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2023-04-17[MRG] Fix circleci_redirector and codecov (#460)Rémi Flamary
* Try circleci_redirector fix * reùove fixed version pytest-cov * use new codecov way to upload * bad return * proper pr in release fle
2023-04-07[MRG] Release 0.9.0 (#452)Rémi Flamary
* relkase text * correct typos
2023-03-09[MRG] Semi-relaxed (fused) gromov-wasserstein divergence and improvements of ↵Cédric Vincent-Cuaz
gromov-wasserstein solvers (#431) * maj gw/ srgw/ generic cg solver * correct pep8 on current state * fix bug previous tests * fix pep8 * fix bug srGW constC in loss and gradient * fix doc html * fix doc html * start updating test_optim.py * update tests gromov and optim - plus fix gromov dependencies * add symmetry feature to entropic gw * add symmetry feature to entropic gw * add exemple for sr(F)GW matchings * small stuff * remove (reg,M) from line-search/ complete srgw tests with backend * remove backend repetitions / rename fG to costG/ fix innerlog to True * fix pep8 * take comments into account / new nx parameters still to test * factor (f)gw2 + test new backend parameters in ot.gromov + harmonize stopping criterions * split gromov.py in ot/gromov/ + update test_gromov with helper_backend functions * manual documentaion gromov * remove circular autosummary * trying stuff * debug documentation * alphabetic ordering of module * merge into branch * add note in entropic gw solvers --------- Co-authored-by: Rémi Flamary <remi.flamary@gmail.com>
2023-02-23[WIP] Wasserstein distance on the circle and Spherical Sliced-Wasserstein (#434)Clément Bonet
* W circle + SSW * Tests + Example SSW_1 * Example Wasserstein Circle + Tests * Wasserstein on the circle wrt Unif * Example SSW unif * pep8 * np.linalg.qr for numpy < 1.22 by batch + add python3.11 to tests * np qr * rm test python 3.11 * update names, tests, backend transpose * Comment error batchs * semidiscrete_wasserstein2_unif_circle example * torch permute method instead of torch.permute for previous versions * update comments and doc * doc wasserstein circle model as [0,1[ * Added ot.utils.get_coordinate_circle to get coordinates on the circle in turn
2023-01-16[MRG] OT for Gaussian distributions (#428)tgnassou
* add gaussian modules * add gaussian modules * add PR to release.md * Apply suggestions from code review Co-authored-by: Alexandre Gramfort <alexandre.gramfort@m4x.org> * Apply suggestions from code review Co-authored-by: Alexandre Gramfort <alexandre.gramfort@m4x.org> * Update ot/gaussian.py * Update ot/gaussian.py * add empirical bures wassertsein distance, fix docstring and test * update to fit with new networkx API * add test for jax et tf" * fix test * fix test? * add empirical_bures_wasserstein_mapping * fix docs * fix doc * fix docstring * add tgnassou to contributors * add more coverage for gaussian.py * add deprecated function * fix doc math" " * fix doc math" " * add remi flamary to authors of gaussiansmodule * fix equation Co-authored-by: Rémi Flamary <remi.flamary@gmail.com> Co-authored-by: Alexandre Gramfort <alexandre.gramfort@m4x.org>
2022-12-15[MRG] New API for OT solver (with pre-computed ground cost matrix) (#388)Rémi Flamary
* new API for OT solver * use itertools for product of parameters * add tests for result class * add tests for result class * add tests for result class last time? * add sinkhorn * make partial OT bckend compatible * add TV as unbalanced flavor * better tests * make smoth backend compatible and add l2 tregularizatio to solve * add reularizedd unbalanced * add test for more complex attibutes * add test for more complex attibutes * add generic unbalaned solver and implement it for ot.solve * add entropy to possible regularization * star of documentation for ot.solv * weird new pep8 * documenttaion for function ot.solve done * pep8 * Update ot/solvers.py Co-authored-by: Alexandre Gramfort <alexandre.gramfort@m4x.org> * update release file * Apply suggestions from code review Co-authored-by: Alexandre Gramfort <alexandre.gramfort@m4x.org> * add test NotImplemented * pep8 * pep8gcmp pep8! * compute kl in backend * debug tensorflow kl backend Co-authored-by: Alexandre Gramfort <alexandre.gramfort@m4x.org>
2022-05-06[WIP] Generalized Wasserstein Barycenters (#372)eloitanguy
* GWB first solver version * tests + example for gwb (untested) + free_bar doc fix * improved doc, fixed minor bugs, better example visu * minor doc + visu fixes * plot GWB pep8 fix * fixed partial gromov test reproductibility * added an animation for the GWB visu * added PR num * minor doc fixes + better gwb logo
2022-04-21[MRG] Release 8.2 (#365)Rémi Flamary
* release text and number * add examples in release fil build wheels * switch gallery to release * add much needed contributors file * debug circleci * une line of logos * working logo * back to stable sphinx galery
2022-03-24[MRG] Add factored coupling (#358)Rémi Flamary
* add gfactored ot * pep8 and add doc * add exmaple for factotred OT * final number of PR * correct test on backends * remove useless loss * better tests
2022-02-11[MRG] GW dictionary learning (#319)Cédric Vincent-Cuaz
* add fgw dictionary learning feature * add fgw dictionary learning feature * plot gromov wasserstein dictionary learning * Update __init__.py * fix pep8 errors exact E501 line too long * fix last pep8 issues * add unitary tests for (F)GW dictionary learning without using autodifferentiable functions * correct tests for (F)GW dictionary learning without using autodiff * correct tests for (F)GW dictionary learning without using autodiff * fix docs and notations * answer to review: improve tests, docs, examples + make node weights optional * fix pep8 and examples * improve docs + tests + thumbnail * make example faster * improve ex * update README.md * make GDL tests faster Co-authored-by: Rémi Flamary <remi.flamary@gmail.com>
2022-02-02[MRG] Add weak OT solver (#341)Rémi Flamary
* add info in release file * update tests * pep8 * add weak OT example * update plot in doc * correction ewample with empirical sinkhorn * better thumbnail * comment from review * update documenation
2022-01-14[WIP] Set dev version and add minigallery to quick start guide (#334)Rémi Flamary
* change version and add minigallery in quickstart guide * remove ot.gpu from documentation because it is deprecated and bacckends should be used * start 0.8.2dev and description in releases.md * typo for gallery sinkhorn2 * test better doc update for files in .githib folder
2021-12-31[MRG] Release 0.8.1.0 and correct doc build (#332)Rémi Flamary
* update ersion and change doc build * update release file * debug release of doc * set version number to 0.8.1.0
2021-12-26[MRG] Release 0.8.1 (#325)Rémi Flamary
* update delease file and add it to doc ith mystè_parser * typos in release file * update PR template * test debug doc build * test debug doc build * wrog circleci * set proper version number * add numpy 1.20 constraint * remove python 3.6 deprecated in december * add python 3.10 * debug pip on windows * proper yml * remoe 3.10 becauqe of troch * next try * try distutils * back * try something * new stuf * debug yaml * test back to old vriso f numpy * try something * windows is worksing?
2021-12-15[WIP] Update version in to 0.8.1dev and release file (#323)Rémi Flamary
* update delease file and add it to doc ith mystè_parser * typos in release file * update PR template
2021-11-05[MRG] Release 0.8 (#289)Rémi Flamary
* working on release * test circleci * try again * cleanup circle ci run * add all PR and releant Issues * update doc * thanks idris * update version + add pyproject.toml * test pyproject.toml * revert tests * build wheels * use windows-latest for tests * add tests python 3.10 * build all whels * all versions * build all wheels * build all wheels * cleanup pep8 and minimal acions * forst shot text release * bettr text * stuff * release text updated * update manifest to allow build from source * update doc again * update release
2021-11-04[MRG] Make gromov loss differentiable wrt matrices and weights (#302)Rémi Flamary
* grmov differentable * new stuff * test gromov gradients * fgwdifferentiable * fgw tested * correc name test * add awesome example with gromov optimizatrion * pep8+ typos * damn pep8 * thunbnail * remove prints
2021-11-02[MRG] Sliced and 1D Wasserstein distances : backend versions (#256)Nicolas Courty
* add numpy and torch backends * stat sets on functions * proper import * install recent torch on windows * install recent torch on windows * now testing all functions in backedn * add jax backedn * clenaup windowds * proper convert for jax backedn * pep8 * try again windows tests * test jax conversion * try proper widows tests * emd fuction ses backedn * better test partial OT * proper tests to_numpy and teplate Backend * pep8 * pep8 x2 * feaking sinkhorn works with torch * sinkhorn2 compatible * working ot.emd2 * important detach * it should work * jax autodiff emd * pep8 * no tast same for jax * new independat tests per backedn * freaking pep8 * add tests for gradients * deprecate ot.gpu * worging dist function * working dist * dist done in backedn * not in * remove indexing * change accuacy for jax * first pull backend * projection simplex * projection simplex * projection simplex * projection simplex no ci * projection simplex no ci * projection simplex no ci * pep8 * add backedn discusion to quickstart guide * projection simplex no ci * projection simplex no ci * projection simplex no ci * pep8 + better doc * proper links * corect doctest * big debug documentation * doctest again * doctest again bis * doctest again ter (last one or i kill myself) * backend test + doc proj simplex * correction test_utils * correction test_utils * correction cumsum * correction flip * correction flip v2 * more debug * more debug * more debug + pep8 * pep8 * argh * proj_simplex * backedn works for sort * proj simplex * jax sucks * update doc * Update test/test_utils.py Co-authored-by: Alexandre Gramfort <alexandre.gramfort@m4x.org> * Update docs/source/quickstart.rst Co-authored-by: Alexandre Gramfort <alexandre.gramfort@m4x.org> * Update docs/source/quickstart.rst Co-authored-by: Alexandre Gramfort <alexandre.gramfort@m4x.org> * Update docs/source/quickstart.rst Co-authored-by: Alexandre Gramfort <alexandre.gramfort@m4x.org> * Update docs/source/readme.rst Co-authored-by: Alexandre Gramfort <alexandre.gramfort@m4x.org> * Update test/test_utils.py Co-authored-by: Alexandre Gramfort <alexandre.gramfort@m4x.org> * Update ot/utils.py Co-authored-by: Alexandre Gramfort <alexandre.gramfort@m4x.org> * Update docs/source/readme.rst Co-authored-by: Alexandre Gramfort <alexandre.gramfort@m4x.org> * Update ot/lp/__init__.py Co-authored-by: Alexandre Gramfort <alexandre.gramfort@m4x.org> * begin comment alex * comment alex part 2 * optimize test gromov * proj_simplex on vectors * add awesome gradient decsnt example on the weights * pep98 of course * proof read example by alex * pep8 again * encoding oos in translation * correct legend * new backend functions for sliced * small indent pb * Optimized backendversion of sliced W * error in sliced W * after master merge * error sliced * error sliced * pep8 * test_sliced pep8 * doctest + precision for sliced * doctest * type win test_backend gather * type win test_backend gather * Update sliced.py change argument of padding pad_width * Update backend.py update redefinition * Update backend.py pep8 * Update backend.py pep 8 again.... * pep8 * build docs * emd2_1D example * refectoring emd_1d and variants * remove unused previous wasserstein_1d * pep8 * upate example * move stuff * tesys should work + implemù random backend * test random generayor functions * correction * better random generation * update sliced * update sliced * proper tests sliced * max sliced * chae file nam * add stuff * example sliced flow and barycenter * correct typo + update readme * exemple sliced flow done * pep8 * solver1d works * pep8 Co-authored-by: Rémi Flamary <remi.flamary@gmail.com> Co-authored-by: Alexandre Gramfort <alexandre.gramfort@m4x.org>
2021-10-25[MRG] Regularization path for l2 UOT (#274)haoran010
* add reg path * debug examples and verify pep8 * pep8 and move the reg path examples in unbalanced folder Co-authored-by: haoran010 <haoran.wu@insa-rennes.fr> Co-authored-by: Rémi Flamary <remi.flamary@gmail.com>
2021-06-01[MRG] POT numpy/torch/jax backends (#249)Rémi Flamary
* add numpy and torch backends * stat sets on functions * proper import * install recent torch on windows * install recent torch on windows * now testing all functions in backedn * add jax backedn * clenaup windowds * proper convert for jax backedn * pep8 * try again windows tests * test jax conversion * try proper widows tests * emd fuction ses backedn * better test partial OT * proper tests to_numpy and teplate Backend * pep8 * pep8 x2 * feaking sinkhorn works with torch * sinkhorn2 compatible * working ot.emd2 * important detach * it should work * jax autodiff emd * pep8 * no tast same for jax * new independat tests per backedn * freaking pep8 * add tests for gradients * deprecate ot.gpu * worging dist function * working dist * dist done in backedn * not in * remove indexing * change accuacy for jax * first pull backend * projection simplex * projection simplex * projection simplex * projection simplex no ci * projection simplex no ci * projection simplex no ci * pep8 * add backedn discusion to quickstart guide * projection simplex no ci * projection simplex no ci * projection simplex no ci * pep8 + better doc * proper links * corect doctest * big debug documentation * doctest again * doctest again bis * doctest again ter (last one or i kill myself) * backend test + doc proj simplex * correction test_utils * correction test_utils * correction cumsum * correction flip * correction flip v2 * more debug * more debug * more debug + pep8 * pep8 * argh * proj_simplex * backedn works for sort * proj simplex * jax sucks * update doc * Update test/test_utils.py Co-authored-by: Alexandre Gramfort <alexandre.gramfort@m4x.org> * Update docs/source/quickstart.rst Co-authored-by: Alexandre Gramfort <alexandre.gramfort@m4x.org> * Update docs/source/quickstart.rst Co-authored-by: Alexandre Gramfort <alexandre.gramfort@m4x.org> * Update docs/source/quickstart.rst Co-authored-by: Alexandre Gramfort <alexandre.gramfort@m4x.org> * Update docs/source/readme.rst Co-authored-by: Alexandre Gramfort <alexandre.gramfort@m4x.org> * Update test/test_utils.py Co-authored-by: Alexandre Gramfort <alexandre.gramfort@m4x.org> * Update ot/utils.py Co-authored-by: Alexandre Gramfort <alexandre.gramfort@m4x.org> * Update docs/source/readme.rst Co-authored-by: Alexandre Gramfort <alexandre.gramfort@m4x.org> * Update ot/lp/__init__.py Co-authored-by: Alexandre Gramfort <alexandre.gramfort@m4x.org> * begin comment alex * comment alex part 2 * optimize test gromov * proj_simplex on vectors * add awesome gradient decsnt example on the weights * pep98 of course * proof read example by alex * pep8 again * encoding oos in translation * correct legend Co-authored-by: Nicolas Courty <ncourty@irisa.fr> Co-authored-by: Alexandre Gramfort <alexandre.gramfort@m4x.org>
2021-04-22[WIP] Build doc in master and stable separately and have both versions on ↵Rémi Flamary
the website (#243) * add bild doc action workflow * new build * build full doc * remove github action and update circleci builder * add versions in doc and change dev number
2020-12-22[WIP] Update documentation "Why OT" section (#220)Rémi Flamary
* add some text + discussion sinkhorn * stating wrk on why POT * fix sphinx warnings + make html-noplot * discussion when not to use POT * add discussion which sinkhorn * edits on quickstart * more * remove warnings :any: * more * done * remove ref Co-authored-by: Alexandre Gramfort <alexandre.gramfort@m4x.org>
2020-10-22[MRG] Sliced wasserstein (#203)AdrienCorenflos
* example for log treatment in bregman.py * Improve doc * Revert "example for log treatment in bregman.py" This reverts commit 9f51c14e * Add comments by Flamary * Delete repetitive description * Added raw string to avoid pbs with backslashes * Implements sliced wasserstein * Changed formatting of string for py3.5 support * Docstest, expected 0.0 and not 0. * Adressed comments by @rflamary * No 3d plot here * add sliced to the docs * Incorporate comments by @rflamary * add link to pdf Co-authored-by: Rémi Flamary <remi.flamary@gmail.com>
2020-04-30change release and update reseale fileRémi Flamary
2020-04-24better doc per moduleRémi Flamary
2020-04-20bump beta version and update setup.pyRémi Flamary
2020-04-15partial with initLaetitia Chapel
2020-04-15partial with testsLaetitia Chapel
2019-09-09merge new unbalancedRémi Flamary
2019-09-04improve docHicham Janati
2019-09-03add unbalanced_barycenter importHicham Janati
2019-08-28remove square in convergence checkHicham Janati
add unbalanced with stabilization add unbalanced tests with stabilization fix doctest examples add xvfb in travis remove explicit call xvfb in travis change alpha to reg_m minor flake8 remove redundant sink definitions + better doc and naming add stabilized unbalanced barycenter + add not converged warnings add test for stable barycenter add generic barycenter func + make method funcs private fix typo + add method test for barycenters fix doc examples + add xml to gitignore fix whitespace in example change logsumexp import - scipy deprecation warning fix doctest improve naming + add stable barycenter in bregman add test for stable bar + test the method arg in bregman
2019-07-05prepare for version 1.0Rémi Flamary
2019-07-03doc in modulesRémi Flamary
2019-07-03test raise with pytets in test_emd_1d_emd2_1dRémi Flamary
2019-06-27Merge branch 'master' into doc_modulesRémi Flamary
2019-06-27Wasserstein defined as the cost itself (do not return transportation matrix)Romain Tavenard
2019-06-27Merge branch 'master' into masterRomain Tavenard
2019-06-27Improved tests and docs for wasserstein_1dRomain Tavenard
2019-06-25Merge branch 'master' into doc_modulesRémi Flamary
2019-06-24update docstrings + initHicham Janati
2019-06-21Sparse G matrix for EMD1d + standard metrics computed without cdistRomain Tavenard
2019-06-20EMD 1d without docRomain Tavenard
2019-06-18fix func names + add more testsHicham Janati
2019-06-12add unbalanced sinkhorn algorithmHicham Janati
2019-06-07debut docRémi Flamary
2019-06-06start documentation otRémi Flamary
2018-10-03pipy releaseRémi Flamary
2018-09-28update realease.mdRémi Flamary
2018-08-29version 0.5.0bRémi Flamary
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