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diff --git a/docs/source/releases.rst b/docs/source/releases.rst new file mode 100644 index 0000000..5a357f3 --- /dev/null +++ b/docs/source/releases.rst @@ -0,0 +1,341 @@ +Releases +======== + +0.7.0 +----- + +*May 2020* + +This is the new stable release for POT. We made a lot of changes in the +documentation and added several new features such as Partial OT, +Unbalanced and Multi Sources OT Domain Adaptation and several bug fixes. +One important change is that we have created the GitHub organization +`PythonOT <https://github.com/PythonOT>`__ that now owns the main POT +repository https://github.com/PythonOT/POT and the repository for the +new documentation is now hosted at https://PythonOT.github.io/. + +This is the first release where the Python 2.7 tests have been removed. +Most of the toolbox should still work but we do not offer support for +Python 2.7 and will close related Issues. + +A lot of changes have been done to the documentation that is now hosted +on https://PythonOT.github.io/ instead of readthedocs. It was a hard +choice but readthedocs did not allow us to run sphinx-gallery to update +our beautiful examples and it was a huge amount of work to maintain. The +documentation is now automatically compiled and updated on merge. We +also removed the notebooks from the repository for space reason and also +because they are all available in the `example +gallery <auto_examples/index.html>`__. Note +that now the output of the documentation build for each commit in the PR +is available to check that the doc builds correctly before merging which +was not possible with readthedocs. + +The CI framework has also been changed with a move from Travis to Github +Action which allows to get faster tests on Windows, MacOS and Linux. We +also now report our coverage on +`Codecov.io <https://codecov.io/gh/PythonOT/POT>`__ and we have a +reasonable 92% coverage. We also now generate wheels for a number of OS +and Python versions at each merge in the master branch. They are +available as outputs of this +`action <https://github.com/PythonOT/POT/actions?query=workflow%3A%22Build+dist+and+wheels%22>`__. +This will allow simpler multi-platform releases from now on. + +In terms of new features we now have `OTDA Classes for unbalanced +OT <https://pythonot.github.io/gen_modules/ot.da.html#ot.da.UnbalancedSinkhornTransport>`__, +a new Domain adaptation class form `multi domain problems +(JCPOT) <auto_examples/domain-adaptation/plot_otda_jcpot.html#sphx-glr-auto-examples-domain-adaptation-plot-otda-jcpot-py>`__, +and several solvers to solve the `Partial Optimal +Transport <auto_examples/unbalanced-partial/plot_partial_wass_and_gromov.html#sphx-glr-auto-examples-unbalanced-partial-plot-partial-wass-and-gromov-py>`__ +problems. + +This release is also the moment to thank all the POT contributors (old +and new) for helping making POT such a nice toolbox. A lot of changes +(also in the API) are comming for the next versions. + +Features +^^^^^^^^ + +- New documentation on https://PythonOT.github.io/ (PR #160, PR #143, + PR #144) +- Documentation build on CircleCI with sphinx-gallery (PR #145,PR #146, + #155) +- Run sphinx gallery in CI (PR #146) +- Remove notebooks from repo because available in doc (PR #156) +- Build wheels in CI (#157) +- Move from travis to GitHub Action for Windows, MacOS and Linux (PR + #148, PR #150) +- Partial Optimal Transport (PR#141 and PR #142) +- Laplace regularized OTDA (PR #140) +- Multi source DA with target shift (PR #137) +- Screenkhorn algorithm (PR #121) + +Closed issues +^^^^^^^^^^^^^ + +- Bug in Unbalanced OT example (Issue #127) +- Clean Cython output when calling setup.py clean (Issue #122) +- Various Macosx compilation problems (Issue #113, Issue #118, PR#130) +- EMD dimension mismatch (Issue #114, Fixed in PR #116) +- 2D barycenter bug for non square images (Issue #124, fixed in PR + #132) +- Bad value in EMD 1D (Issue #138, fixed in PR #139) +- Log bugs for Gromov-Wassertein solver (Issue #107, fixed in PR #108) +- Weight issues in barycenter function (PR #106) + +0.6.0 +----- + +*July 2019* + +This is the first official stable release of POT and this means a jump +to 0.6! The library has been used in the wild for a while now and we +have reached a state where a lot of fundamental OT solvers are available +and tested. It has been quite stable in the last months but kept the +beta flag in its Pypi classifiers until now. + +Note that this release will be the last one supporting officially Python +2.7 (See https://python3statement.org/ for more reasons). For next +release we will keep the travis tests for Python 2 but will make them +non necessary for merge in 2020. + +The features are never complete in a toolbox designed for solving +mathematical problems and research but with the new contributions we now +implement algorithms and solvers from 24 scientific papers (listed in +the README.md file). New features include a direct implementation of the +`empirical Sinkhorn +divergence <all.html#ot.bregman.empirical_sinkhorn_divergence>`__ +, a new efficient (Cython implementation) solver for `EMD in +1D <all.html#ot.lp.emd_1d>`__ and +corresponding `Wasserstein +1D <all.html#ot.lp.wasserstein_1d>`__. +We now also have implementations for `Unbalanced +OT <auto_examples/plot_UOT_1D.html>`__ +and a solver for `Unbalanced OT +barycenters <auto_examples/plot_UOT_barycenter_1D.html>`__. +A new variant of Gromov-Wasserstein divergence called `Fused +Gromov-Wasserstein <all.html?highlight=fused_#ot.gromov.fused_gromov_wasserstein>`__ +has been also contributed with exemples of use on `structured +data <auto_examples/plot_fgw.html>`__ +and computing `barycenters of labeld +graphs <auto_examples/plot_barycenter_fgw.html>`__. + +A lot of work has been done on the documentation with several new +examples corresponding to the new features and a lot of corrections for +the docstrings. But the most visible change is a new `quick start +guide <quickstart.html>`__ for POT +that gives several pointers about which function or classes allow to +solve which specific OT problem. When possible a link is provided to +relevant examples. + +We will also provide with this release some pre-compiled Python wheels +for Linux 64bit on github and pip. This will simplify the install +process that before required a C compiler and numpy/cython already +installed. + +Finally we would like to acknowledge and thank the numerous contributors +of POT that has helped in the past build the foundation and are still +contributing to bring new features and solvers to the library. + +Features +^^^^^^^^ + +- Add compiled manylinux 64bits wheels to pip releases (PR #91) +- Add quick start guide (PR #88) +- Make doctest work on travis (PR #90) +- Update documentation (PR #79, PR #84) +- Solver for EMD in 1D (PR #89) +- Solvers for regularized unbalanced OT (PR #87, PR#99) +- Solver for Fused Gromov-Wasserstein (PR #86) +- Add empirical Sinkhorn and empirical Sinkhorn divergences (PR #80) + +Closed issues +^^^^^^^^^^^^^ + +- Issue #59 fail when using "pip install POT" (new details in doc+ + hopefully wheels) +- Issue #85 Cannot run gpu modules +- Issue #75 Greenkhorn do not return log (solved in PR #76) +- Issue #82 Gromov-Wasserstein fails when the cost matrices are + slightly different +- Issue #72 Macosx build problem + +0.5.0 +----- + +*Sep 2018* + +POT is 2 years old! This release brings numerous new features to the +toolbox as listed below but also several bug correction. + +| Among the new features, we can highlight a `non-regularized + Gromov-Wasserstein + solver <auto_examples/plot_gromov.html>`__, + a new `greedy variant of + sinkhorn <all.html#ot.bregman.greenkhorn>`__, +| `non-regularized <all.html#ot.lp.barycenter>`__, + `convolutional + (2D) <auto_examples/plot_convolutional_barycenter.html>`__ + and `free + support <auto_examples/plot_free_support_barycenter.html>`__ + Wasserstein barycenters and + `smooth <https://github.com/rflamary/POT/blob/prV0.5/notebooks/plot_OT_1D_smooth.html>`__ + and + `stochastic <all.html#ot.stochastic.sgd_entropic_regularization>`__ + implementation of entropic OT. + +POT 0.5 also comes with a rewriting of ot.gpu using the cupy framework +instead of the unmaintained cudamat. Note that while we tried to keed +changes to the minimum, the OTDA classes were deprecated. If you are +happy with the cudamat implementation, we recommend you stay with stable +release 0.4 for now. + +The code quality has also improved with 92% code coverage in tests that +is now printed to the log in the Travis builds. The documentation has +also been greatly improved with new modules and examples/notebooks. + +This new release is so full of new stuff and corrections thanks to the +old and new POT contributors (you can see the list in the +`readme <https://github.com/rflamary/POT/blob/master/README.md>`__). + +Features +^^^^^^^^ + +- Add non regularized Gromov-Wasserstein solver (PR #41) +- Linear OT mapping between empirical distributions and 90% test + coverage (PR #42) +- Add log parameter in class EMDTransport and SinkhornLpL1Transport (PR + #44) +- Add Markdown format for Pipy (PR #45) +- Test for Python 3.5 and 3.6 on Travis (PR #46) +- Non regularized Wasserstein barycenter with scipy linear solver + and/or cvxopt (PR #47) +- Rename dataset functions to be more sklearn compliant (PR #49) +- Smooth and sparse Optimal transport implementation with entropic and + quadratic regularization (PR #50) +- Stochastic OT in the dual and semi-dual (PR #52 and PR #62) +- Free support barycenters (PR #56) +- Speed-up Sinkhorn function (PR #57 and PR #58) +- Add convolutional Wassersein barycenters for 2D images (PR #64) +- Add Greedy Sinkhorn variant (Greenkhorn) (PR #66) +- Big ot.gpu update with cupy implementation (instead of un-maintained + cudamat) (PR #67) + +Deprecation +^^^^^^^^^^^ + +Deprecated OTDA Classes were removed from ot.da and ot.gpu for version +0.5 (PR #48 and PR #67). The deprecation message has been for a year +here since 0.4 and it is time to pull the plug. + +Closed issues +^^^^^^^^^^^^^ + +- Issue #35 : remove import plot from ot/\ **init**.py (See PR #41) +- Issue #43 : Unusable parameter log for EMDTransport (See PR #44) +- Issue #55 : UnicodeDecodeError: 'ascii' while installing with pip + +0.4 +--- + +*15 Sep 2017* + +This release contains a lot of contribution from new contributors. + +Features +^^^^^^^^ + +- Automatic notebooks and doc update (PR #27) +- Add gromov Wasserstein solver and Gromov Barycenters (PR #23) +- emd and emd2 can now return dual variables and have max\_iter (PR #29 + and PR #25) +- New domain adaptation classes compatible with scikit-learn (PR #22) +- Proper tests with pytest on travis (PR #19) +- PEP 8 tests (PR #13) + +Closed issues +^^^^^^^^^^^^^ + +- emd convergence problem du to fixed max iterations (#24) +- Semi supervised DA error (#26) + +0.3.1 +----- + +*11 Jul 2017* + +- Correct bug in emd on windows + +0.3 +--- + +*7 Jul 2017* + +- emd\* and sinkhorn\* are now performed in parallel for multiple + target distributions +- emd and sinkhorn are for OT matrix computation +- emd2 and sinkhorn2 are for OT loss computation +- new notebooks for emd computation and Wasserstein Discriminant + Analysis +- relocate notebooks +- update documentation +- clean\_zeros(a,b,M) for removimg zeros in sparse distributions +- GPU implementations for sinkhorn and group lasso regularization + +V0.2 +---- + +*7 Apr 2017* + +- New dimensionality reduction method (WDA) +- Efficient method emd2 returns only tarnsport (in paralell if several + histograms given) + +0.1.11 +------ + +*5 Jan 2017* + +- Add sphinx gallery for better documentation +- Small efficiency tweak in sinkhorn +- Add simple tic() toc() functions for timing + +0.1.10 +------ + +*7 Nov 2016* \* numerical stabilization for sinkhorn (log domain and +epsilon scaling) + +0.1.9 +----- + +*4 Nov 2016* + +- Update classes and examples for domain adaptation +- Joint OT matrix and mapping estimation + +0.1.7 +----- + +*31 Oct 2016* + +- Original Domain adaptation classes + +0.1.3 +----- + +- pipy works + +First pre-release +----------------- + +*28 Oct 2016* + +It provides the following solvers: \* OT solver for the linear program/ +Earth Movers Distance. \* Entropic regularization OT solver with +Sinkhorn Knopp Algorithm. \* Bregman projections for Wasserstein +barycenter [3] and unmixing. \* Optimal transport for domain adaptation +with group lasso regularization \* Conditional gradient and Generalized +conditional gradient for regularized OT. + +Some demonstrations (both in Python and Jupyter Notebook format) are +available in the examples folder. |