diff --git a/.vscode/settings.json b/.vscode/settings.json
index 0cfcb653850ceb990c5a2ca4b158a9ee52d93b27..b323bd22ab5f1a9fd19dbefd7ede743a850c669d 100644
--- a/.vscode/settings.json
+++ b/.vscode/settings.json
@@ -1,13 +1,10 @@
{
- "python.testing.unittestArgs": [
+ "python.testing.pytestArgs": [
+ "tests/",
"-v",
- "-s",
- "tests",
- "-t",
- "src/vipscore_common",
- "-p",
- "test_*.py"
+ "-k",
+ "test_"
],
- "python.testing.pytestEnabled": false,
- "python.testing.unittestEnabled": true
+ "python.testing.pytestEnabled": true,
+ "python.testing.unittestEnabled": false
}
\ No newline at end of file
diff --git a/LICENSE b/LICENSE
new file mode 100644
index 0000000000000000000000000000000000000000..ad9df02c558eb3280ec8f2638771627970dc3c42
--- /dev/null
+++ b/LICENSE
@@ -0,0 +1,15 @@
+Copyright (c) 2023 NIBIO <http://www.nibio.no/>.
+
+This file is part of VIPSCore-Python-Common.
+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/>.
\ No newline at end of file
diff --git a/pyproject.toml b/pyproject.toml
index 374b58cbf4636f1e28bacf987ac2fe89ed27ccba..6fe23d7c296072e8de5e266a6d07f71860039281 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,5 @@
[build-system]
requires = [
- "setuptools>=42",
- "wheel"
+ "setuptools>=61.0"
]
build-backend = "setuptools.build_meta"
diff --git a/setup.cfg b/setup.cfg
index 91debbde832c40d69b9aa716b3756f306134e501..fdadd5ae110113e667e059447e93b31fd1286d61 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -1,5 +1,5 @@
[metadata]
-name = vipscore-python-common
+name = vipscore_python_common
version = 0.5.0
author = Tor-Einar Skog
author_email = tor-einar.skog@nibio.no
@@ -21,6 +21,7 @@ install_requires =
shapely
pydantic
pytz
+ pandas
[options.packages.find]
where = src
\ No newline at end of file
diff --git a/src/vipscore_common/__init__.py b/src/vipscore_common/__init__.py
index 44e6f454d49ae6d69188abea9994c130cb15629b..8b137891791fe96927ad78e64b0aad7bded08bdc 100755
--- a/src/vipscore_common/__init__.py
+++ b/src/vipscore_common/__init__.py
@@ -1,2 +1 @@
-from .entities import *
-from .vips_model import *
\ No newline at end of file
+
diff --git a/src/vipscore_common/data_utils.py b/src/vipscore_common/data_utils.py
index 6d1abdd4c3b38b43afeb33aaf5afc292926aae96..4bc6acd04183f757a0ca050c8c7a70da0b58b652 100644
--- a/src/vipscore_common/data_utils.py
+++ b/src/vipscore_common/data_utils.py
@@ -26,7 +26,7 @@ import numpy as np
import pandas as pd
from pandas import DataFrame
import json
-from entities import *
+from .entities import *
def get_dataframe_from_weather_observations(weather_observations: list, timezone:datetime.tzinfo) -> DataFrame:
"""
diff --git a/src/vipscore_common/reference_model.py b/src/vipscore_common/reference_model.py
index 717882182d0cd03e24411eff51d93fcee18fa2a7..1fd3bf60229e076bafba12adacc4fb894a598382 100755
--- a/src/vipscore_common/reference_model.py
+++ b/src/vipscore_common/reference_model.py
@@ -18,9 +18,9 @@ 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 vips_model import VIPSModel
-from entities import Result, ModelConfiguration, WeatherObservation
-import data_utils
+from .vips_model import VIPSModel
+from .entities import Result, ModelConfiguration, WeatherObservation
+from .data_utils import *
import numpy as np
class ReferenceModel(VIPSModel):
@@ -46,8 +46,8 @@ class ReferenceModel(VIPSModel):
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 = data_utils.get_dataframe_from_weather_observations(
- data_utils.get_weather_observations_from_json_list(
+ self.df = get_dataframe_from_weather_observations(
+ get_weather_observations_from_json_list(
model_configuration.config_parameters["observations"]
),
self.timezone
@@ -74,7 +74,7 @@ class ReferenceModel(VIPSModel):
# Calculate day degrees from sowingDate and as far as weather data goes
# Adjusting for base temperature
- self.df["TMContrib"] = self.df["TM"].apply(data_utils.get_temp_adjusted_for_base, args=(5,))
+ 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
@@ -84,7 +84,7 @@ class ReferenceModel(VIPSModel):
# 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 = data_utils.get_result_list_from_dataframe(self.df)
+ result = get_result_list_from_dataframe(self.df)
#print(result)
return result
diff --git a/src/vipscore_common/vips_model.py b/src/vipscore_common/vips_model.py
index 175b032de008e14cf16c21f880eb33fdca38e2f0..38e02f9236174e364597ae83aa40ae0c973b3f92 100755
--- a/src/vipscore_common/vips_model.py
+++ b/src/vipscore_common/vips_model.py
@@ -22,7 +22,7 @@ along with VIPSCore-Python-Common. If not, see <http://www.nibio.no/licenses/>.
# @author Tor-Einar Skog <tor-einar.skog@nibio.no>
from abc import ABC, abstractmethod, abstractproperty
-from entities import Result, ModelConfiguration
+from .entities import Result, ModelConfiguration
class VIPSModel(ABC):
diff --git a/src/vipscore_common/tests/__init__.py b/tests/__init__.py
similarity index 100%
rename from src/vipscore_common/tests/__init__.py
rename to tests/__init__.py
diff --git a/src/vipscore_common/tests/test_data_utils.py b/tests/test_data_utils.py
similarity index 81%
rename from src/vipscore_common/tests/test_data_utils.py
rename to tests/test_data_utils.py
index 09dab010aa0f266db0bf92d6cd21a780a5319577..5b0b255c91e0ce509cac9fec011b0b25c7291307 100644
--- a/src/vipscore_common/tests/test_data_utils.py
+++ b/tests/test_data_utils.py
@@ -1,9 +1,8 @@
import unittest
-import data_utils
-from reference_model import *
-from entities import *
+from src.vipscore_common import data_utils
+from src.vipscore_common.entities import *
import pytz
class TestDataUtils(unittest.TestCase):
@@ -11,7 +10,7 @@ class TestDataUtils(unittest.TestCase):
"""
The method can convert a json dict to a list of WeatherObservation objects
"""
- with open ("src/vipscore_common/tests/weather_data_2015_NO_aas_TMD.json") as f:
+ with open ("tests/weather_data_2015_NO_aas_TMD.json") as f:
result = data_utils.get_weather_observations_from_json(f.read())
# Length should be > 0
self.assertGreater(len(result), 0)
@@ -23,7 +22,7 @@ class TestDataUtils(unittest.TestCase):
"""
Lorem Ipsum osv
"""
- with open ("src/vipscore_common/tests/weather_data_2015_NO_aas_TMD.json") as f:
+ with open ("tests/weather_data_2015_NO_aas_TMD.json") as f:
weather_observations = data_utils.get_weather_observations_from_json(f.read())
result = data_utils.get_dataframe_from_weather_observations(weather_observations, pytz.timezone("Europe/Oslo"))
self.assertIsNotNone(result)
diff --git a/src/vipscore_common/tests/test_reference_model.py b/tests/test_reference_model.py
similarity index 94%
rename from src/vipscore_common/tests/test_reference_model.py
rename to tests/test_reference_model.py
index 743855eaa2b6f40a9992d1c3bc4c4b79c85d2342..5d6ba9061c99f27ee57167c63a8687aa0f10fd0a 100644
--- a/src/vipscore_common/tests/test_reference_model.py
+++ b/tests/test_reference_model.py
@@ -2,11 +2,11 @@ import unittest
import json
-from reference_model import *
-from entities import *
+from src.vipscore_common.reference_model import *
+from src.vipscore_common.entities import *
def get_model_configuration():
- with open ("src/vipscore_common/tests/weather_data_2015_NO_aas_TMD.json") as f:
+ with open ("tests/weather_data_2015_NO_aas_TMD.json") as f:
weather_observations = json.load(f)
return ModelConfiguration(
model_id=ReferenceModel.MODEL_ID,
diff --git a/src/vipscore_common/tests/weather_data_2015_NO_aas_TMD.json b/tests/weather_data_2015_NO_aas_TMD.json
similarity index 100%
rename from src/vipscore_common/tests/weather_data_2015_NO_aas_TMD.json
rename to tests/weather_data_2015_NO_aas_TMD.json