integrated into opendrift logging, moved xroms to pip

ci/environment-py3.10.yml

@@ -10,10 +10,11 @@ dependencies:
   - opendrift
   - scipy
   - xarray
-  - xroms
+  # - xroms
   ##############
   - pytest
   - pip:
     - codecov
     - pytest-cov
     - coverage[toml]
+    - xroms  # can't be found on conda-forge for CI

ci/environment-py3.11.yml

@@ -10,10 +10,11 @@ dependencies:
   - opendrift
   - scipy
   - xarray
-  - xroms
+  # - xroms
   ##############
   - pytest
   - pip:
     - codecov
     - pytest-cov
     - coverage[toml]
+    - xroms  # can't be found on conda-forge for CI

ci/environment-py3.9.yml

@@ -10,10 +10,11 @@ dependencies:
   - opendrift
   - scipy
   - xarray
-  - xroms
+  # - xroms
   ##############
   - pytest
   - pip:
     - codecov
     - pytest-cov
     - coverage[toml]
+    - xroms  # can't be found on conda-forge for CI

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`.
 
@@ -88,6 +88,28 @@ m.seed()
 m.run()
 ```
 
-```{code-cell} ipython3
+## Ways to Get Information
+
+Check drifter initialization properties:
+
+```
+m.initial_drifters
+```
+
+Look at reader/ocean model properties:
 
 ```
+m.reader
+```
+
+Get reader/ocean model properties (gathered metadata about model):
+
+```
+m.reader_metadata(key)
+```
+
+Show configuration details — many more details on this in {doc}`configuration`:
+
+```
+m.show_config()
+```

particle_tracking_manager/models/opendrift/model_opendrift.py

@@ -1,6 +1,7 @@
 """Using OpenDrift for particle tracking."""
 import copy
 import datetime
+import logging
 import pathlib
 
 import pandas as pd
@@ -42,6 +43,9 @@
 overall_start_time = datetime.datetime(1999, 1, 1, 0, 0, 0)
 overall_end_time = ciofs_operational_end_time
 
+
+# logger = logging.getLogger("opendrift")
+
 
 # @copydocstring( ParticleTrackingManager )
 class OpenDriftModel(ParticleTrackingManager):
@@ -271,7 +275,7 @@ def __setattr_model__(self, name: str, value) -> None:
                 self, "horizontal_diffusivity"
             ):
 
-                print(
+                self.logger.info(
                     "overriding horizontal_diffusivity parameter with one tuned to reader model"
                 )
 
@@ -296,7 +300,7 @@ def __setattr_model__(self, name: str, value) -> None:
                 and self.horizontal_diffusivity is None
             ):
 
-                print(
+                self.logger.info(
                     "changing horizontal_diffusivity parameter from None to 0.0. Otherwise set it to a specific value."
                 )
 
@@ -311,7 +315,7 @@ def __setattr_model__(self, name: str, value) -> None:
                 "CIOFS_now",
             ]:
 
-                print(
+                self.logger.info(
                     "overriding horizontal_diffusivity parameter with one tuned to reader model"
                 )
 
@@ -341,7 +345,7 @@ def __setattr_model__(self, name: str, value) -> None:
                 "CIOFS_now",
             ]:
 
-                print(
+                self.logger.info(
                     "changing horizontal_diffusivity parameter from None to 0.0. Otherwise set it to a specific value."
                 )
 
@@ -367,15 +371,15 @@ def __setattr_model__(self, name: str, value) -> None:
             and hasattr(self, "o")
         ):
             if self.surface_only and self.drift_model != "Leeway":
-                print("Truncating model output below 0.5 m.")
+                self.logger.info("Truncating model output below 0.5 m.")
                 self.o.set_config("drift:truncate_ocean_model_below_m", 0.5)
             elif (
                 not self.surface_only
                 and self.drift_model != "Leeway"
                 and self.show_config(key="drift:truncate_ocean_model_below_m")["value"]
                 is not None
             ):
-                print("Un-truncating model output below 0.5 m.")
+                self.logger.info("Un-truncating model output below 0.5 m.")
                 self.o.set_config("drift:truncate_ocean_model_below_m", None)
 
         # Leeway doesn't have this option available

particle_tracking_manager/the_manager.py

@@ -3,6 +3,7 @@
 
 # from docstring_inheritance import NumpyDocstringInheritanceMeta
 import datetime
+import logging
 import pathlib
 import warnings
 
@@ -142,6 +143,8 @@ 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__
         # these will also update "value" in the config dict
@@ -198,7 +201,7 @@ def __setattr__(self, name: str, value) -> None:
                     self.__dict__["lon"] += 360
 
         if name == "surface_only" and value:
-            print(
+            self.logger.info(
                 "overriding values for `do3D`, `z`, and `vertical_mixing` because `surface_only` True"
             )
             self.do3D = False
@@ -208,7 +211,7 @@ def __setattr__(self, name: str, value) -> None:
         # in case any of these are reset by user after surface_only is already set
         if name in ["do3D", "z", "vertical_mixing"]:
             if hasattr(self, "surface_only") and self.surface_only:
-                print(
+                self.logger.info(
                     "overriding values for `do3D`, `z`, and `vertical_mixing` because `surface_only` True"
                 )
                 if name == "do3D":
@@ -222,19 +225,19 @@ def __setattr__(self, name: str, value) -> None:
 
             # if not 3D turn off vertical_mixing
             if hasattr(self, "do3D") and not self.do3D:
-                print("turning off vertical_mixing since do3D is False")
+                self.logger.info("turning off vertical_mixing since do3D is False")
                 self.__dict__["vertical_mixing"] = False
                 self.config_ptm["vertical_mixing"]["value"] = False
                 # self.vertical_mixing = False  # this is recursive
 
         # set z to None if seed_seafloor is True
         if name == "seed_seafloor" and value:
-            print("setting z to None since being seeded at seafloor")
+            self.logger.info("setting z to None since being seeded at seafloor")
             self.z = None
 
         # in case z is changed back after initialization
         if name == "z" and value is not None and hasattr(self, "seed_seafloor"):
-            print(
+            self.logger.info(
                 "setting `seed_seafloor` to False since now setting a non-None z value"
             )
             self.seed_seafloor = False
@@ -260,7 +263,7 @@ def __setattr__(self, name: str, value) -> None:
 
         # use reader start time if not otherwise input
         if name == "has_added_reader" and value and self.start_time is None:
-            print("setting reader start_time as simulation start_time")
+            self.logger.info("setting reader start_time as simulation start_time")
             self.start_time = self.reader_metadata("start_time")
 
         # if reader, lon, and lat set, check inputs