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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>
2023-03-09[MRG] Update pymanopt requirement and API for `ot.dr` (#443)Rémi Flamary
* updayte pymanopt API step 1 * add realease information * update requireents for tests on windows
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>
2022-08-18[MRG] Proper subsections in gallery (#395)Rémi Flamary
* add option for preper subsections * cleanup dodecov ignore * cleanup dodecov ignore
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
2022-03-18[MRG] Add logo to POT (#357)Rémi Flamary
* add logo code and logo to doc * update release file
2022-02-23[MRG] Build POT against oldest-supported-numpy (local PR) (#349)Rémi Flamary
* Configure setup to compile against oldest supported numpy version using the meta-package: https://pypi.org/project/oldest-supported-numpy/ - * Set minimum Python requirement to `>=3.7` in setup.py since !328 removed Python 3.6 support * Fix typo in pyproject.toml - * Update setup.py * Update setup.py and * build wheels * remove install dependencies for wheels building and build wheels * Apply suggestions from code review Co-authored-by: David M. Ghiurco <9147386+davidghiurco@users.noreply.github.com> * correct timing test add info in release file and build wheels * pep8 and Co-authored-by: David Ghiurco <9147386+davidghiurco@users.noreply.github.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
2022-01-17[MRG] Default pygment color for doc (#335)Rémi Flamary
* back to default pygment * add images back * move static images and make it work
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
2021-12-17[WIP] Debug doc missing file on merge (#324)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
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
2021-12-09[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
2021-11-19[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
2021-11-05[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
2021-11-02[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] 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
2021-10-25[MRG] Bregman backend (#280)ncassereau-idris
* Bregman * Resolve conflicts * Bug solve * Bregman updated for JAX compatibility * Tests coherence between backend improved * No longer enforcing 64 bits operations on Jax except for tests * Now using mixtures, to make backend dependent tests with less code * Better test skipping code * Pep8 + test optimizations * redundancy removed * Docs * Typo corrected * Typo * Typo * Docs * Docs * pep8 * Backend docs * Prettier docs * Mistake corrected * small changes * Better wording Co-authored-by: Rémi Flamary <remi.flamary@gmail.com>
2021-06-08[MRG] Update example GAN to avoid the 10 minute CircleCI limit (#258)Rémi Flamary
* shortened example GAN * pep8 and typo * awesome animation * small eror pep8 * add animation to doc * better timing animation * tune step
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
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
2020-12-22[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>
2020-08-30Fix minor typo take #2 (#209)Florian Kalinke
As recommended in your comment.
2020-08-24[WIP] add introductory example of OT, EMD and Sinkhorn (#191)aboisbunon
* add introductory example of OT, EMD and Sinkhorn * improve figure and try complying with pep8 * autopep8 * change markdown elements to rst * try solving issue with images * fix issue with images * add a section on varying the sinkhorn hyperparameter * add Sinkhorn algorithm and discussion for comparison between EMD and Sinkhorn * autopep8 again * add subsections and modify figure sizes/shapes * fix bug with print * correct some typos * remove computational time comparison * autopep8 again... Co-authored-by: Aurelie Boisbunon <abb@mydatamodels.com>
2020-05-05update release in docRémi Flamary
2020-05-05correct year in mccan reference for partial otRémi Flamary
2020-05-05add release 0.7.0 in docRémi Flamary
2020-04-27correct url for examplesRémi Flamary
2020-04-24update proper links form readmeRémi Flamary
2020-04-24test new foldeerRémi Flamary
2020-04-24add templateRémi Flamary
2020-04-24awesome mini galleryRémi Flamary
2020-04-24test autosummaryRémi Flamary
2020-04-24Better section name + snhix-gallery tuningRémi Flamary
2020-04-24test options sphinx galleryRémi Flamary
2020-04-24better documentationRémi Flamary
2020-04-24mockj module cupy for gpu focumentationRémi Flamary
2020-04-24add realeasesRémi Flamary
2020-04-24update docRémi Flamary
2020-04-24correct doc for emdRémi Flamary
2020-04-22relative path in docRémi Flamary
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