sections.py modified for merge

Author: daquinterop

DSSATTools/__init__.py

@@ -1,16 +1,46 @@
 '''
-DSSAT library allows the user to create low-code scripts to run simulations with the DSSAT model. The library structure allows to execute the DSSAT model based on four input classes: `Crop`, `SoilProfile`, `WeatherStation` and `Management`.
+DSSATTools library allows the user to create low-code scripts to run simulations
+using the DSSAT modeling framework. The library structure allows to executes DSSAT
+based on four input classes: `Crop`, `SoilProfile`, `Weather` and `Management`.
+The simulation environment is managed by the `DSSAT` Class. There are three stages
+for the simulation to be performed: 
 
-The simulation environment is represented by the `DSSAT` Class. There are three stages for the simulation to be excecuted: 
-#. Initialize a `DSSAT` instance
-#. setup the simulation environment by using the `DSSAT.setup` method
-#. run the simulation using the `DSSAT.run` method.
+1. Initialize a `DSSAT` instance. 
+2. setup the simulation environment by using the `DSSAT.setup` method. When that 
+method is called a new directory is created in the provided location (a tmp 
+directory is default) and all the files that are necessary to run the model are 
+copied in that folder.
+3. run the simulation calling `DSSAT.run` method. That method needs four 
+parameters to be pased. Each parameter indicates the crop, soil, weather, and management.
+This step can be performed as many times as one wants. 
+4. close the environment using `DSSAT.close`. This removes the directory and the
+files created during the environment setup.
 
-During the environment setup (`DSSAT.setup`) a directory is created and all the static files required to run DSSAT are copied in that directory. This directory will be removed when the `DSSAT.close` method is called. After the environment has been set up, the `DSSAT.run` method can be called as many times as you want.
+The next simple example illustrates how to run a simulation using the five 
+aforementioned classes:
 
-Input clases are defined by sections and tabular subsections within some sections. Each section is an attribute of the input instance and is defined as an independent `RowBasedSection` class. This class inherits from `dict`, so you can modify any parameter in the section the same way that you'd modify a `dict`'s item.
+    >>> crop = Crop('maize')
+    >>> weather = Weather(
+            df, # Weather data with a datetime index
+            {"tn": "TMIN", "rad": "SRAD", "prec": "RAIN", "rh": "RHUM", "TMAX": "TMAX"},
+            4.54, -75.1, 1800
+        )
+    >>> soil = SoilProfile(default_class='SIL')
+    >>> man = Management(planting_date=datetime(12, 3, 2020))
+    >>> dssat = DSSAT()
+    >>> dssat.setup()
+    >>> dssat.run(soil, wth, crop, man)
+    >>> growth = dssat.output["PlantGro"] 
+    >>> dssat.close() # Terminate the simulation environment
 
-All of the parameters and attributes of the four basic clases have the same name you find in the DSSAT files (Take a look at the .CDE files in https://github.com/DSSAT/dssat-csm-os/tree/develop/Data).
+The parameters for ecach class are described in their doucmentation. It is very 
+important to highlight that this library will allow the user to run only one treatment
+at a time. If the users are familiar to DSSAT, they must know that DSSAT allows to
+define multiple treatments in the same experimental file.
+
+All of the parameters for the four basic clases have the same names you find in 
+the DSSAT files (Take a look at the .CDE files in 
+https://github.com/DSSAT/dssat-csm-os/tree/develop/Data).
 
 Up to date next crops and models are included:
 
@@ -31,19 +61,20 @@
 Potato               SUBSTOR
 Tomato               CROPGRO
 Cabbage              CROPGRO
+Potato               SUBSTOR             
+Sugarcane            CANEGRO             
 ==================   =====================
-
 '''
 VERSION = '048'
 
-from DSSATTools.crop import Crop
+from DSSATTools.crop import Crop, available_cultivars
 from DSSATTools.soil import SoilProfile, SoilLayer
-from DSSATTools.weather import WeatherStation, WeatherData
+from DSSATTools.weather import Weather
 from DSSATTools.management import Management
 from DSSATTools.run import DSSAT
 from DSSATTools.base.sections import TabularSubsection
 
 __all__ = [
-    'Crop', 'SoilProfile', 'SoilLayer', 'WeatherStation', 'WeatherData',
-    'Management', 'DSSAT', 'TabularSubsection'
+    'Crop', 'SoilProfile', 'SoilLayer', 'Weather', 'Management', 'DSSAT', 
+    'TabularSubsection', "available_cultivars"
     ]