still trying to fix windows error

docs/quick_start.md

@@ -15,7 +15,7 @@ kernelspec:
 
 +++
 
-The simplest way to run `particle-tracking-manager` is to choose a built-in ocean model and select a location to initialize drifters, then use the built-in defaults for everything else (including start time which defaults to the first time step in the model output). You can do this interacting with the software as a Python library or using a command line interface. 
+The simplest way to run `particle-tracking-manager` is to choose a built-in ocean model and select a location to initialize drifters, then use the built-in defaults for everything else (including start time which defaults to the first time step in the model output). You can do this interacting with the software as a Python library or using a command line interface.
 
 Alternatively, you can run the package with new model output by inputting the necessary information into the `Manager`.
 

particle_tracking_manager/models/opendrift/model_opendrift.py

@@ -35,7 +35,7 @@
     if "default" in config_model[key] and is_None(config_model[key]["default"]):
         config_model[key]["default"] = None
 
-        
+
 # logger = logging.getLogger("opendrift")
 
 

particle_tracking_manager/models/opendrift/reader_ROMS_native.py

@@ -43,8 +43,6 @@ def __init__(
         kwargs_xarray=None,
     ):
         """Initialize ROMS model reader."""
-
-        import pdb; pdb.set_trace()
 
         if filename is None:
             raise ValueError("Need filename as argument to constructor")

particle_tracking_manager/the_manager.py

@@ -151,7 +151,7 @@ def __init__(
         sig = signature(ParticleTrackingManager)
 
         self.config_ptm = config_ptm
-        
+
         self.logger = logging.getLogger(model)
 
         # Set all attributes which will trigger some checks and changes in __setattr__
@@ -202,14 +202,22 @@ def __setattr__(self, name: str, value) -> None:
 
         # check start_time relative to ocean_model selection
         if name in ["ocean_model", "start_time"]:
-            if hasattr(self, "start_time") and self.start_time is not None and \
-               hasattr(self, "ocean_model") and self.ocean_model is not None:
+            if (
+                hasattr(self, "start_time")
+                and self.start_time is not None
+                and hasattr(self, "ocean_model")
+                and self.ocean_model is not None
+            ):
                 if value == "NWGOA":
                     assert overall_start_time <= value <= nwgoa_end_time
                 elif value == "CIOFS":
                     assert overall_start_time <= value <= ciofs_end_time
                 elif value == "CIOFS_NOW":
-                    assert ciofs_operational_start_time <= value <= ciofs_operational_end_time
+                    assert (
+                        ciofs_operational_start_time
+                        <= value
+                        <= ciofs_operational_end_time
+                    )
 
         # deal with if input longitudes need to be shifted due to model
         if name == "oceanmodel_lon0_360" and value:

tests/test_cli.py

@@ -2,8 +2,9 @@
 
 import os
 
+from datetime import datetime
+
 import pytest
-from datetime import datetime 
 
 import particle_tracking_manager as ptm
 
@@ -14,13 +15,19 @@ def test_setup():
     No drifters are run due to oceanmodel=None
     """
     ret_value = os.system(
-        f"python {ptm.__path__[0]}/cli.py ocean_model='test' lon=-151 lat=59 use_auto_landmask=True start_time='2000-1-1'"
+        f"python {ptm.__path__[0]}/cli.py ocean_model=test lon=-151 lat=59 use_auto_landmask=True start_time='2000-1-1'"
     )
     assert ret_value == 0
 
 
 def test_setup_library():
     """Same test but with library"""
-
-    m = ptm.OpenDriftModel(ocean_model='test', lon=-151, lat=59, use_auto_landmask=True, start_time=datetime(2000,1,1))
-    m.run_all()
+
+    m = ptm.OpenDriftModel(
+        ocean_model="test",
+        lon=-151,
+        lat=59,
+        use_auto_landmask=True,
+        start_time=datetime(2000, 1, 1),
+    )
+    m.run_all()

tests/test_opendrift_init.py

@@ -1,7 +1,12 @@
 """From Copilot"""
 
 import unittest
-from particle_tracking_manager.models.opendrift.model_opendrift import OpenDriftModel, config_model
+
+from particle_tracking_manager.models.opendrift.model_opendrift import (
+    OpenDriftModel,
+    config_model,
+)
+
 
 class TestOpenDriftModel(unittest.TestCase):
     def setUp(self):
@@ -12,35 +17,79 @@ def test_init(self):
         self.assertEqual(self.odm.radius, config_model["radius"]["default"])
         self.assertEqual(self.odm.radius_type, config_model["radius_type"]["default"])
         # self.assertEqual(self.odm.horizontal_diffusivity, config_model["horizontal_diffusivity"]["default"])
-        self.assertEqual(self.odm.use_auto_landmask, config_model["use_auto_landmask"]["default"])
-        self.assertEqual(self.odm.diffusivitymodel, config_model["diffusivitymodel"]["default"])
+        self.assertEqual(
+            self.odm.use_auto_landmask, config_model["use_auto_landmask"]["default"]
+        )
+        self.assertEqual(
+            self.odm.diffusivitymodel, config_model["diffusivitymodel"]["default"]
+        )
         self.assertEqual(self.odm.stokes_drift, config_model["stokes_drift"]["default"])
-        self.assertEqual(self.odm.mixed_layer_depth, config_model["mixed_layer_depth"]["default"])
-        self.assertEqual(self.odm.coastline_action, config_model["coastline_action"]["default"])
+        self.assertEqual(
+            self.odm.mixed_layer_depth, config_model["mixed_layer_depth"]["default"]
+        )
+        self.assertEqual(
+            self.odm.coastline_action, config_model["coastline_action"]["default"]
+        )
         self.assertEqual(self.odm.max_speed, config_model["max_speed"]["default"])
-        self.assertEqual(self.odm.wind_drift_factor, config_model["wind_drift_factor"]["default"])
-        self.assertEqual(self.odm.wind_drift_depth, config_model["wind_drift_depth"]["default"])
-        self.assertEqual(self.odm.vertical_mixing_timestep, config_model["vertical_mixing_timestep"]["default"])
+        self.assertEqual(
+            self.odm.wind_drift_factor, config_model["wind_drift_factor"]["default"]
+        )
+        self.assertEqual(
+            self.odm.wind_drift_depth, config_model["wind_drift_depth"]["default"]
+        )
+        self.assertEqual(
+            self.odm.vertical_mixing_timestep,
+            config_model["vertical_mixing_timestep"]["default"],
+        )
         self.assertEqual(self.odm.object_type, config_model["object_type"]["default"])
         self.assertEqual(self.odm.diameter, config_model["diameter"]["default"])
-        self.assertEqual(self.odm.neutral_buoyancy_salinity, config_model["neutral_buoyancy_salinity"]["default"])
-        self.assertEqual(self.odm.stage_fraction, config_model["stage_fraction"]["default"])
+        self.assertEqual(
+            self.odm.neutral_buoyancy_salinity,
+            config_model["neutral_buoyancy_salinity"]["default"],
+        )
+        self.assertEqual(
+            self.odm.stage_fraction, config_model["stage_fraction"]["default"]
+        )
         self.assertEqual(self.odm.hatched, config_model["hatched"]["default"])
         self.assertEqual(self.odm.length, config_model["length"]["default"])
         self.assertEqual(self.odm.weight, config_model["weight"]["default"])
         self.assertEqual(self.odm.oil_type, config_model["oil_type"]["default"])
         self.assertEqual(self.odm.m3_per_hour, config_model["m3_per_hour"]["default"])
-        self.assertEqual(self.odm.oil_film_thickness, config_model["oil_film_thickness"]["default"])
-        self.assertEqual(self.odm.droplet_size_distribution, config_model["droplet_size_distribution"]["default"])
-        self.assertEqual(self.odm.droplet_diameter_mu, config_model["droplet_diameter_mu"]["default"])
-        self.assertEqual(self.odm.droplet_diameter_sigma, config_model["droplet_diameter_sigma"]["default"])
-        self.assertEqual(self.odm.droplet_diameter_min_subsea, config_model["droplet_diameter_min_subsea"]["default"])
-        self.assertEqual(self.odm.droplet_diameter_max_subsea, config_model["droplet_diameter_max_subsea"]["default"])
-        self.assertEqual(self.odm.emulsification, config_model["emulsification"]["default"])
+        self.assertEqual(
+            self.odm.oil_film_thickness, config_model["oil_film_thickness"]["default"]
+        )
+        self.assertEqual(
+            self.odm.droplet_size_distribution,
+            config_model["droplet_size_distribution"]["default"],
+        )
+        self.assertEqual(
+            self.odm.droplet_diameter_mu, config_model["droplet_diameter_mu"]["default"]
+        )
+        self.assertEqual(
+            self.odm.droplet_diameter_sigma,
+            config_model["droplet_diameter_sigma"]["default"],
+        )
+        self.assertEqual(
+            self.odm.droplet_diameter_min_subsea,
+            config_model["droplet_diameter_min_subsea"]["default"],
+        )
+        self.assertEqual(
+            self.odm.droplet_diameter_max_subsea,
+            config_model["droplet_diameter_max_subsea"]["default"],
+        )
+        self.assertEqual(
+            self.odm.emulsification, config_model["emulsification"]["default"]
+        )
         self.assertEqual(self.odm.dispersion, config_model["dispersion"]["default"])
         self.assertEqual(self.odm.evaporation, config_model["evaporation"]["default"])
-        self.assertEqual(self.odm.update_oilfilm_thickness, config_model["update_oilfilm_thickness"]["default"])
-        self.assertEqual(self.odm.biodegradation, config_model["biodegradation"]["default"])
+        self.assertEqual(
+            self.odm.update_oilfilm_thickness,
+            config_model["update_oilfilm_thickness"]["default"],
+        )
+        self.assertEqual(
+            self.odm.biodegradation, config_model["biodegradation"]["default"]
+        )
+
 
-if __name__ == '__main__':
-    unittest.main()
+if __name__ == "__main__":
+    unittest.main()

tests/test_ptm_init.py

@@ -1,10 +1,15 @@
 """From Co-pilot"""
 
 import unittest
+
 from datetime import datetime, timedelta
+
 import particle_tracking_manager as ptm
+
+
 # from ptm.the_manager import ParticleTrackingManager
 
+
 class TestParticleTrackingManager(unittest.TestCase):
     def setUp(self):
         self.ptm = ptm.ParticleTrackingManager(model="opendrift")
@@ -74,5 +79,6 @@ def test_set_end_time(self):
         self.ptm.end_time = end_time
         self.assertEqual(self.ptm.end_time, end_time)
 
-if __name__ == '__main__':
-    unittest.main()
+
+if __name__ == "__main__":
+    unittest.main()

tests/test_realistic.py

@@ -23,6 +23,7 @@ def test_run():
     """Set up and run."""
 
     import xroms
+
     seeding_kwargs = dict(lon=-90, lat=28.7, number=1)
     manager = ptm.OpenDriftModel(**seeding_kwargs)