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2021-11-27Ensure dh_numpy3 is called for NumPy ABI generationGard Spreemann
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
2021-11-10Skip test meant to be run from uninstalled sourcesGard Spreemann
2021-11-09Changelog for releaseGard Spreemann
2021-11-09Update files-excludedGard Spreemann
The previously bundled funcsig has been removed upstream. We instead remove the unclearly licensed example data files.
2021-11-09Standards-versionGard Spreemann
2021-11-09Merge branch 'dfsg/latest' into debian/sidGard Spreemann
2021-11-09Remove unclearly licensed example dataGard Spreemann
2021-11-09Merge tag '0.8.0' into dfsg/latestGard Spreemann
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
2021-11-03[MRG] Docs updates (#298)ncassereau-idris
* bregman docs * sliced docs * docs partial * unbalanced docs * stochastic docs * plot docs * datasets docs * utils docs * dr docs * dr docs corrected * smooth docs * docs da * pep8 * docs gromov * more space after min and argmin * docs lp * bregman docs * bregman docs mistake corrected * pep8 Co-authored-by: Rémi Flamary <remi.flamary@gmail.com>
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>
2021-11-02change repo url (#299)Rémi Flamary
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>
2021-11-02[MRG] Backend for gromov (#294)ncassereau-idris
* bregman: small correction * gromov backend first draft * Removing decorators * Reworked casting method * Bug solve * Removing casting * Bug solve * toarray renamed todense ; expand_dims removed * Warning (jax not supporting sparse matrix) moved * Mistake corrected * test backend * Sparsity test for older versions of pytorch * Trying pytorch/1.10 * Attempt to correct torch sparse bug * Backend version of gromov tests * Random state introduced for remaining gromov functions * review changes * code coverage * Docs (first draft, to be continued) * Gromov docs * Prettified docs * mistake corrected in the docs * little change Co-authored-by: Rémi Flamary <remi.flamary@gmail.com>
2021-10-29[MRG] Add tesing on wda (#296)Rémi Flamary
2021-10-29[MRG] add normalization of distances for WDA (#172)Hexuan_Liu
* edit dr.py * Correct normalization + optional parameter * pep8? * final! Co-authored-by: Rémi Flamary <remi.flamary@gmail.com>
2021-10-29[WIP] Debug doc build memory error (#295)Rémi Flamary
* change doker type * try avoid memory error * remove medium+ because no money * remove medium+ because no money
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
2021-10-25[MRG] Backend for optim (#282)ncassereau-idris
* Backend for optim * Bug solve * Doc update * backend tests now with fixture * Unused imports removed * Docs * Docs * Docs * Outer product backend docs * Prettier docs * Pep8 * Mistakes corrected Co-authored-by: Rémi Flamary <remi.flamary@gmail.com>
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>
2021-10-25[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>
2021-10-22Add set_gradients method for JAX backend. (#278)AdrienCorenflos
Co-authored-by: Rémi Flamary <remi.flamary@gmail.com>
2021-09-30[MRG] GPU bugs solve (#288)ncassereau-idris
* gpus tests now passing * pep8 compliance * GPU tests succeeding even if b has rank higher than 1 Co-authored-by: Rémi Flamary <remi.flamary@gmail.com>
2021-09-29[MRG] OpenMP support (#260)kguerda-idris
* Added : OpenMP support Restored : Epsilon and Debug mode Replaced : parmap => multiprocessing is now replace by multithreading * Commit clean up * Number of CPUs correctly calculated on SLURM clusters * Corrected number of processes for cluster slurm * Mistake corrected * parmap is now deprecated * Now a different solver is used depending on the requested number of threads * Tiny mistake corrected * Folders are now in the ot library instead of at the root * Helpers is now correctly placed * Attempt to make compilation work smoothly * OS compatible path * NumThreads now defaults to 1 * Better flags * Mistake corrected in case of OpenMP unavailability * Revert OpenMP flags modification, which do not compile on Windows * Test helper functions * Helpers comments * Documentation update * File title corrected * Warning no longer using print * Last attempt for macos compilation * pls work * atempt * solving a type error * TypeError OpenMP * Compilation finally working on Windows * Bug solve, number of threads now correctly selected * 64 bits solver to avoid overflows for bigger problems * 64 bits EMD corrected Co-authored-by: kguerda-idris <ssos023@jean-zay3.idris.fr> Co-authored-by: ncassereau-idris <84033440+ncassereau-idris@users.noreply.github.com> Co-authored-by: ncassereau <nathan.cassereau@idris.fr> Co-authored-by: Rémi Flamary <remi.flamary@gmail.com>
2021-09-28[MRG] Regularized OT (optim.cg) bug solve (#286)ncassereau-idris
* Line search stops when derphi is 0 instead of bugging out like in some instances * pep8 compliance * Tests
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>
2021-08-17we don't test with 3.5 but we already do with 3.9 so setup was not up to ↵Alexandre Gramfort
date (#269)
2021-08-15Changelog for releasedebian/0.7.0+dfsg-4Gard Spreemann
2021-08-15Fix watch fileGard Spreemann
2021-08-15Fix metadataGard Spreemann
2021-06-17[MRG] Speedup tests (#262)Rémi Flamary
* speedup tests * add color to tests and timings * add test unbalanced * stupid missing -
2021-06-14[MRG] Batch/Lazy Log Sinkhorn Knopp on samples (#259)Huy Tran
* Add batch implementation of Sinkhorn * Reformat to pep8 and modify parameter * Fix error in batch size * Code review and add test * Fix accidental typo in test_empirical_sinkhorn * Remove whitespace * Edit config.yml
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
2021-06-07[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>
2021-06-02[WIP] Add Wasserstein GAN and debug memory leak (#254)Rémi Flamary
* add example and debug memory leak * print stuff * speedup gallery * Apply suggestions from code review Co-authored-by: Alexandre Gramfort <alexandre.gramfort@m4x.org> * test cells * proper header gan exmaple * cleanup sections * last changes ? 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>
2021-05-27Build wheels on ARM and in PR (#253)Rémi Flamary
2021-05-26Docs correction (#252)ncassereau-idris
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
generated by cgit v1.2.3 (git 2.39.1) at 2024-06-02 01:49:41 +0000