openalea · baugetfa · Feb 9, 2026 · Feb 4, 2026 · Feb 4, 2026 · Feb 4, 2026
diff --git a/doc/_autosummary/openalea.rsml.continuous.rst b/doc/_autosummary/openalea.rsml.continuous.rst
@@ -0,0 +1,14 @@
+openalea.rsml.continuous
+========================
+
+.. automodule:: openalea.rsml.continuous
+
+
+   .. rubric:: Functions
+
+   .. autosummary::
+
+      continuous_to_discrete
+      discrete_to_continuous
+      toporder
+
diff --git a/doc/_autosummary/openalea.rsml.hirros.rst b/doc/_autosummary/openalea.rsml.hirros.rst
@@ -0,0 +1,27 @@
+openalea.rsml.hirros
+====================
+
+.. automodule:: openalea.rsml.hirros
+
+
+   .. rubric:: Functions
+
+   .. autosummary::
+
+      dataframes
+      length_and_number
+      main
+      merge_and_compute_primaries
+      merge_and_compute_secondaries
+      primaries
+      process
+      read
+      run
+      run_all
+      secondary
+      sequence_length
+      times
+      walk
+      write_xls
+      write_xls_all
+
diff --git a/doc/_autosummary/openalea.rsml.io.rst b/doc/_autosummary/openalea.rsml.io.rst
@@ -0,0 +1,23 @@
+openalea.rsml.io
+================
+
+.. automodule:: openalea.rsml.io
+
+
+   .. rubric:: Functions
+
+   .. autosummary::
+
+      mtg2rsml
+      read_xml_tree
+      rsml2mtg
+      str2datetime
+
+   .. rubric:: Classes
+
+   .. autosummary::
+
+      Annotation
+      Dumper
+      Parser
+
diff --git a/doc/_autosummary/openalea.rsml.matching.rst b/doc/_autosummary/openalea.rsml.matching.rst
@@ -0,0 +1,14 @@
+openalea.rsml.matching
+======================
+
+.. automodule:: openalea.rsml.matching
+
+
+   .. rubric:: Functions
+
+   .. autosummary::
+
+      match_plants
+      match_roots
+      one_to_one_match
+
diff --git a/doc/_autosummary/openalea.rsml.measurements.rst b/doc/_autosummary/openalea.rsml.measurements.rst
@@ -0,0 +1,19 @@
+openalea.rsml.measurements
+==========================
+
+.. automodule:: openalea.rsml.measurements
+
+
+   .. rubric:: Functions
+
+   .. autosummary::
+
+      parent_position
+      root_length
+
+   .. rubric:: Classes
+
+   .. autosummary::
+
+      RSML_Measurements
+
diff --git a/doc/_autosummary/openalea.rsml.metadata.rst b/doc/_autosummary/openalea.rsml.metadata.rst
@@ -0,0 +1,15 @@
+openalea.rsml.metadata
+======================
+
+.. automodule:: openalea.rsml.metadata
+
+
+   .. rubric:: Functions
+
+   .. autosummary::
+
+      add_property_definition
+      filter_literal
+      rsml_type
+      set_metadata
+
diff --git a/doc/_autosummary/openalea.rsml.misc.rst b/doc/_autosummary/openalea.rsml.misc.rst
@@ -0,0 +1,16 @@
+openalea.rsml.misc
+==================
+
+.. automodule:: openalea.rsml.misc
+
+
+   .. rubric:: Functions
+
+   .. autosummary::
+
+      hausdorff_distance
+      plant_vertices
+      root_order
+      root_tree
+      root_vertices
+
diff --git a/doc/_autosummary/openalea.rsml.plot.rst b/doc/_autosummary/openalea.rsml.plot.rst
@@ -0,0 +1,14 @@
+openalea.rsml.plot
+==================
+
+.. automodule:: openalea.rsml.plot
+
+
+   .. rubric:: Functions
+
+   .. autosummary::
+
+      multiple_plot
+      plot2d
+      plot3d
+
diff --git a/doc/_autosummary/openalea.rsml.properties.rst b/doc/_autosummary/openalea.rsml.properties.rst
@@ -0,0 +1,17 @@
+openalea.rsml.properties
+========================
+
+.. automodule:: openalea.rsml.properties
+
+
+   .. rubric:: Functions
+
+   .. autosummary::
+
+      set_accession
+      set_ids
+      set_label
+      set_parent_position
+      set_root_length
+      set_rsml_properties
+
diff --git a/doc/_static/RSML_tutorial.png b/doc/_static/RSML_tutorial.png
diff --git a/doc/_static/quick_start.png b/doc/_static/quick_start.png
diff --git a/doc/api.rst b/doc/api.rst
@@ -0,0 +1,16 @@
+OpenAlea RSML's API
+===================
+
+.. toctree::
+    :maxdepth: 4
+    :caption: Contents:
+
+    ./user/api_continuous.rst
+    ./user/api_hirros.rst
+    ./user/api_io.rst
+    ./user/api_matching.rst
+    ./user/api_measurements.rst
+    ./user/api_metadata.rst
+    ./user/api_misc.rst
+    ./user/api_plot.rst
+    ./user/api_properties.rst
diff --git a/doc/api_other_option.rst b/doc/api_other_option.rst
@@ -0,0 +1,18 @@
+==============
+API References
+==============
+
+.. autosummary::
+    :toctree: _autosummary
+    :template: 
+    :recursive:
+
+    openalea.rsml.continuous
+    openalea.rsml.hirros
+    openalea.rsml.io
+    openalea.rsml.matching
+    openalea.rsml.measurements
+    openalea.rsml.metadata
+    openalea.rsml.misc
+    openalea.rsml.plot
+    openalea.rsml.properties
diff --git a/doc/conf.py b/doc/conf.py
@@ -118,6 +118,11 @@
 # Output file base name for HTML help builder.
 htmlhelp_basename = project + '_documentation'
 
+# images used for the nbgallery
+nbsphinx_thumbnails = {
+    "example/RSML_tutorial": "_static/RSML_tutorial.png",
+}
+
 # Add infomation about github repository
 html_context = {
     # "github_url": "https://github.com", # or your GitHub Enterprise site

diff --git a/example/RSML_Readme_tutorial.ipynb → doc/example/RSML_Readme_tutorial.ipynb b/example/RSML_Readme_tutorial.ipynb → doc/example/RSML_Readme_tutorial.ipynb
diff --git a/example/RSML_Readme_tutorial.py → doc/example/RSML_Readme_tutorial.py b/example/RSML_Readme_tutorial.py → doc/example/RSML_Readme_tutorial.py
diff --git a/doc/example/RSML_tutorial.ipynb b/doc/example/RSML_tutorial.ipynb
diff --git a/example/data/arabidopsis-simple.rsml → doc/example/data/arabidopsis-simple.rsml b/example/data/arabidopsis-simple.rsml → doc/example/data/arabidopsis-simple.rsml
diff --git a/example/data/lupin_aero.rsml → doc/example/data/lupin_aero.rsml b/example/data/lupin_aero.rsml → doc/example/data/lupin_aero.rsml
diff --git a/example/demo_plot_rsml.py → doc/example/demo_plot_rsml.py b/example/demo_plot_rsml.py → doc/example/demo_plot_rsml.py
diff --git a/example/testing_rsml.py → doc/example/testing_rsml.py b/example/testing_rsml.py → doc/example/testing_rsml.py
diff --git a/doc/gallery.rst b/doc/gallery.rst
@@ -0,0 +1,8 @@
+.. _gallery-label:
+
+=======
+Gallery
+=======
+
+.. nbgallery::
+    example/RSML_tutorial.ipynb
diff --git a/doc/index.rst b/doc/index.rst
@@ -1,55 +1,32 @@
-.. Do not edit this file. Edit user/overview.txt, user/index user/autosum 
-.. You may add as many files as you want in ./user.
 
-.. _rsml:
+Welcome to OpenAlea RSML's documentation!
+#########################################
 
-.. module:: openales.rsml
+RootSystemML (RSML) is a file format to represent root architectural data (see https://rootsystemml.github.io/ ).
 
-RSML documentation
-#########################################################################
+OpenAlea RSML is a python package that provides:
 
-Module description
-==================
-
-.. sidebar:: Summary
-
-    :Version: |version|
-    :Release: |release|
-    :Date: |today|
-    :Author: See `Authors`_ section
-    :ChangeLog: See `ChangeLog`_ section
-
-.. topic:: Overview
+- import/export between .rsml files and MTG
+- 2D and 3D plot
+- standard root system measurements
+- export to table file
 
-    .. include:: user/overview.txt
-
-Documentation
-=============
 
 .. toctree::
-    :maxdepth: 2
-
-    User Guide<user/index.rst>   
-    Reference Guide<user/autosum.rst>
-
-- A `PDF <../latex/rsml.pdf>`_ version of |rsml| documentation is 
-  available.
+    :maxdepth: 1
+    :caption: Contents:
 
-.. seealso::
-
-   More documentation can be found on the
-   `openalea <https://openalea.rtfd.io>`__ documentation.
+    installation.rst
+    quick_start.rst
+    gallery.rst
+    api.rst
+    references.rst
 
 Authors
 =======
 
 .. include:: ../AUTHORS.txt
 
-ChangeLog
-=========
-
-.. include:: ../ChangeLog.txt
-
 License
 =======
 
@@ -59,3 +36,10 @@ License
     license is a LGPL compatible license.
 
 .. |rsml| replace:: openalea.rsml
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`
diff --git a/doc/installation.rst b/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 RSML may by installed simply on a conda environments:
+
+::
+
+    mamba create -n rsml -c conda-forge -c openalea3 openalea.rsml
+    mamba activate rsml
+
+That creates a conda environment called *rsml*, install in it *openalea.rsml* 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/rsml) 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 rsml
+    pip install -e .[options]
+
+This will first create a conda environment called *rsml_dev* with the proper dependencies, then the environment will be activated,
+and finally openalea.rsml 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", ...)
diff --git a/doc/quick_start.rst b/doc/quick_start.rst
@@ -0,0 +1,24 @@
+===============
+Quick start
+===============
+
+Import necessay libray
+
+.. code-block:: python
+
+    from openalea import rsml
+    from openalea.rsml.data import data_dir
+    from openalea.rsml.plot import plot2d, plot3d
+
+Read and convert rsml file to MTG
+.. code-block:: python
+
+    g = rsml.rsml2mtg(data_dir/'lupin_aero.rsml')
+
+plot it in 2D
+
+.. code-block:: python
+
+    plot2d(g)  # requires matplotlib
+
+.. figure:: _static/quick_start.png
diff --git a/doc/references.rst b/doc/references.rst
@@ -0,0 +1,5 @@
+==========
+References
+==========
+
+Guillaume Lobet, Michael P. Pound, Julien Diener, Christophe Pradal, Xavier Draye, Christophe Godin, Mathieu Javaux, Daniel Leitner, Félicien Meunier, Philippe Nacry, Tony P. Pridmore, Andrea Schnepf, Root System Markup Language: Toward a Unified Root Architecture Description Language, Plant Physiology, Volume 167, Issue 3, March 2015, Pages 617–627, https://doi.org/10.1104/pp.114.253625