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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 <[email protected]> Co-authored-by: Sambit Panda <[email protected]> * 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 <[email protected]> * 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 <[email protected]> * 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 <[email protected]> * add description Co-authored-by: Ronan Perry <[email protected]> * be more clear about descriptions Co-authored-by: Ronan Perry <[email protected]> * Update examples/permutation_tree.py Co-authored-by: Ronan Perry <[email protected]> Co-authored-by: Ronan Perry <[email protected]> * 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 <[email protected]> * 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 <[email protected]> Co-authored-by: Sambit Panda <[email protected]> * 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 <[email protected]> * 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 <[email protected]> * 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 <[email protected]> * 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 <[email protected]> * 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 <[email protected]> * 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> * docs: add ebridge2 as a contributor for bug, ideas (#279) * docs: update README.md [skip ci] * docs: update .all-contributorsrc [skip ci] Co-authored-by: allcontributors[bot] 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Signed-off-by: dependabot[bot] <[email protected]> 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 <[email protected]> * 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 <[email protected]> Co-authored-by: Sambit Panda <[email protected]> * 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 <[email protected]> Co-authored-by: Sambit Panda <[email protected]> Co-authored-by: Sambit Panda <[email protected]> * 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 <[email protected]> Co-authored-by: Sambit Panda <[email protected]> * 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 <[email protected]> Co-authored-by: Sambit Panda <[email protected]> * 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 <[email protected]> * 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 <[email protected]> * 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 <[email protected]> Co-authored-by: Haoyin Xu <[email protected]> Co-authored-by: Hadas Arik <[email protected]> Co-authored-by: kareef928 <[email protected]> Co-authored-by: Verathagnus <[email protected]> Co-authored-by: dlee0156 <[email protected]> Co-authored-by: najmieh <[email protected]> Co-authored-by: MatthewZhao26 <[email protected]> Co-authored-by: TacticalFallacy <[email protected]> Co-authored-by: darsh-patel <[email protected]> Co-authored-by: zdbzdb123123 <[email protected]> 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 <[email protected]> Co-authored-by: Alexander Oakley <[email protected]> Co-authored-by: Harsh Gupta <[email protected]> Co-authored-by: Jaewon Chung <[email protected]> Co-authored-by: Prabhat Kr. Gupta <[email protected]> Co-authored-by: prabhat.kumar <[email protected]> Co-authored-by: Victoria Shevchenko <[email protected]>
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