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0.5.0

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Remove source/target masks (#603)

* Remove `{src,tgt}_mask`

* Remove `nan{mean,max,median}`

* Reintroduce subset function

* Bump macOS runners

* Fwd-port `jnp.isscalar`

0.4.9

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Feature/batched vmap (#588)

* Start batched vmap

* Initial `batched_vmap` impl

* Nicer formatting

* Fix getting shape

* Remove private API usage

* Fix new args

* Add a TODO

* Canonicalize axes

* Add `batched_vmap` to docs

* Removed batched transport functions

* Remove `_norm_{x,y}` from `CostFn`

* Implement `apply_lse_kernel`

* Implememt `apply_kernel`

* Implement `apply_cost`

* Remove old functions

* Make function private

* Refactor `apply_cost` to have consistent shapes

* Use `_apply_cost_to_vec` in `PointCloud`

* Remoeve TODO

* Formatting

* Simplify `_apply_sqeucl_cost`

* Fix `RecusionError`

* Remove docstring of a private method

* Fix `apply_lse_kernel`

* Squeeze only 1 axis of the cost

* Add TODO

* Rename function, make a property

* Remove unused helper function

* Compute mean summary online

* Compute mean online

* Compute max cost matrix

* Update error message

* Remove TODO

* Flatten out axes

* Fix missing cross terms in the costs

* Fix geom tests

* Fix dtype

* Start implementing transport functions

* Implement online transport functions

* Fix solver tests

* Fix Bures test

* Don't use `pairwise` in tests

* Update notebook that uses `norm`

* Fix bug in `UnbalancedBures`

* Rename `pairwise -> __call__`

* Remove old shape code

* Always instantiate the cost for online

* Remove old TODO

* Extract `_apply_cost_to_vec_fast`

* Update max cost in LRCGeom

* Fix test, use more `multi_dot`

* Remove `batch_size` from `LRCGeometry`

* Add better warning error

* Reorder properties

* Add docs to `batched_vmap`

* Start adding tests

* Reorder functions in test

* Fix axes, add a test

* Update test fn

* Move out assert

* Dont canon out_axes

* Check max traces

* Test memory of batched vmap

* Install `typing_extensions`

* Remove `.` from description

* Add more `out_axes` tests

* Add `in_axes` test

* Fix negative axes

* Increase memory limit in the test

* Add in_axes pytree test

* Remove old warnings filters

* Update fixtures

* Update SqEucl cost.

* Update docstrings

* Remove unused imports from the docs

* Revert test pre-commits

* Fix ICNN init notebook

Was broken by #551

* Improve error message

0.4.8

Fix test

0.4.7

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Refactor regularized TI costs (#553)

* Update docs

Add new costs

Update tests

Final polishing

* Decrease tolerance in `test_l2_moreau_envelope`

* Fix not passing `kwargs`

* Expose initial estimate in `h_transform`

* Test for `x_init`

* Change variable name in `h_transform`

* Better `h_transform` parameterization

* Add more references

* Add a missing reference

* Update docs of p-norm

* Improve the docs of `RegTICost.h_transform`

* Rename `is_squared` -> `is_factor`

* Better `h_legendre` docs

* Expose solver in `TICost.h_transform`

0.4.6

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bug fix: avoid mixing up linear and quadratic in genot (#517)

* bug fix: avoid mixing up linear and quadratic part by returning Dict in genot prepare_data()

* fix data_match_fn() setup in genot tests

* prepare_data() in GENOT now returns a tuple instead of a dict; change order of args in utils.match_quadratic()

* Update docs

* Fix typo

---------

Co-authored-by: Michal Klein <46717574+michalk8@users.noreply.github.com>

0.4.5

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Add low-rank kernel geometry (#440)

* Add Gaussian kernel

* Make runnable with Sinkhorn

* Fix epsilon

* Use the same random vectors, fix epsilon

* Add arccos kernel

* Add citation

* Fix citation, start working on docs

* Addd LambertW

* Polish docstrings

* Update Lambert W docs

* Format references

* Remove useless TYPE_CHECKING

* Update docstring

* Add test skeletons

* Add rank test

* Update tests

* Start working on arccos cost

* Add arccos to docs

* Add `s=2` option for `Arccos`

* Fix LRK tests

* Fix tests and tree API

* Rename argument

* Add generic order using `jax.grad`

* Test also the implementation of `J(theta)`

* Polish flaky test

* Address comments

0.4.4

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Feature/ulrgw (#410)

* Remove low-rank from GromovWasserstein solver

* First skeleton loop

* Add LRGW implementation

* Add ULFGW

* Revert change

* Add a TODO

* Fix `grad_g` in the fused case

* Update docs

* Remove duplicate citation

* Fix cost for the fused case

* Fix bugs in TI

* Remove unused import

* Change way array extraction in LR init works

* Disallow LR in the old GW solver

* Disallow LR in old GW class

* Remove `is_entropic` property

* Use `jnp.linalg.norm`

* Simplify initializers in GW

* Simplify initializer creation for low-rank

* Remove temporary name

* Fix norms

* Fix linkcheck

* Remove old initializers test

* Fix more initializer tests

* Remove `LRQuadraticInitializer`, `reg_ot_cost -> reg_gw_cost`

* `host_callback` -> `io_callback`

* Fix more initializers tests

* Fix more tests

* Remove initializer mention from the docs

* Remove mention of LR initializer

* Start incorporating GWLoss

* Simplify reg GW cost computation

* Finish `primal_cost`

* Don't calculate unbal. grads in balanced case

* Fix `primal_cost` in balanced case

* Update GW LR notebook

* Convert quad problem to LR if possible

* Convert quad problem to LR if possible

* Regenerate GWLR Sinkhorn

* Regenerate `LRSinkhorn`

* [ci skip] Fix linter

* Fix convergence metric

* Undo TODO

* Fix factor

* Regenerate notebooks

* Add tests

0.4.3

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Test `default_progress_fn`, skip `types.py` (#404)

* Test `default_progress_fn`, skip `types.py`

* Fix ignore path

* [ci skip] Use glob

0.4.2

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fix #375, `converged` flag when predefined number of iterations. (#386)

* fix 375

* handle conversion of `threshold` in SinkhornOutput

* fix bug in converged when static_b is True

* take Michal comments into account + pydocs

* shape issue in the convergence[0]

0.4.1

remove announcement