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2022-06-01[MRG] numItermax in 64 bits in EMD solver (#380)Nathan Cassereau
* Correct test_mm_convergence for cupy * Fix bug where number of iterations is limited to 2^31 * Update RELEASES.md * Replace size_t with long long * Use uint64_t instead of long long
2022-05-16[MRG] dist: check metric is a string before calling a str method (#379)Zachary Kurtz
2022-05-13remove calls to cerr (#377)Jay Stanley
typo in releases
2022-05-11[WIP] Graphical tweaks for GWB + fixed seed method for the partial gromov ↵eloitanguy
test (#376) * 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 * GWB graphical tweaks + better seed method for partial gromov test * fixed PR number * refixed seed issue * seed fix fix fix Co-authored-by: Rémi Flamary <remi.flamary@gmail.com>
2022-05-09[MRG] Fix barycenter mass (#375)Hicham Janati
* fix transpose in sinkhorn barycenters * add test for assymetric cost barycenters * fix pep8 Co-authored-by: Hicham Janati <hicham.janati@inria.fr>
2022-05-06[MRG] Torch random generator not working for Cuda tensor (#373)Nathan Cassereau
* Solve bug * Update release file
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] Center gradients for mass of emd2 and gw2 (#363)Rémi Flamary
* center gradients for mass of emd2 and gw2 * debug fgw gradient * debug fgw
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
2022-04-04[WIP] Add backend dual loss and plan computation for stochastic optimization ↵Rémi Flamary
or regularized OT (#360) * add losses and plan computations and exmaple for dual oiptimization * pep8 * add nice exmaple * update awesome example stochasti dual * add all tests * pep8 + speedup exmaple * add release info
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
2022-03-24[MRG] Domain adaptation and unbalanced solvers with backend support (#343)Nathan Cassereau
* First draft * Add matrix inverse and square root to backend * Eigen decomposition for older versions of pytorch (1.8.1 and older) * Corrected eigen decomposition for pytorch 1.8.1 and older * Spectral theorem is a thing * Optimization * small optimization * More functions converted * pep8 * remove a warning and prepare torch meshgrid for future torch release (which will change default indexing) * dots and pep8 * Meshgrid corrected for older version and prepared for future versions changes * New backend functions * Base transport * LinearTransport * All transport classes + pep8 * PR added to release file * Jcpot barycenter test * unbalanced with backend * pep8 * bug solve * test of domain adaptation with backends * solve bug for tic toc & macos * solving scipy deprecation warning * solving scipy deprecation warning attempt2 * solving scipy deprecation warning attempt3 * A warning is triggered when a float->int conversion is detected * bug solve * docs * release file updated * Better handling of float->int conversion in EMD * Corrected test for is_floating_point * docs * release file updated * cupy does not allow implicit cast * fromnumpy * added test * test da tf jax * test unbalanced with no provided histogram * using type_as argument in unif function correctly * pep8 * transport plan cast in emd changed behaviour, now trying to cast as histogram's dtype, defaulting to cost matrix Co-authored-by: Rémi Flamary <remi.flamary@gmail.com>
2022-03-18[MRG] Add logo to POT (#357)Rémi Flamary
* add logo code and logo to doc * update release file
2022-03-09[MRG] minor spelling fix (#353)Keiland
2022-03-02[MRG] Gromov_Wasserstein2 not performing backward properly on GPU (#352)Nathan Cassereau
* Resolves gromov wasserstein backward bug * release file updated
2022-02-23[MRG] Proper links in release file in documentation (#350)Rémi Flamary
* propreer links in release file in documentation * add pr in 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>
2022-02-11[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
2022-01-28[MRG] Backend implementation of the free support barycenter (#340)Rémi Flamary
* backend version barycenter * new tests * cleanup release file and doc * f*ing pep8 * remove unused variable
2022-01-21[MRG] Implement Sinkhorn in log-domain for WDA (#336)Jakub Zadrożny
* [MRG] Implement Sinkhorn in log-domain for WDA * for small values of the regularization parameter (reg) the current implementation runs into numerical issues (nans and infs) * this can be resolved by using log-domain implementation of the sinkhorn algorithm * Add feature to RELEASES and contributor name * Add 'sinkhorn_method' parameter to WDA * use the standard Sinkhorn solver by default (faster) * use log-domain Sinkhorn if asked by the user Co-authored-by: Jakub Zadrożny <jz@qed.ai> Co-authored-by: Rémi Flamary <remi.flamary@gmail.com>
2022-01-19[MRG] Fix instantiation of `ValFunction` (which raises a warning with ↵Bastian Rieck
PyTorch) (#338) * Not instantiating `ValFunction` `ValFunction` should not be instantiated since `autograd` functions are supposed to only ever use static methods. This solves a warning message raised by PyTorch. * Updated release information * Fixed PR number
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
2021-12-31[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
2021-12-31Don't install benchmarks (#333)gspr
2021-12-31minor changes for better doc generation in GW with Pytorch example (#330)Binh Nguyen
2021-12-27debug doc deply on tagRémi Flamary
2021-12-27[MRG] Remove python 3.6 properly for all wheel building (#328)Rémi Flamary
* remove python3.6 properly
2021-12-27[MRG] Remove Python3.6 from wheels (#327)Rémi Flamary
* remove wheel 3.6
2021-12-26[MRG] Change numpy version (due to ABI change) (#326)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? * proper version numpy * update release file
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?
2021-12-17[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
2021-12-06[MRG] Fix issue 317 (#318)Hongwei Jin
* Fix issue 317 * Update with docs and tests Co-authored-by: Rémi Flamary <remi.flamary@gmail.com>
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
2021-11-17[MRG] SinkhornL1L2 bug solve (#313)Nathan Cassereau
* Now limiting alpha to a minimum value as well as a max value * Docs * typo
2021-11-17[MRG] SinkhornL1L2Transport bug (#312)Nathan Cassereau
* solve bug * Linesearch no longer return None as alpha, only 0
2021-11-16[WIP] Fix gradient scaling bug in emd (#310)Rémi Flamary
* orrect gradient bug in emd2 * small comment in test * deploy properly on tag release * subplot fail
2021-11-08[MRG] Distance calculation bug solve (#306)Nathan Cassereau
* solve bug * Weights & docs * tests for dist * test dist * pep8
2021-11-05update classifiersRémi Flamary
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
2021-11-05[MRG] Tests with types/device on sliced/bregman/gromov functions (#303)ncassereau-idris
* First draft : making pytest use gpu for torch testing * bug solve * Revert "bug solve" This reverts commit 29b013abd162f8693128f26d8129186b79923609. * Revert "First draft : making pytest use gpu for torch testing" This reverts commit 2778175bcc338016c704efa4187d132fe5162e3a. * sliced * sliced * ot 1dsolver * bregman * better print * jax works with sinkhorn, sinkhorn_log and sinkhornn_stabilized, no need to skip them * gromov & entropic gromov
2021-11-04[MRG] Add tests about type and GPU for emd/emd2 + 1d variants + ↵Rémi Flamary
wasserstein1d (#304) * new test gpu * pep 8 of couse * debug torch * jax with gpu * device put * device put * it works * emd1d and emd2_1d working * emd_1d and emd2_1d done * cleanup * of course * should work on gpu now * tests done+ pep8
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
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