updated the doc's format and content

Author: RamiALBASHA

AUTHORS.rst

@@ -4,16 +4,8 @@ Credits
 Development Lead
 ----------------
 
-.. {# pkglts, doc
-
 * Rami Albasha, <[email protected]>
-* Christian Fournier, <christian.fournier@inra.fr>
+* Christian Fournier, <christian.fournier@inrae.fr>
 * Christophe Pradal, <[email protected]>
 * Eric Lebon
 
-.. #}
-
-Contributors
-------------
-
-None yet. Why not be the first?

HISTORY.rst

@@ -3,7 +3,14 @@
 History
 =======
 
-creation (TODAY)
-------------------------
+creation
+--------
 
-* First release on PyPI.
+HydroShoot was created by Rami ALBASHA during his postdoctoral research (July 2015 to December 2016)
+under the supervision of Eric LEBON†, in close collaboration with Christian FOURNIER and Christophe PRADAL.
+
+The model is partly based on prior developments led by Gaëtan LOUARN and Jorge PRIETO who developed the FSPM TOPVINE
+(`Louarn et al., 2008 <https://academic.oup.com/aob/article/101/8/1167/159779>`_,
+`Prieto et al., 2012 <https://onlinelibrary.wiley.com/doi/10.1111/j.1365-3040.2012.02491.x>`_).
+The main difference between TOPVINE and HydroShoot is that the latter simulates explicitly the hydraulic network of the
+shoot, which is coupled to both energy and gas exchange processes.

doc/conf.py

@@ -18,6 +18,7 @@
 
 
 # -- Project information -----------------------------------------------------
+import sphinx_rtd_theme
 
 project = u'HydroShoot'
 copyright = u'2019, Rami Albasha'
@@ -45,6 +46,7 @@
     'sphinx.ext.ifconfig',
     'sphinx.ext.viewcode',
     'sphinx.ext.githubpages',
+    'sphinx_rtd_theme'
 ]
 
 # Add any paths that contain templates here, relative to this directory.
@@ -82,7 +84,7 @@
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 #
-html_theme = 'alabaster'
+html_theme = "sphinx_rtd_theme"
 
 # Theme options are theme-specific and customize the look and feel of a theme
 # further.  For a list of options available for each theme, see the

doc/ecophysio_solver.rst

@@ -4,7 +4,7 @@ Processes interactions
 
 Interactions among the physiological processes occur.
 
-.. figure:: figs/ecophysio_solver.svg
+.. figure:: figs/ecophysio_solver_1.svg
     :align: center
 
     Solving the interactions between leaf's water potential, transpiration rate and temperature !
@@ -36,7 +36,7 @@ the hydraulic, energy and gas-exchange processes is handled in HydroShoot.
 
 .. _fig_2:
 
-.. figure:: figs/fig_2_ecophysio_solver.png
+.. figure:: figs/ecophysio_solver_2.png
 
     Schematic representation of the numerical resolution of HydroShoot. Meteorological inputs that are common
     to all leaves are air temperature (:math:`T_{air}, \ K`), air relative humidity (:math:`RH, \ -`), air

doc/energy.rst

@@ -80,7 +80,7 @@ This refers to the method used to calculate the lumped sky and soil form factors
 
 In order to reduce calculation costs, :math:`k_{sky}` and :math:`k_{soil}`) are obtained by flip flopping the canopy:
 
-.. figure:: figs/energy_pirouete_cacahute.png
+.. figure:: figs/energy_3.png
     :align: center
 
 At first, the canopy is turned downwards. A unit irradiance is emitted from each sky sector and irradiance that is

doc/figs/ecophysio_solver.svg doc/figs/ecophysio_solver_1.svg

@@ -17,9 +17,11 @@ Welcome to HydroShoot's documentation!
 
 
 
-Indices and tables
-==================
+Further reading
+===============
 
-* :ref:`genindex`
-* :ref:`modindex`
-* :ref:`search`
+.. toctree::
+
+   authors
+   history
+   contributing

doc/figs/fig_2_ecophysio_solver.png doc/figs/ecophysio_solver_2.png

@@ -2,8 +2,9 @@
 Model description
 =================
 
-All information in this section are taken from HydroShoot's paper **(`Albasha et al., 2019 <https://doi.org/10.1093/insilicoplants/diz007>`_)**. Please refer to the this
-paper for a thorough description of model's formulae and evaluation.
+All information in this section are taken from HydroShoot's paper
+(`Albasha et al., 2019 <https://doi.org/10.1093/insilicoplants/diz007>`_).
+Please refer to the this paper for a detailed description of model's formulae and evaluation.
 
 
 .. toctree::