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2023-03-24[WIP] Build donc in GH Action and report warnings + move contributing and ↵Rémi Flamary
code of conduct in documentation (#441) * use action for doc with wraning visible * remove space * remove space again * test pre commands * install pot properly * install compiler... * try composite action * remoe warning in sliced exmaple * pep8 * move contributing and code of conduct * cleanup * underline too short * update quickstart * replace version selector by static list to avoid jsQuery bug
2023-03-22[MRG] CO-Optimal Transport solver (#447)Huy Tran
* Allow warmstart in sinkhorn and sinkhorn_log * Added argument for warmstart of dual vectors in Sinkhorn-based methods in * Add the number of the PR * [WIP] CO-Optimal Transport * Revert "[WIP] CO-Optimal Transport" This reverts commit f3d36b2705013409ac69b346585e311bc25fcfb7. * reformat with PEP8 * Fix W291 trailing whitespace error in pep8 test * Rearange position of warmstart argument and edit its description * Implementation of CO-Optimal Transport * Optimize code and edit documentation * fix backend bug in test cases * fix backend bug * fix backend bug * Add examples on COOT * Modify API and edit example * Edit API * minor edit of examples and release * fix bug in coot * fix doc examples * more fix of doc * restart CI * reordering ref * add more tests * add more tests * add test verbose * fix PEP8 bug * fix PEP8 bug * fix PEP8 bug * fix pytest bug * edit doc for better display --------- Co-authored-by: Rémi Flamary <remi.flamary@gmail.com> Co-authored-by: Alexandre Gramfort <agramfort@fb.com>
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
2022-06-13[MRG] Correct pointer overflow in EMD (#381)Nathan Cassereau
* avoid overflow on openmp version of emd solver * monothread version updated * Fixed typo in readme * added PR in releases * typo in releases.md * added a precision to releases.md * added a precision to releases.md * correct readme * forgot to cast * lower error
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
2022-04-11[MRG] MM algorithms for UOT (#362)Laetitia Chapel
* bugfix * update refs partial OT * fixes small typos in plot_partial_wass_and_gromov * fix small bugs in partial.py * update README * pep8 bugfix * modif doctest * fix bugtests * update on test_partial and test on the numerical precision on ot/partial * resolve merge pb * Delete partial.py * update unbalanced: mm algo+plot * update unbalanced: mm algo+plot * update unbalanced: mm algo+plot * update unbalanced: mm algo+plot * update unbalanced: mm algo+plot * add test mm algo unbalanced OT * add test mm algo unbalanced OT * add test mm algo unbalanced OT * add test mm algo unbalanced OT * add test mm algo unbalanced OT * add test mm algo unbalanced OT * add test mm algo unbalanced OT * add test mm algo unbalanced OT * update unbalanced: mm algo+plot * update unbalanced: mm algo+plot * update releases.md with new MM UOT algorithms Co-authored-by: Rémi Flamary <remi.flamary@gmail.com>
2022-04-07[MRG] Remove deprecated ot.gpu submodule (#361)Rémi Flamary
* remove all cpu submodule and tests * speedup tests gromov
2022-04-05[MRG] Update examples in the doc (#359)Rémi Flamary
* add transparent color logo * add transparent color logo * move screenkhorn * move stochastic and install ffmpeg on circleci * try something * add sudo * install ffmpeg before python * cleanup examples * test svg scrapper * add animation for reg path * better example OT sivergence * update ttles and add plots * update free support * proper figure indexes * have less frame sin animation * update readme and release file * add tests for python 3.10
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
2021-12-09[MRG] Tensorflow backend & Benchmarker & Myst_parser (#316)Nathan Cassereau
* First batch of tf methods (to be continued) * Second batch of method (yet to debug) * tensorflow for cpu * add tf requirement * pep8 + bug * small changes * attempt to solve pymanopt bug with tf2 * attempt #2 * attempt #3 * attempt 4 * docstring * correct pep8 violation introduced in merge conflicts resolution * attempt 5 * attempt 6 * just a random try * Revert "just a random try" This reverts commit 8223e768bfe33635549fb66cca2267514a60ebbf. * GPU tests for tensorflow * pep8 * attempt to solve issue with m2r2 * Remove transpose backend method * first draft of benchmarker (need to correct time measurement) * prettier bench table * Bitsize and prettier device methods * prettified table bench * Bug corrected (results were mixed up in the final table) * Better perf counter (for GPU support) * pep8 * EMD bench * solve bug if no GPU available * pep8 * warning about tensorflow numpy api being required in the backend.py docstring * Bug solve in backend docstring * not covering code which requires a GPU * Tensorflow gradients manipulation tested * Number of warmup runs is now customizable * typo * Remove some warnings while building docs * Change prettier_device to device_type in backend * Correct JAX mistakes preventing to see the CPU if a GPU is present * Attempt to solve JAX bug in case no GPU is found * Reworked benchmarks order and results storage & clear GPU after usage by benchmark * Add bench to backend docstring * better benchs * remove useless stuff * Better device_type * Now using MYST_PARSER and solving links issue in the README.md / online docs
2021-12-03[MRG] Cupy backend (#315)Nathan Cassereau
* Cupy backend * pep8 + bug * working even if cupy not installed * attempt to force codecov to ignore cupy because no gpu can be used for testing on github * docstring * readme
2021-11-19[MRG] Solve bug of contribution link in docs + automated insert of readme in ↵Nathan Cassereau
doc (#301) * first try * bug solve * attempt to use m2r2 * More elegant dependency * readme.rst now generated automatically from readme.md * weird attempt * Revert "weird attempt" This reverts commit b45f0e6495148877ad3e93ad608b3b0cfe9bbb16. * fixing readme links * Revert "fixing readme links" This reverts commit 0c6ca7612ea297674a3afc50f8e6538c58c27701. * full link for readme * correct CONTRIBUTING guidelines mistakes
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
2021-11-03[WIP] Add debiased barycenter (Sinkhorn + convolutional sinkhorn) (#291)Hicham Janati
* add debiased sinkhorn barycenter + make loops pythonic * add debiased arg in tests * add 1d and 2d examples of debiased barycenters * fix doctest * fix flake8 * pep8 + make func private + add convergence warnings * remove rel paths + add rng + pylab to pyplot * fix stopping criterion debiased * pass alex * change params with new API * add logdomain barycenters + separate debiased API * test new API * fix jax read-only ? * raise error for jax * test catch jax error * fix pytest catch error * fix relative path * fix flake8 * add warn arg everywhere * fix ref number * catch warnings in tests * add contrib to readme + change ref number * fix convolution example + gallery thumbnails * increase coverage * fix flake Co-authored-by: Hicham Janati <hicham.janati@inria.fr> Co-authored-by: Rémi Flamary <remi.flamary@gmail.com> Co-authored-by: Alexandre Gramfort <alexandre.gramfort@m4x.org>
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>
2021-10-27[WIP] POT build without installing cython first (#293)Rémi Flamary
* test build with no dep * cleaning up stuff * build wheels
2021-10-27[WIP] Sinkhorn in log space (#290)Rémi Flamary
* adda sinkhorn log and working sinkhorn2 function * more tests pass * more tests pass * it works but not by default yet * remove warningd * update circleci doc * update circleci doc * new sinkhorn implemeted but not by default * better * doctest pass * test doctest * new test utils * remove pep8 errors * remove pep8 errors * doc new implementtaion with log * test sinkhorn 2 * doc for log implementation
2021-09-17[MRG] Implementation of two news algorithms: SaGroW and PoGroW. (#275)Tanguy
* Add two new algorithms to solve Gromov Wasserstein: Sampled Gromov Wasserstein and Pointwise Gromov Wasserstein. * Correct some lines in SaGroW and PoGroW to follow pep8 guide. * Change nb_samples name. Use rdm state. Change symmetric check. * Change names of len(p) and len(q) in SaGroW and PoGroW. * Re-add some deleted lines in the comments of gromov.py Co-authored-by: Rémi Flamary <remi.flamary@gmail.com>
2021-09-06[MRG] Projection Robust Wasserstein (#267)Minhui Huang
* ot.dr: PRW code; text.text_dr: PRW test code. * ot.dr: PRW code; test.test_dr: PRW test code. * fix errors: pep8(3.8) * fix errors: pep8(3.8) * modified readme; prw code review * fix pep error * edit comment * modified math comment Co-authored-by: Rémi Flamary <remi.flamary@gmail.com>
2021-06-07[WIP] Spell correction in README.md (#257)kguerda-idris
* Spell correction in README.md * Update README.md Co-authored-by: Alexandre Gramfort <alexandre.gramfort@m4x.org> Co-authored-by: kguerda-idris <ssos023@jean-zay1.idris.fr> Co-authored-by: Rémi Flamary <remi.flamary@gmail.com> Co-authored-by: Alexandre Gramfort <alexandre.gramfort@m4x.org>
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>
2021-04-10pass on readme (#234)Alexandre Gramfort
2021-04-08[MRG] Add Mathieu Blondel in acknoledgements (#232)Rémi Flamary
* add Mathieu in acknoledgements
2021-04-08[MRG] ADD JMLR paper to the readme and documentation (#231)Rémi Flamary
* add JMLR reefrence to eradme and doc
2020-10-22[MRG] Fix bugs for partial OT (#215)Laetitia Chapel
* bugfix * update refs partial OT * fixes small typos in plot_partial_wass_and_gromov * fix small bugs in partial.py * update README * pep8 bugfix * modif doctest * fix bugtests * update on test_partial and test on the numerical precision on ot/partial * resolve merge pb Co-authored-by: Rémi Flamary <remi.flamary@gmail.com>
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>
2020-05-22[MRG] Templates (#181)Ayush Karnawat
* Add a PR template * move github contrib + code of conduct * fix links * add feature request template * ask for gpu info * address comments * add gitter in README
2020-05-11Update README.mdRémi Flamary
make build badge on master only
2020-05-05correct year in mccan reference for partial otRémi Flamary
2020-05-04[WIP] Improved docs and changed scipy version (#163)Romain Tavenard
* Improved docs and changed scipy version * Fixed dependency bug in setup.py * dependencies set to minimal versions for tests * add requirements file * added minimal version build for scipy (testing 1.2) * bugfix in minimal deps build * (yet another) bugfix in minimal deps build * minimal deps now reflect README.md * minimal deps: no autograd nor pymanopt * refactored workflow names * minimal deps: no doctests * minimal deps: numpy 1.16 * trigger GH Actions on PR * better merge * re-add minimal-deps... * bugfix in yaml * enforce np>=1.16 * enforce scipy and cython versions too * requires / install_requires * requires / install_requires / requires * setup_requires Co-authored-by: Rémi Flamary <remi.flamary@gmail.com>
2020-04-27correct url for examplesRémi Flamary
2020-04-24update proper links form readmeRémi Flamary
2020-04-23Merge branch 'master' into rm_travisRémi Flamary
2020-04-23Update README.mdRémi Flamary
Co-Authored-By: Alexandre Gramfort <alexandre.gramfort@m4x.org>
2020-04-23update redame for install from gitRémi Flamary
2020-04-22awesome new readmeRémi Flamary
2020-04-22re-org readmeRémi Flamary
2020-04-22remove notebooks and cleanup readme and docRémi Flamary
2020-04-21fix GH Action badge in readme (#153)Alexandre Gramfort
2020-04-21[MRG] Actually run sphinx-gallery (#146)Rémi Flamary
* generate gallery * remove mock * add sklearn to requirermnt?txt for example * remove latex from fgw example * add networks for graph example * remove all * add requirement.txt rtd * rtd debug * update readme * eradthedoc with redirection * add conf rtd
2020-04-21rm travisAlexandre Gramfort
2020-04-21Windows CI (#148)Alexandre Gramfort
* add Windows build on GH actions
2020-04-21add codecov buttonAlexandre Gramfort
2020-04-20update readme + notebooksRémi Flamary
2020-04-20Change rflamary to PythonOT in ReadmeRémi Flamary
2020-04-20readme with laplaceievred
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