Creating a goodness-of-fit module in hyppo #232
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sampan501
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Dec 6, 2021
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You need to modify the CircleCI config file so that your tests are actually run.
Is this taken from here: https://github.com/wittawatj/fsic-test. If so, you have to attribute where you got this code from. I noticed that much of it was copied and pasted, and does not follow hyppo conventions or Python conventions. Also, much of the code, while appropriate for a Python 2.7 paper, is not necessary to include in a Python 3.8 version like our package. Please rewrite to remove these redundancies and replace with functions calls already in scipy, numpy, or scikit-learn.
I gave a couple of examples in the review so far, but since this will likely require a major rewrite and removing of code, I would remove all the extraneous functions first, and then I can review the code again and go through all the lines.
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I'm sorry, I meant to attribute the implementation to the Wittawat implementation in a README file located within the module that I was going to include following first pass of the draft. That's my mistake. Will sort through your comments and remove any redundancies and extraneous lines. Where would you like me to give credit to the original author? |
As a comment at the location of the code. Link to the repo |
sampan501
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Dec 10, 2021
sampan501
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Dec 17, 2021
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Docstrings are formatted incorrectly. See this as an example for a base class. See this as an example for your methods class. Make sure that tabbing and description is there for all your parameters, otherwise the documentation will not render correctly.
Make sure you edit this so your tutorial shows up on the website
sampan501
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Dec 20, 2021
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Few documentation errors on this page and the tutorial is not building. Also problems here for the misc functions not rendering
sampan501
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Dec 20, 2021
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* Update permutation tree/block docstrings (#157) * perm tree docs * base docstrings * create wrapper class for Energy (#160) * sort imports * fix docs error short underline * add energy source code * fix tutorials not rendering * add more detail to compute distance and kernel * Move to Circle CI (#163) * 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 (#164) * 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 (#165) * 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 (#166) * update readme badges * update readme badges * Update README.md * improve documentation (#167) * 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 * Release v0.2.0 (#169) * fix overview rendering issue * increment version * update changelog * fix changelog release date * remove make clean in netlify toml * README codecov typo * change pypi long description format * release v0.2.1 (#179) * 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 * rename badges to main in README * make file names for benchmarks lower case * Remove extraneous benchmarks (#180) * 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 * make changes to improve diversity and inclusion (#189) * update maxmargin fast dcorr * add accessibility changes * change l1 distance to l2 for median heuristic (#191) * add reference to paper within fast docstring * reformat to black * make median kernel default for rbf and gaussian (#196) * make median kernel default for rbf and gaussian * recache dependencies * increment cache key * Switch to MIT license (#198) * Update LICENSE * Switch to MIT license * Switch to MIT license * Added typing to output of test methods. Updated requirements. (#201) * Added typing to output of test methods. Updated requirements. * Removed inheritance of namedtuple because it doesn't work as expected. * Removed unnecessary requirements. * fix docs website formatting issues (#197) * 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 * update preprints to published version (#202) * add CITATION.cff (#204) * add bibtex to docs (#205) * remove master references (#208) * 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 * remove file references in bibtex * EHN update pytest orbs version (#217) * Reproducibility to Perm Tests (#212) * 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 (#224) * MAINT update license in setup * MAINT update license * MGC redundancy warning (#125) (#220) * MGC redundancy warning (#125) MGC redundancy warning (#125) MGC redundancy warning (#125) MGC redundancy warning (#125) MGC redundancy warning (#125) * make MGC Map warning more descriptive * rename testing class so pytest finds it Co-authored-by: Sambit Panda <36676569+sampan501@users.noreply.github.com> * Fix #228 (#230) * Fix #228 Adds `rng.permutation` reproducibility to `perm_test` @kareef928 * fix linter req * enable rng None default * always use permuter * add 3.9 support (#223) * test new python versions * test correct python versions * add new classifiers in setup.py * MAINT update badge versions * python versions are decided through pypi * iterate cache key circleci * limit to 3.9 since 3.10 the dependencies don't install * remove testing 3.10 Co-authored-by: Haoyin Xu <haoyinxu@gmail.com> * release hyppo 0.2.2 (#236) * fix inccorect p-value in unit tests * fix MGC unit tests * update version to 0.2.2 * release hyppo 0.2.2 (#236) (#237) (#241) * fix inccorect p-value in unit tests * fix MGC unit tests * update version to 0.2.2 * add permutation test example to docs (#242) * add permutation test example to docs * update heading underline * lower replications and datasets so example runs * change KMERF to Dcorr Co-authored-by: Ronan Perry <rflperry@gmail.com> * add description Co-authored-by: Ronan Perry <rflperry@gmail.com> * be more clear about descriptions Co-authored-by: Ronan Perry <rflperry@gmail.com> * Update examples/permutation_tree.py Co-authored-by: Ronan Perry <rflperry@gmail.com> Co-authored-by: Ronan Perry <rflperry@gmail.com> * Adding dHSIC (#233) * Create basic outline of dhsic.py * Making preliminary modifications to base class * Create skeleton for multivariate.py * Update multivariate.py skeleton * Update dhsic.py * Creating multivariate module * Add multivariate permutation test to tools * Add multi_compute_kern to tools * Add stat method to dhsic.py * Add tests for multi_compute_kern * Create _utils for multivariate class * Add skeleton for test method in dhsic.py * Adding unit tests for multi_perm_test * updating dhsic * Update dhsic.py * Adding docstring to dhsic * Fixing bugs * Add unit tests for dhsic * Adding dhsic to tutorial * Fixing pvalue bug and adding dhsic tutorial * Running black on modified files * Modify variable names and docstrings * Add tutorial for dHsic * Add unit tests for error checking functions * Add reference * Running black * Modify checks to be within class for coverage * Add tests for power.py * Running black on test_power.py * Documentation changes and fix rendering errors * Fix rendering error * Fixing rendering error * Fix math equation formatting * Add documentation to website * Edited the types in the documentation section. (#244) * I replaced ndarray with ndarray of floats * I replaced the types in the documentation * edited the documentation to float only * Edited the types in the documentation section of discrim_two_samp * Edited the args type in the base.py * edited types in dhsic.py * edited types in base.py * Edited types in base.py in independece * Edited types in cca.py in independence * Edited types in dorr.py in independence * Edited types in hhg.py in independence * Edited types in hsic.py * edited types in kmerf.py in independence * Edited types in max_margin.py * Edited types in mgc.py in independence * Edited types in rv.py in independence * Edited types in base.py in ksample * Edited types in disco.py in ksample * edited types in energy.py in ksample * Edited types in hotelling.py in ksample * Edited types in ksamp.py in ksample * Edited types in manova.py in ksample * Edited types in mmd.py in ksample * Edited types in base.py in time_series * Edited types in dcorrx.py in time_series * Edited types in mgcx.py in time_series * Edited types in common.py in tools * Edited types in the indep_sim.py in tools * Edited types in ksample_sim.py in tools * Edtited types in power.py in tools * Edited types in time_series_sim.py in tools * Types Update * Types update in base.py Co-authored-by: Sambit Panda <36676569+sampan501@users.noreply.github.com> * Fast tstest (#234) * Create smoothCF.py * Added mean_embedding * updated inheritance from IndependenceTest * Updated SmoothCF and ME tests to match author code output * Updated SmoothCF and ME inheritance, started editing tutorial * Updated documentation * Enabled numba, added docstrings * Minor change * Response to initial PR comments * Added random state to SmoothCF * ran black * ran black again * remove blank * quotes * Changed example * black * deleted * black + more changes * random_state added to ME * coverage * tests * black * more tests * tests * reformatting * reformat * reformat * added journal to citation (Fast 2-sample) * corrected docstring math format * formatting update, helper docstring update * Formatting changes, renaming of helpers, moved random_state * fix tabbing issue in ksample * added __init__ variable explanantions to tutorial * minor formatting change to tutorial * fix tutorial rendering issue Co-authored-by: Haoyin Xu <haoyinxu@gmail.com> Co-authored-by: Sambit Panda <36676569+sampan501@users.noreply.github.com> * Fast HHG Test (#238) * Integrated Fast HHG into original HHG code * Update hhg.py * Create Fast HHG Tester.ipynb * Update hhg.py * Update Fast HHG Tester.ipynb * Update Fast HHG Tester.ipynb * FastHHG Tester * Update * Update Fast HHG Tester.ipynb * Added Power Sample Size Results * Fast HHG updated with Hoeffdings and docstrings * Update hhg.py * Edited independence tutorial * Delete Fast HHG Tester.ipynb * Delete indep_power_sampsize (center).pdf * Delete OGTest1Figure.png * Delete OGTest1.png * Delete Function Outline.docx * release hyppo 0.2.2 (#236) (#237) * fix inccorect p-value in unit tests * fix MGC unit tests * update version to 0.2.2 * Black sampling and edits to tutorial * Black format check * Imported IndependenceTestOutput * Formatting Changes * Black formating * Black Formatting * Adjustments to Requested Changes Remove cdist - replace with compute_dist, modified description, changed 'fast' to 'auto' and simplifying of hoeffding's implementation to basic formula. * Edited Hoeffding Function * Added Unit Tests for Fast HHG Unit tests cover replicability, Type 1 Error, distance statistic implementation and 1D linear test. * Add citations to refs and to code * Black Formatting Sweep * Minor Edits * Transfer Fast HHG description to notes section * Removed Fast HHG description Added 'fast implementation' as a pro instead. * Updated Unit Tests * Adjustments Made 'auto' in test function instead of _init_. Adjustments all-around to match. Adjusted Hoeffding function to implement jit on inner function. Achieved much higher speeds thanks to it. * Added Toy Implementation to tutorial * Update independence.py * Black Formatting Sweep * Adjustments * Formatting sweep * Updated test to cover Hoeffding Statistic Function * Disabled JIT during test to possibly improve code coverage * Formatting * Removed unneeded import. * Fixed JIT coverage error + Black Format Sweep * [skip-ci] link to p-value method Co-authored-by: Sambit Panda <36676569+sampan501@users.noreply.github.com> * Creating a goodness-of-fit module in hyppo (#232) * Created kgof module * Added tutorial documentation * Resolved an import statement issue * first pass of removal of extraneous code * removed majority of extraneous functions in _utils.py * Further removal of redundancies + addition of citations * Removal of redundancies / unnecessary features * Removed NumpySeedContext to resolve redundancies with numpy.random default_rng * Removed further dependencies on np.random and replaced with default_rng() * Removed subsample_ind * added testing file for kernel.py * black formatting applied * added testing file for density.py and replaces all instances of np.random with default_rng() in data.py * Update index.rst * Updated circleci so tests run * Cleaned up docstrings and moved around functions (formatting) * Lots of cleanup and PR comments addressed * Rewrote necessary unit tests with pytest * Black reformatting * Removed extraneous imports * Dependencies installation attempt * Changed dependencies * removed extraneous imports * removed dependency on future * Fixed imports * Update fssd.py * fixed circular import issue * Black reformatting * Fixed import statements in unit test files * removed unittest * Modified import statements * Made testing edits * Testing edits * Black reformatting * Update test_fssd.py * Testing edits * Removed extraneous functions, rewrote tests * Update test_density.py * Removed extraneous functions from density.py * Removed extraneous functions and imports * Added test for density.Normal * Added tests for kernel.py * Fixed import error in test_kernel * Removed extraneous function from density.py * Removed extraneous GaussianMixture support * Added tests for data.py and removed extraneous function from data.py * Added tests for fssd.py * Added tests to test_kernel.py * Made changes to fssd syntax and added more tests for fssd * Added tests for fssd.py * black reformatting * Added more tests for data,py * density.py and data.py tests added * Removed extraneous code * Added more tests for fssd.py * Formatting fix * Changed description of base class. * Added kgof tutorial to index.rst, reformatted docstrings * Black reformatting in base.py * Fixed docstrings in fssd.py * Reformatted kgof tutorial * Fixed documentation and tutorial rendering issues * Fixed issues for misc functions not building * add current module back to misc and base class * Tutorial formatting changes * [skip ci] fix nabla math symbol Co-authored-by: Sambit Panda <36676569+sampan501@users.noreply.github.com> * Friedman Rafsky PR (#239) * Add files via upload * Add files via upload * Update and rename _friedmanRafsky.py to test_friedmanRafsky.py * Update test_friedmanRafsky.py * Update test_friedmanRafsky.py * Update test_friedmanRafsky.py * Update test_friedmanRafsky.py * Delete test_friedmanRafsky.py * Delete friedmanRafsky.py * Add files via upload * Delete friedmanRafsky.py * Add files via upload * Delete friedmanRafsky.py * Add files via upload * Update friedmanRafsky.py * Delete friedmanRafsky.py * Add files via upload * Update independence.py * Add files via upload * Update independence.py * Update friedmanRafsky.py * Delete friedmanRafsky.py * Add files via upload * Rename Update.py to friedmanRafsky.py * Update friedmanRafsky.py * Update friedmanRafsky.py * Add files via upload * Update index.rst * Update friedmanRafsky.py * Update friedmanRafsky.py * Update test_friedmanRafsky.py * Update __init__.py * Update test_friedmanRafsky.py * Rename friedmanRafsky.py to friedman_rafsky.py * Update __init__.py * Update and rename test_friedmanRafsky.py to test_friedman_rafsky.py * Update test_friedman_rafsky.py * Update __init__.py * Update test_friedman_rafsky.py * Update friedman_rafsky.py * Update index.rst * Update friedman_rafsky.py * Update friedman_rafsky.py * Update friedman_rafsky.py * Update friedman_rafsky.py * Update friedman_rafsky.py * Update friedman_rafsky.py * Update friedman_rafsky.py * Update friedman_rafsky.py * Update friedman_rafsky.py * Update friedman_rafsky.py * Update friedman_rafsky.py * Delete friedman_rafsky.py * Add files via upload * Rename Update.py to friedman_rafsky.py * Update friedman_rafsky.py * Update test_friedman_rafsky.py * Update friedman_rafsky.py * Update friedman_rafsky.py * Update test_friedman_rafsky.py * Update test_friedman_rafsky.py * Update friedman_rafsky.py * Update friedman_rafsky.py * Update test_friedman_rafsky.py * Update test_friedman_rafsky.py * Update test_friedman_rafsky.py * Update test_friedman_rafsky.py * Update test_friedman_rafsky.py * Update test_friedman_rafsky.py * Update test_friedman_rafsky.py * Update friedman_rafsky.py * Update test_friedman_rafsky.py * Update friedman_rafsky.py * Update independence.py * Delete friedman_rafsky.py * Add files via upload * Rename Update.py to friedman_rafsky.py * Update friedman_rafsky.py * Update friedman_rafsky.py * Update friedman_rafsky.py * Delete friedman_rafsky.py * Add files via upload * Rename Update.py to friedman_rafsky.py * Update friedman_rafsky.py * Update friedman_rafsky.py * Update friedman_rafsky.py * Update friedman_rafsky.py * Update friedman_rafsky.py * Update refs.bib * Update friedman_rafsky.py * Update friedman_rafsky.py * Update independence.py * Update friedman_rafsky.py * Update independence.py * Update independence.py * Update independence.py * Update independence.py * Update independence.py * Update independence.py * Update independence.py * Update 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Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Copy SciPy private `_contains_nan` function (#304) * copy scipy private contains nan function * update formatting based on black spec * reformatted before switching branches Co-authored-by: Sambit Panda <sampanda501@gmail.com> * release v0.3.0 * run jobs in parallel * release v0.3.0 * add autograd as a dependency * release v0.3.1 * remove emojis so windows can build package * release v0.3.2 * run pytest in parallel (#310) * run pytest in parallel * test files hyppo * install pytest * upload to codecov * fix codecov * compute coverage * run coverage * install pytest-cov * add coverage location * remove rep tests because random_state parameter * change reps to 3 * [skip ci] add change to changelog * add skip decorator for two sample circleci tests (#321) * update sphinx to fix jinja error (#319) * Refactor kgof module (#318) * Created kgof module * Added tutorial documentation * Resolved an import statement issue * first pass of removal of extraneous code * removed majority of extraneous functions in _utils.py * Further removal of redundancies + addition of citations * Removal of redundancies / unnecessary features * Removed NumpySeedContext to resolve redundancies with numpy.random default_rng * Removed further dependencies on np.random and replaced with default_rng() * Removed subsample_ind * added testing file for kernel.py * black formatting applied * added testing file for density.py and replaces all instances of np.random with default_rng() in data.py * Update index.rst * Updated circleci so tests run * Cleaned up docstrings and moved around functions (formatting) * Lots of cleanup and PR comments addressed * Rewrote necessary unit tests with pytest * Black reformatting * Removed extraneous imports * Dependencies installation attempt * Changed dependencies * removed extraneous imports * removed dependency on future * Fixed imports * Update fssd.py * fixed circular import issue * Black reformatting * Fixed import statements in unit test files * removed unittest * Modified import statements * Made testing edits * Testing edits * Black reformatting * Update test_fssd.py * Testing edits * Removed extraneous functions, rewrote tests * Update test_density.py * Removed extraneous functions from density.py * Removed extraneous functions and imports * Added test for density.Normal * Added tests for kernel.py * Fixed import error in test_kernel * Removed extraneous function from density.py * Removed extraneous GaussianMixture support * Added tests for data.py and removed extraneous function from data.py * Added tests for fssd.py * Added tests to test_kernel.py * Made changes to fssd syntax and added more tests for fssd * Added tests for fssd.py * black reformatting * Added more tests for data,py * density.py and data.py tests added * Removed extraneous code * Added more tests for fssd.py * Formatting fix * Changed description of base class. * Added kgof tutorial to index.rst, reformatted docstrings * Black reformatting in base.py * Fixed docstrings in fssd.py * Reformatted kgof tutorial * Fixed documentation and tutorial rendering issues * Fixed issues for misc functions not building * add current module back to misc and base class * Tutorial formatting changes * [skip ci] fix nabla math symbol * Removed helper functions from fssd class file * Made changes to test new modified fssd.py * Removed Data object inputs and replaced them with numpy array inputs * Removed Data dependent tests * Continued edits to testing files following Data removal * Removed redundant code, used compute_kern from tools * Updated kernel testing file to evaluate usage of tools functions * Added scipy.stats functionality to density sims * Update kernel.py * Removed extraneous references to Data * Black reformatting * Black reformatting * Made edits to the testing files to run more robust tests * black reformatting * Installed newest black build and reformatted files * Update config.yml * Resolved circular import issue * fixed import statement * Delete data.py * Fixed unexpected argument issue * Removed extraneous testing code * fixed autograd ArrayBox TypeError * Testing ArrayBox issue * Reformatting * Update test_density.py * Update test_density.py * Edits based on comments * Addressed comments and made testing changes * Raised ValueErrors, testing changes * Update test_density.py * Made small testing edits * Updates to datasources * Small testing edits * Update test_density.py * Update test_density.py * testing edits * Update test_density.py * Density + datasource testing edits * Update test_density.py * Update test_density.py * Update test_density.py * Update test_density.py * Update test_density.py * Removed extraneous function * Testing edit * Updated index.rst based on instruction * Minor changes to index.rst and kernel testing addressed * Added T0D0 for removal of kernel.py * fix spaces in index.rst Co-authored-by: Sambit Panda <36676569+sampan501@users.noreply.github.com> Co-authored-by: Sambit Panda <sampanda501@gmail.com> * FCIT (#315) * Create smoothCF.py * Added mean_embedding * updated inheritance from IndependenceTest * Updated SmoothCF and ME tests to match author code output * Updated SmoothCF and ME inheritance, started editing tutorial * Updated documentation * Enabled numba, added docstrings * Minor change * Response to initial PR comments * Added random state to SmoothCF * ran black * ran black again * remove blank * quotes * Changed example * black * deleted * black + more changes * random_state added to ME * coverage * tests * black * more tests * tests * reformatting * reformat * reformat * added journal to citation (Fast 2-sample) * corrected docstring math format * formatting update, helper docstring update * Formatting changes, renaming of helpers, moved random_state * fix tabbing issue in ksample * added __init__ variable explanantions to tutorial * minor formatting change to tutorial * fix tutorial rendering issue * Create FCIT.py * Creating new conditional independence module * Update cond'l ind module + bib * updated index.rst * updated config.yml * added tests, updated hyppo init * updated tests FCIT * Update FCIT.py * added FCIT documentation * black update, documentation update FCIT * added tutorial * Update conditional.py * rst edits * minor doc changes Co-authored-by: Haoyin Xu <haoyinxu@gmail.com> Co-authored-by: Sambit Panda <36676569+sampan501@users.noreply.github.com> Co-authored-by: Sambit Panda <sampanda501@gmail.com> * KCI Dev Pull Request (#317) * Update __init__.py * Create __init__.py * Create base.py * Create kci.py * Update kci.py * Create __init__.py * Create test_kci.py * Rename hyppo/conditional_independence/__init__.py to hyppo/conditional/__init__.py * Rename hyppo/conditional_independence/base.py to hyppo/conditional/base.py * Update base.py * Update and rename hyppo/conditional_independence/kci.py to hyppo/conditional/kci.py * Rename hyppo/conditional_independence/tests/__init__.py to hyppo/conditional/tests/__init__.py * Rename hyppo/conditional_independence/tests/test_kci.py to hyppo/conditional/tests/test_kci.py * Update base.py * Update base.py * Update base.py * Update kci.py * Update kci.py * Update kci.py * Update test_kci.py * Update __init__.py * Update __init__.py * Update __init__.py * Update base.py * Update base.py * Update __init__.py * Update __init__.py * Update kci.py * Update kci.py * Update index.rst * Update kci.py * Update kci.py * Update conditional.py * Update conditional.py * Update conditional.py * Update kci.py * Update conditional.py * Update conditional.py * Update kci.py * Update kci.py * Update conditional.py * Update __init__.py * Update conditional.py * Update conditional.py * Update conditional.py * Update __init__.py * Update conditional.py Co-authored-by: Sambit Panda <sampanda501@gmail.com> Co-authored-by: Sambit Panda <36676569+sampan501@users.noreply.github.com> * Fast HHG 2-Sample Test (#314) * Integrated Fast HHG into original HHG code * Update hhg.py * Create Fast HHG Tester.ipynb * Update hhg.py * Update Fast HHG Tester.ipynb * Update Fast HHG Tester.ipynb * FastHHG Tester * Update * Update Fast HHG Tester.ipynb * Added Power Sample Size Results * Fast HHG updated with Hoeffdings and docstrings * Update hhg.py * Edited independence tutorial * Delete Fast HHG Tester.ipynb * Delete indep_power_sampsize (center).pdf * Delete OGTest1Figure.png * Delete OGTest1.png * Delete Function Outline.docx * release hyppo 0.2.2 (#236) (#237) * fix inccorect p-value in unit tests * fix MGC unit tests * update version to 0.2.2 * Black sampling and edits to tutorial * Black format check * Imported IndependenceTestOutput * Formatting Changes * Black formating * Black Formatting * Adjustments to Requested Changes Remove cdist - replace with compute_dist, modified description, changed 'fast' to 'auto' and simplifying of hoeffding's implementation to basic formula. * Edited Hoeffding Function * Added Unit Tests for Fast HHG Unit tests cover replicability, Type 1 Error, distance statistic implementation and 1D linear test. * Add citations to refs and to code * Black Formatting Sweep * Minor Edits * Transfer Fast HHG description to notes section * Removed Fast HHG description Added 'fast implementation' as a pro instead. * Updated Unit Tests * Adjustments Made 'auto' in test function instead of _init_. Adjustments all-around to match. Adjusted Hoeffding function to implement jit on inner function. Achieved much higher speeds thanks to it. * Added Toy Implementation to tutorial * Update independence.py * Black Formatting Sweep * Adjustments * Formatting sweep * Updated test to cover Hoeffding Statistic Function * Disabled JIT during test to possibly improve code coverage * Formatting * Removed unneeded import. * Fixed JIT coverage error + Black Format Sweep * [skip-ci] link to p-value method * Create HHG KSample Tester.ipynb * Adding Fast HHG K-Sample Class Currently center-of-mass AD version * Completed addition of Multipoint Version * Renaming module file to match independence format * Begin code of unit tests for HHG Ksample * Edit ksample init.py * Update Unit Test Added Type 1 Error and replicability test * Corrected error in hhg ksample module Allowed option of mode * Remove Center of Mass Version * Update documentation * Black formatting * Update Stat vs test function * Start user guide * Update documentation. * Update unit tests * Updated Ksample tutorial * Black formating * Change unit test for better coverage * Consolidated functions * Correct error in tutorial * Removed mistakenly added testing notebook * Change class name to KSampleHHG, Distinguish from independence HHG. All references also updated as well. * change file name to ksamplehhg * Change test function to use statistic function * Separate function to add numba to relevant section * Added parameter headings * Complete parameter headings * Black Formatting * Removed accidental loop * Fix for coverage * Requested changes made! * Updated API index for class doc Co-authored-by: Sambit Panda <36676569+sampan501@users.noreply.github.com> Co-authored-by: Sambit Panda <sampanda501@gmail.com> * fix typos (#327) * Stat ranges to docs (#331) * Add range of Friedman Rafsky test statistic to docs * improve range documentation Co-authored-by: Sambit Panda <36676569+sampan501@users.noreply.github.com> * DOC remove extra comma in dcorr docstring (#335) * Update dcorr.py * Update dcorr.py * don't normalize kmerf importances * make k-sample error more clear * MANOVA rank errors if circle used here * update netlify image * make docs clear about FR corrected stat (#336) * make docs clear about FR corrected stat * need null distribution calculation * test now returns three outputs * fix two typos in docs (#337) * Fix typo in distance covariance equation (#340) The distance covariance equation needs the distance matrix to be both left and right multiplied by the centering matrix `H`. * bugfix: reduce maximum dependency of numpy to 1.23.5 to maintain compatibility with numba & numpy libraries (#345) Co-authored-by: prabhat.kumar <prabhat.kumar@sprinklr.com> * Add null distribution to DiscrimOneSampleTestOutput (#346) * Null distribution from the permutation test Return the distribution along with the stats for subsequent visualization * Update test_discrim_one_samp.py --------- Co-authored-by: Ronan Perry <rflperry@gmail.com> Co-authored-by: Haoyin Xu <haoyinxu@gmail.com> Co-authored-by: Hadas Arik <39025628+hadasarik@users.noreply.github.com> Co-authored-by: kareef928 <51966539+kareef928@users.noreply.github.com> Co-authored-by: Verathagnus <59093644+Verathagnus@users.noreply.github.com> Co-authored-by: dlee0156 <47963020+dlee0156@users.noreply.github.com> Co-authored-by: najmieh <najmieh.safarabadi@protonmail.com> Co-authored-by: MatthewZhao26 <52184663+MatthewZhao26@users.noreply.github.com> Co-authored-by: TacticalFallacy <56208921+TacticalFallacy@users.noreply.github.com> Co-authored-by: darsh-patel <70541374+darsh-patel@users.noreply.github.com> Co-authored-by: zdbzdb123123 <95720890+zdbzdb123123@users.noreply.github.com> Co-authored-by: allcontributors[bot] <46447321+allcontributors[bot]@users.noreply.github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Benjamin Pedigo <benjamindpedigo@gmail.com> Co-authored-by: Alexander Oakley <2579439+oakla@users.noreply.github.com> Co-authored-by: Harsh Gupta <harshgupta204016@gmail.com> Co-authored-by: Jaewon Chung <jaewonc78@gmail.com> Co-authored-by: Prabhat Kr. Gupta <42283586+prabhatkgupta@users.noreply.github.com> Co-authored-by: prabhat.kumar <prabhat.kumar@sprinklr.com> Co-authored-by: Victoria Shevchenko <49495286+victoris93@users.noreply.github.com>
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* Update permutation tree/block docstrings (#157) * perm tree docs * base docstrings * create wrapper class for Energy (#160) * sort imports * fix docs error short underline * add energy source code * fix tutorials not rendering * add more detail to compute distance and kernel * Move to Circle CI (#163) * 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 (#164) * 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 (#165) * 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 (#166) * update readme badges * update readme badges * Update README.md * improve documentation (#167) * 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 * Release v0.2.0 (#169) * fix overview rendering issue * increment version * update changelog * fix changelog release date * remove make clean in netlify toml * README codecov typo * change pypi long description format * release v0.2.1 (#179) * 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 * rename badges to main in README * make file names for benchmarks lower case * Remove extraneous benchmarks (#180) * 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 * 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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 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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 * make changes to improve diversity and inclusion (#189) * update maxmargin fast dcorr * add accessibility changes * change l1 distance to l2 for median heuristic (#191) * add reference to paper within fast docstring * reformat to black * make median kernel default for rbf and gaussian (#196) * make median kernel default for rbf and gaussian * recache dependencies * increment cache key * Switch to MIT license (#198) * Update LICENSE * Switch to MIT license * Switch to MIT license * Added typing to output of test methods. Updated requirements. (#201) * Added typing to output of test methods. Updated requirements. * Removed inheritance of namedtuple because it doesn't work as expected. * Removed unnecessary requirements. * fix docs website formatting issues (#197) * 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 * update preprints to published version (#202) * add CITATION.cff (#204) * add bibtex to docs (#205) * remove master references (#208) * 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 * remove file references in bibtex * EHN update pytest orbs version (#217) * Reproducibility to Perm Tests (#212) * 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 (#224) * MAINT update license in setup * MAINT update license * MGC redundancy warning (#125) (#220) * MGC redundancy warning (#125) MGC redundancy warning (#125) MGC redundancy warning (#125) MGC redundancy warning (#125) MGC redundancy warning (#125) * make MGC Map warning more descriptive * rename testing class so pytest finds it Co-authored-by: Sambit Panda <36676569+sampan501@users.noreply.github.com> * Fix #228 (#230) * Fix #228 Adds `rng.permutation` reproducibility to `perm_test` @kareef928 * fix linter req * enable rng None default * always use permuter * add 3.9 support (#223) * test new python versions * test correct python versions * add new classifiers in setup.py * MAINT update badge versions * python versions are decided through pypi * iterate cache key circleci * limit to 3.9 since 3.10 the dependencies don't install * remove testing 3.10 Co-authored-by: Haoyin Xu <haoyinxu@gmail.com> * release hyppo 0.2.2 (#236) * fix inccorect p-value in unit tests * fix MGC unit tests * update version to 0.2.2 * release hyppo 0.2.2 (#236) (#237) (#241) * fix inccorect p-value in unit tests * fix MGC unit tests * update version to 0.2.2 * add permutation test example to docs (#242) * add permutation test example to docs * update heading underline * lower replications and datasets so example runs * change KMERF to Dcorr Co-authored-by: Ronan Perry <rflperry@gmail.com> * add description Co-authored-by: Ronan Perry <rflperry@gmail.com> * be more clear about descriptions Co-authored-by: Ronan Perry <rflperry@gmail.com> * Update examples/permutation_tree.py Co-authored-by: Ronan Perry <rflperry@gmail.com> Co-authored-by: Ronan Perry <rflperry@gmail.com> * Adding dHSIC (#233) * Create basic outline of dhsic.py * Making preliminary modifications to base class * Create skeleton for multivariate.py * Update multivariate.py skeleton * Update dhsic.py * Creating multivariate module * Add multivariate permutation test to tools * Add multi_compute_kern to tools * Add stat method to dhsic.py * Add tests for multi_compute_kern * Create _utils for multivariate class * Add skeleton for test method in dhsic.py * Adding unit tests for multi_perm_test * updating dhsic * Update dhsic.py * Adding docstring to dhsic * Fixing bugs * Add unit tests for dhsic * Adding dhsic to tutorial * Fixing pvalue bug and adding dhsic tutorial * Running black on modified files * Modify variable names and docstrings * Add tutorial for dHsic * Add unit tests for error checking functions * Add reference * Running black * Modify checks to be within class for coverage * Add tests for power.py * Running black on test_power.py * Documentation changes and fix rendering errors * Fix rendering error * Fixing rendering error * Fix math equation formatting * Add documentation to website * Edited the types in the documentation section. (#244) * I replaced ndarray with ndarray of floats * I replaced the types in the documentation * edited the documentation to float only * Edited the types in the documentation section of discrim_two_samp * Edited the args type in the base.py * edited types in dhsic.py * edited types in base.py * Edited types in base.py in independece * Edited types in cca.py in independence * Edited types in dorr.py in independence * Edited types in hhg.py in independence * Edited types in hsic.py * edited types in kmerf.py in independence * Edited types in max_margin.py * Edited types in mgc.py in independence * Edited types in rv.py in independence * Edited types in base.py in ksample * Edited types in disco.py in ksample * edited types in energy.py in ksample * Edited types in hotelling.py in ksample * Edited types in ksamp.py in ksample * Edited types in manova.py in ksample * Edited types in mmd.py in ksample * Edited types in base.py in time_series * Edited types in dcorrx.py in time_series * Edited types in mgcx.py in time_series * Edited types in common.py in tools * Edited types in the indep_sim.py in tools * Edited types in ksample_sim.py in tools * Edtited types in power.py in tools * Edited types in time_series_sim.py in tools * Types Update * Types update in base.py Co-authored-by: Sambit Panda <36676569+sampan501@users.noreply.github.com> * Fast tstest (#234) * Create smoothCF.py * Added mean_embedding * updated inheritance from IndependenceTest * Updated SmoothCF and ME tests to match author code output * Updated SmoothCF and ME inheritance, started editing tutorial * Updated documentation * Enabled numba, added docstrings * Minor change * Response to initial PR comments * Added random state to SmoothCF * ran black * ran black again * remove blank * quotes * Changed example * black * deleted * black + more changes * random_state added to ME * coverage * tests * black * more tests * tests * reformatting * reformat * reformat * added journal to citation (Fast 2-sample) * corrected docstring math format * formatting update, helper docstring update * Formatting changes, renaming of helpers, moved random_state * fix tabbing issue in ksample * added __init__ variable explanantions to tutorial * minor formatting change to tutorial * fix tutorial rendering issue Co-authored-by: Haoyin Xu <haoyinxu@gmail.com> Co-authored-by: Sambit Panda <36676569+sampan501@users.noreply.github.com> * Fast HHG Test (#238) * Integrated Fast HHG into original HHG code * Update hhg.py * Create Fast HHG Tester.ipynb * Update hhg.py * Update Fast HHG Tester.ipynb * Update Fast HHG Tester.ipynb * FastHHG Tester * Update * Update Fast HHG Tester.ipynb * Added Power Sample Size Results * Fast HHG updated with Hoeffdings and docstrings * Update hhg.py * Edited independence tutorial * Delete Fast HHG Tester.ipynb * Delete indep_power_sampsize (center).pdf * Delete OGTest1Figure.png * Delete OGTest1.png * Delete Function Outline.docx * release hyppo 0.2.2 (#236) (#237) * fix inccorect p-value in unit tests * fix MGC unit tests * update version to 0.2.2 * Black sampling and edits to tutorial * Black format check * Imported IndependenceTestOutput * Formatting Changes * Black formating * Black Formatting * Adjustments to Requested Changes Remove cdist - replace with compute_dist, modified description, changed 'fast' to 'auto' and simplifying of hoeffding's implementation to basic formula. * Edited Hoeffding Function * Added Unit Tests for Fast HHG Unit tests cover replicability, Type 1 Error, distance statistic implementation and 1D linear test. * Add citations to refs and to code * Black Formatting Sweep * Minor Edits * Transfer Fast HHG description to notes section * Removed Fast HHG description Added 'fast implementation' as a pro instead. * Updated Unit Tests * Adjustments Made 'auto' in test function instead of _init_. Adjustments all-around to match. Adjusted Hoeffding function to implement jit on inner function. Achieved much higher speeds thanks to it. * Added Toy Implementation to tutorial * Update independence.py * Black Formatting Sweep * Adjustments * Formatting sweep * Updated test to cover Hoeffding Statistic Function * Disabled JIT during test to possibly improve code coverage * Formatting * Removed unneeded import. * Fixed JIT coverage error + Black Format Sweep * [skip-ci] link to p-value method Co-authored-by: Sambit Panda <36676569+sampan501@users.noreply.github.com> * Creating a goodness-of-fit module in hyppo (#232) * Created kgof module * Added tutorial documentation * Resolved an import statement issue * first pass of removal of extraneous code * removed majority of extraneous functions in _utils.py * Further removal of redundancies + addition of citations * Removal of redundancies / unnecessary features * Removed NumpySeedContext to resolve redundancies with numpy.random default_rng * Removed further dependencies on np.random and replaced with default_rng() * Removed subsample_ind * added testing file for kernel.py * black formatting applied * added testing file for density.py and replaces all instances of np.random with default_rng() in data.py * Update index.rst * Updated circleci so tests run * Cleaned up docstrings and moved around functions (formatting) * Lots of cleanup and PR comments addressed * Rewrote necessary unit tests with pytest * Black reformatting * Removed extraneous imports * Dependencies installation attempt * Changed dependencies * removed extraneous imports * removed dependency on future * Fixed imports * Update fssd.py * fixed circular import issue * Black reformatting * Fixed import statements in unit test files * removed unittest * Modified import statements * Made testing edits * Testing edits * Black reformatting * Update test_fssd.py * Testing edits * Removed extraneous functions, rewrote tests * Update test_density.py * Removed extraneous functions from density.py * Removed extraneous functions and imports * Added test for density.Normal * Added tests for kernel.py * Fixed import error in test_kernel * Removed extraneous function from density.py * Removed extraneous GaussianMixture support * Added tests for data.py and removed extraneous function from data.py * Added tests for fssd.py * Added tests to test_kernel.py * Made changes to fssd syntax and added more tests for fssd * Added tests for fssd.py * black reformatting * Added more tests for data,py * density.py and data.py tests added * Removed extraneous code * Added more tests for fssd.py * Formatting fix * Changed description of base class. * Added kgof tutorial to index.rst, reformatted docstrings * Black reformatting in base.py * Fixed docstrings in fssd.py * Reformatted kgof tutorial * Fixed documentation and tutorial rendering issues * Fixed issues for misc functions not building * add current module back to misc and base class * Tutorial formatting changes * [skip ci] fix nabla math symbol Co-authored-by: Sambit Panda <36676569+sampan501@users.noreply.github.com> * Friedman Rafsky PR (#239) * Add files via upload * Add files via upload * Update and rename _friedmanRafsky.py to test_friedmanRafsky.py * Update test_friedmanRafsky.py * Update test_friedmanRafsky.py * Update test_friedmanRafsky.py * Update test_friedmanRafsky.py * Delete test_friedmanRafsky.py * Delete friedmanRafsky.py * Add files via upload * Delete friedmanRafsky.py * Add files via upload * Delete friedmanRafsky.py * Add files via upload * Update friedmanRafsky.py * Delete friedmanRafsky.py * Add files via upload * Update independence.py * Add files via upload * Update independence.py * Update friedmanRafsky.py * Delete friedmanRafsky.py * Add files via upload * Rename Update.py to friedmanRafsky.py * Update friedmanRafsky.py * Update friedmanRafsky.py * Add files via upload * Update index.rst * Update friedmanRafsky.py * Update friedmanRafsky.py * Update test_friedmanRafsky.py * Update __init__.py * Update test_friedmanRafsky.py * Rename friedmanRafsky.py to friedman_rafsky.py * Update __init__.py * Update and rename test_friedmanRafsky.py to test_friedman_rafsky.py * Update test_friedman_rafsky.py * Update __init__.py * Update test_friedman_rafsky.py * Update friedman_rafsky.py * Update index.rst * Update friedman_rafsky.py * Update friedman_rafsky.py * Update friedman_rafsky.py * Update friedman_rafsky.py * Update friedman_rafsky.py * Update friedman_rafsky.py * Update friedman_rafsky.py * Update friedman_rafsky.py * Update friedman_rafsky.py * Update friedman_rafsky.py * Update friedman_rafsky.py * Delete friedman_rafsky.py * Add files via upload * Rename Update.py to friedman_rafsky.py * Update friedman_rafsky.py * Update test_friedman_rafsky.py * Update friedman_rafsky.py * Update friedman_rafsky.py * Update test_friedman_rafsky.py * Update test_friedman_rafsky.py * Update friedman_rafsky.py * Update friedman_rafsky.py * Update test_friedman_rafsky.py * Update test_friedman_rafsky.py * Update test_friedman_rafsky.py * Update test_friedman_rafsky.py * Update test_friedman_rafsky.py * Update test_friedman_rafsky.py * Update test_friedman_rafsky.py * Update friedman_rafsky.py * Update test_friedman_rafsky.py * Update friedman_rafsky.py * Update independence.py * Delete friedman_rafsky.py * Add files via upload * Rename Update.py to friedman_rafsky.py * Update friedman_rafsky.py * Update friedman_rafsky.py * Update friedman_rafsky.py * Delete friedman_rafsky.py * Add files via upload * Rename Update.py to friedman_rafsky.py * Update friedman_rafsky.py * Update friedman_rafsky.py * Update friedman_rafsky.py * Update friedman_rafsky.py * Update friedman_rafsky.py * Update refs.bib * Update friedman_rafsky.py * Update friedman_rafsky.py * Update independence.py * Update friedman_rafsky.py * Update independence.py * Update independence.py * Update independence.py * Update independence.py * Update independence.py * Update independence.py * Update independence.py * Update independence.py * Update independence.py * remove fr test images Co-authored-by: Sambit Panda <36676569+sampan501@users.noreply.github.com> * refactor docs and add contribution bot (#248) * change from sphinx rtd theme to pydata sphinx theme * add changelog for next version * add kgof to docs * add all contributors bot * change to README.md * add myst_parser to docs * change hosting to https * [skip ci] add description to markdown * docs: add sampan501 as a contributor for bug, code, doc, ideas, maintenance, review (#251) * docs: update README.md [skip ci] * docs: create .all-contributorsrc [skip ci] * follow add-contributors spec Co-authored-by: allcontributors[bot] <46447321+allcontributors[bot]@users.noreply.github.com> Co-authored-by: Sambit Panda <36676569+sampan501@users.noreply.github.com> * docs: add cshen6 as a contributor for code (#274) * docs: update README.md [skip ci] * docs: update .all-contributorsrc [skip ci] * [skip ci] fix badge updates * [skip ci] add research contribution * [skip ci] add research Co-authored-by: allcontributors[bot] <46447321+allcontributors[bot]@users.noreply.github.com> Co-authored-by: Sambit Panda <36676569+sampan501@users.noreply.github.com> * fix all-contrib errors * change research to ideas (#275) * docs: add jovo as a contributor for fundingFinding, mentoring, ideas (#276) * docs: update README.md [skip ci] * docs: update .all-contributorsrc [skip ci] Co-authored-by: allcontributors[bot] <46447321+allcontributors[bot]@users.noreply.github.com> * docs: add tpsatish95 as a contributor for code, ideas (#277) * docs: update README.md [skip ci] * docs: update .all-contributorsrc [skip ci] Co-authored-by: allcontributors[bot] <46447321+allcontributors[bot]@users.noreply.github.com> * docs: add junhaobearxiong as a contributor for code, ideas (#278) * docs: update README.md [skip ci] * docs: update .all-contributorsrc [skip ci] Co-authored-by: allcontributors[bot] <46447321+allcontributors[bot]@users.noreply.github.com> * 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docs: add darsh-patel as a contributor for code (#296) * docs: update README.md [skip ci] * docs: update .all-contributorsrc [skip ci] Co-authored-by: allcontributors[bot] <46447321+allcontributors[bot]@users.noreply.github.com> * docs: add zdbzdb123123 as a contributor for code (#297) * docs: update README.md [skip ci] * docs: update .all-contributorsrc [skip ci] Co-authored-by: allcontributors[bot] <46447321+allcontributors[bot]@users.noreply.github.com> * Bump ipython from 7.19.0 to 7.31.1 in /docs (#299) Bumps [ipython](https://github.com/ipython/ipython) from 7.19.0 to 7.31.1. - [Release notes](https://github.com/ipython/ipython/releases) - [Commits](https://github.com/ipython/ipython/compare/7.19.0...7.31.1) --- updated-dependencies: - dependency-name: ipython dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Copy SciPy private `_contains_nan` function (#304) * copy scipy private contains nan function * update formatting based on black spec * reformatted before switching branches Co-authored-by: Sambit Panda <sampanda501@gmail.com> * release v0.3.0 * run jobs in parallel * release v0.3.0 * add autograd as a dependency * release v0.3.1 * remove emojis so windows can build package * release v0.3.2 * run pytest in parallel (#310) * run pytest in parallel * test files hyppo * install pytest * upload to codecov * fix codecov * compute coverage * run coverage * install pytest-cov * add coverage location * remove rep tests because random_state parameter * change reps to 3 * [skip ci] add change to changelog * add skip decorator for two sample circleci tests (#321) * update sphinx to fix jinja error (#319) * Refactor kgof module (#318) * Created kgof module * Added tutorial documentation * Resolved an import statement issue * first pass of removal of extraneous code * removed majority of extraneous functions in _utils.py * Further removal of redundancies + addition of citations * Removal of redundancies / unnecessary features * Removed NumpySeedContext to resolve redundancies with numpy.random default_rng * Removed further dependencies on np.random and replaced with default_rng() * Removed subsample_ind * added testing file for kernel.py * black formatting applied * added testing file for density.py and replaces all instances of np.random with default_rng() in data.py * Update index.rst * Updated circleci so tests run * Cleaned up docstrings and moved around functions (formatting) * Lots of cleanup and PR comments addressed * Rewrote necessary unit tests with pytest * Black reformatting * Removed extraneous imports * Dependencies installation attempt * Changed dependencies * removed extraneous imports * removed dependency on future * Fixed imports * Update fssd.py * fixed circular import issue * Black reformatting * Fixed import statements in unit test files * removed unittest * Modified import statements * Made testing edits * Testing edits * Black reformatting * Update test_fssd.py * Testing edits * Removed extraneous functions, rewrote tests * Update test_density.py * Removed extraneous functions from density.py * Removed extraneous functions and imports * Added test for density.Normal * Added tests for kernel.py * Fixed import error in test_kernel * Removed extraneous function from density.py * Removed extraneous GaussianMixture support * Added tests for data.py and removed extraneous function from data.py * Added tests for fssd.py * Added tests to test_kernel.py * Made changes to fssd syntax and added more tests for fssd * Added tests for fssd.py * black reformatting * Added more tests for data,py * density.py and data.py tests added * Removed extraneous code * Added more tests for fssd.py * Formatting fix * Changed description of base class. * Added kgof tutorial to index.rst, reformatted docstrings * Black reformatting in base.py * Fixed docstrings in fssd.py * Reformatted kgof tutorial * Fixed documentation and tutorial rendering issues * Fixed issues for misc functions not building * add current module back to misc and base class * Tutorial formatting changes * [skip ci] fix nabla math symbol * Removed helper functions from fssd class file * Made changes to test new modified fssd.py * Removed Data object inputs and replaced them with numpy array inputs * Removed Data dependent tests * Continued edits to testing files following Data removal * Removed redundant code, used compute_kern from tools * Updated kernel testing file to evaluate usage of tools functions * Added scipy.stats functionality to density sims * Update kernel.py * Removed extraneous references to Data * Black reformatting * Black reformatting * Made edits to the testing files to run more robust tests * black reformatting * Installed newest black build and reformatted files * Update config.yml * Resolved circular import issue * fixed import statement * Delete data.py * Fixed unexpected argument issue * Removed extraneous testing code * fixed autograd ArrayBox TypeError * Testing ArrayBox issue * Reformatting * Update test_density.py * Update test_density.py * Edits based on comments * Addressed comments and made testing changes * Raised ValueErrors, testing changes * Update test_density.py * Made small testing edits * Updates to datasources * Small testing edits * Update test_density.py * Update test_density.py * testing edits * Update test_density.py * Density + datasource testing edits * Update test_density.py * Update test_density.py * Update test_density.py * Update test_density.py * Update test_density.py * Removed extraneous function * Testing edit * Updated index.rst based on instruction * Minor changes to index.rst and kernel testing addressed * Added T0D0 for removal of kernel.py * fix spaces in index.rst Co-authored-by: Sambit Panda <36676569+sampan501@users.noreply.github.com> Co-authored-by: Sambit Panda <sampanda501@gmail.com> * FCIT (#315) * Create smoothCF.py * Added mean_embedding * updated inheritance from IndependenceTest * Updated SmoothCF and ME tests to match author code output * Updated SmoothCF and ME inheritance, started editing tutorial * Updated documentation * Enabled numba, added docstrings * Minor change * Response to initial PR comments * Added random state to SmoothCF * ran black * ran black again * remove blank * quotes * Changed example * black * deleted * black + more changes * random_state added to ME * coverage * tests * black * more tests * tests * reformatting * reformat * reformat * added journal to citation (Fast 2-sample) * corrected docstring math format * formatting update, helper docstring update * Formatting changes, renaming of helpers, moved random_state * fix tabbing issue in ksample * added __init__ variable explanantions to tutorial * minor formatting change to tutorial * fix tutorial rendering issue * Create FCIT.py * Creating new conditional independence module * Update cond'l ind module + bib * updated index.rst * updated config.yml * added tests, updated hyppo init * updated tests FCIT * Update FCIT.py * added FCIT documentation * black update, documentation update FCIT * added tutorial * Update conditional.py * rst edits * minor doc changes Co-authored-by: Haoyin Xu <haoyinxu@gmail.com> Co-authored-by: Sambit Panda <36676569+sampan501@users.noreply.github.com> Co-authored-by: Sambit Panda <sampanda501@gmail.com> * KCI Dev Pull Request (#317) * Update __init__.py * Create __init__.py * Create base.py * Create kci.py * Update kci.py * Create __init__.py * Create test_kci.py * Rename hyppo/conditional_independence/__init__.py to hyppo/conditional/__init__.py * Rename hyppo/conditional_independence/base.py to hyppo/conditional/base.py * Update base.py * Update and rename hyppo/conditional_independence/kci.py to hyppo/conditional/kci.py * Rename hyppo/conditional_independence/tests/__init__.py to hyppo/conditional/tests/__init__.py * Rename hyppo/conditional_independence/tests/test_kci.py to hyppo/conditional/tests/test_kci.py * Update base.py * Update base.py * Update base.py * Update kci.py * Update kci.py * Update kci.py * Update test_kci.py * Update __init__.py * Update __init__.py * Update __init__.py * Update base.py * Update base.py * Update __init__.py * Update __init__.py * Update kci.py * Update kci.py * Update index.rst * Update kci.py * Update kci.py * Update conditional.py * Update conditional.py * Update conditional.py * Update kci.py * Update conditional.py * Update conditional.py * Update kci.py * Update kci.py * Update conditional.py * Update __init__.py * Update conditional.py * Update conditional.py * Update conditional.py * Update __init__.py * Update conditional.py Co-authored-by: Sambit Panda <sampanda501@gmail.com> Co-authored-by: Sambit Panda <36676569+sampan501@users.noreply.github.com> * Fast HHG 2-Sample Test (#314) * Integrated Fast HHG into original HHG code * Update hhg.py * Create Fast HHG Tester.ipynb * Update hhg.py * Update Fast HHG Tester.ipynb * Update Fast HHG Tester.ipynb * FastHHG Tester * Update * Update Fast HHG Tester.ipynb * Added Power Sample Size Results * Fast HHG updated with Hoeffdings and docstrings * Update hhg.py * Edited independence tutorial * Delete Fast HHG Tester.ipynb * Delete indep_power_sampsize (center).pdf * Delete OGTest1Figure.png * Delete OGTest1.png * Delete Function Outline.docx * release hyppo 0.2.2 (#236) (#237) * fix inccorect p-value in unit tests * fix MGC unit tests * update version to 0.2.2 * Black sampling and edits to tutorial * Black format check * Imported IndependenceTestOutput * Formatting Changes * Black formating * Black Formatting * Adjustments to Requested Changes Remove cdist - replace with compute_dist, modified description, changed 'fast' to 'auto' and simplifying of hoeffding's implementation to basic formula. * Edited Hoeffding Function * Added Unit Tests for Fast HHG Unit tests cover replicability, Type 1 Error, distance statistic implementation and 1D linear test. * Add citations to refs and to code * Black Formatting Sweep * Minor Edits * Transfer Fast HHG description to notes section * Removed Fast HHG description Added 'fast implementation' as a pro instead. * Updated Unit Tests * Adjustments Made 'auto' in test function instead of _init_. Adjustments all-around to match. Adjusted Hoeffding function to implement jit on inner function. Achieved much higher speeds thanks to it. * Added Toy Implementation to tutorial * Update independence.py * Black Formatting Sweep * Adjustments * Formatting sweep * Updated test to cover Hoeffding Statistic Function * Disabled JIT during test to possibly improve code coverage * Formatting * Removed unneeded import. * Fixed JIT coverage error + Black Format Sweep * [skip-ci] link to p-value method * Create HHG KSample Tester.ipynb * Adding Fast HHG K-Sample Class Currently center-of-mass AD version * Completed addition of Multipoint Version * Renaming module file to match independence format * Begin code of unit tests for HHG Ksample * Edit ksample init.py * Update Unit Test Added Type 1 Error and replicability test * Corrected error in hhg ksample module Allowed option of mode * Remove Center of Mass Version * Update documentation * Black formatting * Update Stat vs test function * Start user guide * Update documentation. * Update unit tests * Updated Ksample tutorial * Black formating * Change unit test for better coverage * Consolidated functions * Correct error in tutorial * Removed mistakenly added testing notebook * Change class name to KSampleHHG, Distinguish from independence HHG. All references also updated as well. * change file name to ksamplehhg * Change test function to use statistic function * Separate function to add numba to relevant section * Added parameter headings * Complete parameter headings * Black Formatting * Removed accidental loop * Fix for coverage * Requested changes made! * Updated API index for class doc Co-authored-by: Sambit Panda <36676569+sampan501@users.noreply.github.com> Co-authored-by: Sambit Panda <sampanda501@gmail.com> * fix typos (#327) * Stat ranges to docs (#331) * Add range of Friedman Rafsky test statistic to docs * improve range documentation Co-authored-by: Sambit Panda <36676569+sampan501@users.noreply.github.com> * DOC remove extra comma in dcorr docstring (#335) * Update dcorr.py * Update dcorr.py * don't normalize kmerf importances * make k-sample error more clear * MANOVA rank errors if circle used here * update netlify image * make docs clear about FR corrected stat (#336) * make docs clear about FR corrected stat * need null distribution calculation * test now returns three outputs * fix two typos in docs (#337) * Fix typo in distance covariance equation (#340) The distance covariance equation needs the distance matrix to be both left and right multiplied by the centering matrix `H`. * start * update sims * Update kernel estimation * Update and fix computation * Add permutation test * Add input checks * Fix errors * Separate cdcorr and cdcov * combine cdcov and cdcorr * Update init * Add docstrings * Add more options * update docstring * Add docstrings, update random_state * Add more sims * Update simulations * Fix statistics bug * Fix bugs in sims * Update rand to random * Add more checks and features * Add conditional tests to power function * Add script * Fix error in sim * Add partial correlation * Add partial correlation * Update * Update * Add pdcorr * Fix error * Fix indepedent lognormal sim * Update lognormal sim * Deal with zero variance * Tests for utils * add cdcorr tests * Update * Fix errors * Update covariance * Fix simultation * Update docstrings * Fix docstring warnings * Partial Correlation tests * Update cdcorr test * Fix errors * PDcorr tests * Fix tests * Update test * Fix imports * Update docstrings and fix RF error * fix tests failing * Update conditional independence simulation tests * Add no pragma for cov/corr computation * Add more tests * More unit tests and black * add support for constant input z for cdcorr --------- Co-authored-by: Ronan Perry <rflperry@gmail.com> Co-authored-by: Sambit Panda <36676569+sampan501@users.noreply.github.com> Co-authored-by: Haoyin Xu <haoyinxu@gmail.com> Co-authored-by: Hadas Arik <39025628+hadasarik@users.noreply.github.com> Co-authored-by: kareef928 <51966539+kareef928@users.noreply.github.com> Co-authored-by: Verathagnus <59093644+Verathagnus@users.noreply.github.com> Co-authored-by: dlee0156 <47963020+dlee0156@users.noreply.github.com> Co-authored-by: najmieh <najmieh.safarabadi@protonmail.com> Co-authored-by: MatthewZhao26 <52184663+MatthewZhao26@users.noreply.github.com> Co-authored-by: TacticalFallacy <56208921+TacticalFallacy@users.noreply.github.com> Co-authored-by: darsh-patel <70541374+darsh-patel@users.noreply.github.com> Co-authored-by: zdbzdb123123 <95720890+zdbzdb123123@users.noreply.github.com> Co-authored-by: allcontributors[bot] <46447321+allcontributors[bot]@users.noreply.github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Benjamin Pedigo <benjamindpedigo@gmail.com> Co-authored-by: Sambit Panda <sampanda501@gmail.com> Co-authored-by: Alexander Oakley <2579439+oakla@users.noreply.github.com> Co-authored-by: Harsh Gupta <harshgupta204016@gmail.com>
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Reference issue
Closes issue #103.
Type of change
Feature request
What does this implement/fix?
Implements a linear-time kernel goodness of fit test for a Gaussian kernel. Developed so that other types of distributions may be added in the future.
Additional information