add realeases

Author: rflamary

Makefile

@@ -59,7 +59,10 @@ release_test :
 rdoc :
 	pandoc --from=markdown --to=rst --output=docs/source/readme.rst README.md
 	sed -i 's,https://pythonot.github.io/auto_examples/,auto_examples/,g' docs/source/readme.rst 
-
+	pandoc --from=markdown --to=rst --output=docs/source/releases.rst RELEASES.md
+	sed -i 's,https://pot.readthedocs.io/en/latest/,,g' docs/source/releases.rst
+	sed -i 's,https://github.com/rflamary/POT/blob/master/notebooks/,auto_examples/,g' docs/source/releases.rst 
+	sed -i 's,.ipynb,.html/,g' docs/source/releases.rst 
 notebook :
 	ipython notebook --matplotlib=inline  --notebook-dir=notebooks/
 

RELEASES.md

@@ -1,4 +1,4 @@
-# POT Releases
+# Releases
 
 
 ## 0.6 Year 3

docs/source/conf.py

@@ -67,7 +67,7 @@ def __getattr__(cls, name):
     'sphinx.ext.ifconfig',
     'sphinx.ext.viewcode',
     'sphinx.ext.napoleon',
-    #'sphinx_gallery.gen_gallery',
+    'sphinx_gallery.gen_gallery',
 ]
 
 napoleon_numpy_docstring = True

docs/source/index.rst

@@ -10,12 +10,13 @@ Contents
 --------
 
 .. toctree::
-   :maxdepth: 2
+   :maxdepth: 1
 
    self
    quickstart
    all
    auto_examples/index
+   releases
 
 .. include:: readme.rst
     :start-line: 5

docs/source/releases.rst

@@ -0,0 +1,260 @@
+POT Releases
+============
+
+0.6 Year 3
+----------
+
+*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 Year 2
+------------
+
+*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 Community edition
+---------------------
+
+*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 Summer release
+------------------
+
+*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)
+
+V0.1.11 New years resolution
+----------------------------
+
+*5 Jan 2017*
+
+-  Add sphinx gallery for better documentation
+-  Small efficiency tweak in sinkhorn
+-  Add simple tic() toc() functions for timing
+
+V0.1.10
+-------
+
+*7 Nov 2016* \* numerical stabilization for sinkhorn (log domain and
+epsilon scaling)
+
+V0.1.9 DA classes and mapping
+-----------------------------
+
+*4 Nov 2016*
+
+-  Update classes and examples for domain adaptation
+-  Joint OT matrix and mapping estimation
+
+V0.1.7
+------
+
+*31 Oct 2016*
+
+-  Original Domain adaptation classes
+
+PyPI version 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.