Merge branch 'main' of https://github.com/daquinterop/Py_DSSATTools

DSSATTools/base/sections.py

@@ -40,7 +40,7 @@
     'Tomato':       'A6,1X,A20,1X,A1,1X,A6,2(1X,F5.2),3(1X,F5.1),3(1X,F5.2),1X,F5.0,1X,F5.1,1X,F5.2,1X,F5.4,4(1X,F5.1),2(1X,F5.3)',
     'Cabbage':      'A6,1X,A16,1X,A5,1X,A6,1X,F5.2,1X,F5.3,3(1X,F5.1),2(1X,F5.2),1X,F5.3,1X,F5.0,1X,F5.1,1X,F5.3,1X,F5.2,1X,F5.1,1X,F5.2,2(1X,F5.1),2(1X,F5.3)',
     'Sugarcane':    'A6,1X,A16,1X,A5,1X,A6,22(1X,F14.4)',
-    "Wheat":        "A6,1X,A16,1X,A5,1X,A6,5(1X,F5.1),1X,F5.2,1X,F5.1"
+    "Wheat":        "A6,1X,A16,1X,A5,1X,A6,5(1X,F5.1),1X,F5.2,1X,F5.0"
 }
 ECOTYPE_HEADER_FMT = {
     'Maize':        'A5,1X,1X,A16,1X,11(1X,A5)',

DSSATTools/crop.py

@@ -172,9 +172,9 @@ def available_cultivars(crop_name):
     cul_path = os.path.join(GENOTYPE_PATH, f'{CODE}{SMODEL[2:]}{VERSION}.CUL')
     with open(cul_path, "r") as f:
         lines = f.readlines()
-    lines = [l for l in lines if l[:1] not in ["@", "*", "!"]]
+    lines = [l for l in lines if l[:1] not in ["@", "*", "!", "$"]]
     lines = [l for l in lines if len(l) > 5]
-    return [l.split()[0] for l in lines]
+    return [l.split()[0] for l in lines if len(l.strip()) > 6]
 
 class Crop:
     def __init__(self, crop_name:str='Maize', cultivar_code:str=None):

DSSATTools/management.py

@@ -203,7 +203,7 @@ def __init__(
                 'table': TabularSubsection({
                     'IDATE': [planting_date.strftime('%y%j'),],
                     'IROP': ['IR001',],
-                    'IVAL': [0,]
+                    'IRVAL': [0,]
                 })														
             }
         )
@@ -314,7 +314,7 @@ def write(self, filename='EXP', expname='DEFAULT'):
 
         outstr += '*TREATMENTS                        -------------FACTOR LEVELS------------\n'
         outstr += '@N R O C TNAME.................... CU FL SA IC MP MI MF MR MC MT ME MH SM\n'
-        self._treatmentOptions["MI"] = min(1, self.irrigation['table']["IVAL"].sum())
+        self._treatmentOptions["MI"] = min(1, self.irrigation['table']["IRVAL"].sum())
         self._treatmentOptions["MF"] = min(1, self.fertilizers["table"][["FAMN", "FAMP", "FAMK", "FAMC", "FAMO"]].values.max())
         self._treatmentOptions["MH"] = min(1, int(self.harvest_details["HDATE"] is not None))
         outstr += f' 1 1 0 0 DEFAULT TREATMENT          {"  ".join(map(str, IMPLEMENTED_SECTIONS.values()))}\n\n'

DSSATTools/run.py

@@ -34,22 +34,35 @@
 from DSSATTools.base.sections import TabularSubsection
 
 OS = platform.system().lower()
-OUTPUTS = ['PlantGro', "Weather", "SoilWat", "SoilOrg"]
+OUTPUTS = ['PlantGro', "Weather", "SoilWat", "SoilOrg", "SoilNi"]
 OUTPUT_MAP = {
     "PlantGro": "GROUT",  "SoilWat": "WAOUT", "SoilOrg": "CAOUT",
-    "Weather": "GROUT"
+    "Weather": "GROUT", "SoilNi": "NIOUT"
 }
+SOIL_LAYER_OUTPUTS = ["SoilNi"]
 
 PERENIAL_FORAGES = ['Alfalfa', 'Bermudagrass', 'Brachiaria', 'Bahiagrass']
 ROOTS = ['Potato']
 
 # Paths to DSSAT and Env variables
 BASE_PATH = os.path.dirname(module_path)
 STATIC_PATH = os.path.join(BASE_PATH, 'static')
-STATIC_PATH = STATIC_PATH + os.sep
-STD_PATH = os.path.join(STATIC_PATH, 'StandardData')
-CRD_PATH = os.path.join(STATIC_PATH, 'Genotype')
-SLD_PATH = os.path.join(STATIC_PATH, 'Soil')
+TMP =  tempfile.gettempdir()
+DSSAT_HOME = os.path.join(TMP, f"DSSAT{VERSION}"+os.sep)
+STD_PATH = os.path.join(DSSAT_HOME, 'StandardData')
+CRD_PATH = os.path.join(DSSAT_HOME, 'Genotype')
+SLD_PATH = os.path.join(DSSAT_HOME, 'Soil')
+
+# Creates a folder with DSSAT files. This is done to avoid long path names
+# that exceed the defined lenght for path variables in DSSAT.
+if not os.path.exists(DSSAT_HOME):
+    os.mkdir(DSSAT_HOME)
+for file in os.listdir(STATIC_PATH):
+    file_link = os.path.join(DSSAT_HOME, file)
+    if os.path.exists(file_link):
+        os.remove(file_link)
+    os.symlink(os.path.join(STATIC_PATH, file), file_link)
+
 if 'windows'in OS:
     BIN_PATH = os.path.join(STATIC_PATH, 'bin', 'dscsm048.exe')
     CONFILE = 'DSSATPRO.V48'
@@ -225,14 +238,14 @@ def run(self,
             else:
                 f.write(f'M{crop._CODE}    {self._RUN_PATH} dscsm048 {crop._SMODEL}{VERSION}\n')
             f.write(f'CRD    {CRD_PATH}\n')
-            f.write(f'PSD    {os.path.join(STATIC_PATH, "Pest")}\n')
+            f.write(f'PSD    {os.path.join(DSSAT_HOME, "Pest")}\n')
             f.write(f'SLD    {SLD_PATH}\n')
             f.write(f'STD    {STD_PATH}\n')
 
         exc_args = [BIN_PATH, 'C', os.path.basename(management_filename), '1']
         excinfo = subprocess.run(exc_args, 
             cwd=self._RUN_PATH, capture_output=True, text=True,
-            env={"DSSAT_HOME": STATIC_PATH, }
+            env={"DSSAT_HOME": DSSAT_HOME, }
         )
         excinfo.stdout = re.sub("\n{2,}", "\n", excinfo.stdout)
         excinfo.stdout = re.sub("\n$", "", excinfo.stdout)
@@ -259,16 +272,21 @@ def run(self,
             assert f'{file}.OUT' in OUTPUT_FILES, \
                 f'{file}.OUT does not exist in {self._RUN_PATH}'
             table_start = -1
+            init_lines = []
             with open(os.path.join(self._RUN_PATH, f'{file}.OUT'), 'r', encoding='cp437') as f:
                 while True:
                     table_start += 1
-                    if '@' in f.readline():
+                    init_lines.append(f.readline())
+                    if '@' in init_lines[-1][:10]:
                         break
+
             try:  
                 df = pd.read_csv(
                     os.path.join(self._RUN_PATH, f'{file}.OUT'),
                     skiprows=table_start, sep=' ', skipinitialspace=True
                 )
+                df = df.dropna(how="all", axis=1)
+
             except UnicodeDecodeError:
                 with open(os.path.join(self._RUN_PATH, f'{file}.OUT'), 'r', encoding='cp437') as f:
                     lines = f.readlines()

DSSATTools/weather.py

@@ -97,7 +97,7 @@ def __init__(self, df:DataFrame, pars:dict, lat:float=None, lon:float=None,
         '''
         Initialize a Weather instance. This instance contains the weather data,
         as well as the parameters that define the weather station that the data
-        represents,nsuch as the latitude, longitude and elevation.
+        represents, such as the latitude, longitude and elevation.
 
         Arguments
         ----------
@@ -212,7 +212,7 @@ def write(self, folder:str='', **kwargs):
         ])
         outstr += weather_data_header(self.data.columns)
 
-        df = self.data.applymap(lambda x: f"{x:5.1f}")
+        df = self.data.map(lambda x: f"{x:5.1f}")
         df['day'] = df.index.strftime("%Y%j")
         df = df [["day"]+list(self.data.columns)]
         outstr += "\n".join(map(lambda x: " ".join(x), df.values))

README.md

@@ -6,7 +6,7 @@ pip install DSSATTools
 ```
 ## v2.1 Updates
 For the latest version the next changes were implemented:
-- Everything is based in the fact that each simulation includes only one treatment. That involves a single option for cultivars, irrigation, fertilizer, field, etc. 
+- The library simultes only one treatment. Therefore, only one option for cultivars, irrigation, fertilizer, field, etc. can be defined. 
 - Every set of defined crop or management parameters is a section. Each section is an attribute of the `Crop` or `Management` class. Sections won't be created by the user. The user can only modify the value of the parameters of the section, they can't create or add new parameters.
 - The weather is now managed by a single `Weather` class.
 - A `__repr__` method was implemented for the four basic classes (`Crop`, `Management`, `Weather` and `SoilProfile`), and the `Section` class. 

setup.py

@@ -13,7 +13,7 @@
 
 setuptools.setup(
     name="DSSATTools",
-    version="2.1.2",
+    version="2.1.4",
     author="Diego Quintero",
     author_email="[email protected]",
     description="A DSSAT's Python implementation",

tests/test_run.py

@@ -395,7 +395,7 @@ def test_run_soybean():
     man.irrigation["table"] = TabularSubsection({
         'IDATE': ["85183", "85189", "85196", "85200", "85214", "85221"],
         'IROP': ["IR001"]*6,
-        'IVAL': [41, 54, 56, 51, 40, 25],
+        'IRVAL': [41, 54, 56, 51, 40, 25],
     })
     #  *SIMULATION CONTROLS
     # @N GENERAL     NYERS NREPS START SDATE RSEED SNAME.................... SMODEL
@@ -569,7 +569,7 @@ def test_run_tomato():
             '94170','94171','94172','94173','94174','94175'
         ],
         'IROP': ["IR007"]*126,
-        'IVAL': [
+        'IRVAL': [
             3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,4,4,3,3,4,3,3,4,4,3,3,3,4,
             4,4,3,4,4,4,4,4,4,5,4,4,4,4,4,4,4,4,3,3,4,4,3,4,4,4,5,5,4,5,5,5,
             5,5,5,5,4,5,4,5,4,4,5,5,5,3,3,5,4,5,5,5,5,5,5,5,5,4,4,5,5,3,2,2,

tests/test_weather.py

@@ -6,11 +6,9 @@
 import numpy as np
 import shutil
 import os
-import platform
-if 'windows' in platform.system().lower():
-    BASE_PATH = 'C:/Users/daqui/'
-else:
-    BASE_PATH='/home/diego'
+from pathlib import Path
+
+PROJECT_ROOT = Path(__file__).parent.parent
 
 DATES = pd.date_range('2000-01-01', '2010-12-31')
 N = len(DATES)
@@ -34,7 +32,7 @@
 
 class TestWeather:  
     def test_write(self):
-        folder = os.path.join(BASE_PATH, 'Py_DSSATTools', 'wth_test')
+        folder = os.path.join(PROJECT_ROOT, 'tests', 'wth_test')
         if os.path.exists(folder): shutil.rmtree(folder)
         wth = Weather(df, variables, 4.54, -75.1, 1800)
         wth.write(folder)
@@ -157,4 +155,4 @@ def test_co2_value(self):
         dssat.run(
             soil, wth, crop, man
         )
-        assert np.isclose(dssat.output["Weather"]["CO2D"].iloc[0], 500., atol=1)
+        assert np.isclose(dssat.output["Weather"]["CO2D"].iloc[0], 500., atol=1)