Merge pull request #52 from aquacropos/update-docs

update docs in line with newest mkdocs version
aquacropos · Jun 27, 2022 · 6f6b93d · 6f6b93d
2 parents ec9b2d9 + 7b698f1
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diff --git a/.vscode/settings.json b/.vscode/settings.json
@@ -1,6 +1,6 @@
 {
     "python.linting.enabled": true,
-    "python.linting.flake8Enabled": true,
+    "python.linting.flake8Enabled": false,
     "python.linting.mypyEnabled": true,
     "python.linting.flake8Args": [
         "--max-line-length=200",

diff --git a/README.md b/README.md
@@ -7,6 +7,8 @@ Soil-Crop-Water model based on AquaCrop-OS.
 ![last-commit](https://badgen.net/github/last-commit/aquacropos/aquacrop)
 ![license](https://badgen.net/pypi/license/aquacrop)
 ![python-version](https://badgen.net/pypi/python/aquacrop)
+[![image](https://pepy.tech/badge/aquacrop)](https://pepy.tech/project/aquacrop)
+[![Downloads](https://pepy.tech/badge/aquacrop/month)](https://pepy.tech/project/aquacrop)
 
 
 ```python
@@ -27,7 +29,7 @@ model_results = model_os.get_simulation_results().head()
 print(model_results)
 ```
 
-## ABOUT
+## About
 
 AquaCrop-OSPy is a python implementation of the popular crop-water model AquaCrop, built from the AquaCrop-OS source code.
 

diff --git a/aquacrop/core.py b/aquacrop/core.py
@@ -55,7 +55,7 @@ class AquaCropModel:
     This is the main class of the AquaCrop-OSPy model.
     It is in charge of executing all the operations.
 
-    Arguments:
+    Parameters:
 
         sim_start_time (str): YYYY/MM/DD, Simulation start date
 

diff --git a/aquacrop/entities/clockStruct.py b/aquacrop/entities/clockStruct.py
@@ -8,41 +8,37 @@ class ClockStruct:
     """
     Contains model information regarding dates and step times etc.
 
-    Atributes:\n
+    Attributes:
 
-    `time_step_counter` : `int`: Keeps track of current timestep
+        time_step_counter (int): Keeps track of current timestep
 
-    `model_is_finished` : `Bool`: False unless model has finished
+        model_is_finished (Bool): False unless model has finished
 
-    `simulation_start_date` : `np.Datetime64`: Date of simulation start
+        simulation_start_date (np.Datetime64): Date of simulation start
 
-    `simulation_end_date` : `np.Datetime64`: Date of simulation end
+        simulation_end_date (np.Datetime64): Date of simulation end
 
-    `time_step` : `int`: time step (evaluation needed)
+        time_step (int): time step (evaluation needed
 
-    `n_steps` : `int`: total number of days of simulation
+        n_steps (int): total number of days of simulation
 
-    `time_span` : `np.array`: all dates (np.Datetime64) that
-        lie within the start and end dates of simulation
+        time_span (np.array): all dates that lie within the start and end dates of simulation
 
-    `step_start_time` : `np.Datetime64`: Date at start of timestep
+        step_start_time (np.Datetime64): Date at start of timestep
 
-    `step_end_time` : `np.Datetime64`: Date at end of timestep
+        step_end_time (np.Datetime64): Date at end of timestep
 
-    `evap_time_steps` : `int`: Number of time-steps (per day) for soil
-        evaporation calculation
+        evap_time_steps (int): Number of time-steps (per day) for soil evaporation calculation
 
-    `sim_off_season` : `str`: 'Y' if you want to simulate the off season,
-    'N' otherwise
+        sim_off_season (str): 'Y' if you want to simulate the off season,'N' otherwise
 
-    `planting_dates` : `list-like`: list of planting dates in datetime format
+        planting_dates (list-like): list of planting dates in datetime format
 
-    `harvest_dates` : `list-like`: list of harvest dates in datetime format
+        harvest_dates (list-like): list of harvest dates in datetime format
 
-    `n_seasons` : `int`: Total number of seasons to be simulated
+        n_seasons (int): Total number of seasons to be simulated
 
-    `season_counter` : `int`: counter to keep track of which season we are
-        currenlty simulating
+        season_counter (int): counter to keep track of which season we are currenlty simulating
 
 
     """

diff --git a/aquacrop/entities/co2.py b/aquacrop/entities/co2.py
@@ -11,12 +11,11 @@ class CO2(object):
 
     """
 
-    **Attributes:**\n
+    Attributes:
 
+        ref_concentration (float): reference CO2 concentration
 
-    `ref_concentration` : `float` : reference CO2 concentration
-
-    `current_concentration` : `float` : current CO2 concentration
+        current_concentration (float): current CO2 concentration
 
     """
 

diff --git a/aquacrop/entities/crop.py b/aquacrop/entities/crop.py
@@ -13,34 +13,26 @@
 
 class Crop:
     """
-    The Crop Class contains Paramaters and variables of the crop used in the simulation
+    The Crop Class contains paramaters and variables of the crop used in the simulation
 
+    Most Crop attributes can be found in the `crops.crop_params.py` file
+    
+    A number of default program properties of type float are also specified during initialisation
 
-    **Attributes**:\n
+    ```
+    Initialization example:
+    
+    crop = Crop('Maize', planting_date='05/01')
+    ```
 
-    `c_name`: `str`: crop name ('custom' or one of built in defaults e.g. 'Maize')
+    Attributes:
 
-    `planting_date` : `str` : Planting Date (mm/dd)
+        c_name (str): crop name ('custom' or one of built in defaults e.g. 'Maize')
 
-    `harvest_date` : `str` : Latest Harvest Date (mm/dd)
+        planting_date (str): Planting Date (mm/dd)
 
-    `CropType` : `int` : Crop Type (1 = Leafy vegetable, 2 = Root/tuber, 3 = Fruit/grain)
+        harvest_date (str): Latest Harvest Date (mm/dd)
 
-    `PlantMethod` : `int` : Planting method (0 = Transplanted, 1 =  Sown)
-
-    `CalendarType` : `int` : Calendar Type (1 = Calendar days, 2 = Growing degree days)
-
-    `SwitchGDD` : `int` : Convert calendar to gdd mode if inputs are given in calendar days (0 = No; 1 = Yes)
-
-
-
-    `IrrMngt`: `dict` :  dictionary containting irrigation management information
-
-    `IrrSchd` : `pandas.DataFrame` :  pandas DataFrame containing the Irrigation Schedule if predefined
-
-    `FieldMngt` : `dict` :   Dictionary containing field management variables for the growing season of the crop
-
-     A number of default program properties of type float are also specified during initialisation
 
     """
 
@@ -336,11 +328,7 @@ def calculate_additional_params(
 
 class CropStruct(object):
     """
-    The Crop Class contains Paramaters and variables of the crop used in the simulation
-
-
-    **Attributes**:\n
-
+    Duplicate crop object for Jit compilation
 
 
     """

diff --git a/aquacrop/entities/fieldManagement.py b/aquacrop/entities/fieldManagement.py
@@ -1,33 +1,29 @@
-
 from numba import float64, int64, boolean, types
 
 
 class FieldMngt:
     """
-    Field Management Class
-
-    **Attributes:**\n
-
-
-    `mulches` : `bool` :  Soil surface covered by mulches (yield_ or N)
+    Field Management Class containing mulches and bunds parameters
 
-    `bunds` : `bool` :  Surface bunds present (yield_ or N)
+    Attributes:
 
-    `curve_number_adj` : `bool` : Field conditions affect curve number (yield_ or N)
+        mulches (bool):  Soil surface covered by mulches (yield_ or N)
 
-    `sr_inhb` : `bool` : Management practices fully inhibit surface runoff (yield_ or N)
+        bunds (bool):  Surface bunds present (yield_ or N)
 
+        curve_number_adj (bool): Field conditions affect curve number (yield_ or N)
 
+        sr_inhb (bool): Management practices fully inhibit surface runoff (yield_ or N)
 
-    `mulch_pct` : `float` :  Area of soil surface covered by mulches (%)
+        mulch_pct (float):  Area of soil surface covered by mulches (%)
 
-    `f_mulch` : `float` : Soil evaporation adjustment factor due to effect of mulches
+        f_mulch (float): Soil evaporation adjustment factor due to effect of mulches
 
-    `z_bund` : `float` : Bund height (m)
+        z_bund (float): Bund height (m)
 
-    `bund_water` : `float` : Initial water height in surface bunds (mm)
+        bund_water (float): Initial water height in surface bunds (mm)
 
-    `curve_number_adj_pct` : `float` : Percentage change in curve number (positive or negative)
+        curve_number_adj_pct (float): Percentage change in curve number (positive or negative)
 
     """
 

diff --git a/aquacrop/entities/groundWater.py b/aquacrop/entities/groundWater.py
@@ -4,16 +4,15 @@ class GroundWater:
     """
     Ground Water Class stores information on water table params
 
-    **Attributes:**\n
+    Attributes:
 
+        water_table (str):  Water table considered (yield_ or N)
 
-    `water_table` : `str` :  Water table considered (yield_ or N)
+        method (str):  Water table input data ('Constant' or 'Variable')
 
-    `method` : `str` :  Water table input data ('Constant' or 'Variable')
+        dates (list): water table observation dates
 
-    `dates` : `list` : water table observation dates
-
-    `values` : `list` : water table observation depths
+        values (list): water table observation depths
 
     """
 

diff --git a/aquacrop/entities/inititalWaterContent.py b/aquacrop/entities/inititalWaterContent.py
@@ -4,15 +4,15 @@ class InitialWaterContent:
     """
     Initial water content Class defines water content at start of sim
 
-    **Attributes:**\n
+    Attributes:
 
-    `wc_type` : `str` :  Type of value ('Prop' = 'WP'/'FC'/'SAT'; 'Num' = XXX m3/m3; 'Pct' = % taw))
+        wc_type (str):  Type of value ('Prop' = 'WP'/'FC'/'SAT'; 'Num' = XXX m3/m3; 'Pct' = % taw))
 
-    `method` : `str` :  method ('Depth' = Interpolate depth points; 'Layer' = Constant value for each soil layer)
+        method (str):  method ('Depth' = Interpolate depth points; 'Layer' = Constant value for each soil layer)
 
-    `depth_layer` : `list` : location in soil profile (soil layer or depth)
+        depth_layer (list): location in soil profile (soil layer or depth)
 
-    `value` : `list` : value at that location
+        value (list): value at each location given in depth_layer
 
     """
 

diff --git a/aquacrop/entities/irrigationManagement.py b/aquacrop/entities/irrigationManagement.py
@@ -6,31 +6,29 @@
 class IrrigationManagement:
 
     """
-    Farmer Class defines irrigation strategy
+    IrrigationManagement Class defines irrigation strategy
 
-    **Attributes:**\n
+    Attributes:
 
 
-    `Name` : `str` :  name
+        irrigation_method (int):  Irrigation method {0: rainfed, 1: soil moisture targets, 2: set time interval,
+                                                3: predifined schedule, 4: net irrigation, 5: constant depth }
 
-    `irrigation_method` : `int` :  Irrigation method {0: rainfed, 1: soil moisture targets, 2: set time interval,
-                                              3: predifined schedule, 4: net irrigation, 5: constant depth }
+        WetSurf (int): Soil surface wetted by irrigation (%)
 
-    `WetSurf` : `int` : Soil surface wetted by irrigation (%)
+        AppEff (int): Irrigation application efficiency (%)
 
-    `AppEff` : `int` : Irrigation application efficiency (%)
+        MaxIrr (float): Maximum depth (mm) that can be applied each day
 
-    `MaxIrr` : `float` : Maximum depth (mm) that can be applied each day
+        SMT (list):  Soil moisture targets (%taw) to maintain in each growth stage (only used if irrigation method is equal to 1)
 
-    `SMT` : `list` :  Soil moisture targets (%taw) to maintain in each growth stage (only used if irrigation method is equal to 1)
+        IrrInterval (int): Irrigation interval in days (only used if irrigation method is equal to 2)
 
-    `IrrInterval` : `int` : Irrigation interval in days (only used if irrigation method is equal to 2)
+        Schedule (pandas.DataFrame): DataFrame containing dates and depths
 
-    `Schedule` : `pandas.DataFrame` : DataFrame containing dates and depths
+        NetIrrSMT (float): Net irrigation threshold moisture level (% of taw that will be maintained, for irrigation_method=4)
 
-    `NetIrrSMT` : `float` : Net irrigation threshold moisture level (% of taw that will be maintained, for irrigation_method=4)
-
-    `Depth` : `float` : constant depth to apply on each day
+        Depth (float): constant depth to apply on each day
 
     """
 

diff --git a/aquacrop/entities/moistureDepletion.py b/aquacrop/entities/moistureDepletion.py
@@ -9,14 +9,14 @@
 
 
 class Dr:
-
     """
+    Depletion class to hold the rootzone and topsoil depletion
 
-    **Attributes:**\n
+    Attributes:
 
-    `Rz` : `float` : .
+    Rz (float): Root zone soil-water depletion
 
-    `Zt` : `float` : .
+    Zt (float): Top soil depletion
 
 
     """

diff --git a/aquacrop/entities/output.py b/aquacrop/entities/output.py
@@ -6,16 +6,18 @@ class Output:
     """
     Class to hold output data
 
-    **Atributes**:\n
+    During Simulation these are numpy arrays and are converted to pandas dataframes
+    at the end of the simulation
 
-    `water_storage` : `numpy` : Water storage in soil. TODO: it is numpy or pandas?
+    Atributes:
+    
+        water_flux (pandas.DataFrame, numpy.array): Daily water flux changes
 
-    TODO: water_flux and crop_growth are numpy arrays during simulation. I think it should be clearer
-    `water_flux` : `pandas.DataFrame` : Water flux
+        water_storage (pandas.DataFrame, numpy array): daily water content of each soil compartment
 
-    `crop_growth` : `pandas.DataFrame` : crop growth
+        crop_growth (pandas.DataFrame, numpy array): daily crop growth variables
 
-    `final_stats` : `pandas.DataFrame` : final stats
+        final_stats (pandas.DataFrame, numpy array): final stats at end of each season
 
     """