Merge branch 'main' of https://gitlab.cesbio.omp.eu/auclairj/modspa_pixel into main

.gitignore

@@ -9,6 +9,9 @@ config/config_modspa_*
 parameters/csv_files/params_samir_test_dev.csv
 parameters/csv_files/params_samir_Sigpac_test.csv
 
+# figures
+*.png
+
 # Byte-compiled, backup..
 *__pycache__*
 __pycache__/

config/select_config_modspa.py

@@ -16,14 +16,15 @@ import shutil  # file management
 
 if __name__ == '__main__':
     if len(sys.argv) == 1:
-        
+
         prog = os.path.basename(sys.argv[0])
-        print('      ',sys.argv[0],' [data selected]') 
-        
+        print('      ', sys.argv[0], ' [data selected]')
+
     else:
         currentdir = os.path.dirname(os.path.realpath(__file__))
-        source_file = currentdir + os.sep + 'config_modspa_' + sys.argv[1]+'.json'
-        if not os.path.exists(source_file) : source_file = currentdir + os.sep + sys.argv[1]
+        source_file = currentdir + os.sep + 'config_modspa.' + sys.argv[1]+'.json'
+        if not os.path.exists(source_file):
+            source_file = currentdir + os.sep + sys.argv[1]
         dest_file = currentdir + os.sep + 'config_modspa.json'
         print('source file:', source_file)
         print('destination file:', dest_file)

docs/source/setup/conda_env.rst

-Installing the conda environnment
+Installing the conda environment
 =================================
 
 If you have not yet installed **conda** on your machine, you should start with this step : `conda installation <https://conda.io/projects/conda/en/latest/user-guide/install/index.html>`_.
 
-A ``yaml`` file is included to automatically create a conda virtual environnment with the correct libraries and dependencies installed. To install it run this command in the root directory of the modspa_pixel project:
+A ``yml`` file is included to automatically create a conda virtual environnment with the correct libraries and dependencies installed. To install it run this command in the root directory of the modspa_pixel project:
 
 .. code:: bash
 
-    (base) /modspa_pixel$ conda env create -f modspa_pixel_env.yaml
+    (base) /modspa_pixel$ conda env create -f modspa_pixel_env.yml
 
-To activate the environnment:
+To activate the environment:
 
 .. code:: bash
 

docs/source/setup/json_config_file.rst

@@ -3,18 +3,18 @@
 Understanding the json config file
 ==================================
 
-All the global paramters for the modspa processing chain are located in the ``json`` (**/modspa_pixel/config/config_modspa.json**). 
+All the global paramters for the modspa processing chain are located in the ``json`` (**/modspa_pixel/config/config_modspa.json**) configuration file. 
 
 This allows you to choose where and how to run the modspa_pixel processing chain. Different parts of the processing chain are detailed in the **inputs** and **samir** sections. You can have multiple configuration files with name extensions (``_name_ext`` corresponds to the file ``config_modspa_name_ext.json``), to select one configuration file for the run, use the ``select_config_modspa.py`` (in the **modspa_pixel/config:** directory) as follows:
 
 .. code:: bash
 
    (modspa_pixel) $ python select_config_modspa.py name_ext
-   source file: /modspa_pixel/config/config_modspa_name_ext.json
+   source file: /modspa_pixel/config/config_modspa.name_ext.json
    destination file: /modspa_pixel/config/config_modspa.json
    /modspa_pixel/config/config_modspa.json updated
 
-the name extension argument ``name_ext`` (withou the underscore **_**) is used to select the file content you want and copy it in the **/modspa_pixel/config/config_modspa.json** file.
+the name extension argument ``name_ext`` is used to select the file content you want and copy it in the regular **/modspa_pixel/config/config_modspa.json** file.
 
 Example of a configuration file:
 

docs/source/setup/setup.rst

 Setting up the correct environnment and parameters
 ==================================================
 
-This section will help you set-up the correct environnment and parameters to run the **modspa_pixel** scripts.
+This section will help you set-up the correct environment and parameters to run the **modspa_pixel** scripts and perform a simulation.
 
 To begin, clone the project from the `github <https://gitlab.cesbio.omp.eu/auclairj/modspa_pixel>`_ page with the following command:
 
 .. code:: bash
 
-   (base) /modspa_pixel$ git clone https://gitlab.cesbio.omp.eu/auclairj/modspa_pixel.git
+   > git clone https://gitlab.cesbio.omp.eu/auclairj/modspa_pixel.git
    
 This should create a ``modspa_pixel`` directory in your current directory.
 
 .. warning::
 
-   Thz scripts have been developped and tested on **Linux** (Ubuntu) operating systems. Some tools or packages might not work on other operating systems like **Windows** or **Mac-OS**.
+   The scripts have been developped and tested on **Linux** (Ubuntu) operating systems. Some tools or packages might not work on other operating systems like **Windows** or **Mac-OS**.
 
 .. toctree::
    :maxdepth: 2

parameters/csv_files/params_samir_Aurade_test.csv

 ClassName,scale_factor,Default,no_sim,straw_cereal,oilseed,soy,sunflower,corn,grassland,orchard,vineyards,broadleaf_forest,conifer_forest,heathland 
 ClassNumber,1,0,1,2,3,4,5,6,7,8,9,10,11,12
-FCmax,1000,1,0,,,,,,,,,,,
-Fslope,1000,1.4,0,,,,,,,,,,,
-Foffset,1000,-0.075,0,,,,,,,,,,,
-Kcmax,0,1.15,0,,,,,,,,,,,
-Kslope,1000,1.2,0,,,,,,,,,,,
-Koffset,1000,-0.24,0,,,,,,,,,,,
-NDVIsol,1,0.15,,,,,,,
-NDVImax,1,0.85,,,,,,,
-Zsoil,1,2000,,,,,,,,,,,,
-Ze,1,300,,,,,,,,,,,,
-Init_RU,1000,0.87,,,,,,,,,,,,
-DiffE,1,1,0,,,,,,,,,,,
-DiffR,1,5,0,,,,,,,,,,,
-REW,1,0,,,,,,,,,,,,
-minZr,1,150,0,,,,,,,,,,,
-maxZr,1,600,0,,,,,,,,,,,
-p,1000,0.55,0,,,,,,,,,,,
-FW,1000,1,0,,,,,,,,,,,
-Irrig_auto,1,1,0,,,,,,,,,,,
-Irrig_man,1,0,0,,,,,,,,,,,
+NDVIsol,1,0.15,,0.15,0.15,,,,
+NDVImax,1,0.85,,0.85,0.85,,,,
+FCmax,1000,1,0,1,,,,,,,,,,
+Fslope,1000,1.4,0,1.18,1.22,,,,,,,,,
+Foffset,1000,-0.075,0,-0.165,-0.17,,,,,,,,,
+Kcmax,0,1.15,0,1.15,0.7,,,,,,,,,
+Kslope,1000,1.2,0,1.47,1.35,,,,,,,,,
+Koffset,1000,-0.24,0,-0.17,-0.16,,,,,,,,,
+Zsoil,1,2000,,2000,2000,,,,,,,,,
+Ze,1,300,,125,125,,,,,,,,,
+Init_RU,1000,0.87,,0.5,0.5,,,,,,,,,
+DiffE,1,1,0,0,0,,,,,,,,,
+DiffR,1,5,0,0,0,,,,,,,,,
+REW,1,0,,9,9,,,,,,,,,
+minZr,1,150,0,125,125,,,,,,,,,
+maxZr,1,600,0,1250,1450,,,,,,,,,
+p,1000,0.55,0,0.55,0.65,,,,,,,,,
+FW,1000,1,0,1,1,,,,,,,,,
+Irrig_auto,1,1,0,1,1,,,,,,,,,
+Irrig_man,1,0,0,0,0,,,,,,,,,
 Kcb_stop_irrig,1,0.5,0,,,,,,,,,,,
\ No newline at end of file