Merge pull request #19 from rflamary/pytest

rflamary · web-flow · commit 7638d019b43e · 2017-07-26T15:25:53.000+02:00
Pytest with 89% coverage Fixes #19
diff --git a/.gitignore b/.gitignore
@@ -100,3 +100,6 @@ ENV/
 
 # Mac stuff
 .DS_Store
+
+# coverage output folder
+cov_html/
diff --git a/.travis.yml b/.travis.yml
@@ -13,6 +13,10 @@ matrix:
           python: 2.7
 before_install:
   - ./.travis/before_install.sh
+before_script: # configure a headless display to test plot generation
+  - "export DISPLAY=:99.0"
+  - "sh -e /etc/init.d/xvfb start"
+  - sleep 3 # give xvfb some time to start
 # command to install dependencies
 install:
   - pip install -r requirements.txt
diff --git a/Makefile b/Makefile
@@ -38,10 +38,10 @@ pep8 :
 	flake8 examples/ ot/ test/
 
 test : FORCE pep8
-	python -m py.test -v test/
+	python -m py.test -v test/ --cov=ot --cov-report html:cov_html
 	
 pytest : FORCE 
-	python -m py.test -v test/	
+	python -m py.test -v test/ --cov=ot
 
 uploadpypi :
 	#python setup.py register
diff --git a/examples/plot_OTDA_2D.py b/examples/plot_OTDA_2D.py
@@ -6,6 +6,10 @@
 
 """
 
+# Author: Remi Flamary <remi.flamary@unice.fr>
+#
+# License: MIT License
+
 import numpy as np
 import matplotlib.pylab as pl
 import ot
diff --git a/examples/plot_OTDA_classes.py b/examples/plot_OTDA_classes.py
@@ -6,6 +6,10 @@
 
 """
 
+# Author: Remi Flamary <remi.flamary@unice.fr>
+#
+# License: MIT License
+
 import matplotlib.pylab as pl
 import ot
 
diff --git a/examples/plot_OTDA_color_images.py b/examples/plot_OTDA_color_images.py
@@ -9,6 +9,10 @@
 SIAM Journal on Imaging Sciences, 7(3), 1853-1882.
 """
 
+# Author: Remi Flamary <remi.flamary@unice.fr>
+#
+# License: MIT License
+
 import numpy as np
 from scipy import ndimage
 import matplotlib.pylab as pl
diff --git a/examples/plot_OTDA_mapping.py b/examples/plot_OTDA_mapping.py
@@ -9,6 +9,10 @@
     Neural Information Processing Systems (NIPS), 2016.
 """
 
+# Author: Remi Flamary <remi.flamary@unice.fr>
+#
+# License: MIT License
+
 import numpy as np
 import matplotlib.pylab as pl
 import ot
diff --git a/examples/plot_OTDA_mapping_color_images.py b/examples/plot_OTDA_mapping_color_images.py
@@ -11,6 +11,10 @@
 
 """
 
+# Author: Remi Flamary <remi.flamary@unice.fr>
+#
+# License: MIT License
+
 import numpy as np
 from scipy import ndimage
 import matplotlib.pylab as pl
diff --git a/examples/plot_OT_1D.py b/examples/plot_OT_1D.py
@@ -4,9 +4,12 @@
 1D optimal transport
 ====================
 
-@author: rflamary
 """
 
+# Author: Remi Flamary <remi.flamary@unice.fr>
+#
+# License: MIT License
+
 import numpy as np
 import matplotlib.pylab as pl
 import ot
diff --git a/examples/plot_OT_2D_samples.py b/examples/plot_OT_2D_samples.py
@@ -4,9 +4,12 @@
 2D Optimal transport between empirical distributions
 ====================================================
 
-@author: rflamary
 """
 
+# Author: Remi Flamary <remi.flamary@unice.fr>
+#
+# License: MIT License
+
 import numpy as np
 import matplotlib.pylab as pl
 import ot
diff --git a/examples/plot_OT_L1_vs_L2.py b/examples/plot_OT_L1_vs_L2.py
@@ -8,9 +8,12 @@
 https://arxiv.org/pdf/1706.07650.pdf
 
 
-@author: rflamary
 """
 
+# Author: Remi Flamary <remi.flamary@unice.fr>
+#
+# License: MIT License
+
 import numpy as np
 import matplotlib.pylab as pl
 import ot
diff --git a/examples/plot_WDA.py b/examples/plot_WDA.py
@@ -4,9 +4,12 @@
 Wasserstein Discriminant Analysis
 =================================
 
-@author: rflamary
 """
 
+# Author: Remi Flamary <remi.flamary@unice.fr>
+#
+# License: MIT License
+
 import numpy as np
 import matplotlib.pylab as pl
 
diff --git a/examples/plot_barycenter_1D.py b/examples/plot_barycenter_1D.py
@@ -4,10 +4,12 @@
 1D Wasserstein barycenter demo
 ==============================
 
-
-@author: rflamary
 """
 
+# Author: Remi Flamary <remi.flamary@unice.fr>
+#
+# License: MIT License
+
 import numpy as np
 import matplotlib.pylab as pl
 import ot
diff --git a/examples/plot_compute_emd.py b/examples/plot_compute_emd.py
@@ -4,9 +4,12 @@
 1D optimal transport
 ====================
 
-@author: rflamary
 """
 
+# Author: Remi Flamary <remi.flamary@unice.fr>
+#
+# License: MIT License
+
 import numpy as np
 import matplotlib.pylab as pl
 import ot
diff --git 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 @@
 
 __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
@@ -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 sink():
                                        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 sink():
                                        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 get_Gamma(alpha, beta, u, v):
 
         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 get_reg(n):  # exponential decreasing
             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
@@ -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
@@ -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
@@ -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
@@ -4,4 +4,9 @@
 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
@@ -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
@@ -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
@@ -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
@@ -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
diff --git a/ot/plot.py b/ot/plot.py
diff --git a/ot/utils.py b/ot/utils.py
diff --git a/test/test_bregman.py b/test/test_bregman.py
diff --git a/test/test_da.py b/test/test_da.py
diff --git a/test/test_dr.py b/test/test_dr.py
diff --git a/test/test_gpu.py b/test/test_gpu.py
diff --git a/test/test_optim.py b/test/test_optim.py
diff --git a/test/test_ot.py b/test/test_ot.py
diff --git a/test/test_plot.py b/test/test_plot.py
diff --git a/test/test_utils.py b/test/test_utils.py
