Merge pull request #143 from PythonOT/doc_travis

[WIP] Update travis test and documentation (examples)

1 files changed, 153 insertions, 68 deletions

diff --git a/docs/source/auto_examples/index.rst b/docs/source/auto_examples/index.rst
index fe6702d..9f05263 100644
--- a/docs/source/auto_examples/index.rst
+++ b/docs/source/auto_examples/index.rst
@@ -1,5 +1,9 @@
 :orphan:
 
+
+
+.. _sphx_glr_auto_examples:
+
 POT Examples
 ============
 
@@ -13,9 +17,9 @@ This is a gallery of all the POT example files.
 
 .. only:: html
 
-    .. figure:: /auto_examples/images/thumb/sphx_glr_plot_OT_1D_thumb.png
+ .. figure:: /auto_examples/images/thumb/sphx_glr_plot_OT_1D_thumb.png
 
-        :ref:`sphx_glr_auto_examples_plot_OT_1D.py`
+     :ref:`sphx_glr_auto_examples_plot_OT_1D.py`
 
 .. raw:: html
 
@@ -33,9 +37,9 @@ This is a gallery of all the POT example files.
 
 .. only:: html
 
-    .. figure:: /auto_examples/images/thumb/sphx_glr_plot_UOT_1D_thumb.png
+ .. figure:: /auto_examples/images/thumb/sphx_glr_plot_UOT_1D_thumb.png
 
-        :ref:`sphx_glr_auto_examples_plot_UOT_1D.py`
+     :ref:`sphx_glr_auto_examples_plot_UOT_1D.py`
 
 .. raw:: html
 
@@ -49,13 +53,13 @@ This is a gallery of all the POT example files.
 
 .. raw:: html
 
-    <div class="sphx-glr-thumbcontainer" tooltip="Illustrates the use of the generic solver for regularized OT with user-designed regularization ...">
+    <div class="sphx-glr-thumbcontainer" tooltip="This example illustrates the computation of Screenkhorn: Screening Sinkhorn Algorithm for Optim...">
 
 .. only:: html
 
-    .. figure:: /auto_examples/images/thumb/sphx_glr_plot_optim_OTreg_thumb.png
+ .. figure:: /auto_examples/images/thumb/sphx_glr_plot_screenkhorn_1D_thumb.png
 
-        :ref:`sphx_glr_auto_examples_plot_optim_OTreg.py`
+     :ref:`sphx_glr_auto_examples_plot_screenkhorn_1D.py`
 
 .. raw:: html
 
@@ -65,17 +69,17 @@ This is a gallery of all the POT example files.
 .. toctree::
    :hidden:
 
-   /auto_examples/plot_optim_OTreg
+   /auto_examples/plot_screenkhorn_1D
 
 .. raw:: html
 
-    <div class="sphx-glr-thumbcontainer" tooltip="Illustration of 2D Wasserstein barycenters if discributions that are weighted sum of diracs.">
+    <div class="sphx-glr-thumbcontainer" tooltip="Illustrates the use of the generic solver for regularized OT with user-designed regularization ...">
 
 .. only:: html
 
-    .. figure:: /auto_examples/images/thumb/sphx_glr_plot_free_support_barycenter_thumb.png
+ .. figure:: /auto_examples/images/thumb/sphx_glr_plot_optim_OTreg_thumb.png
 
-        :ref:`sphx_glr_auto_examples_plot_free_support_barycenter.py`
+     :ref:`sphx_glr_auto_examples_plot_optim_OTreg.py`
 
 .. raw:: html
 
@@ -85,7 +89,7 @@ This is a gallery of all the POT example files.
 .. toctree::
    :hidden:
 
-   /auto_examples/plot_free_support_barycenter
+   /auto_examples/plot_optim_OTreg
 
 .. raw:: html
 
@@ -93,9 +97,9 @@ This is a gallery of all the POT example files.
 
 .. only:: html
 
-    .. figure:: /auto_examples/images/thumb/sphx_glr_plot_OT_1D_smooth_thumb.png
+ .. figure:: /auto_examples/images/thumb/sphx_glr_plot_OT_1D_smooth_thumb.png
 
-        :ref:`sphx_glr_auto_examples_plot_OT_1D_smooth.py`
+     :ref:`sphx_glr_auto_examples_plot_OT_1D_smooth.py`
 
 .. raw:: html
 
@@ -109,13 +113,13 @@ This is a gallery of all the POT example files.
 
 .. raw:: html
 
-    <div class="sphx-glr-thumbcontainer" tooltip="This example is designed to show how to use the Gromov-Wassertsein distance computation in POT....">
+    <div class="sphx-glr-thumbcontainer" tooltip="Illustration of 2D Wasserstein barycenters if discributions that are weighted sum of diracs.">
 
 .. only:: html
 
-    .. figure:: /auto_examples/images/thumb/sphx_glr_plot_gromov_thumb.png
+ .. figure:: /auto_examples/images/thumb/sphx_glr_plot_free_support_barycenter_thumb.png
 
-        :ref:`sphx_glr_auto_examples_plot_gromov.py`
+     :ref:`sphx_glr_auto_examples_plot_free_support_barycenter.py`
 
 .. raw:: html
 
@@ -125,7 +129,7 @@ This is a gallery of all the POT example files.
 .. toctree::
    :hidden:
 
-   /auto_examples/plot_gromov
+   /auto_examples/plot_free_support_barycenter
 
 .. raw:: html
 
@@ -133,9 +137,9 @@ This is a gallery of all the POT example files.
 
 .. only:: html
 
-    .. figure:: /auto_examples/images/thumb/sphx_glr_plot_compute_emd_thumb.png
+ .. figure:: /auto_examples/images/thumb/sphx_glr_plot_compute_emd_thumb.png
 
-        :ref:`sphx_glr_auto_examples_plot_compute_emd.py`
+     :ref:`sphx_glr_auto_examples_plot_compute_emd.py`
 
 .. raw:: html
 
@@ -149,13 +153,33 @@ This is a gallery of all the POT example files.
 
 .. raw:: html
 
+    <div class="sphx-glr-thumbcontainer" tooltip="This example is designed to show how to use the Gromov-Wassertsein distance computation in POT....">
+
+.. only:: html
+
+ .. figure:: /auto_examples/images/thumb/sphx_glr_plot_gromov_thumb.png
+
+     :ref:`sphx_glr_auto_examples_plot_gromov.py`
+
+.. raw:: html
+
+    </div>
+
+
+.. toctree::
+   :hidden:
+
+   /auto_examples/plot_gromov
+
+.. raw:: html
+
     <div class="sphx-glr-thumbcontainer" tooltip="This example is designed to illustrate how the Convolutional Wasserstein Barycenter function of...">
 
 .. only:: html
 
-    .. figure:: /auto_examples/images/thumb/sphx_glr_plot_convolutional_barycenter_thumb.png
+ .. figure:: /auto_examples/images/thumb/sphx_glr_plot_convolutional_barycenter_thumb.png
 
-        :ref:`sphx_glr_auto_examples_plot_convolutional_barycenter.py`
+     :ref:`sphx_glr_auto_examples_plot_convolutional_barycenter.py`
 
 .. raw:: html
 
@@ -173,9 +197,9 @@ This is a gallery of all the POT example files.
 
 .. only:: html
 
-    .. figure:: /auto_examples/images/thumb/sphx_glr_plot_otda_linear_mapping_thumb.png
+ .. figure:: /auto_examples/images/thumb/sphx_glr_plot_otda_linear_mapping_thumb.png
 
-        :ref:`sphx_glr_auto_examples_plot_otda_linear_mapping.py`
+     :ref:`sphx_glr_auto_examples_plot_otda_linear_mapping.py`
 
 .. raw:: html
 
@@ -189,13 +213,13 @@ This is a gallery of all the POT example files.
 
 .. raw:: html
 
-    <div class="sphx-glr-thumbcontainer" tooltip="This example illustrate the use of WDA as proposed in [11].">
+    <div class="sphx-glr-thumbcontainer" tooltip="Illustration of 2D optimal transport between discributions that are weighted sum of diracs. The...">
 
 .. only:: html
 
-    .. figure:: /auto_examples/images/thumb/sphx_glr_plot_WDA_thumb.png
+ .. figure:: /auto_examples/images/thumb/sphx_glr_plot_OT_2D_samples_thumb.png
 
-        :ref:`sphx_glr_auto_examples_plot_WDA.py`
+     :ref:`sphx_glr_auto_examples_plot_OT_2D_samples.py`
 
 .. raw:: html
 
@@ -205,17 +229,17 @@ This is a gallery of all the POT example files.
 .. toctree::
    :hidden:
 
-   /auto_examples/plot_WDA
+   /auto_examples/plot_OT_2D_samples
 
 .. raw:: html
 
-    <div class="sphx-glr-thumbcontainer" tooltip="Illustration of 2D optimal transport between discributions that are weighted sum of diracs. The...">
+    <div class="sphx-glr-thumbcontainer" tooltip="This example illustrate the use of WDA as proposed in [11].">
 
 .. only:: html
 
-    .. figure:: /auto_examples/images/thumb/sphx_glr_plot_OT_2D_samples_thumb.png
+ .. figure:: /auto_examples/images/thumb/sphx_glr_plot_WDA_thumb.png
 
-        :ref:`sphx_glr_auto_examples_plot_OT_2D_samples.py`
+     :ref:`sphx_glr_auto_examples_plot_WDA.py`
 
 .. raw:: html
 
@@ -225,7 +249,7 @@ This is a gallery of all the POT example files.
 .. toctree::
    :hidden:
 
-   /auto_examples/plot_OT_2D_samples
+   /auto_examples/plot_WDA
 
 .. raw:: html
 
@@ -233,9 +257,9 @@ This is a gallery of all the POT example files.
 
 .. only:: html
 
-    .. figure:: /auto_examples/images/thumb/sphx_glr_plot_stochastic_thumb.png
+ .. figure:: /auto_examples/images/thumb/sphx_glr_plot_stochastic_thumb.png
 
-        :ref:`sphx_glr_auto_examples_plot_stochastic.py`
+     :ref:`sphx_glr_auto_examples_plot_stochastic.py`
 
 .. raw:: html
 
@@ -253,9 +277,9 @@ This is a gallery of all the POT example files.
 
 .. only:: html
 
-    .. figure:: /auto_examples/images/thumb/sphx_glr_plot_otda_color_images_thumb.png
+ .. figure:: /auto_examples/images/thumb/sphx_glr_plot_otda_color_images_thumb.png
 
-        :ref:`sphx_glr_auto_examples_plot_otda_color_images.py`
+     :ref:`sphx_glr_auto_examples_plot_otda_color_images.py`
 
 .. raw:: html
 
@@ -273,9 +297,9 @@ This is a gallery of all the POT example files.
 
 .. only:: html
 
-    .. figure:: /auto_examples/images/thumb/sphx_glr_plot_barycenter_1D_thumb.png
+ .. figure:: /auto_examples/images/thumb/sphx_glr_plot_barycenter_1D_thumb.png
 
-        :ref:`sphx_glr_auto_examples_plot_barycenter_1D.py`
+     :ref:`sphx_glr_auto_examples_plot_barycenter_1D.py`
 
 .. raw:: html
 
@@ -289,13 +313,33 @@ This is a gallery of all the POT example files.
 
 .. raw:: html
 
+    <div class="sphx-glr-thumbcontainer" tooltip="This example introduces a domain adaptation in a 2D setting and OTDA approach with Laplacian re...">
+
+.. only:: html
+
+ .. figure:: /auto_examples/images/thumb/sphx_glr_plot_otda_laplacian_thumb.png
+
+     :ref:`sphx_glr_auto_examples_plot_otda_laplacian.py`
+
+.. raw:: html
+
+    </div>
+
+
+.. toctree::
+   :hidden:
+
+   /auto_examples/plot_otda_laplacian
+
+.. raw:: html
+
     <div class="sphx-glr-thumbcontainer" tooltip="OT for domain adaptation with image color adaptation [6] with mapping estimation [8].">
 
 .. only:: html
 
-    .. figure:: /auto_examples/images/thumb/sphx_glr_plot_otda_mapping_colors_images_thumb.png
+ .. figure:: /auto_examples/images/thumb/sphx_glr_plot_otda_mapping_colors_images_thumb.png
 
-        :ref:`sphx_glr_auto_examples_plot_otda_mapping_colors_images.py`
+     :ref:`sphx_glr_auto_examples_plot_otda_mapping_colors_images.py`
 
 .. raw:: html
 
@@ -313,9 +357,9 @@ This is a gallery of all the POT example files.
 
 .. only:: html
 
-    .. figure:: /auto_examples/images/thumb/sphx_glr_plot_UOT_barycenter_1D_thumb.png
+ .. figure:: /auto_examples/images/thumb/sphx_glr_plot_UOT_barycenter_1D_thumb.png
 
-        :ref:`sphx_glr_auto_examples_plot_UOT_barycenter_1D.py`
+     :ref:`sphx_glr_auto_examples_plot_UOT_barycenter_1D.py`
 
 .. raw:: html
 
@@ -333,9 +377,9 @@ This is a gallery of all the POT example files.
 
 .. only:: html
 
-    .. figure:: /auto_examples/images/thumb/sphx_glr_plot_otda_mapping_thumb.png
+ .. figure:: /auto_examples/images/thumb/sphx_glr_plot_otda_mapping_thumb.png
 
-        :ref:`sphx_glr_auto_examples_plot_otda_mapping.py`
+     :ref:`sphx_glr_auto_examples_plot_otda_mapping.py`
 
 .. raw:: html
 
@@ -349,13 +393,13 @@ This is a gallery of all the POT example files.
 
 .. raw:: html
 
-    <div class="sphx-glr-thumbcontainer" tooltip="This example introduces a semi supervised domain adaptation in a 2D setting. It explicits the p...">
+    <div class="sphx-glr-thumbcontainer" tooltip="This example illustrates the computation of FGW for 1D measures[18].">
 
 .. only:: html
 
-    .. figure:: /auto_examples/images/thumb/sphx_glr_plot_otda_semi_supervised_thumb.png
+ .. figure:: /auto_examples/images/thumb/sphx_glr_plot_fgw_thumb.png
 
-        :ref:`sphx_glr_auto_examples_plot_otda_semi_supervised.py`
+     :ref:`sphx_glr_auto_examples_plot_fgw.py`
 
 .. raw:: html
 
@@ -365,17 +409,17 @@ This is a gallery of all the POT example files.
 .. toctree::
    :hidden:
 
-   /auto_examples/plot_otda_semi_supervised
+   /auto_examples/plot_fgw
 
 .. raw:: html
 
-    <div class="sphx-glr-thumbcontainer" tooltip="This example illustrates the computation of FGW for 1D measures[18].">
+    <div class="sphx-glr-thumbcontainer" tooltip="This example introduces a semi supervised domain adaptation in a 2D setting. It explicits the p...">
 
 .. only:: html
 
-    .. figure:: /auto_examples/images/thumb/sphx_glr_plot_fgw_thumb.png
+ .. figure:: /auto_examples/images/thumb/sphx_glr_plot_otda_semi_supervised_thumb.png
 
-        :ref:`sphx_glr_auto_examples_plot_fgw.py`
+     :ref:`sphx_glr_auto_examples_plot_otda_semi_supervised.py`
 
 .. raw:: html
 
@@ -385,7 +429,7 @@ This is a gallery of all the POT example files.
 .. toctree::
    :hidden:
 
-   /auto_examples/plot_fgw
+   /auto_examples/plot_otda_semi_supervised
 
 .. raw:: html
 
@@ -393,9 +437,9 @@ This is a gallery of all the POT example files.
 
 .. only:: html
 
-    .. figure:: /auto_examples/images/thumb/sphx_glr_plot_otda_classes_thumb.png
+ .. figure:: /auto_examples/images/thumb/sphx_glr_plot_otda_classes_thumb.png
 
-        :ref:`sphx_glr_auto_examples_plot_otda_classes.py`
+     :ref:`sphx_glr_auto_examples_plot_otda_classes.py`
 
 .. raw:: html
 
@@ -409,13 +453,33 @@ This is a gallery of all the POT example files.
 
 .. raw:: html
 
+    <div class="sphx-glr-thumbcontainer" tooltip="This example is designed to show how to use the Partial (Gromov-)Wassertsein distance computati...">
+
+.. only:: html
+
+ .. figure:: /auto_examples/images/thumb/sphx_glr_plot_partial_wass_and_gromov_thumb.png
+
+     :ref:`sphx_glr_auto_examples_plot_partial_wass_and_gromov.py`
+
+.. raw:: html
+
+    </div>
+
+
+.. toctree::
+   :hidden:
+
+   /auto_examples/plot_partial_wass_and_gromov
+
+.. raw:: html
+
     <div class="sphx-glr-thumbcontainer" tooltip="This example introduces a domain adaptation in a 2D setting. It explicits the problem of domain...">
 
 .. only:: html
 
-    .. figure:: /auto_examples/images/thumb/sphx_glr_plot_otda_d2_thumb.png
+ .. figure:: /auto_examples/images/thumb/sphx_glr_plot_otda_d2_thumb.png
 
-        :ref:`sphx_glr_auto_examples_plot_otda_d2.py`
+     :ref:`sphx_glr_auto_examples_plot_otda_d2.py`
 
 .. raw:: html
 
@@ -433,9 +497,9 @@ This is a gallery of all the POT example files.
 
 .. only:: html
 
-    .. figure:: /auto_examples/images/thumb/sphx_glr_plot_OT_L1_vs_L2_thumb.png
+ .. figure:: /auto_examples/images/thumb/sphx_glr_plot_OT_L1_vs_L2_thumb.png
 
-        :ref:`sphx_glr_auto_examples_plot_OT_L1_vs_L2.py`
+     :ref:`sphx_glr_auto_examples_plot_OT_L1_vs_L2.py`
 
 .. raw:: html
 
@@ -449,13 +513,33 @@ This is a gallery of all the POT example files.
 
 .. raw:: html
 
+    <div class="sphx-glr-thumbcontainer" tooltip="This example introduces a target shift problem with two 2D source and 1 target domain.">
+
+.. only:: html
+
+ .. figure:: /auto_examples/images/thumb/sphx_glr_plot_otda_jcpot_thumb.png
+
+     :ref:`sphx_glr_auto_examples_plot_otda_jcpot.py`
+
+.. raw:: html
+
+    </div>
+
+
+.. toctree::
+   :hidden:
+
+   /auto_examples/plot_otda_jcpot
+
+.. raw:: html
+
     <div class="sphx-glr-thumbcontainer" tooltip="This example illustrates the computation of regularized Wasserstein Barycenter as proposed in [...">
 
 .. only:: html
 
-    .. figure:: /auto_examples/images/thumb/sphx_glr_plot_barycenter_lp_vs_entropic_thumb.png
+ .. figure:: /auto_examples/images/thumb/sphx_glr_plot_barycenter_lp_vs_entropic_thumb.png
 
-        :ref:`sphx_glr_auto_examples_plot_barycenter_lp_vs_entropic.py`
+     :ref:`sphx_glr_auto_examples_plot_barycenter_lp_vs_entropic.py`
 
 .. raw:: html
 
@@ -473,9 +557,9 @@ This is a gallery of all the POT example files.
 
 .. only:: html
 
-    .. figure:: /auto_examples/images/thumb/sphx_glr_plot_barycenter_fgw_thumb.png
+ .. figure:: /auto_examples/images/thumb/sphx_glr_plot_barycenter_fgw_thumb.png
 
-        :ref:`sphx_glr_auto_examples_plot_barycenter_fgw.py`
+     :ref:`sphx_glr_auto_examples_plot_barycenter_fgw.py`
 
 .. raw:: html
 
@@ -493,9 +577,9 @@ This is a gallery of all the POT example files.
 
 .. only:: html
 
-    .. figure:: /auto_examples/images/thumb/sphx_glr_plot_gromov_barycenter_thumb.png
+ .. figure:: /auto_examples/images/thumb/sphx_glr_plot_gromov_barycenter_thumb.png
 
-        :ref:`sphx_glr_auto_examples_plot_gromov_barycenter.py`
+     :ref:`sphx_glr_auto_examples_plot_gromov_barycenter.py`
 
 .. raw:: html
 
@@ -508,22 +592,23 @@ This is a gallery of all the POT example files.
    /auto_examples/plot_gromov_barycenter
 .. raw:: html
 
-    <div style='clear:both'></div>
+    <div class="sphx-glr-clear"></div>
 
 
 
 .. only :: html
 
  .. container:: sphx-glr-footer
+    :class: sphx-glr-footer-gallery
 
 
-  .. container:: sphx-glr-download
+  .. container:: sphx-glr-download sphx-glr-download-python
 
     :download:`Download all examples in Python source code: auto_examples_python.zip <//home/rflamary/PYTHON/POT/docs/source/auto_examples/auto_examples_python.zip>`
 
 
 
-  .. container:: sphx-glr-download
+  .. container:: sphx-glr-download sphx-glr-download-jupyter
 
     :download:`Download all examples in Jupyter notebooks: auto_examples_jupyter.zip <//home/rflamary/PYTHON/POT/docs/source/auto_examples/auto_examples_jupyter.zip>`
 
@@ -532,4 +617,4 @@ This is a gallery of all the POT example files.
 
  .. rst-class:: sphx-glr-signature
 
-    `Gallery generated by Sphinx-Gallery <https://sphinx-gallery.readthedocs.io>`_
+    `Gallery generated by Sphinx-Gallery <https://sphinx-gallery.github.io>`_