Merge pull request #19 from rflamary/pytest

Pytest with 89% coverage

Fixes #19 

13 files changed, 78 insertions, 16 deletions

diff --git a/ot/__init__.py b/ot/__init__.py
index a79a5ce..6d4c4c6 100644
--- a/ot/__init__.py
+++ b/ot/__init__.py
@@ -4,6 +4,10 @@
 
 """
 
+# Author: Remi Flamary <remi.flamary@unice.fr>
+#
+# License: MIT License
+
 
 # All submodules and packages
 from . import lp
@@ -24,6 +28,6 @@ from .utils import dist, unif, tic, toc, toq
 
 __version__ = "0.3.1"
 
-__all__ = ["emd", "emd2", "sinkhorn","sinkhorn2", "utils", 'datasets',
+__all__ = ["emd", "emd2", "sinkhorn", "sinkhorn2", "utils", 'datasets',
            'bregman', 'lp', 'plot', 'tic', 'toc', 'toq',
            'dist', 'unif', 'barycenter', 'sinkhorn_lpl1_mm', 'da', 'optim']
diff --git a/ot/bregman.py b/ot/bregman.py
index fe10880..d63c51d 100644
--- a/ot/bregman.py
+++ b/ot/bregman.py
@@ -3,6 +3,11 @@
 Bregman projections for regularized OT
 """
 
+# Author: Remi Flamary <remi.flamary@unice.fr>
+#         Nicolas Courty <ncourty@irisa.fr>
+#
+# License: MIT License
+
 import numpy as np
 
 
@@ -103,8 +108,9 @@ def sinkhorn(a, b, M, reg, method='sinkhorn', numItermax=1000, stopThr=1e-9, ver
                                        stopThr=stopThr, verbose=verbose, log=log, **kwargs)
     elif method.lower() == 'sinkhorn_epsilon_scaling':
         def sink():
-            return sinkhorn_epsilon_scaling(a, b, M, reg, numItermax=numItermax,
-                                            stopThr=stopThr, verbose=verbose, log=log, **kwargs)
+            return sinkhorn_epsilon_scaling(
+                a, b, M, reg, numItermax=numItermax,
+                stopThr=stopThr, verbose=verbose, log=log, **kwargs)
     else:
         print('Warning : unknown method using classic Sinkhorn Knopp')
 
@@ -211,8 +217,9 @@ def sinkhorn2(a, b, M, reg, method='sinkhorn', numItermax=1000, stopThr=1e-9, ve
                                        stopThr=stopThr, verbose=verbose, log=log, **kwargs)
     elif method.lower() == 'sinkhorn_epsilon_scaling':
         def sink():
-            return sinkhorn_epsilon_scaling(a, b, M, reg, numItermax=numItermax,
-                                            stopThr=stopThr, verbose=verbose, log=log, **kwargs)
+            return sinkhorn_epsilon_scaling(
+                a, b, M, reg, numItermax=numItermax,
+                stopThr=stopThr, verbose=verbose, log=log, **kwargs)
     else:
         print('Warning : unknown method using classic Sinkhorn Knopp')
 
@@ -588,7 +595,7 @@ def sinkhorn_stabilized(a, b, M, reg, numItermax=1000, tau=1e3, stopThr=1e-9, wa
 
         cpt = cpt + 1
 
-    #print('err=',err,' cpt=',cpt)
+    # print('err=',err,' cpt=',cpt)
     if log:
         log['logu'] = alpha / reg + np.log(u)
         log['logv'] = beta / reg + np.log(v)
@@ -773,7 +780,7 @@ def sinkhorn_epsilon_scaling(a, b, M, reg, numItermax=100, epsilon0=1e4, numInne
             loop = False
 
         cpt = cpt + 1
-    #print('err=',err,' cpt=',cpt)
+    # print('err=',err,' cpt=',cpt)
     if log:
         log['alpha'] = alpha
         log['beta'] = beta
@@ -960,16 +967,16 @@ def unmix(a, D, M, M0, h0, reg, reg0, alpha, numItermax=1000, stopThr=1e-3, verb
 
     """
 
-    #M = M/np.median(M)
+    # M = M/np.median(M)
     K = np.exp(-M / reg)
 
-    #M0 = M0/np.median(M0)
+    # M0 = M0/np.median(M0)
     K0 = np.exp(-M0 / reg0)
     old = h0
 
     err = 1
     cpt = 0
-    #log = {'niter':0, 'all_err':[]}
+    # log = {'niter':0, 'all_err':[]}
     if log:
         log = {'err': []}
 
diff --git a/ot/da.py b/ot/da.py
index 5039fbd..4f9bce5 100644
--- a/ot/da.py
+++ b/ot/da.py
@@ -3,6 +3,12 @@
 Domain adaptation with optimal transport
 """
 
+# Author: Remi Flamary <remi.flamary@unice.fr>
+#         Nicolas Courty <ncourty@irisa.fr>
+#         Michael Perrot <michael.perrot@univ-st-etienne.fr>
+#
+# License: MIT License
+
 import numpy as np
 from .bregman import sinkhorn
 from .lp import emd
@@ -472,7 +478,7 @@ def joint_OT_mapping_kernel(xs, xt, mu=1, eta=0.001, kerneltype='gaussian', sigm
         Kp[:ns, :ns] = K
 
         # ls regu
-        #K0 = K1.T.dot(K1)+eta*I
+        # K0 = K1.T.dot(K1)+eta*I
         # Kreg=I
 
         # RKHS regul
@@ -484,7 +490,7 @@ def joint_OT_mapping_kernel(xs, xt, mu=1, eta=0.001, kerneltype='gaussian', sigm
         I = np.eye(ns)
 
         # ls regul
-        #K0 = K1.T.dot(K1)+eta*I
+        # K0 = K1.T.dot(K1)+eta*I
         # Kreg=I
 
         # proper kernel ridge
diff --git a/ot/datasets.py b/ot/datasets.py
index 4371a23..e4fe118 100644
--- a/ot/datasets.py
+++ b/ot/datasets.py
@@ -2,6 +2,10 @@
 Simple example datasets for OT
 """
 
+# Author: Remi Flamary <remi.flamary@unice.fr>
+#
+# License: MIT License
+
 
 import numpy as np
 import scipy as sp
diff --git a/ot/dr.py b/ot/dr.py
index 77cbae2..d30ab30 100644
--- a/ot/dr.py
+++ b/ot/dr.py
@@ -3,6 +3,10 @@
 Dimension reduction with optimal transport
 """
 
+# Author: Remi Flamary <remi.flamary@unice.fr>
+#
+# License: MIT License
+
 from scipy import linalg
 import autograd.numpy as np
 from pymanopt.manifolds import Stiefel
diff --git a/ot/gpu/__init__.py b/ot/gpu/__init__.py
index 40b11c0..c8f9433 100644
--- a/ot/gpu/__init__.py
+++ b/ot/gpu/__init__.py
@@ -4,4 +4,9 @@ from . import bregman
 from . import da
 from .bregman import sinkhorn
 
+# Author: Remi Flamary <remi.flamary@unice.fr>
+#         Leo Gautheron <https://github.com/aje> 
+#
+# License: MIT License
+
 __all__ = ["bregman", "da", "sinkhorn"]
diff --git a/ot/gpu/bregman.py b/ot/gpu/bregman.py
index 2302f80..47939c4 100644
--- a/ot/gpu/bregman.py
+++ b/ot/gpu/bregman.py
@@ -3,6 +3,11 @@
 Bregman projections for regularized OT with GPU
 """
 
+# Author: Remi Flamary <remi.flamary@unice.fr>
+#         Leo Gautheron <https://github.com/aje>
+#
+# License: MIT License
+
 import numpy as np
 import cudamat
 
diff --git a/ot/gpu/da.py b/ot/gpu/da.py
index c66e755..05c580f 100644
--- a/ot/gpu/da.py
+++ b/ot/gpu/da.py
@@ -3,6 +3,14 @@
 Domain adaptation with optimal transport with GPU implementation
 """
 
+# Author: Remi Flamary <remi.flamary@unice.fr>
+#         Nicolas Courty <ncourty@irisa.fr>
+#         Michael Perrot <michael.perrot@univ-st-etienne.fr>
+#         Leo Gautheron <https://github.com/aje>
+#
+# License: MIT License
+
+
 import numpy as np
 from ..utils import unif
 from ..da import OTDA
diff --git a/ot/lp/__init__.py b/ot/lp/__init__.py
index db3da78..6e0bdb8 100644
--- a/ot/lp/__init__.py
+++ b/ot/lp/__init__.py
@@ -3,6 +3,10 @@
 Solvers for the original linear program OT problem
 """
 
+# Author: Remi Flamary <remi.flamary@unice.fr>
+#
+# License: MIT License
+
 import numpy as np
 # import compiled emd
 from .emd_wrap import emd_c, emd2_c
diff --git a/ot/lp/emd_wrap.pyx b/ot/lp/emd_wrap.pyx
index 46794ab..46c96c1 100644
--- a/ot/lp/emd_wrap.pyx
+++ b/ot/lp/emd_wrap.pyx
@@ -1,9 +1,12 @@
 # -*- coding: utf-8 -*-
 """
-Created on Thu Sep 11 08:42:08 2014
-
-@author: rflamary
+Cython linker with C solver
 """
+
+# Author: Remi Flamary <remi.flamary@unice.fr>
+#
+# License: MIT License
+
 import numpy as np
 cimport numpy as np
 
diff --git a/ot/optim.py b/ot/optim.py
index adad95e..1d09adc 100644
--- a/ot/optim.py
+++ b/ot/optim.py
@@ -3,6 +3,10 @@
 Optimization algorithms for OT
 """
 
+# Author: Remi Flamary <remi.flamary@unice.fr>
+#
+# License: MIT License
+
 import numpy as np
 from scipy.optimize.linesearch import scalar_search_armijo
 from .lp import emd
@@ -300,7 +304,7 @@ def gcg(a, b, M, reg1, reg2, f, df, G0=None, numItermax=10, numInnerItermax=200,
         Mi = M + reg2 * df(G)
 
         # solve linear program with Sinkhorn
-        #Gc = sinkhorn_stabilized(a,b, Mi, reg1, numItermax = numInnerItermax)
+        # Gc = sinkhorn_stabilized(a,b, Mi, reg1, numItermax = numInnerItermax)
         Gc = sinkhorn(a, b, Mi, reg1, numItermax=numInnerItermax)
 
         deltaG = Gc - G
diff --git a/ot/plot.py b/ot/plot.py
index 61afc9f..784a372 100644
--- a/ot/plot.py
+++ b/ot/plot.py
@@ -2,6 +2,9 @@
 Functions for plotting OT matrices
 """
 
+# Author: Remi Flamary <remi.flamary@unice.fr>
+#
+# License: MIT License
 
 import numpy as np
 import matplotlib.pylab as pl
diff --git a/ot/utils.py b/ot/utils.py
index 1dee932..2b2f8b3 100644
--- a/ot/utils.py
+++ b/ot/utils.py
@@ -2,6 +2,11 @@
 """
 Various function that can be usefull
 """
+
+# Author: Remi Flamary <remi.flamary@unice.fr>
+#
+# License: MIT License
+
 import multiprocessing
 from functools import reduce
 import time