CropGym update for new PCSE version

.github/workflows/test.yml

@@ -6,19 +6,21 @@ jobs:
       strategy:
         matrix:
           os: [ubuntu-latest]
-          python-version: ['3.11']
+          python-version: ['3.9']
       steps:
       - uses: actions/checkout@v3
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v3
+        uses: actions/setup-python@v4
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
           pip install flake8 pytest pytest-cov
           pip uninstall -y --quiet pcse
           git clone https://github.com/ajwdewit/pcse.git /tmp/pcse
-          cd /tmp/pcse && git switch develop_WOFOST_v8_1 && git apply --ignore-space-change --ignore-whitespace ${GITHUB_WORKSPACE}/notebooks/nitrogen-winterwheat/pcse-lintul3.patch && pip install --quiet -e . && cd ${GITHUB_WORKSPACE}
-          pip install stable_baselines3 sb3-contrib gymnasium lib_programname tensorboard scipy tqdm pandas numpy
+          cd /tmp/pcse && git switch develop_wofost81 && git reset --hard 67a3d0c3a46280bddcf7617de3b27c82e5cb0a40 && pip install --quiet -e . && cd ${GITHUB_WORKSPACE}
+          pip install dotmap
+          pip install stable_baselines3 sb3-contrib
+          pip install gymnasium==0.28.1 lib_programname tensorboard scipy tqdm pandas numpy
       - name: Lint with flake8
         run: |
           # stop the build if there are Python syntax errors or undefined names

.gitignore

@@ -2,3 +2,4 @@
 _notebooks_old/nitrogen-winterwheat/tensorboard_logs
 _notebooks_old/nitrogen-winterwheat/.ipynb_checkpoints
 .pyc
+/comet/

notebooks/nitrogen-winterwheat/wofost_results_lt.csv

@@ -0,0 +1,66 @@
+"IDCROP_PARAMETRIZATION","IDSEASON","DECADE","IDGRID","POTENTIAL_YIELD_BIOMASS","POTENTIAL_YIELD_STORAGE","WATER_LIM_YIELD_BIOMASS","WATER_LIM_YIELD_STORAGE","POTENTIAL_LEAF_AREA_INDEX","WATER_LIM_LEAF_AREA_INDEX","DEVELOPMENT_STAGE","RELATIVE_SOIL_MOISTURE","TOTAL_WATER_CONSUMPTION","TOTAL_WATER_REQUIREMENT","FSM","FSMUR","LEAVES_DIED_BY_COLD","RUNOFF","SOIL_EVAPORATION","LOSS_TO_SUBSOIL"
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pcse_gym/envs/common_env.py

@@ -1,5 +1,6 @@
 import datetime
 import os
+import copy
 
 import numpy as np
 import yaml
@@ -18,41 +19,198 @@
 """
 
 
-def replace_years(agro_management, years):
+class AgroManagementContainer:
+    def __init__(self, agro_management: list):
+        self.agro_structure = agro_management
+        self.campaign_date: datetime.date = list(agro_management[0].keys())[0]
+        self.crop_name: str = agro_management[0][self.campaign_date]['CropCalendar']['crop_name']
+        self.crop_variety: str = agro_management[0][self.campaign_date]['CropCalendar']['variety_name']
+        self.crop_start_date: datetime.date = agro_management[0][self.campaign_date]['CropCalendar']['crop_start_date']
+        self.crop_start_type: str = agro_management[0][self.campaign_date]['CropCalendar']['crop_start_type']
+        self.crop_end_date: datetime.date = agro_management[0][self.campaign_date]['CropCalendar']['crop_end_date']
+        self.crop_end_type: str = agro_management[0][self.campaign_date]['CropCalendar']['crop_end_type']
+        self.max_duration: int = agro_management[0][self.campaign_date]['CropCalendar']['max_duration']
+
+        self.structure = None
+        self.build_structure()
+
+    def build_structure(self):
+        self.structure = yaml.load(f'''
+                    - {self.campaign_date}:
+                        CropCalendar:
+                            crop_name: {self.crop_name}
+                            variety_name: {self.crop_variety}
+                            crop_start_date: {self.crop_start_date}
+                            crop_start_type: {self.crop_start_type}
+                            crop_end_date: {self.crop_end_date}
+                            crop_end_type: {self.crop_end_type}
+                            max_duration: {self.max_duration}
+                        TimedEvents: null
+                        StateEvents: null
+                ''', Loader=yaml.SafeLoader)
+
+    def replace_years(self, y):
+        """
+            Years replaced are the harvest date. Campaign start and sow date starts a year before.
+        """
+        if isinstance(y, list):
+            y = y[0]
+        if self.campaign_date.year == self.crop_end_date.year:
+            yprev = y
+        else:
+            yprev = y - 1
+        self.campaign_date = self.campaign_date.replace(year=yprev)
+        self.crop_start_date = self.crop_start_date.replace(year=yprev)
+        self.crop_end_date = self.crop_end_date.replace(year=y)
+
+        self.build_structure()
+        return self.structure
+
+    def replace_sow_date(self, year, month, day):
+        self.crop_start_date = self.crop_start_date.replace(year=year, month=month, day=day)
+
+        self.build_structure()
+        return self.structure
+
+    def replace_harvest_date(self, year, month, day):
+        self.crop_end_date = self.crop_end_date.replace(year=year, month=month, day=day)
+
+        self.build_structure()
+        return self.structure
+
+    def replace_start_type(self, start):
+        assert start == 'sowing' or start == 'emergence'
+        self.crop_start_type = start
+
+        self.build_structure()
+        return self.structure
+
+    @property
+    def get_structure(self):
+        return self.structure
+
+    @property
+    def get_start_date(self):
+        return self.crop_start_date
+
+    @property
+    def get_end_date(self):
+        return self.crop_end_date
+
+
+def replace_years_(agro_management, years):  # deprecated
     if not isinstance(years, list):
         years = [years]
 
-    updated_agro_management = [{k.replace(year=year): v for k, v in agro.items()} for agro, year in
-                               zip(agro_management, years)]
-
-    def replace_year_value(d, year):
+    # TODO: refactor date_keys so it's lighter,
+    #  direct reference is a bit tricky with the dictionary name (2006-10-01)
+    agro = agro_management[0]
+    date_keys = [[v2.year for v1 in v.values() if isinstance(v1, dict) for v2 in v1.values()
+                  if isinstance(v2, datetime.date)] for v in agro.values()]
+    date_keys = date_keys[0]
+    if date_keys[0] < date_keys[1]:
+        updated_agro_management = [{k.replace(year=year - 1): v for k, v in agro.items()} for agro, year in
+                                   zip(agro_management, years)]
+    else:
+        updated_agro_management = [{k.replace(year=year): v for k, v in agro.items()} for agro, year in
+                                   zip(agro_management, years)]
+
+    def replace_year_value(d, year, y_sow=None):
         for k, v in d.items():
             if isinstance(v, dict):
-                replace_year_value(v, year)
+                replace_year_value(v, year, y_sow)
             else:
-                if isinstance(v, datetime.date):
+                if isinstance(v, datetime.date) and y_sow and k == 'crop_start_date':
+                    up_dict = {k: v.replace(year=y_sow)}
+                    d.update(up_dict)
+                elif isinstance(v, datetime.date):
                     up_dict = {k: v.replace(year=year)}
                     d.update(up_dict)
 
     for agro, year in zip(updated_agro_management, years):
-        replace_year_value(agro, year)
+        if date_keys[0] < date_keys[1]:
+            year_sow = year - 1
+            replace_year_value(agro, year, year_sow)
+        else:
+            replace_year_value(agro, year)
     return updated_agro_management
 
 
-def get_weather_data_provider(location) -> pcse.db.NASAPowerWeatherDataProvider:
-    wdp = pcse.db.NASAPowerWeatherDataProvider(*location)
+def get_weather_data_provider(location, random_weather=False) -> pcse.db.NASAPowerWeatherDataProvider or pcse.fileinput.CSVWeatherDataProvider:
+    if random_weather:
+        wdp = get_random_weather_provider(location)
+    else:
+        wdp = pcse.db.NASAPowerWeatherDataProvider(*location)
+    return wdp
+
+
+def get_random_weather_provider(location) -> pcse.fileinput.CSVWeatherDataProvider:
+    path_to_file = os.path.dirname(os.path.realpath(__file__))
+    lat, lon = location
+    csv_name = f'{lat}-{lon}_random_weather.csv'
+    filename = os.path.join(path_to_file[:-4], 'utils', 'weather_utils', 'random_weather_csv', csv_name)
+    wdp = pcse.fileinput.CSVWeatherDataProvider(filename)
     return wdp
 
 
 class Engine(pcse.engine.Engine):
     """
-    Wraps around the PCSE engine/crop model to set a flag when the simulation has terminated
+    Wraps around the PCSE engine/crop model for correct rate updates after fertilization action and
+    to set a flag when the simulation has terminated
     """
 
     def __init__(self, *args, **kwargs):
         super().__init__(*args, **kwargs)
         self._flag_terminated = False
 
+    def _run(self, action):
+        """Make one time step of the simulation.
+        """
+
+        # Update timer
+        self.day, delt = self.timer()
+
+        # State integration
+        self.integrate(self.day, delt)
+
+        # Driving variables
+        self.drv = self._get_driving_variables(self.day)
+
+        # Agromanagement decisions
+        self.agromanager(self.day, self.drv)
+
+        if action > 0:
+            self._send_signal(signal=pcse.signals.apply_n,
+                              amount=action,
+                              application_depth=10.,
+                              cnratio=0.,
+                              f_orgmat=0.,
+                              f_NH4N=0.5,
+                              f_NO3N=0.5,
+                              initial_age=0,
+                              recovery=0.7
+                              )
+
+        # Rate calculation
+        self.calc_rates(self.day, self.drv)
+
+        if self.flag_terminate is True:
+            self._terminate_simulation(self.day)
+
+    def run(self, days=1, action=0):
+        """Advances the system state with given number of days"""
+
+        # do action at end of time step
+        days_counter = days
+        days_done = 0
+        while (days_done < days) and (self.flag_terminate is False):
+            days_done += 1
+            days_counter -= 1
+            if days_counter > 0:
+                self._run(0)
+            else:
+                self._run(action)
+
     @property
     def terminated(self):
         return self._flag_terminated
@@ -129,27 +287,34 @@ def __init__(self,
 
         # Set location
         if location is None:
-            location = (52, 5.5)
+            location = (52.0, 5.5)
         self._location = location
         self._timestep = timestep
 
         # Store the crop/soil/site parameters
         self._crop_params = crop_parameters
         self._site_params = site_parameters
+        self._site_params_ = site_parameters
         self._soil_params = soil_parameters
 
+        # Agent will have no access to weather
+        self.no_weather = kwargs.get('no_weather', False)
+
         # Store the agro-management config
         with open(agro_config, 'r') as f:
             self._agro_management = yaml.load(f, Loader=yaml.SafeLoader)
 
+        # Initialize Agromanagement Container Class
+        self.agmt = AgroManagementContainer(self._agro_management)
+
         if years is not None:
-            self._agro_management = replace_years(self._agro_management, years)
+            self._agro_management = self.agmt.replace_years(years)
 
         # Store the PCSE Engine config
         self._model_config = model_config
 
         # Get the weather data source
-        self._weather_data_provider = get_weather_data_provider(self._location)
+        self._weather_data_provider = get_weather_data_provider(self._location, kwargs.get('random_weather'))
 
         # Create a PCSE engine / crop growth model
         self._model = self._init_pcse_model()
@@ -165,7 +330,12 @@ def __init__(self,
         # Define Gym action space
         self.action_space = self._get_action_space()
 
-    def _init_pcse_model(self, *args, **kwargs) -> Engine:
+    def _init_pcse_model(self, options=None, *args, **kwargs) -> Engine:
+
+        # Inject different initial condition every episode if it specified in args
+        if options is not None:
+            self._site_params['NH4I'] = options['NH4I']
+            self._site_params['NO3I'] = options['NO3I']
 
         # Combine the config files in a single PCSE ParameterProvider object
         self._parameter_provider = pcse.base.ParameterProvider(cropdata=self._crop_params,
@@ -294,10 +464,10 @@ def step(self, action) -> tuple:
         # Apply action
         if isinstance(action, np.ndarray):
             action = action[0]
-        self._apply_action(action)
+        action = self._apply_action(action)  # is subclassed by sb3
 
         # Run the crop growth model
-        self._model.run(days=self._timestep)
+        self._model.run(days=self._timestep, action=action)
         # Get the model output
         output = self._model.get_output()[-self._timestep:]
         info['days'] = [day['day'] for day in output]
@@ -408,7 +578,7 @@ def reset(self,
         info = dict()
 
         # Create a PCSE engine / crop growth model
-        self._model = self._init_pcse_model()
+        self._model = self._init_pcse_model(options)
         output = self._model.get_output()[-self._timestep:]
         o = self._get_observation(output)
         info['date'] = self.date

pcse_gym/envs/configs/Wofost81_NWLP_FD.conf

@@ -24,7 +24,7 @@ OUTPUT_VARS = ["DVS","LAI", "TAGP", "TWSO", "TWLV", "TWST",
                "WRT", "TRA", "RD", "SM", "WWLOW", "RFTRA",
                 "NAVAIL", "Ndemand", "RNuptake", "NuptakeTotal",
                "NamountSO", "NamountLV", "NamountST", "NamountRT",
-               "NfixTotal", "NlossesTotal"]
+               "NfixTotal", "NlossesTotal", "IDWST"]
 # interval for OUTPUT signals, either "daily"|"dekadal"|"monthly"
 # For daily output you change the number of days between successive
 # outputs using OUTPUT_INTERVAL_DAYS. For dekadal and monthly