First commit

.gitignore

+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
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+
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+.coverage.*
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+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
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+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/#use-with-ide
+.pdm.toml
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
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+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
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+# Spyder project settings
+.spyderproject
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+# Rope project settings
+.ropeproject
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+# mkdocs documentation
+/site
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+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
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+# pytype static type analyzer
+.pytype/
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+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/
+

.vscode/settings.json

+{
+    "python.testing.pytestArgs": [
+        "tests",
+        "-v"
+    ],
+    "python.testing.unittestEnabled": false,
+    "python.testing.pytestEnabled": true
+}
\ No newline at end of file

LICENSE

+Copyright (c) 2023 NIBIO <http://www.nibio.no/>. 
+
+This file is part of ReferenceModel.
+ReferenceModel is free software: you can redistribute it and/or modify
+it under the terms of the NIBIO Open Source License as published by 
+NIBIO, either version 1 of the License, or (at your option) any
+later version.
+ 
+ReferenceModel is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+NIBIO Open Source License for more details.
+
+You should have received a copy of the NIBIO Open Source License
+along with ReferenceModel.  If not, see <http://www.nibio.no/licenses/>.
\ No newline at end of file

README.md

+# ReferenceModel
\ No newline at end of file

pyproject.toml

+[build-system]
+requires = [
+    "setuptools>=61.0"
+]
+build-backend = "setuptools.build_meta"

setup.cfg

+[metadata]
+name = reference_model
+version = 0.5.0
+author = Tor-Einar Skog
+author_email = tor-einar.skog@nibio.no
+description = Example VIPS model, showcasing functionality
+long_description = file: README.md
+long_description_content_type = text/markdown
+url = https://www.vips-landbruk.no
+classifiers =
+    Programming Language :: Python :: 3
+    License :: NIBIO Open Source License
+    Operating System :: OS Independent
+
+[options]
+package_dir =
+    = src
+packages = find:
+python_requires = >=3.7
+install_requires = 
+    shapely
+    pydantic
+    pytz
+    pandas
+
+[options.packages.find]
+where = src
\ No newline at end of file

src/reference_model/reference_model.py

+#!/usr/bin/python3
+
+LICENSE = """
+Copyright (c) 2023 NIBIO <http://www.nibio.no/>. 
+
+This file is part of ReferenceModel.
+VIPSCore-Python-Common is free software: you can redistribute it and/or modify
+it under the terms of the NIBIO Open Source License as published by 
+NIBIO, either version 1 of the License, or (at your option) any
+later version.
+ 
+VIPSCore-Python-Common is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+NIBIO Open Source License for more details.
+
+You should have received a copy of the NIBIO Open Source License
+along with VIPSCore-Python-Common.  If not, see <http://www.nibio.no/licenses/>.
+"""
+
+from vipscore_common.vips_model import VIPSModel
+from vipscore_common.entities import Result, ModelConfiguration, WeatherObservation
+from vipscore_common.data_utils import *
+import numpy as np
+
+class ReferenceModel(VIPSModel):
+    """
+        A reference implementation of the VIPSModel abstract class. Showcasing core functionality
+        and best practices
+    """
+
+    MODEL_ID        = "REFERENCEM"
+    COPYRIGHT       = "(c) 2023 NIBIO"
+
+    THRESHOLD_LOW = 100.0
+    THRESHOLD_MEDIUM = 300.0
+    THRESHOLD_HIGH = 500.0
+ 
+    def set_configuration(self, model_configuration: ModelConfiguration):
+        if not isinstance(model_configuration, ModelConfiguration):
+            raise ValueError("%s is not a ModelConfiguration object" % model_configuration)
+        if model_configuration.model_id != ReferenceModel.MODEL_ID:
+            raise ValueError("%s is not the correct model ID!" % model_configuration.model_id)
+        
+        # Input data check
+        self.sowing_date = model_configuration.get_config_parameter_as_date("sowingDate")
+        self.timezone = model_configuration.get_config_parameter_as_timezone("timeZone")
+        # Weather data is turned into Pandas dataframe
+        self.df = get_dataframe_from_weather_observations(
+                get_weather_observations_from_json_list(
+                    model_configuration.config_parameters["observations"]
+                    ),
+                self.timezone
+            )
+
+    
+
+    def determine_warning_status(self, TMDD: float) -> int:
+        """
+        Used in get_result as a dataframe operation. Determines the warning status
+        based on the model thresholds
+        """
+        if TMDD < ReferenceModel.THRESHOLD_MEDIUM:
+            return  Result.WARNING_STATUS_NO_WARNING
+        if TMDD < ReferenceModel.THRESHOLD_HIGH:
+            return Result.WARNING_STATUS_MINOR_RISK
+        else:
+            return Result.WARNING_STATUS_HIGH_RISK
+
+        
+    
+    def get_result(self) -> list[Result]:
+        """Get the results as a list of Result objects (TODO ref)"""
+        
+        # Calculate day degrees from sowingDate and as far as weather data goes
+        # Adjusting for base temperature
+        self.df["TMContrib"] = self.df["TM"].apply(get_temp_adjusted_for_base, args=(5,))
+        # Aggregating the day degrees
+        self.df["TMDD"] = self.df["TMContrib"].cumsum()
+        # Adding the thresholds to the data frame
+        self.df["THRESHOLD_LOW"] = ReferenceModel.THRESHOLD_LOW
+        self.df["THRESHOLD_MEDIUM"] = ReferenceModel.THRESHOLD_MEDIUM
+        self.df["THRESHOLD_HIGH"] = ReferenceModel.THRESHOLD_HIGH
+        # For each day: check accumulated day-degrees and decide warning status
+        self.df["WARNING_STATUS"] = self.df["TMDD"].apply(self.determine_warning_status)
+        #print(self.df)
+        result = get_result_list_from_dataframe(self.df)
+        #print(result)
+        return result
+        
+
+    @property
+    def model_id(self) -> str:
+        """10-character ID of the model. Must be unique (at least in the current system)"""
+        return ReferenceModel.MODEL_ID
+
+    
+    @property
+    def license(self) -> str:
+        """Returns the license for this piece of software"""
+        return LICENSE
+
+    @property
+    def copyright(self) -> str:
+        """Name of person/organization that holds the copyright, and contact information"""
+        return ReferenceModel.COPYRIGHT
+    
+    @property
+    def sample_config(self) -> dict:
+        """A sample configuration in JSON format (TODO check relation with Dict)"""
+        return """
+        {
+	model_id:'REFERENCEM',
+	config_parameters: {
+		'sowingDate': '2022-03-01', 
+		'observations': [
+			{'timeMeasured': '2015-03-01T00:00:00+01:00', 'elementMeasurementTypeId': 'TM', 'logIntervalId': '2', 'value': '1.41025'}, 
+			{'timeMeasured': '2015-03-02T00:00:00+01:00', 'elementMeasurementTypeId': 'TM', 'logIntervalId': '2', 'value': '2.87608333333333'}, 
+			{'timeMeasured': '2015-03-03T00:00:00+01:00', 'elementMeasurementTypeId': 'TM', 'logIntervalId': '2', 'value': '1.00854166666667'}, 
+			{'timeMeasured': '2015-03-04T00:00:00+01:00', 'elementMeasurementTypeId': 'TM', 'logIntervalId': '2', 'value': '-1.44675'}
+		]
+	}
+}
+        """
+
+    def get_model_name(self, language = VIPSModel.default_language) -> str:
+        """Returns the model name in the specified language (<a href="http://www.loc.gov/standards/iso639-2/php/English_list.php">ISO-639-2</a>)"""
+        return "Reference Model"     
+
+    def get_model_description(self, language = VIPSModel.default_language) -> str:
+        """Returns the model description in the specified language (<a href="http://www.loc.gov/standards/iso639-2/php/English_list.php">ISO-639-2</a>)"""
+        return """
+        The model is a reference model for developers, showcasing best practices and functionalities of a model.
+        It's a simple day degree model for an imagined pest, and when thresholds are passed, the warning status progresses.
+        """
+
+    def get_warning_status_interpretation(self, language = VIPSModel.default_language) -> str:
+        """How to interpret the warning status (red-yellow-green, what does it mean?) in the specified language (<a href="http://www.loc.gov/standards/iso639-2/php/English_list.php">ISO-639-2</a>)"""
+        return """
+        Gray   status (warning status == 0): Warning not applicable
+        Blue   status (warning status == 1): Missing data
+        Green  status (warning status == 2): No risk. Sleep well
+        Yellow status (warning status == 3): The day-degree hreshold for medium risk has been passed. Be on the alert, inspect your field
+        Red status    (warning status == 4): The day-degree threshold for high risk has been passed. When the going gets tough, the tough get going
+        """
+
+    def get_model_usage(self, language = VIPSModel.default_language) -> str:
+        """Technical manual for this model, in the specified language  (<a href="http://www.loc.gov/standards/iso639-2/php/English_list.php">ISO-639-2</a>)"""
+        return "TODO"
+
+    
\ No newline at end of file

tests/test_reference_model.py

+import unittest
+
+import json
+
+from src.reference_model.reference_model import *
+from vipscore_common.entities import *
+
+def get_model_configuration():
+    with open ("tests/weather_data_2015_NO_aas_TMD.json") as f:
+        weather_observations = json.load(f)
+        return ModelConfiguration(
+            model_id=ReferenceModel.MODEL_ID,
+            config_parameters={
+                "sowingDate": "2022-03-01",
+                "timeZone" : "Europe/Oslo",
+                "observations": weather_observations
+            }
+        )
+
+class TestReferenceModel(unittest.TestCase):
+    def test_set_configuration(self):
+        """
+        Passing a configuration object does not fail
+        """
+        #print(get_model_configuration())
+        instance = ReferenceModel()
+        instance.set_configuration(get_model_configuration())
+
+    def test_get_result(self):
+        """
+        We get a series of results from the calculation,
+        and the TMDD is as expected
+        """
+        instance = ReferenceModel()
+        instance.set_configuration(get_model_configuration())
+        result_list = instance.get_result()
+        self.assertIsNotNone(result_list)
+        last_result = result_list[len(result_list)-1]
+        self.assertEqual(555.8507083333333, last_result.all_values["TMDD"])
+
+    def test_get_model_id(self):
+         """
+         The model returns the correct ID
+         """
+         instance = ReferenceModel()
+         self.assertEqual(instance.model_id, ReferenceModel.MODEL_ID)
+        
+    def test_get_license(self):
+        """
+        The model returns its license
+        """
+        instance = ReferenceModel()
+        self.assertIsNotNone(instance.license)
+
+    def test_get_copyright(self):
+        """
+        The model returns its copyright notice
+        """
+        instance = ReferenceModel()
+        self.assertEqual(instance.copyright, ReferenceModel.COPYRIGHT)
+    
+    def test_get_sample_config(self):
+        """
+        The model returns its sample configuration
+        """
+        instance = ReferenceModel()
+        self.assertIsNotNone(instance.sample_config)
+    
+    def test_get_model_name(self):
+        """
+        The model returns its name in the default language
+        """
+        instance = ReferenceModel()
+        self.assertEqual(instance.get_model_name(), "Reference Model")
+    
+    def test_get_model_description(self):
+        """
+        The model returns a description
+        """
+        instance = ReferenceModel()
+        self.assertIsNotNone(instance.get_model_description())
+    
+    def test_get_warning_status_interpretation(self):
+        """
+        The model returns a warning status interpretation
+        """
+        instance = ReferenceModel()
+        self.assertIsNotNone(instance.get_warning_status_interpretation())
+
+    def test_get_model_usage(self):
+        """
+        The model returns a description of usage
+        """
+
+if __name__ == '__main__':
+    unittest.main()
\ No newline at end of file

tests/weather_data_2015_NO_aas_TMD.json

+[{"timeMeasured": "2015-03-01T00:00:00+01:00","elementMeasurementTypeId":"TM", "logIntervalId":"2", "value":"1.41025"},
+{"timeMeasured": "2015-03-02T00:00:00+01:00","elementMeasurementTypeId":"TM", "logIntervalId":"2", "value":"2.87608333333333"},
+{"timeMeasured": "2015-03-03T00:00:00+01:00","elementMeasurementTypeId":"TM", "logIntervalId":"2", "value":"1.00854166666667"},
+{"timeMeasured": "2015-03-04T00:00:00+01:00","elementMeasurementTypeId":"TM", "logIntervalId":"2", "value":"-1.44675"},
+{"timeMeasured": "2015-03-05T00:00:00+01:00","elementMeasurementTypeId":"TM", "logIntervalId":"2", "value":"0.506208333333333"},
+{"timeMeasured": "2015-03-06T00:00:00+01:00","elementMeasurementTypeId":"TM", "logIntervalId":"2", "value":"5.055"},
+{"timeMeasured": "2015-03-07T00:00:00+01:00","elementMeasurementTypeId":"TM", "logIntervalId":"2", "value":"5.29470833333333"},
+{"timeMeasured": "2015-03-08T00:00:00+01:00","elementMeasurementTypeId":"TM", "logIntervalId":"2", "value":"5.78691666666667"},
+{"timeMeasured": "2015-03-09T00:00:00+01:00","elementMeasurementTypeId":"TM", "logIntervalId":"2", "value":"3.44725"},
+{"timeMeasured": "2015-03-10T00:00:00+01:00","elementMeasurementTypeId":"TM", "logIntervalId":"2", "value":"6.848625"},
+{"timeMeasured": "2015-03-11T00:00:00+01:00","elementMeasurementTypeId":"TM", "logIntervalId":"2", "value":"5.59816666666667"},
+{"timeMeasured": "2015-03-12T00:00:00+01:00","elementMeasurementTypeId":"TM", "logIntervalId":"2", "value":"2.78283333333333"},
+{"timeMeasured": "2015-03-13T00:00:00+01:00","elementMeasurementTypeId":"TM", "logIntervalId":"2", "value":"0.640458333333333"},
+{"timeMeasured": "2015-03-14T00:00:00+01:00","elementMeasurementTypeId":"TM", "logIntervalId":"2", "value":"1.04645833333333"},
+{"timeMeasured": "2015-03-15T00:00:00+01:00","elementMeasurementTypeId":"TM", "logIntervalId":"2", "value":"2.46125"},
+{"timeMeasured": "2015-03-16T00:00:00+01:00","elementMeasurementTypeId":"TM", "logIntervalId":"2", "value":"3.87916666666667"},
+{"timeMeasured": "2015-03-17T00:00:00+01:00","elementMeasurementTypeId":"TM", "logIntervalId":"2", "value":"3.67829166666667"},
+{"timeMeasured": "2015-03-18T00:00:00+01:00","elementMeasurementTypeId":"TM", "logIntervalId":"2", "value":"3.16966666666667"},
+{"timeMeasured": "2015-03-19T00:00:00+01:00","elementMeasurementTypeId":"TM", "logIntervalId":"2", "value":"2.41620833333333"},
+{"timeMeasured": "2015-03-20T00:00:00+01:00","elementMeasurementTypeId":"TM", "logIntervalId":"2", "value":"3.30125"},
+{"timeMeasured": "2015-03-21T00:00:00+01:00","elementMeasurementTypeId":"TM", "logIntervalId":"2", "value":"-0.05"},
+{"timeMeasured": "2015-03-22T00:00:00+01:00","elementMeasurementTypeId":"TM", "logIntervalId":"2", "value":"0.198625"},
+{"timeMeasured": "2015-03-23T00:00:00+01:00","elementMeasurementTypeId":"TM", "logIntervalId":"2", "value":"4.522"},
+{"timeMeasured": "2015-03-24T00:00:00+01:00","elementMeasurementTypeId":"TM", "logIntervalId":"2", "value":"5.11220833333333"},
+{"timeMeasured": "2015-03-25T00:00:00+01:00","elementMeasurementTypeId":"TM", "logIntervalId":"2", "value":"1.92391666666667"},
+{"timeMeasured": "2015-03-26T00:00:00+01:00","elementMeasurementTypeId":"TM", "logIntervalId":"2", "value":"-0.728625"},
+{"timeMeasured": "2015-03-27T00:00:00+01:00","elementMeasurementTypeId":"TM", "logIntervalId":"2", "value":"1.34791666666667"},
+{"timeMeasured": "2015-03-28T00:00:00+01:00","elementMeasurementTypeId":"TM", "logIntervalId":"2", "value":"1.19704166666667"},
+{"timeMeasured": "2015-03-29T00:00:00+01:00","elementMeasurementTypeId":"TM", "logIntervalId":"2", "value":"3.0285"},
+{"timeMeasured": "2015-03-30T00:00:00+02:00","elementMeasurementTypeId":"TM", "logIntervalId":"2", "value":"2.43166666666667"},
+{"timeMeasured": "2015-03-31T00:00:00+02:00","elementMeasurementTypeId":"TM", "logIntervalId":"2", "value":"1.33133333333333"},
+{"timeMeasured": "2015-04-01T00:00:00+02:00","elementMeasurementTypeId":"TM", "logIntervalId":"2", "value":"2.65516666666667"},
+{"timeMeasured": "2015-04-02T00:00:00+02:00","elementMeasurementTypeId":"TM", "logIntervalId":"2", "value":"4.430875"},
+{"timeMeasured": "2015-04-03T00:00:00+02:00","elementMeasurementTypeId":"TM", "logIntervalId":"2", "value":"3.55983333333333"},
+{"timeMeasured": "2015-04-04T00:00:00+02:00","elementMeasurementTypeId":"TM", "logIntervalId":"2", "value":"2.77170833333333"},
+{"timeMeasured": "2015-04-05T00:00:00+02:00","elementMeasurementTypeId":"TM", "logIntervalId":"2", "value":"1.38383333333333"},
+{"timeMeasured": "2015-04-06T00:00:00+02:00","elementMeasurementTypeId":"TM", "logIntervalId":"2", "value":"3.98670833333333"},
+{"timeMeasured": "2015-04-07T00:00:00+02:00","elementMeasurementTypeId":"TM", "logIntervalId":"2", "value":"9.01775"},
+{"timeMeasured": "2015-04-08T00:00:00+02:00","elementMeasurementTypeId":"TM", "logIntervalId":"2", "value":"8.91166666666667"},
+{"timeMeasured": "2015-04-09T00:00:00+02:00","elementMeasurementTypeId":"TM", "logIntervalId":"2", "value":"7.22270833333333"},
+{"timeMeasured": "2015-04-10T00:00:00+02:00","elementMeasurementTypeId":"TM", "logIntervalId":"2", "value":"6.97625"},
+{"timeMeasured": "2015-04-11T00:00:00+02:00","elementMeasurementTypeId":"TM", "logIntervalId":"2", "value":"5.57629166666667"},
+{"timeMeasured": "2015-04-12T00:00:00+02:00","elementMeasurementTypeId":"TM", "logIntervalId":"2", "value":"7.04654166666667"},
+{"timeMeasured": "2015-04-13T00:00:00+02:00","elementMeasurementTypeId":"TM", "logIntervalId":"2", "value":"4.99058333333333"},
+{"timeMeasured": "2015-04-14T00:00:00+02:00","elementMeasurementTypeId":"TM", "logIntervalId":"2", "value":"2.80320833333333"},
+{"timeMeasured": "2015-04-15T00:00:00+02:00","elementMeasurementTypeId":"TM", "logIntervalId":"2", "value":"4.93241666666667"},
+{"timeMeasured": "2015-04-16T00:00:00+02:00","elementMeasurementTypeId":"TM", "logIntervalId":"2", "value":"5.9735"},
+{"timeMeasured": "2015-04-17T00:00:00+02:00","elementMeasurementTypeId":"TM", "logIntervalId":"2", "value":"7.18533333333333"},
+{"timeMeasured": "2015-04-18T00:00:00+02:00","elementMeasurementTypeId":"TM", "logIntervalId":"2", "value":"6.27766666666667"},
+{"timeMeasured": "2015-04-19T00:00:00+02:00","elementMeasurementTypeId":"TM", "logIntervalId":"2", "value":"9.67808333333333"},
+{"timeMeasured": "2015-04-20T00:00:00+02:00","elementMeasurementTypeId":"TM", "logIntervalId":"2", "value":"12.619375"},
+{"timeMeasured": "2015-04-21T00:00:00+02:00","elementMeasurementTypeId":"TM", "logIntervalId":"2", "value":"9.36679166666667"},
+{"timeMeasured": "2015-04-22T00:00:00+02:00","elementMeasurementTypeId":"TM", "logIntervalId":"2", "value":"10.2030416666667"},
+{"timeMeasured": "2015-04-23T00:00:00+02:00","elementMeasurementTypeId":"TM", "logIntervalId":"2", "value":"10.283375"},
+{"timeMeasured": "2015-04-24T00:00:00+02:00","elementMeasurementTypeId":"TM", "logIntervalId":"2", "value":"6.46583333333333"},
+{"timeMeasured": "2015-04-25T00:00:00+02:00","elementMeasurementTypeId":"TM", "logIntervalId":"2", "value":"6.93266666666667"},
+{"timeMeasured": "2015-04-26T00:00:00+02:00","elementMeasurementTypeId":"TM", "logIntervalId":"2", "value":"5.83495833333333"},
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