Merge pull request #42 from EcoExtreML/refactor_save_to_netcdf

Refactor save to netcdf: change config.model to config_file

PyStemmusScope/save.py

@@ -24,6 +24,7 @@
 import numpy as np
 import pandas as pd
 import xarray as xr
+from PyStemmusScope import config_io
 from PyStemmusScope import forcing_io
 from . import variable_conversion as vc
 
@@ -250,18 +251,21 @@ def _update_dataset_attrs_dims(dataset: xr.Dataset, forcing_dict: Dict) -> xr.Da
     return dataset
 
 
-def to_netcdf(config: Dict, cf_filename: str) -> str:
+def to_netcdf(config_file: str, cf_filename: str) -> str:
     """Save csv files generated by Stemmus_Scope model to a netcdf file using
         information provided by ALMA conventions.
 
     Args:
-        config(Dict): PyStemmusScope configuration dictionary.
+        config_file(str): Path to the config file.
         cf_filename(str): Path to a csv file for ALMA conventions.
 
     Returns:
         str: path to a csv file under the output directory.
     """
 
+    # read config file
+    config = config_io.read_config(config_file)
+
     # list of required forcing variables, Alma_short_name: forcing_io_name, # model_name
     var_names = {
         "RH": "rh", # RH
@@ -274,16 +278,13 @@ def to_netcdf(config: Dict, cf_filename: str) -> str:
         "Precip": "precip_conv", # Pre
     }
 
-    # Number of time steps from configuration file
-    time_steps = config["NumberOfTimeSteps"]
-
     # read forcing file into a dict
     forcing_dict = forcing_io.read_forcing_data(
         Path(config["ForcingPath"]) / config["ForcingFileName"]
     )
 
     # get time info
-    time = _shorten_data_array(forcing_dict["time"], time_steps)
+    time = _shorten_data_array(forcing_dict["time"], config["NumberOfTimeSteps"])
 
     # read convention file
     conventions = pd.read_csv(cf_filename)
@@ -297,7 +298,7 @@ def to_netcdf(config: Dict, cf_filename: str) -> str:
         if alma_name in var_names:
             # select data
             data_array = _select_forcing_variables(forcing_dict, var_names[alma_name], alma_name)
-            data_array = _shorten_data_array(data_array, time_steps)
+            data_array = _shorten_data_array(data_array, config["NumberOfTimeSteps"])
 
         # create data array
         elif alma_name in {"SoilTemp", "SoilMoist"}:

notebooks/run_model_in_notebook.ipynb

@@ -217,7 +217,7 @@
    "source": [
     "# save output in netcdf format\n",
     "required_netcdf_variables = \"./required_netcdf_variables.csv\"\n",
-    "nc_file_name = save.to_netcdf(model.config, required_netcdf_variables)\n",
+    "nc_file_name = save.to_netcdf(config_path, required_netcdf_variables)\n",
     "print(nc_file_name)"
    ]
   },
@@ -268,7 +268,7 @@
     "    print(result)\n",
     "    \n",
     "    # save results in a netcdf file\n",
-    "    nc_file_name = save.to_netcdf(model.config, required_netcdf_variables)\n",
+    "    nc_file_name = save.to_netcdf(config_path, required_netcdf_variables)\n",
     "    print(nc_file_name)\n",
     "    "
    ]

notebooks/run_model_in_notebook_dev.ipynb

@@ -235,7 +235,7 @@
    ],
    "source": [
     "required_netcdf_variables = path_to_model / \"utils\" / \"csv_to_nc\" / \"required_netcdf_variables.csv\"\n",
-    "nc_file_name = save.to_netcdf(model.config, required_netcdf_variables)\n",
+    "nc_file_name = save.to_netcdf(config_path, required_netcdf_variables)\n",
     "print(nc_file_name)"
    ]
   },

tests/test_save.py

@@ -45,16 +45,16 @@ def model_with_setup(self, tmp_path):
         with patch("time.strftime") as mocked_time:
             mocked_time.return_value = "2022-08-01-1200"
 
-            _ = model.setup(
+            config_path = model.setup(
                 WorkDir = str(tmp_path),
                 ForcingFileName = "dummy_forcing_file.nc",
                 NumberOfTimeSteps = "3", # less than forcing temporal range
                 )
-            return model
+            return model, config_path
 
     def test_save_to_netcdf(self, cf_convention, model_with_setup):
-        model = model_with_setup
-        saved_nc_file = save.to_netcdf(model.config, cf_convention)
+        model, config_path = model_with_setup
+        saved_nc_file = save.to_netcdf(config_path, cf_convention)
 
         expected_nc_file = (
             "tests/test_data/directories/output/dummy-2022-08-01-1200/dummy-2022-08-01-1200_STEMMUS_SCOPE.nc"
@@ -110,16 +110,16 @@ def model_with_setup(self, tmp_path):
         with patch("time.strftime") as mocked_time:
             mocked_time.return_value = "2022-08-01-1200"
 
-            _ = model.setup(
+            config_path = model.setup(
                 WorkDir = str(tmp_path),
                 ForcingFileName = "dummy_forcing_file.nc",
                 NumberOfTimeSteps = "NA", # use temporal range of forcing data
                 )
-            return model
+            return model, config_path
 
     @pytest.fixture(name="_make_csv_file")
     def fixture_make_csv_file(self, model_with_setup):
-        model = model_with_setup
+        model, _ = model_with_setup
         data = [
             "simulation_number,year,DoY,Netlong",
             ",,,W m-2",
@@ -134,8 +134,8 @@ def fixture_make_csv_file(self, model_with_setup):
         write_csv(data, csv_file)
 
     def test_save_to_netcdf(self, cf_convention, _make_csv_file, model_with_setup):
-        model = model_with_setup
-        saved_nc_file = save.to_netcdf(model.config, cf_convention)
+        model, config_path = model_with_setup
+        saved_nc_file = save.to_netcdf(config_path, cf_convention)
 
         expected_nc_file = (
             "tests/test_data/directories/output/dummy-2022-08-01-1200/dummy-2022-08-01-1200_STEMMUS_SCOPE.nc"
@@ -193,16 +193,16 @@ def model_with_setup(self, tmp_path):
         with patch("time.strftime") as mocked_time:
             mocked_time.return_value = "2022-08-01-1200"
 
-            _ = model.setup(
+            config_path = model.setup(
                 WorkDir = str(tmp_path),
                 ForcingFileName = "dummy_forcing_file.nc",
                 NumberOfTimeSteps = "5",
                 )
-            return model
+            return model, config_path
 
     @pytest.fixture(name="_make_csv_file")
     def fixture_make_csv_file(self, model_with_setup):
-        model = model_with_setup
+        model, _ = model_with_setup
         data = [
             "1,2,3,5",
             "1,1,1,2",
@@ -218,8 +218,8 @@ def fixture_make_csv_file(self, model_with_setup):
         write_csv(data, csv_file)
 
     def test_save_to_netcdf(self, cf_convention, _make_csv_file, model_with_setup):
-        model = model_with_setup
-        saved_nc_file = save.to_netcdf(model.config, cf_convention)
+        model, config_path = model_with_setup
+        saved_nc_file = save.to_netcdf(config_path, cf_convention)
 
         expected_nc_file = (
             "tests/test_data/directories/output/dummy-2022-08-01-1200/dummy-2022-08-01-1200_STEMMUS_SCOPE.nc"
@@ -282,16 +282,16 @@ def model_with_setup(self, tmp_path):
         with patch("time.strftime") as mocked_time:
             mocked_time.return_value = "2022-08-01-1200"
 
-            _ = model.setup(
+            config_path = model.setup(
                 WorkDir = str(tmp_path),
                 ForcingFileName = "dummy_forcing_file.nc",
                 NumberOfTimeSteps = "NA",
                 )
-            return model
+            return model, config_path
 
     @pytest.fixture(name="_make_csv_file")
     def fixture_make_csv_file(self, model_with_setup):
-        model = model_with_setup
+        model, _ = model_with_setup
         data = [
             "1,2,3,5",
             "1,1,1,2",
@@ -318,8 +318,8 @@ def fixture_make_csv_file(self, model_with_setup):
         write_csv(data, csv_file)
 
     def test_save_to_netcdf(self, cf_convention, _make_csv_file, model_with_setup):
-        model = model_with_setup
-        saved_nc_file = save.to_netcdf(model.config, cf_convention)
+        model, config_path = model_with_setup
+        saved_nc_file = save.to_netcdf(config_path, cf_convention)
 
         expected_nc_file = (
             "tests/test_data/directories/output/dummy-2022-08-01-1200/dummy-2022-08-01-1200_STEMMUS_SCOPE.nc"