merge new unbalanced

Author: rflamary

.gitignore

@@ -59,6 +59,9 @@ coverage.xml
 *.mo
 *.pot
 
+# xml
+*.xml
+
 # Django stuff:
 *.log
 local_settings.py

.travis.yml

@@ -25,6 +25,9 @@ matrix:
     #   language: shell       # 'language: python' is an error on Travis CI Windows
     #   before_install: choco install python
     #   env: PATH=/c/Python37:/c/Python37/Scripts:$PATH
+# before_script: # configure a headless display to test plot generation
+#   - "export DISPLAY=:99.0"
+#   - sleep 3 # give xvfb some time to start
 before_install:
   - ./.travis/before_install.sh
 # command to install dependencies
@@ -34,6 +37,8 @@ install:
   - pip install flake8 pytest "pytest-cov<2.6"
   - pip install .
 # command to run tests + check syntax style
+services:
+  - xvfb
 script:
   - python setup.py develop
   - flake8 examples/ ot/ test/

Makefile

@@ -85,4 +85,7 @@ dist : wheels
 	$(PYTHON) setup.py sdist
 
 
+pydocstyle :
+	pydocstyle ot
+
 FORCE :

docs/source/quickstart.rst

@@ -102,7 +102,7 @@
 problems.append([A, [bary_l2, bary_wass, bary_wass2]])
 
 ##############################################################################
-# Dirac Data
+# Stair Data
 # ----------
 
 #%% parameters
@@ -168,6 +168,11 @@
 pl.title('Barycenters')
 pl.tight_layout()
 
+
+##############################################################################
+# Dirac Data
+# ----------
+
 #%% parameters
 
 a1 = np.zeros(n)

examples/plot_barycenter_lp_vs_entropic.py

@@ -62,7 +62,7 @@
 pl.figure(1)
 for (x_i, b_i) in zip(measures_locations, measures_weights):
     color = np.random.randint(low=1, high=10 * N)
-    pl.scatter(x_i[:, 0], x_i[:, 1], s=b * 1000, label='input measure')
+    pl.scatter(x_i[:, 0], x_i[:, 1], s=b_i * 1000, label='input measure')
 pl.scatter(X[:, 0], X[:, 1], s=b * 1000, c='black', marker='^', label='2-Wasserstein barycenter')
 pl.title('Data measures and their barycenter')
 pl.legend(loc=0)

examples/plot_free_support_barycenter.py

@@ -1,7 +1,7 @@
 """
 
-This is the main module of the POT toolbox. It provides easy access to 
-a number of sub-modules and functions described below. 
+This is the main module of the POT toolbox. It provides easy access to
+a number of sub-modules and functions described below.
 
 .. note::
 
@@ -14,27 +14,27 @@
     - :any:`ot.lp` contains OT solvers for the exact (Linear Program) OT problems.
     - :any:`ot.smooth` contains OT solvers for the regularized (l2 and kl) smooth OT
       problems.
-    - :any:`ot.gromov` contains solvers for Gromov-Wasserstein and Fused Gromov 
+    - :any:`ot.gromov` contains solvers for Gromov-Wasserstein and Fused Gromov
       Wasserstein problems.
-    - :any:`ot.optim` contains generic solvers OT based optimization problems 
+    - :any:`ot.optim` contains generic solvers OT based optimization problems
     - :any:`ot.da` contains classes and function related to Monge mapping
       estimation and Domain Adaptation (DA).
     - :any:`ot.gpu` contains GPU (cupy) implementation of some OT solvers
-    - :any:`ot.dr` contains Dimension Reduction (DR) methods such as Wasserstein 
+    - :any:`ot.dr` contains Dimension Reduction (DR) methods such as Wasserstein
       Discriminant Analysis.
-    - :any:`ot.utils` contains utility functions such as distance computation and 
-      timing.  
+    - :any:`ot.utils` contains utility functions such as distance computation and
+      timing.
     - :any:`ot.datasets` contains toy dataset generation functions.
     - :any:`ot.plot` contains visualization functions
     - :any:`ot.stochastic` contains stochastic solvers for regularized OT.
     - :any:`ot.unbalanced` contains solvers for regularized unbalanced OT.
 
 .. warning::
-    The list of automatically imported sub-modules is as follows: 
+    The list of automatically imported sub-modules is as follows:
     :py:mod:`ot.lp`, :py:mod:`ot.bregman`, :py:mod:`ot.optim`
     :py:mod:`ot.utils`, :py:mod:`ot.datasets`,
     :py:mod:`ot.gromov`, :py:mod:`ot.smooth`
-    :py:mod:`ot.stochastic`    
+    :py:mod:`ot.stochastic`
 
     The following sub-modules are not imported due to additional dependencies:
 
@@ -65,17 +65,17 @@
 # OT functions
 from .lp import emd, emd2, emd_1d, emd2_1d, wasserstein_1d
 from .bregman import sinkhorn, sinkhorn2, barycenter
-from .unbalanced import sinkhorn_unbalanced, barycenter_unbalanced
+from .unbalanced import sinkhorn_unbalanced, barycenter_unbalanced, sinkhorn_unbalanced2
 from .da import sinkhorn_lpl1_mm
 
 # utils functions
 from .utils import dist, unif, tic, toc, toq
 
-__version__ = "1.0.0"
+__version__ = "0.6.0"
 
-__all__ = ["emd", "emd2", 'emd_1d','emd2_1d', 'wasserstein_1d', 
-           "sinkhorn", "sinkhorn2", 'barycenter',
-           'sinkhorn_lpl1_mm', 
-           'sinkhorn_unbalanced', "barycenter_unbalanced",
-           'dist', 'unif', 'tic', 'toc', 'toq',
-            "utils", 'datasets', 'bregman', 'lp',  'gromov', 'da', 'optim']
+__all__ = ['emd', 'emd2', 'emd_1d', 'sinkhorn', 'sinkhorn2', 'utils', 'datasets',
+           'bregman', 'lp', 'tic', 'toc', 'toq', 'gromov',
+           'emd_1d', 'emd2_1d', 'wasserstein_1d',
+           'dist', 'unif', 'barycenter', 'sinkhorn_lpl1_mm', 'da', 'optim',
+           'sinkhorn_unbalanced', 'barycenter_unbalanced',
+           'sinkhorn_unbalanced2']