Ott-jax

What's Changed
* Re-run and refactoring of some docs/tutorials + minor changes by marcocuturi in https://github.com/ott-jax/ott/pull/431
* Feature/quadratic solve by michalk8 in https://github.com/ott-jax/ott/pull/433
* Fix `n_iters` by michalk8 in https://github.com/ott-jax/ott/pull/437
* Fix/rank2 init by michalk8 in https://github.com/ott-jax/ott/pull/442
* nn.dataset.GaussianMixture: minor fix to the docstring and standard deviation parameter name by bamos in https://github.com/ott-jax/ott/pull/445
* introduce multivariate cdf / quantiles by marcocuturi in https://github.com/ott-jax/ott/pull/447
* Feature/update jax version by michalk8 in https://github.com/ott-jax/ott/pull/448
* Histogram Transport Implementation by Daniel-Packer in https://github.com/ott-jax/ott/pull/444
* Doc refresh by marcocuturi in https://github.com/ott-jax/ott/pull/450
* Fix/jax prng deprecation by michalk8 in https://github.com/ott-jax/ott/pull/455
* Added CDF distance to Univariate Solver by Daniel-Packer in https://github.com/ott-jax/ott/pull/451
* Use PyPI trusted publishers by michalk8 in https://github.com/ott-jax/ott/pull/459
* first lb -> third lb by Daniel-Packer in https://github.com/ott-jax/ott/pull/462
* Restructure neural module by michalk8 in https://github.com/ott-jax/ott/pull/466
* refactoring ``UnivariateSolver`` by marcocuturi in https://github.com/ott-jax/ott/pull/472
* Feature/geodesic sinkhorn by guillaumehu in https://github.com/ott-jax/ott/pull/457
* Enable 3.12 CI by michalk8 in https://github.com/ott-jax/ott/pull/475
* Feature/apply lse mode by michalk8 in https://github.com/ott-jax/ott/pull/474
* Fix/neural docs by michalk8 in https://github.com/ott-jax/ott/pull/473
* Add quadratic layers and enhance ICNNs, update tutorial by nvesseron in https://github.com/ott-jax/ott/pull/477
* Fix heat scaling by guillaumehu in https://github.com/ott-jax/ott/pull/481
* Add low-rank kernel geometry by michalk8 in https://github.com/ott-jax/ott/pull/440

New Contributors
* Daniel-Packer made their first contribution in https://github.com/ott-jax/ott/pull/444
* guillaumehu made their first contribution in https://github.com/ott-jax/ott/pull/457
* nvesseron made their first contribution in https://github.com/ott-jax/ott/pull/477

**Full Changelog**: https://github.com/ott-jax/ott/compare/0.4.4...0.4.5

What's Changed
* introduce new `norm` operator that can differentiate through `lambda x: norm(x-x)` + lighter tests across the board by marcocuturi in https://github.com/ott-jax/ott/pull/411
* Feature/better io callbacks by michalk8 in https://github.com/ott-jax/ott/pull/413
* Feature/optional dependencies by michalk8 in https://github.com/ott-jax/ott/pull/412
* Update pre-commits by michalk8 in https://github.com/ott-jax/ott/pull/416
* Feature/move solve by michalk8 in https://github.com/ott-jax/ott/pull/418
* Feature/lineax ridge by michalk8 in https://github.com/ott-jax/ott/pull/424
* Feature/ulrgw by michalk8 in https://github.com/ott-jax/ott/pull/410


**Full Changelog**: https://github.com/ott-jax/ott/compare/0.4.3...0.4.4

What's Changed
* A few changes to increase Coverage by marcocuturi in https://github.com/ott-jax/ott/pull/390
* rename `ent_reg_cost` in sinkhorn solver by marcocuturi in https://github.com/ott-jax/ott/pull/391
* Increase coverage of NN modules by including init in tests by marcocuturi in https://github.com/ott-jax/ott/pull/392
* add tests for plots in ``potentials`` by marcocuturi in https://github.com/ott-jax/ott/pull/393
* test `Plot` class in `tools` module to increase coverage by marcocuturi in https://github.com/ott-jax/ott/pull/394
* Add soft `topk_mask` operator, fix `ranks` docs and tests by marcocuturi in https://github.com/ott-jax/ott/pull/396
* Add `relative_epsilon` option to `GromovWasserstein` by michalk8 in https://github.com/ott-jax/ott/pull/355
* [ENH]: Fix misc typos in soft_sort doc by pierreablin in https://github.com/ott-jax/ott/pull/397
* Update docs by michalk8 in https://github.com/ott-jax/ott/pull/398
* add ability to add titles on animation plots by marcocuturi in https://github.com/ott-jax/ott/pull/400
* Update contributing visibility by michalk8 in https://github.com/ott-jax/ott/pull/399
* update nb by marcocuturi in https://github.com/ott-jax/ott/pull/403
* Fix not being able to jit the soft quantile by michalk8 in https://github.com/ott-jax/ott/pull/408
* Test `default_progress_fn`, skip `types.py` by michalk8 in https://github.com/ott-jax/ott/pull/404


**Full Changelog**: https://github.com/ott-jax/ott/compare/0.4.2...0.4.3

What's Changed
* Add a tuto about sparse monge displacements by pierreablin in https://github.com/ott-jax/ott/pull/374
* introduce `ent_reg_cost` / `kl_reg_cost` in Sinkhorn to clarify which is returned to the user in `SinkhornOutput` objects. by marcocuturi in https://github.com/ott-jax/ott/pull/376
* more precise pydocs for 376 by marcocuturi in https://github.com/ott-jax/ott/pull/377
* Update sinkhorn.py by marcocuturi in https://github.com/ott-jax/ott/pull/378
* Compute multiple soft-quantiles in one execution without using `vmap` by marcocuturi in https://github.com/ott-jax/ott/pull/382
* incorporate feedback in 382 by marcocuturi in https://github.com/ott-jax/ott/pull/385
* Update soft_sort.py by marcocuturi in https://github.com/ott-jax/ott/pull/387
* Add elastic-net type costs with an orthogonal linear transformation of the input before it is fed into the regularizer by michalk8 in https://github.com/ott-jax/ott/pull/383
* Add monge gap by theouscidda6 in https://github.com/ott-jax/ott/pull/361
* Feature/unbalanced LR sinkhorn by michalk8 in https://github.com/ott-jax/ott/pull/379
* changes in definition of Monge gap by marcocuturi in https://github.com/ott-jax/ott/pull/389
* fix 375, `converged` flag when predefined number of iterations. by marcocuturi in https://github.com/ott-jax/ott/pull/386


**Full Changelog**: https://github.com/ott-jax/ott/compare/0.4.1...0.4.2

Highlights:
- reformatted tutorial NBs
- progressbars for Sinkhorn
- low-rank Sinkhorn solvers can run in kernel mode
- `discrete_barycenter` is refactored using the Solver/Problem model, rather than a simple function.
- soft-DTW added as a cost function.
- Sparsity inducing (in displacements) costs, see https://arxiv.org/abs/2302.04065


What's Changed
* Fix typo: Wasserstein-4 -> Wasserstein-2 by bamos in https://github.com/ott-jax/ott/pull/249
* Fix/warnings lint by michalk8 in https://github.com/ott-jax/ott/pull/260
* Addresses 229: Copyrights unification by AWehenkel in https://github.com/ott-jax/ott/pull/261
* fixed the docs about the implicit_diff argument by gjhuizing in https://github.com/ott-jax/ott/pull/270
* Correct package requirements for tests. by AWehenkel in https://github.com/ott-jax/ott/pull/271
* Add pre-commit CI cache by michalk8 in https://github.com/ott-jax/ott/pull/279
* Fix flake8 `D10{1,2,3}` errors by giovp in https://github.com/ott-jax/ott/pull/269
* Added CostFn and Plot to the documentation by gjhuizing in https://github.com/ott-jax/ott/pull/288
* add `primal_cost` property to output of GW, to compute cost without any regularization. by marcocuturi in https://github.com/ott-jax/ott/pull/286
* add `ruff` and remove redundant pre-commits by giovp in https://github.com/ott-jax/ott/pull/278
* Remove `matplotlib` dependency by michalk8 in https://github.com/ott-jax/ott/pull/304
* Fix/epsilon regularization by michalk8 in https://github.com/ott-jax/ott/pull/310
* Address 252 - Make soft ranking notebook self contained by AWehenkel in https://github.com/ott-jax/ott/pull/301
* Fix small TODOs by michalk8 in https://github.com/ott-jax/ott/pull/311
* Add CI tests for upstream JAX by michalk8 in https://github.com/ott-jax/ott/pull/313
* Subsample initializer by JTT94 in https://github.com/ott-jax/ott/pull/309
* feat: add progress reporting to Sinkhorn by bosr in https://github.com/ott-jax/ott/pull/228
* Refactor `discrete_barycenter` as solver, cf. issue 255 by marcocuturi in https://github.com/ott-jax/ott/pull/316
* Make random seeding consistent with PRNG keys everywhere instead of seeds by othmanesebbouh in https://github.com/ott-jax/ott/pull/290
* Add `Soft-DTW` cost function by michalk8 in https://github.com/ott-jax/ott/pull/318
* Fix/sinkdiv hessian by michalk8 in https://github.com/ott-jax/ott/pull/321
* Enable `D*` checks by michalk8 in https://github.com/ott-jax/ott/pull/319
* Fix spelling by michalk8 in https://github.com/ott-jax/ott/pull/323
* Remove ignoring passed params in ICNN by michalk8 in https://github.com/ott-jax/ott/pull/325
* Fix spelling by michalk8 in https://github.com/ott-jax/ott/pull/326
* neuraldual: fix issues with objective-based amortization and no-fine-tuning by bamos in https://github.com/ott-jax/ott/pull/327
* Parameter to make line strength proportional to coupling strength in Plot by gjhuizing in https://github.com/ott-jax/ott/pull/280
* Remove sparse option in `Graph` geometry by michalk8 in https://github.com/ott-jax/ott/pull/329
* gh: refactor community files by SauravMaheshkar in https://github.com/ott-jax/ott/pull/331
* Have a simpler "getting started" notebook by pierreablin in https://github.com/ott-jax/ott/pull/296
* update NBs by marcocuturi in https://github.com/ott-jax/ott/pull/332
* Docs/fix minor issues by michalk8 in https://github.com/ott-jax/ott/pull/334
* Small fix in soft_sort.quantile docstring by pierreablin in https://github.com/ott-jax/ott/pull/336
* Fix/jit inside jit by michalk8 in https://github.com/ott-jax/ott/pull/335
* typos by marcocuturi in https://github.com/ott-jax/ott/pull/339
* Remove assertions in cost functions by michalk8 in https://github.com/ott-jax/ott/pull/340
* Fix `EntropicPotentials`'s test by michalk8 in https://github.com/ott-jax/ott/pull/343
* Added tutorial on Sinkhorn divergence by gjhuizing in https://github.com/ott-jax/ott/pull/282
* Pin `chex` version in GPU CI by michalk8 in https://github.com/ott-jax/ott/pull/346
* Feature/unscaled gw cost by michalk8 in https://github.com/ott-jax/ott/pull/348
* Fix typos in notebook by michalk8 in https://github.com/ott-jax/ott/pull/350
* docs/progress bar by bosr in https://github.com/ott-jax/ott/pull/347
* Fix/default prng by michalk8 in https://github.com/ott-jax/ott/pull/353
* tracking progress of gromov-wasserstein by bosr in https://github.com/ott-jax/ott/pull/351
* Store individual costs to in the GW barycenter by michalk8 in https://github.com/ott-jax/ott/pull/354
* Update brain notebook by michalk8 in https://github.com/ott-jax/ott/pull/358
* add dtype to kernel by MUCDK in https://github.com/ott-jax/ott/pull/365
* Neural OT notebook: add more 2d datasets by bamos in https://github.com/ott-jax/ott/pull/303
* New kernel lr by meyerscetbon in https://github.com/ott-jax/ott/pull/324
* Fine grained control of Bures barycenters by marcocuturi in https://github.com/ott-jax/ott/pull/366
* use lineax to solve linear system in implicit diff by marcocuturi in https://github.com/ott-jax/ott/pull/370
* Fix .readthedocs.yaml by michalk8 in https://github.com/ott-jax/ott/pull/372

New Contributors
* AWehenkel made their first contribution in https://github.com/ott-jax/ott/pull/261
* gjhuizing made their first contribution in https://github.com/ott-jax/ott/pull/270
* giovp made their first contribution in https://github.com/ott-jax/ott/pull/269
* bosr made their first contribution in https://github.com/ott-jax/ott/pull/228
* othmanesebbouh made their first contribution in https://github.com/ott-jax/ott/pull/290
* pierreablin made their first contribution in https://github.com/ott-jax/ott/pull/296

**Full Changelog**: https://github.com/ott-jax/ott/compare/0.4.0...0.4.1

What's Changed
* Fix badges by michalk8 in https://github.com/ott-jax/ott/pull/211
* Feature/faster gw init by michalk8 in https://github.com/ott-jax/ott/pull/213
* Fix/device array check by michalk8 in https://github.com/ott-jax/ott/pull/216
* Remove support for Python 3.7 by michalk8 in https://github.com/ott-jax/ott/pull/227
* chore: add yapf config to `pyproject.toml` by SauravMaheshkar in https://github.com/ott-jax/ott/pull/230
* Remove functional API by michalk8 in https://github.com/ott-jax/ott/pull/222
* Docs/notebooks myst by michalk8 in https://github.com/ott-jax/ott/pull/233
* [ci skip] Add `environment.yml` for `binder` by michalk8 in https://github.com/ott-jax/ott/pull/236
* Use `lax.cond` when computing error in Sinkhorn by michalk8 in https://github.com/ott-jax/ott/pull/235
* Fix/debiased entropic map by michalk8 in https://github.com/ott-jax/ott/pull/238
* Misc/tox by michalk8 in https://github.com/ott-jax/ott/pull/239
* Re-add `jit` argument by michalk8 in https://github.com/ott-jax/ott/pull/221
* Add GPU test runner by michalk8 in https://github.com/ott-jax/ott/pull/242
* Remove old `Transport` interface by michalk8 in https://github.com/ott-jax/ott/pull/243
* Remove shape check in `LRCGeometry` by michalk8 in https://github.com/ott-jax/ott/pull/247
* Add regularized costs by michalk8 in https://github.com/ott-jax/ott/pull/244
* Check only whether problem can be LR by michalk8 in https://github.com/ott-jax/ott/pull/248
* Improvements to the neural dual solver by bamos in https://github.com/ott-jax/ott/pull/219

New Contributors
* SauravMaheshkar made their first contribution in https://github.com/ott-jax/ott/pull/230

**Full Changelog**: https://github.com/ott-jax/ott/compare/0.3.1...0.4.0