WIP updating doc

Author: baugetfa

README.md

@@ -1,6 +1,4 @@
 # Visualea
-
-# Package Name
 [![Docs](https://readthedocs.org/projects/visualea/badge/?version=latest)](https://visualea.readthedocs.io/)
 [![Build Status](https://github.com/openalea/visualea/actions/workflows/conda-package-build.yml/badge.svg?branch=master)](https://github.com/openalea/visualea/actions/workflows/conda-package-build.yml?query=branch%3Amaster)
 [![Python Version](https://img.shields.io/badge/python-3.8%20%7C%203.9%20%7C%203.10%20%7C%203.11%20%7C%203.12-blue)](https://www.python.org/downloads/)
@@ -34,14 +32,16 @@ CecILL-C
 OpenAlea.Visualea is the Visual Programming Environment of OpenAlea. It allows using OpenAlea packages 
 without programming language knowledge and to build dataflow graphically.
 
-## Installation user mode
+## Installation 
+
+### user mode
 
 ```bash
 mamba create -n visualea -c openalea3 -c conda-forge openalea.visualea
 mamba activate visualea
 ```
 
-## for developer, in an existing environment
+### for developer, in an existing environment
 
 ```bash
 git clone 'https://github.com/openalea/visualea.git'
@@ -53,7 +53,7 @@ pip install -e .[options]
 defined in the `[project.optional-dependencies]` section of your 
 pyproject.toml file (usually "dev", or "doc", ...)
 
-## for developer, in a new clean isolated environment
+### for developer, in a new clean isolated environment
 ```bash
 mamba env create -f conda/environment.yml 
 mamba activate visualea

doc/_static/visualea.png

@@ -1,49 +1,36 @@
-OpenAlea Visualea documentation
-###############################
+Welcome to Visualea's documentation!
+=====================================
 
-Module description
-==================
+.. include:: ../README.md
+   :parser: myst_parser.sphinx_
 
-.. sidebar:: Summary
+Contact & Contributing
+----------------------
 
-    :Version: |version|
-    :Release: |release|
-    :Date: |today|
-    :Author: See `Authors`_ section
-    :ChangeLog: See `ChangeLog`_ section
+For any question, please submit to https://github.com/openalea/visualea/issues.
 
-.. topic:: Overview
 
-    .. include:: user/overview.txt
+Versioning
+----------
+
+Sources are versioned on an Git repository hosted by platform GitHub: https://github.com/openalea/visualea.
+If you want to make your own development of the model, please fork the repository.
 
 Documentation
-=============
+-------------
 
 .. toctree::
     :maxdepth: 1
+    :caption: Contents:
 
-    User Guide<user/index.rst>   
-    Reference Guide<user/autosum.rst>
-
-- A `PDF <../latex/main.pdf>`_ version of |visualea| documentation is 
-  available.
-
-Authors
-=======
-
-.. include:: ../AUTHORS.txt
-
-ChangeLog
-=========
-
-.. include:: ../ChangeLog.txt
+    user/manual.rst
+    user/autosum.rst
 
-License
-=======
 
-|visualea| is released under a Cecill-C License.
+Indices and tables
+------------------
 
-.. note:: `Cecill-C <http://www.cecill.info/licences/Licence_CeCILL-C_V1-en.html>`_ 
-    license is a LGPL compatible license.
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`
 
-.. |visualea| replace:: OpenAlea.Visualea

doc/index.rst

@@ -1,28 +1,28 @@
 VisuAlea Manual
 ###############
 
-Visualea is a high level visual programming GUI for OpenAlea
+Visualea is a high level visual programming GUI for OpenAlea.
 
-On Linux, in a shell, run the following command::
+On Linux, run the following command in the conda environement
 
-    $visualea
+.. code-block:: bash
 
-On Windows::
+    visualea
 
-    Use start→ OpenAlea → Visualea
-    Main Window
+On Windows
+
+.. code-block:: bash
+
+    visualea.exe
 
-CHANGE THIS PICTURE
 .. image:: ../_static/visualea.png
-   :scale: 75
    :align: left
 
 The main window is composed of :
     * The package manager (lists nodes),
-    * The workspaces where one can graphically assemble dataflows,
+    * The workspaces where dataflows are graphically assembled,
     * Each node has it's own graphical interface,
     * The python interpreter for low level interaction (with code completion)
-    * Python code editor
 
 Package Manager
 ===============
@@ -54,15 +54,17 @@ A package has several associated informations like :
 These package informations are accessible from the context menu:
 
     * Package Context Menu
-      o Open Url : Open associated url
-      o Infos : Display meta informations
+
+      - Open Url : Open associated url
+      - Infos : Display meta informations
 
 Each package element has also a context menu :
 
     * Node (Component) Context Menu
-      o Open : Open the node
-      o Edit : Edit the node (Code Editor for Python node, Dataflow for Composite node)
-      o Remove : Remove the node from the package
+
+      - Open : Open the node
+      - Edit : Edit the node (Code Editor for Python node, Dataflow for Composite node)
+      - Remove : Remove the node from the package
 
 .. note:: Tooltip are available by moving the mouse pointer on an object.
 
@@ -79,9 +81,10 @@ Package Manager operations (menu)
     * → Reload all packages : search all packages on the local system
     * → Find Nodes : Open the search tab
     * → Create
-      o → Package : Create a new user package
-      o → Python Node : Create a new component based on python code
-      o → Composite Node : Create a new component based on other components (Macro node)
+
+      - → Package : Create a new user package
+      - → Python Node : Create a new component based on python code
+      - → Composite Node : Create a new component based on other components (Macro node)
 
 Workspaces
 ----------
@@ -137,9 +140,10 @@ The graph of nodes form an expression.
 To evaluate the expression :
 
     * Menu → Workspace → Run will evaluate all the graph
-    * Context Menu → Run on a particular node will evaluate only the selected node and its dependencies.
+    * Context Menu → Run on a particular node will evaluate only the selected node and its parents.
 
-If you change a value of a node, the evaluation algorithm will compute only the changed nodes and their dependencies, avoiding to do several times the same computation.
+If you change a value of a node, the evaluation algorithm will compute only the changed nodes and their dependencies,
+avoiding to do several times the same computation.
 
 .. deprecated::
     The node contained in a graph can be in different states/ The color of a node depends of its state:
@@ -240,9 +244,9 @@ At any moment, you can use the python interpreter to launch python command or sc
 
 CHANGE THIS PICTURE
 .. image:: ../_static/ipython.png
-   :width: 80%
-   :height: 200px
-   :scale: 100
+    :width: 80%
+    :height: 200px
+    :scale: 100
 
 The interpreter defines special variables :