[WIP] Build donc in GH Action and report warnings + move contributing and code of conduct in documentation (#441)

* use action for doc with wraning visible

* remove space

* remove space again

* test pre commands

* install pot properly

* install compiler...

* try composite action

* remoe warning in sliced exmaple

* pep8

* move contributing and code of conduct

* cleanup

* underline too short

* update quickstart

* replace version selector by static list to avoid jsQuery bug

10 files changed, 134 insertions, 90 deletions

diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md
index 9bc8e87..168ffb3 100644
--- a/.github/CONTRIBUTING.md
+++ b/.github/CONTRIBUTING.md
@@ -1,4 +1,3 @@
-
 Contributing to POT
 ===================
 
diff --git a/.github/workflows/build_doc.yml b/.github/workflows/build_doc.yml
new file mode 100644
index 0000000..93bd113
--- /dev/null
+++ b/.github/workflows/build_doc.yml
@@ -0,0 +1,44 @@
+name: Build doc
+
+on:
+  workflow_dispatch:
+  pull_request:
+  push:
+    branches:
+      - 'master'  
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v1
+    # Standard drop-in approach that should work for most people.
+
+    - name: Set up Python 3.8
+      uses: actions/setup-python@v1
+      with:
+        python-version: 3.8
+
+    - name: Get Python running
+      run: |
+        python -m pip install --user --upgrade --progress-bar off pip
+        python -m pip install --user --upgrade --progress-bar off -r requirements.txt
+        python -m pip install --user --upgrade --progress-bar off -r docs/requirements.txt
+        python -m pip install --user --upgrade --progress-bar off ipython "https://api.github.com/repos/sphinx-gallery/sphinx-gallery/zipball/master" memory_profiler
+        python -m pip install --user -e .
+    # Look at what we have and fail early if there is some library conflict
+    - name: Check installation
+      run: |
+        which python
+        python -c "import ot"
+    # Build docs
+    - name: Generate HTML docs
+      uses: rickstaa/sphinx-action@master
+      with:
+        docs-folder: "docs/"
+    - uses: actions/upload-artifact@v1
+      with:
+        name: Documentation
+        path: docs/build/html/
\ No newline at end of file
diff --git a/README.md b/README.md
index 9c5e07e..2a81e95 100644
--- a/README.md
+++ b/README.md
@@ -192,7 +192,7 @@ POT has benefited from the financing or manpower from the following partners:
 
 ## Contributions and code of conduct
 
-Every contribution is welcome and should respect the [contribution guidelines](.github/CONTRIBUTING.md). Each member of the project is expected to follow the [code of conduct](.github/CODE_OF_CONDUCT.md).
+Every contribution is welcome and should respect the [contribution guidelines](https://pythonot.github.io/master/contributing.html). Each member of the project is expected to follow the [code of conduct](https://pythonot.github.io/master/code_of_conduct.html).
 
 ## Support
 
diff --git a/docs/source/_templates/versions.html b/docs/source/_templates/versions.html
index f48ab86..5b1021a 100644
--- a/docs/source/_templates/versions.html
+++ b/docs/source/_templates/versions.html
@@ -1,47 +1,50 @@
 <div class="rst-versions" data-toggle="rst-versions" role="note"
 aria-label="versions">
-  <!--  add shift_up to the class for force viewing -->
-    <span class="rst-current-version" data-toggle="rst-current-version">
+  <!--  add shift_up to the class for force viewing ,
+  data-toggle="rst-current-version" -->
+    <span class="rst-current-version"  style="margin-bottom:1mm;">
       <span class="fa fa-book"> Python Optimal Transport</span>
-      versions
-      <span class="fa fa-caret-down"></span>
+      <hr  style="margin-bottom:1.5mm;margin-top:5mm;">
+     <!--  versions
+      <span class="fa fa-caret-down"></span>-->
+      <span class="rst-current-version" style="display: inline-block;padding:
+      0px;color:#fcfcfcab;float:left;font-size: 100%;">
+        Versions: 
+        <a href="https://pythonot.github.io/" 
+        style="padding: 3px;color:#fcfcfc;font-size: 100%;">Release</a>
+        <a href="https://pythonot.github.io/master" 
+        style="padding: 3px;color:#fcfcfc;font-size: 100%;">Development</a>
+        <a href="https://github.com/PythonOT/POT"
+        style="padding: 3px;color:#fcfcfc;font-size: 100%;">Code</a>
+
+      </span>
+
+     
     </span>
-    <div class="rst-other-versions"><!-- Inserted RTD Footer -->
+  
+     <!--
+    <div class="rst-other-versions">
+
+      
 
 <div class="injected">
 
-      
-      
-      <dl>
-        <dt>Versions</dt>
-
-        <dd><a href="https://pythonot.github.io/">Release</a></dd>
-        
-        <dd><a href="https://pythonot.github.io/master">Development</a></dd>
-       
-        
-        
-      </dl>
-      
+    
+  <dl>
+    <dt>Versions</dt>
 
+    <dd><a href="https://pythonot.github.io/">Release</a></dd>
     
-      
-      <dl>
-        <dt>On GitHub</dt>
-        <dd>
-          <a href="https://github.com/PythonOT/POT">Code on Github</a>
-        </dd>
-        
-      </dl>
-      
+    <dd><a href="https://pythonot.github.io/master">Development</a></dd>
+   
     
-      
-      
 
-      <hr>
-      
+    <dt><a href="https://github.com/PythonOT/POT">Code on Github</a></dt>       
 
+    
+  </dl>
+  <hr>
 
-</div>
-</div>
+</div> 
+</div>-->
   </div>
\ No newline at end of file
diff --git a/docs/source/all.rst b/docs/source/all.rst
index 1b8d13c..a9d7fe2 100644
--- a/docs/source/all.rst
+++ b/docs/source/all.rst
@@ -37,7 +37,7 @@ API and modules
    
 
 Main :py:mod:`ot` functions
---------------
+---------------------------
 
 .. automodule:: ot
    :members:
diff --git a/docs/source/.github/CODE_OF_CONDUCT.rst b/docs/source/code_of_conduct.rst
index d4c5cec..40b432e 100644
--- a/docs/source/.github/CODE_OF_CONDUCT.rst
+++ b/docs/source/code_of_conduct.rst
@@ -1,6 +1,6 @@
-Code of Conduct
+Code of conduct
 ===============
 
-.. include:: ../../../.github/CODE_OF_CONDUCT.md
+.. include:: ../../.github/CODE_OF_CONDUCT.md
     :parser: myst_parser.sphinx_
     :start-line: 2
diff --git a/docs/source/.github/CONTRIBUTING.rst b/docs/source/contributing.rst
index aef24e9..8dec19a 100644
--- a/docs/source/.github/CONTRIBUTING.rst
+++ b/docs/source/contributing.rst
@@ -1,6 +1,6 @@
 Contributing to POT
 ===================
 
-.. include:: ../../../.github/CONTRIBUTING.md
+.. include:: ../../.github/CONTRIBUTING.md
     :parser: myst_parser.sphinx_
-    :start-line: 3
+    :start-line: 2
diff --git a/docs/source/index.rst b/docs/source/index.rst
index 3d53ef4..0f04738 100644
--- a/docs/source/index.rst
+++ b/docs/source/index.rst
@@ -21,9 +21,9 @@ Contents
    all
    auto_examples/index
    releases
-   .github/CONTRIBUTING
    contributors
-   .github/CODE_OF_CONDUCT
+   contributing
+   code_of_conduct
 
 
 .. include:: ../../README.md
diff --git a/docs/source/quickstart.rst b/docs/source/quickstart.rst
index c8eac30..1dc9f71 100644
--- a/docs/source/quickstart.rst
+++ b/docs/source/quickstart.rst
@@ -127,14 +127,6 @@ been used to solve both graph Laplacian regularization OT and Gromov
 Wasserstein [30]_.
 
 
-.. note::
-
-    POT is originally designed to solve OT problems with Numpy interface and
-    is not yet compatible with Pytorch API. We are currently working on a torch
-    submodule that will provide OT solvers and losses for the most common deep
-    learning configurations.
-
-
 When not to use POT
 """""""""""""""""""
 
@@ -692,42 +684,8 @@ A list of the provided implementation is given in the following note.
     :heading-level: "
 
 
-Other applications
-------------------
-
-We discuss in the following several OT related problems and tools that has been
-proposed in the OT and machine learning community.
-
-Wasserstein Discriminant Analysis
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-Wasserstein Discriminant Analysis [11]_ is a generalization of `Fisher Linear Discriminant
-Analysis <https://en.wikipedia.org/wiki/Linear_discriminant_analysis>`__ that
-allows discrimination between classes that are not linearly separable. It
-consists in finding a linear projector optimizing the following criterion
-
-.. math::
-    P = \text{arg}\min_P \frac{\sum_i OT_e(\mu_i\#P,\mu_i\#P)}{\sum_{i,j\neq i}
-    OT_e(\mu_i\#P,\mu_j\#P)}
-
-where :math:`\#` is the push-forward operator, :math:`OT_e` is the entropic OT
-loss and :math:`\mu_i` is the
-distribution of samples from class :math:`i`.  :math:`P` is also constrained to
-be in the Stiefel manifold. WDA can be solved in POT using function
-:any:`ot.dr.wda`. It requires to have installed :code:`pymanopt` and
-:code:`autograd` for manifold optimization and automatic differentiation
-respectively. Note that we also provide the Fisher discriminant estimator in
-:any:`ot.dr.fda` for easy comparison.
-
-.. warning::
-
-    Note that due to the hard dependency on  :code:`pymanopt` and
-    :code:`autograd`, :any:`ot.dr` is not imported by default. If you want to
-    use it you have to specifically import it with :code:`import ot.dr` .
-
-.. minigallery:: ot.dr.wda
-    :add-heading: Examples of the use of WDA
-    :heading-level: "
+Unbalanced and partial OT
+-------------------------
 
 
 
@@ -845,10 +803,11 @@ regularization of the problem.
     :heading-level: "
 
 
+Gromov Wasserstein and extensions
+---------------------------------
 
-
-Gromov-Wasserstein
-^^^^^^^^^^^^^^^^^^
+Gromov Wasserstein(GW)
+^^^^^^^^^^^^^^^^^^^^^^
 
 Gromov Wasserstein (GW) is a generalization of OT to distributions that do not lie in
 the same space [13]_. In this case one cannot compute distance between samples
@@ -877,6 +836,8 @@ There also exists an entropic regularized variant of GW that has been proposed i
     :add-heading: Examples of computation of GW, regularized G and FGW
     :heading-level: "
 
+Gromov Wasserstein barycenters
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 Note that similarly to Wasserstein distance GW allows for the definition of GW
 barycenters that can be expressed as
@@ -905,6 +866,43 @@ The implementations of FGW and FGW barycenter is provided in functions
     :heading-level: "
 
 
+Other applications
+------------------
+
+We discuss in the following several OT related problems and tools that has been
+proposed in the OT and machine learning community.
+
+Wasserstein Discriminant Analysis
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+Wasserstein Discriminant Analysis [11]_ is a generalization of `Fisher Linear Discriminant
+Analysis <https://en.wikipedia.org/wiki/Linear_discriminant_analysis>`__ that
+allows discrimination between classes that are not linearly separable. It
+consists in finding a linear projector optimizing the following criterion
+
+.. math::
+    P = \text{arg}\min_P \frac{\sum_i OT_e(\mu_i\#P,\mu_i\#P)}{\sum_{i,j\neq i}
+    OT_e(\mu_i\#P,\mu_j\#P)}
+
+where :math:`\#` is the push-forward operator, :math:`OT_e` is the entropic OT
+loss and :math:`\mu_i` is the
+distribution of samples from class :math:`i`.  :math:`P` is also constrained to
+be in the Stiefel manifold. WDA can be solved in POT using function
+:any:`ot.dr.wda`. It requires to have installed :code:`pymanopt` and
+:code:`autograd` for manifold optimization and automatic differentiation
+respectively. Note that we also provide the Fisher discriminant estimator in
+:any:`ot.dr.fda` for easy comparison.
+
+.. warning::
+
+    Note that due to the hard dependency on  :code:`pymanopt` and
+    :code:`autograd`, :any:`ot.dr` is not imported by default. If you want to
+    use it you have to specifically import it with :code:`import ot.dr` .
+
+.. minigallery:: ot.dr.wda
+    :add-heading: Examples of the use of WDA
+    :heading-level: "
+
 
 Solving OT with Multiple backends on CPU/GPU
 --------------------------------------------
diff --git a/examples/backends/plot_ssw_unif_torch.py b/examples/backends/plot_ssw_unif_torch.py
index d1de5a9..7ccc2af 100644
--- a/examples/backends/plot_ssw_unif_torch.py
+++ b/examples/backends/plot_ssw_unif_torch.py
@@ -50,7 +50,7 @@ def plot_sphere(ax):
     r = np.linspace(1.0, 1.0, 50)
     X, Y = np.meshgrid(xlist, ylist)
 
-    Z = np.sqrt(r**2 - X**2 - Y**2)
+    Z = np.sqrt(np.maximum(r**2 - X**2 - Y**2, 0))
 
     ax.plot_wireframe(X, Y, Z, color="gray", alpha=.3)
     ax.plot_wireframe(X, Y, -Z, color="gray", alpha=.3)  # Now plot the bottom half