homogenization documentation with OpenAlea

doc/index.rst

@@ -5,33 +5,31 @@
 
 .. module:: adel
 
-Openalea Adel documentation
-#########################################################################
+Welcome to Openalea Adel's documentation
+########################################
+.. figure:: _static/adel.png
 
-Module description
-==================
+OpenAlea.Adel (Architectural model of DEvelopment based on L-systems)
+allows to simulate the 3D architectural development of the shoot of
+gramineaous plant.
+The package hosts generic data structure and simulation tools for
+gramineaous plants (Fournier & Pradal, unpublished), the Adel-Maize
+[fournier1999]_, Adel-Wheat [fournier2003]_ models,
+together with the wheat parameterization model of [abichou2013]_
+and the plastic leaf model of [fournier2012]_.
 
-.. sidebar:: Summary
-
-    :Version: |version|
-    :Release: |release|
-    :Date: |today|
-    :Author: See `Authors`_ section
-    :ChangeLog: See `ChangeLog`_ section
-
-.. topic:: Overview
-
-    .. include:: user/overview.txt
 
 Documentation
 =============
 
 .. toctree::
     :maxdepth: 2
 
+    ./installation.rst
     User Guide<user/index.rst>
     Notebook example<example/notebook.rst>
     Reference Guide<user/autosum.rst>
+    ./references.rst
 
 - A `PDF <../latex/adel.pdf>`_ version of |adel| documentation is 
   available.

doc/installation.rst

@@ -0,0 +1,42 @@
+============
+Installation
+============
+
+First install miniforge following the instructions given here https://docs.conda.io/projects/conda/en/latest/user-guide/install/index.html
+
+User installation
+---------------------
+
+OpenAlea Adel may by installed simply on a conda environments:
+
+::
+
+    mamba create -n adel -c conda-forge -c openalea3 openalea.adel
+    mamba activate adel
+
+That creates a conda environment called *adel*, install in it *openalea.adel* with all the dependencies and
+activate the environment. Then just open an Ipython session and enjoy.
+
+If you want notebook support, run for example:
+
+::
+
+    mamba install jupyterlab
+
+Developer installation
+-------------------------
+
+First fork the git repository (https://github.com/openalea/adel) and clone it locally see https://docs.github.com/en/get-started/quickstart/fork-a-repo.
+
+Just run the following command:
+
+::
+
+    mamba create -f conda/environment.yml
+    mamba activate adel
+    pip install -e .[options]
+
+This will first create a conda environment called *adel_dev* with the proper dependencies, then the environment will be activated,
+and finally openalea.adel will be installed in development mode. As above to have notebook support run `mamba install jupyterlab`.
+[options] is optional, and allows to install additional dependencies defined in the [project.optional-dependencies] section of your
+pyproject.toml file (usually "dev", or "doc", ...)

doc/references.rst

@@ -0,0 +1,8 @@
+==========
+References
+==========
+
+.. [fournier1999] Christian Fournier, Bruno Andrieu. ADEL-maize: an L-system based model for the integration of growth processes from the organ to the canopy. Application to regulation of morphogenesis by light availability. Agronomie, 1999, 19 (3-4), pp.313-327, https://hal.science/hal-00885933v1.
+.. [fournier2003] Christian Fournier, B. Andrieu, S. Ljutovac, Sébastien Saint-Jean. ADEL-Wheat: a 3D Architectural Model of wheat development. Hu, B.-G. and Jaeger, M. Plant Growth Modeling and Applications, Springer Verlag, pp.54-63, 2003, https://hal.science/hal-00909184v1.
+.. [fournier2012] Christian Fournier, Christophe Pradal. A Plastic, Dynamic and Reducible 3D Geometric Model for Simulating Gramineous Leaves. International Symposium on Plant Growth Modeling, Simulation, Visualization and Applications, Oct 2012, Shanghai, China. pp.125-132, https://inria.hal.science/hal-01543498v2.
+.. [abichou2013] Mariem Abichou, Christian Fournier, Tino Dornbusch, Camille Chambon, Rim Baccar, et al.. Re-parametrisation of Adel-wheat allows reducing the experimental effort to simulate the 3D develop-ment of winter wheat. 7. International Conference on Functional Structure Plant Models, Jun 2013, Saariselkä, Finland, https://hal.science/hal-01512123v1.