Refactor the documentation organization & sections & subsection so th…

…e menu looks ok

bindings/Sofa/src/SofaPython3/Sofa/Core/Binding_Base_doc.h

@@ -74,7 +74,7 @@ static auto getLinkPath =
 
         .. code-block:: python
 
-            # returns is @"/child1/object" if getPathName() is @"/child1/object"
+            # prints @"/child1/object" if getPathName() is "/child1/object"
             print(object.linkPath)
 
         )";

docs/sphinx/source/conf.py

@@ -37,6 +37,7 @@
     'sphinxcontrib.contentui',
     'sphinx.ext.viewcode',
     'sphinx.ext.napoleon',
+    'sphinx_search.extension',
     ]
 
 import sys

docs/sphinx/source/content/Compilation.rst

@@ -213,3 +213,10 @@ Let's now pull the source code of the plugin, configure the build and start the
 
 That's it, you are now ready to use SofaPython3. Keep the environment variable **SOFA_ROOT** and **SP3_ROOT** close by
 for the upcoming sections.
+
+* If you `compiled SofaPython3 out-of-tree <https://sofapython3.readthedocs.io/en/latest/content/Compilation.html#out-of-tree-build>`_, you can load the SofaPython3 following one of this step:
+
+  * use the "-l" of runSofa: ``runSofa -l /path/to/SofaPython3_build/lib/libSofaPython3.so <scene>``
+  * or use the environment variable ``SOFA_PLUGIN_PATH=/path/to/SofaPython3_build/``
+  * or add the component ``<AddPluginRepository path="/path/to/SofaPython3_build/"/>`` in your scene
+  * or start runSofa, manually load the SofaPython3 library using *Edit->Plugin Manager->Add* , then restart runSofa: the plugin should load automatically

docs/sphinx/source/content/Installation.rst

@@ -0,0 +1,160 @@
+#######
+Install
+#######
+
+The SofaPython3 plugins allows you to embed a python3 interpreter into an existing SOFA application (eg: runSofa) and to create/launch SOFA simulations from a python environment.
+Depending on your use case you may have different step to follow to get a fully working SofaPython3 environnement.
+
+***************
+Get SofaPython3
+***************
+
+Latest version of the SofaPython3 plugins are now shipped directly by the Sofa-Constortium directly from the `Sofa website <https://www.sofa-framework.org/download/>`
+
+
+*****
+Setup
+*****
+
+First make sure you have the same version of python installed on your computer as the one that is used in the binary version.
+
+.. content-tabs::
+
+	.. tab-container:: tab1
+		:title: Ubuntu
+
+			Run in a terminal:
+
+			.. code-block:: bash
+
+				sudo add-apt-repository ppa:deadsnakes/ppa
+				sudo apt install libpython3.8 python3.8 python3-pip
+				python3.8 -m pip install numpy
+
+			if you want to launch the runSofa:
+
+			.. code-block:: bash
+
+				sudo apt install libopengl0
+
+
+	.. tab-container:: tab2
+		:title: MacOS
+
+			Run in a terminal:
+
+			.. code-block:: bash
+
+				brew install python@3.8
+				export PATH="/usr/local/opt/python@3.8/bin/:$PATH"
+
+			BigSur only:
+
+			.. code-block:: bash
+
+				pip3 install --upgrade pip
+				python3.8 -m pip install numpy
+
+			Catalina only:
+
+			.. code-block:: bash
+
+				pip3 install numpy
+
+
+	.. tab-container:: tab3
+		:title: Windows
+
+		Download and install `Python 3.8 64bit <https://www.python.org/ftp/python/3.8.10/python-3.8.10-amd64.exe>`_
+
+
+***************************
+Check everything is correct
+***************************
+
+using runSofa
+*************
+
+Using SofaPython3 in runSofa requires loading the SofaPython3 plugin in your runSofa environment.
+
+
+* If you downloaded and installed SOFA and its headers from the `SOFA website <https://www.sofa-framework.org/download/>`_, or if you `compiled SofaPython3 in-tree <https://sofapython3.readthedocs.io/en/latest/content/Compilation.html#in-tree-build>`_, you can load the SofaPython3 plugin using the PluginManager (in the GUI) or by auto-loading the plugin in runSofa: simply copy the file **plugin_list.conf.default** in *<SOFA_build>/lib*, and rename it **plugin_list.conf**, then add the line:
+
+	.. code-block:: text 
+
+		SofaPython3 NO_VERSION
+
+	..
+		Note that adding the line to the file **plugin_list.conf.default** in *<SOFA_build>/lib* would work, but you would need to add the line everytime you compile the code.
+
+	Having the SofaPython3 plugin active will allow you to open scene files using the ".py, .py3, .pyscn, .pyscn3" file extension in runSofa, with the command :
+
+	.. code-block:: bash
+
+		<SOFA_build>/bin/runSofa <your_python_file>
+
+
+using python3
+*************
+
+Before running your simulations, you must make sure to define the following environment variables:
+
+
+.. content-tabs::
+
+	.. tab-container:: tab1
+		:title: Ubuntu
+
+			Run in a terminal:
+
+			.. code-block:: bash
+
+				export SOFA_ROOT=/path/to/SOFA_install
+				export PYTHONPATH=/path/to/SofaPython3/lib/python3/site-packages:$PYTHONPATH
+
+	.. tab-container:: tab2
+		:title: MacOS
+
+			Run in a terminal:
+
+			.. code-block:: bash
+
+				export SOFA_ROOT=/path/to/SOFA_install
+				export PYTHONPATH=/path/to/SofaPython3/lib/python3/site-packages:$PYTHONPATH
+				export PATH="/usr/local/opt/python@3.8/bin/:$PATH"
+
+
+	.. tab-container:: tab3
+		:title: Windows
+
+		    * Create a system variable **SOFA_ROOT** and set it to ``<SOFA-install-directory>``
+		    * Create a system variable **PYTHON_ROOT** and set it to ``<Python3-install-directory>``
+		    * Create a system variable **PYTHONPATH** and set it to ``%SOFA_ROOT%\plugins\SofaPython3\lib\python3\site-packages``
+		    * Edit the system variable **Path** and add at the end ``;%PYTHON_ROOT%;%PYTHON_ROOT%\DLLs;%PYTHON_ROOT%\Lib;%SOFA_ROOT%\bin;``
+		    * Open a Console (cmd.exe) and run ``python -V && python -m pip install numpy scipy``
+
+		After that, all you need to do is open a Console (cmd.exe) and run: ``runSofa -lSofaPython3``
+
+
+
+It is possible to use SOFA in any python3 interpreter.
+The following code should cover most basic SOFA elements:
+
+.. code-block:: python
+
+        # to be able to create SOFA objects you need to first load the plugins that implement them.
+        # For simplicity you can load the plugin "Sofa.Component" that will load all most
+        # common sofa objects.
+        import SofaRuntime
+        SofaRuntime.importPlugin("Sofa.Component")
+
+        # to create elements like Node or objects
+	import Sofa.Core
+
+
+Get support
+***********
+
+To freely get technical assistance from the community, please do not hesitate to join the `SofaPython3 GitHub forum <https://github.com/sofa-framework/sofapython3/discussions>`_ and post there any question related to SofaPython3.
+
+To quickly level up on SOFA, never hesitate to request `SOFA training sessions <https://www.sofa-framework.org/sofa-events/sofa-training-sessions/>`_.

docs/sphinx/source/content/Modules.rst

@@ -3,7 +3,21 @@ Modules
 #######
 
 .. toctree::
+    :titlesonly:
+    :hidden:
 
     modules/Sofa/index
     modules/SofaRuntime/index
     modules/SofaExporter/index
+
+
+The SofaPython3 binding is highly modular allowing to select only the modules strictly relevant to your needs. 
+Most commonly used modules provided by the Sofa-consortium are:
+
+.. autosummary::
+
+    Sofa
+    SofaRuntime
+    SofaExporter
+
+

docs/sphinx/source/content/modules/Sofa/additionalmodules.rst

@@ -0,0 +1,12 @@
+Additional modules
+==================
+
+.. autosummary::
+   :toctree: generated
+   :template: autosummary/sub-modules.rst
+   :recursive:
+
+   Sofa.SofaBaseTopology
+   Sofa.SofaConstraintSolver
+   Sofa.SofaDeformable
+   Sofa.SofaGL   

docs/sphinx/source/content/modules/Sofa/index.rst

@@ -5,12 +5,16 @@ Sofa
 
 .. automodule:: Sofa
 
-Sub-modules
-===========
+
+.. toctree::
+   :hidden:
+
+   submodules
+
+**Sub-modules**
+
 .. autosummary::
-   :toctree: generated
    :template: autosummary/sub-modules.rst
-   :recursive:
 
    Simulation
    Core
@@ -19,26 +23,32 @@ Sub-modules
    Types
    SofaTypes
    prefab
-   constants
+   constants   
+
+.. toctree::
+   :hidden:
+
+   utilityfunctions
+
+**Utility Functions**
 
-Utility Functions
-=================
 .. autosummary::
-   :toctree: generated
    :template: autosummary/base.rst
-   :recursive:
 
    msg_error
    msg_info
    msg_warning
    msg_deprecated
 
-Additional modules
-==================
+.. toctree::
+   :hidden:
+
+   additionalmodules
+
+**Additional modules**
+
 .. autosummary::
-   :toctree: generated
    :template: autosummary/sub-modules.rst
-   :recursive:
 
    SofaBaseTopology
    SofaConstraintSolver

docs/sphinx/source/content/modules/Sofa/submodules.rst

@@ -0,0 +1,16 @@
+Sub-modules
+===========
+
+.. autosummary::
+   :toctree: generated
+   :template: autosummary/sub-modules.rst
+   :recursive:
+
+   Sofa.Simulation
+   Sofa.Core
+   Sofa.Gui
+   Sofa.Helper
+   Sofa.Types
+   Sofa.SofaTypes
+   Sofa.prefab
+   Sofa.constants

docs/sphinx/source/content/modules/Sofa/utilityfunctions.rst

@@ -0,0 +1,12 @@
+Utility Functions
+=================
+
+.. autosummary::
+   :toctree: generated
+   :template: autosummary/base.rst
+   :recursive:
+
+   Sofa.msg_error
+   Sofa.msg_info
+   Sofa.msg_warning
+   Sofa.msg_deprecated

docs/sphinx/source/index.rst

@@ -1,3 +1,6 @@
+Welcome to SofaPython3 documentation !
+======================================
+
 The SofaPython3 project brings python bindings for the `SOFA simulation framework <https://www.sofa-framework.org>`_.
 Thereby, it allows users to use most of the components and features found in SOFA directly into their python scripts.
 
@@ -21,15 +24,21 @@ interpreter without requiring the load of the plugin.
     :width: 400
 
 .. toctree::
+    :hidden:
     :maxdepth: 5
     :caption: Content
-    :includehidden:
-    :numbered:
+    :numbered: 3
 
-    content/Compilation
-    content/UsingThePlugin
+    content/Installation
+    content/FirstSteps
     content/Modules
     content/PythonLibraries
     content/CustomModule
+    content/Compilation
     content/Contributing 
 
+Indices and tables
+==================
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`