ToFuProject · Didou09 · Nov 20, 2019 · Oct 28, 2019 · Oct 29, 2019 · Oct 29, 2019
diff --git a/README.md b/README.md
@@ -100,68 +100,46 @@ If IMAS is not available, tofu will simply display a warning stating that the im
 tofu can thus easily load and handle multiple IDSs (IMAS data structure units) and provide command-line tools for exporting IMAS data to other general tofu classes (e.g.: Cameras, Plasma2D...) and for interactive plotting.
 All tofu objects have methods to facailitate in-python-console introspection, the ``__repr__`` method is overloaded to display relevant information, an dthis is widely used to explore the data loaded from IMAS.
 
-Do you want to use **tofu** on IMAS and don't know where to start? [See our wiki.](https://github.com/ToFuProject/tofu/wiki/Using-tofu-on-IMAS-server)
+Do you want to use **tofu** on IMAS and don't know where to start?
+[See our documetation.](https://tofuproject.github.io/tofu/installation.html#using-tofu-on-a-iter-cluster)
 
 ----
 
 
 ## Installing tofu
 
-
-### For Windows
-
-
-- [Follow this link to know how to configure your Windows to code on ToFu !](https://github.com/ToFuProject/tofu/wiki/Installing-tofu-on-windows)
-
-### For Ubuntu / Mac
+### For Ubuntu
 
 #### Standard mode
 
    ``` conda install -c tofuproject tofu ```
 
-#### Developer mode
-
-Install dependencies
-
-
-    python (>= 3.6)
-    numpy
-    scipy
-    matplotlib
-    cython >= 0.26
-    nose
-    pygments
-    pandas
-
-
-Checkout the tofu git repository and from the top directory
-
-
-    python setup.py build_ext --inplace
-    python setup.py install
-
-
-## Getting Started
-
-See our wiki's page: [Getting started](https://github.com/ToFuProject/tofu/wiki/Getting-started)
+## For Developers and other platforms
 
+[See our documentation.](https://tofuproject.github.io/tofu/installation.html)
 -----
 
 
-**Licensing** 
+**Licensing**
 
-It is distributed under the MIT license and aims at providing the fusion community with 
-a transparent and modular tool for creating / designing diagnostics and using them for 
-synthetic diagnostic (direct problem) and tomography (inverse problem).
+It is distributed under the MIT license and aims at providing the fusion
+community with a transparent and modular tool for creating / designing
+diagnostics and using them for synthetic diagnostic (direct problem)
+and tomography (inverse problem).
 
 **History**
 
-It was first created at the Max-Planck Institute for Plasma Physics (IPP) in Garching, Germany, 
-by Didier Vezinet, and is now maintained / debugged / updated by a team of contributors.
+It was first created at the Max-Planck Institute for Plasma Physics (IPP)
+in Garching, Germany, by Didier Vezinet, and is now maintained, debugged
+and updated by a team of contributors.
 
 
 -----
 
 **Warning**
 This Pypi package focuses on tomography for fusion research.
-It uses the same name as a previous package dedicated to a testing framework coupling fixtures and tests loosely, now renamed **reahl-tofu** and developped by Iwan Vosloo since 2006. If you ended up here looking for a web-oriented library, you should probably redirect to the more recent [**reahl-tofu**](https://pypi.python.org/pypi/reahl-tofu) page.
+It uses the same name as a previous package dedicated to a testing framework
+coupling fixtures and tests loosely, now renamed **reahl-tofu** and developped
+by Iwan Vosloo since 2006. If you ended up here looking for a web-oriented
+library, you should probably redirect to the more recent
+[**reahl-tofu**](https://pypi.python.org/pypi/reahl-tofu) page.
diff --git a/doc/source/conf.py b/doc/source/conf.py
@@ -14,6 +14,7 @@
 import sys
 import tofu as tf
 import sphinx_bootstrap_theme
+from sphinx_gallery.sorting import FileNameSortKey
 
 # Getting tofu version
 tf_version = tf.__version__[:3]
@@ -354,6 +355,8 @@
 sphinx_gallery_conf = {
     "examples_dirs": "../../examples",  # path to your example scripts
     "gallery_dirs": "auto_examples",  # path to save gallery generated output
+    "within_subsection_order": FileNameSortKey,
+    'filename_pattern': '/tuto_plot_',
 }
 
 

diff --git a/doc/source/contributing.rst b/doc/source/contributing.rst
@@ -1,11 +1,29 @@
+Contribute to tofu
+==================
 
-Contributing to tofu
-====================
-
-You found a bug, or you want to add something to the library ? This
+You found a bug, or you want to add something to the library? This
 tutorial will show you how to get the repository and the first steps to
 contribute to the project.
 
+Bug reports and suggestions
+----------------------------
+
+If you found a bug in **tofu**, or if you have a suggestion, the best is to open
+an issue directly on our `github page <https://github.com/ToFuProject/tofu/issues>`_.
+If you are opening an issue related to a bug found, please specify the version
+of the librairies (**tofu**, python, etc.) you are using, any configuration
+information that might be helpful to us (OS, server, how you installed
+**tofu**), a minimal example to recreate the bug (if possible), and the log
+files or errors you might have got.
+
+
+
+Developping in the code
+-----------------------
+
+The basic tools
+"""""""""""""""
+
 There are many tools and concepts to get familiar with when contributing
 to an **open-source python library**. A good place to get started is the
 `scikit-project <https://github.com/nathanshammah/scikit-project>`__.
@@ -66,12 +84,20 @@ environment.
 -  Make sure tests are running ``nosetests``
 
 
+Where to start?
+"""""""""""""""
 
 If you wish to contribute, but don't know where to start, check `our
 open issues <https://github.com/ToFuProject/tofu/issues>`__. You can
 also read `this
 tutorial <https://github.com/firstcontributions/first-contributions>`__,
-on how to contribute to a github project. Before modifying the code, you
+on how to contribute to a github project.
+
+
+Git branches and pull requests
+""""""""""""""""""""""""""""""
+
+Before modifying the code, you
 should create a new branch (based on the *devel* branch) and switch to it.
 
 ::
@@ -88,3 +114,23 @@ page <https://github.com/ToFuProject/tofu/pulls>`__, from your branch,
 accept it.
 
 
+
+Continuous integration
+""""""""""""""""""""""
+
+For each pull request (PR) on github, there will be a series of tests run to
+make sure the modifications introduced to the library did not introduce any
+errors. If all tests pass, you should see something like the image below.
+
+.. image:: images/travis.png
+
+If there is an error (red cross instead of green check) it can be either that
+your code is breaking the normal functionning of the code, or (less probably)
+that there is a bug in the unit tests. Please try and understand what went wrong.
+If you cannot find the problem, you can ask for help by commenting on the PR.
+Additionally to the unit tests, we have integrated pep8speaks_, a bot that will
+check your coding style.
+
+.. _pep8speaks: https://pep8speaks.com/
+
+.. image:: images/pep8speaks.png
diff --git a/doc/source/images/pep8speaks.png b/doc/source/images/pep8speaks.png
diff --git a/doc/source/images/travis.png b/doc/source/images/travis.png
diff --git a/doc/source/index.rst b/doc/source/index.rst
@@ -35,20 +35,25 @@ interactive plots.
     <div style="clear: both"></div>
     <div class="container-fluid hidden-xs hidden-sm">
       <div class="row">
-        <a href="auto_examples/tutorials/plot_basic_tutorial.html">
-          <div class="col-md-4 thumbnail">
-            <img src="_images/sphx_glr_plot_basic_tutorial_thumb.png">
+        <a href="auto_examples/tutorials/tuto_plot_basic.html">
+          <div class="col-md-3 thumbnail">
+            <img src="_images/sphx_glr_tuto_plot_basic_thumb.png">
           </div>
         </a>
-	<a href="auto_examples/tutorials/plot_create_geometry.html">
-          <div class="col-md-4 thumbnail">
-            <img src="_images/sphx_glr_plot_create_geometry_thumb.png">
+	<a href="auto_examples/tutorials/tuto_plot_create_geometry.html">
+          <div class="col-md-3 thumbnail">
+            <img src="_images/sphx_glr_tuto_plot_create_geometry_thumb.png">
+          </div>
+        </a>
+	<a href="auto_examples/tutorials/tuto_plot_custom_emissivity.html">
+          <div class="col-md-3 thumbnail">
+            <img src="_images/sphx_glr_tuto_plot_custom_emissivity_thumb.png">
           </div>
         </a>
       </div>
     </div>
 
-Contents:
+Contents
 ---------
 
 **Tutorials and how to's:**
@@ -60,7 +65,6 @@ Contents:
    A guide to contributing to tofu <contributing.rst>
    Tutorials and examples <auto_examples/index.rst>
 
-
 * How to create / handle a diagnostic geometry
    - Visit the basic_ tutorial for getting started: create, plot and save
      your first configuration: a vessel and its structures;
@@ -75,11 +79,10 @@ Contents:
    - Use existing diagnostic geometry and signals to solve the inverse problem
      and compute tomographic inversions using a choice of discretization basis
      functions and regularisation functionals.
-     How to contribute (todos_)
 
-.. _basic: auto_examples/tutorials/plot_create_geometry.html
-.. _cameras: auto_examples/tutorials/plot_basic_tutorial.html
-.. _tutorial: Tutorial_Geom_SynthDiag_Basic.html
+.. _basic: auto_examples/tutorials/tuto_plot_create_geometry.html
+.. _cameras: auto_examples/tutorials/tuto_plot_basic.html
+.. _tutorial: auto_examples/tutorials/tuto_plot_custom_emissivity.html
 .. _todos: Todos.html
 
 

diff --git a/doc/source/installation.rst b/doc/source/installation.rst
@@ -39,7 +39,7 @@ your choice).
 
 ::
 
-   python -c "import tofu; print(tofu.__version__)"
+   $ python -c "import tofu; print(tofu.__version__)"
 
 Now you can `follow a tutorial. <auto_examples/index.html>`__
 
@@ -128,7 +128,7 @@ To install tofu as a developer, we recommend using the conda ecosystem (Minicond
 -  Move to where you would like to install your local copy of ToFu ``$ cd some_path``
 -  ``$ git clone https://github.com/ToFuProject/tofu.git`` (make sure you
    remember the path where you are installing, if you want to install it
-   into your home repository, just make sure to ``cd ~`` before the
+   into your home repository, just make sure to ``$ cd ~`` before the
    ``git clone...``)
 -  Move to the "cloned" tofu directory that has been created by the git clone command:
    ``cd ~/tofu``
@@ -142,4 +142,3 @@ To install tofu as a developer, we recommend using the conda ecosystem (Minicond
    tofu Cython extensions and install it into your conda environment while you can still
    modify the source files in the current repository.`
 -  Make sure tofu tests are running by typing ``nosetests``
-
diff --git a/doc/source/modules.rst b/doc/source/modules.rst
@@ -0,0 +1,7 @@
+tofu
+====
+
+.. toctree::
+   :maxdepth: 5
+
+   tofu
diff --git a/doc/source/tofu.data.rst b/doc/source/tofu.data.rst
@@ -1,6 +1,11 @@
 tofu.data package
 =================
 
+.. automodule:: tofu.data
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
 Submodules
 ----------
 
@@ -20,6 +25,14 @@ tofu.data.\_core module
    :undoc-members:
    :show-inheritance:
 
+tofu.data.\_core\_new module
+----------------------------
+
+.. automodule:: tofu.data._core_new
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
 tofu.data.\_def module
 ----------------------
 
@@ -44,11 +57,3 @@ tofu.data.\_plot module
    :undoc-members:
    :show-inheritance:
 
-
-Module contents
----------------
-
-.. automodule:: tofu.data
-   :members:
-   :undoc-members:
-   :show-inheritance:
diff --git a/doc/source/tofu.dumpro.rst b/doc/source/tofu.dumpro.rst
@@ -1,6 +1,11 @@
 tofu.dumpro package
 ===================
 
+.. automodule:: tofu.dumpro
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
 Submodules
 ----------
 
@@ -52,11 +57,3 @@ tofu.dumpro.\_plot module
    :undoc-members:
    :show-inheritance:
 
-
-Module contents
----------------
-
-.. automodule:: tofu.dumpro
-   :members:
-   :undoc-members:
-   :show-inheritance:
diff --git a/doc/source/tofu.dust.rst b/doc/source/tofu.dust.rst
@@ -1,6 +1,11 @@
 tofu.dust package
 =================
 
+.. automodule:: tofu.dust
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
 Submodules
 ----------
 
@@ -28,11 +33,3 @@ tofu.dust.\_plot module
    :undoc-members:
    :show-inheritance:
 
-
-Module contents
----------------
-
-.. automodule:: tofu.dust
-   :members:
-   :undoc-members:
-   :show-inheritance: