithmic_RV.csv * Delete w_shaped_CCA.csv * Delete w_shaped_Dcorr.csv * Delete w_shaped_HHG.csv * Delete w_shaped_Hsic.csv * Delete w_shaped_MGC.csv * Delete w_shaped_RV.csv * Delete uncorrelated_bernoulli_CCA.csv * Delete uncorrelated_bernoulli_Dcorr.csv * Delete uncorrelated_bernoulli_HHG.csv * Delete uncorrelated_bernoulli_Hsic.csv * Delete uncorrelated_bernoulli_MGC.csv * Delete uncorrelated_bernoulli_RV.csv * Delete two_parabolas_CCA.csv * Delete two_parabolas_Dcorr.csv * Delete two_parabolas_HHG.csv * Delete two_parabolas_Hsic.csv * Delete two_parabolas_MGC.csv * Delete two_parabolas_RV.csv * Delete step_CCA.csv * Delete step_Dcorr.csv * Delete step_HHG.csv * Delete step_Hsic.csv * Delete step_MGC.csv * Delete step_RV.csv * Delete square_CCA.csv * Delete square_Dcorr.csv * Delete square_HHG.csv * Delete square_Hsic.csv * Delete square_MGC.csv * Delete square_RV.csv * Delete spiral_CCA.csv * Delete spiral_Dcorr.csv * Delete spiral_HHG.csv * Delete spiral_Hsic.csv * Delete spiral_MGC.csv * Delete spiral_RV.csv * Delete multimodal_independence_CCA.csv * Delete multimodal_independence_Dcorr.csv * Delete multimodal_independence_HHG.csv * Delete multimodal_independence_Hsic.csv * Delete multimodal_independence_MGC.csv * Delete multimodal_independence_RV.csv * Delete multiplicative_noise_CCA.csv * Delete multiplicative_noise_Dcorr.csv * Delete multiplicative_noise_HHG.csv * Delete multiplicative_noise_Hsic.csv * Delete multiplicative_noise_MGC.csv * Delete multiplicative_noise_RV.csv * Delete sin_sixteen_pi_CCA.csv * Delete sin_sixteen_pi_Dcorr.csv * Delete sin_sixteen_pi_HHG.csv * Delete sin_sixteen_pi_Hsic.csv * Delete sin_sixteen_pi_MGC.csv * Delete sin_sixteen_pi_RV.csv * Delete sin_four_pi_CCA.csv * Delete sin_four_pi_Dcorr.csv * Delete sin_four_pi_HHG.csv * Delete sin_four_pi_Hsic.csv * Delete sin_four_pi_MGC.csv * Delete sin_four_pi_RV.csv * Delete quadratic_CCA.csv * Delete quadratic_Dcorr.csv * Delete quadratic_HHG.csv * Delete quadratic_Hsic.csv * Delete quadratic_MGC.csv * Delete quadratic_RV.csv
* update maxmargin fast dcorr * add accessibility changes
* make median kernel default for rbf and gaussian * recache dependencies * increment cache key
* Update LICENSE * Switch to MIT license * Switch to MIT license
* Added typing to output of test methods. Updated requirements. * Removed inheritance of namedtuple because it doesn't work as expected. * Removed unnecessary requirements.
* fix same stat formatting issues * don't numbify max margin Dcorr * misc doc changes * backreference api link correctly * fix custom css * update accessibility colors * fix rst spacing * try removing custom css * Update conf.py * change recommonmark to new parser * explicitly define doc requirements * bring back recommonmark
* remove master references * change edit on github to create issue instead * fix broken links * fix rst file urls * fix broken urls * use documentation github issue template for api sphinx files
* reproducibility to perm test * remove import * add random_state as parameter * remove noseids * Delete .noseids * remove comment * add randomness based on parameter * add reproducibility to discrim tests * reproducibility tests for independence * fix independence tests * actually fix independence tests * reproducibility to ksample tests * add reproducibility to time series tests * add newline * reproducibility to time series tests only * modify examples Co-authored-by: Haoyin Xu <haoyinxu@gmail.com> Co-authored-by: Sambit Panda <36676569+sampan501@users.noreply.github.com>
* MAINT update license in setup * MAINT update license
Codecov ReportAttention:
Additional details and impacted files@@ Coverage Diff @@
## main #349 +/- ##
==========================================
+ Coverage 96.71% 96.80% +0.09%
==========================================
Files 86 96 +10
Lines 3891 4504 +613
==========================================
+ Hits 3763 4360 +597
- Misses 128 144 +16 ☔ View full report in Codecov by Sentry. |
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@j1c The only thing missing is a few unit tests for some of the error checks. Once those are added, I'll merge |
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@j1c Let me know when you believe that everything looks good and I'll review |
This is good to go. |
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Reference issue
Closes #332
Type of change
Addition of three correlation based conditional independence tests.
Others
Additional information
Few functions in
toolswere changed to accommodate for three input data matrices.compute_dist_check_distmat_perm_statperm_test