working through precommit

Author: kthyng

.pre-commit-config.yaml

@@ -41,7 +41,7 @@ repos:
     language_version: python3
 
 - repo: https://github.com/pre-commit/mirrors-mypy
-  rev: v0.982
+  rev: v1.15.0
   hooks:
   - id: mypy
     additional_dependencies: [types-setuptools,types-PyYAML]
@@ -54,3 +54,4 @@ repos:
     - id: codespell
       args:
         - --quiet-level=2
+      exclude: 'particle_tracking_manager/models/opendrift/config_opendrift.py'

docs/ocean_models.md

@@ -158,5 +158,3 @@ The built-in models in PTM have wet/dry masks from ROMS so they have had to be s
 
 * (DEFAULT) Use the typical, static, ROMS masks (`mask_rho`, `mask_u`, `mask_v`). For ROMS simulations run in [wet/dry mode](https://www.myroms.org/wiki/WET_DRY), grid cells in `mask_rho` are 0 if they are permanently dry and 1 if they are ever wet. This saves some computational time but is inconsistent with the ROMS output files in some places since the drifters may be allowed (due to the static mask) to enter a cell they wouldn't otherwise. However, it doesn't make much of a difference for simulations that aren't in the tidal flats.
 * Use the time-varying wet/dry masks (`wetdry_mask_rho`, `wetdry_mask_u`, `wetdry_mask_v`). This costs some more computational time but is fully consistent with the ROMS output files. This option should be selected if drifters are expected to run in the tidal flats.
-
-

particle_tracking_manager/__init__.py

@@ -2,12 +2,19 @@
 
 import logging
 
+
 # Set log levels for third paries to WARNING
-logging.getLogger('fsspec').setLevel(logging.WARNING)
-logging.getLogger('kerchunk').setLevel(logging.WARNING)
-logging.getLogger('opendrift').setLevel(logging.WARNING)
-logging.getLogger('numcodecs').setLevel(logging.WARNING)
+logging.getLogger("fsspec").setLevel(logging.WARNING)
+logging.getLogger("kerchunk").setLevel(logging.WARNING)
+logging.getLogger("opendrift").setLevel(logging.WARNING)
+logging.getLogger("numcodecs").setLevel(logging.WARNING)
 
-from .models.opendrift.config_opendrift import OpenDriftConfig, LarvalFishModelConfig, LeewayModelConfig, OceanDriftModelConfig, OpenOilModelConfig
+from .config_the_manager import TheManagerConfig
+from .models.opendrift.config_opendrift import (
+    LarvalFishModelConfig,
+    LeewayModelConfig,
+    OceanDriftModelConfig,
+    OpenDriftConfig,
+    OpenOilModelConfig,
+)
 from .models.opendrift.opendrift import OpenDriftModel
-from .config_the_manager import TheManagerConfig

particle_tracking_manager/cli.py

@@ -3,6 +3,7 @@
 # Standard library imports
 import argparse
 import ast
+
 from datetime import datetime
 
 # Third-party imports

particle_tracking_manager/config_logging.py

@@ -1,7 +1,5 @@
 """Defines LoggerConfig to set up and manage logs."""
 
-"""Defines LoggerConfig to set up and manage logs."""
-
 # Standard library imports
 import logging
 
@@ -11,13 +9,16 @@
 # Local imports
 from .config_the_manager import LogLevelEnum, TheManagerConfig
 
+
 logger = logging.getLogger()
 
 
 class LoggerConfig(BaseModel):
     """Methods for loggers."""
 
-    log_level: LogLevelEnum = Field(TheManagerConfig.model_json_schema()["properties"]["log_level"]["default"])
+    log_level: LogLevelEnum = Field(
+        TheManagerConfig.model_json_schema()["properties"]["log_level"]["default"]
+    )
 
     def close_loggers(self, logger: logging.Logger) -> None:
         """Close and remove all handlers from the logger."""
@@ -36,11 +37,11 @@ def setup_logger(self, logfile_name: str) -> logging.Logger:
         logger.setLevel(getattr(logging, self.log_level))
 
         # Add handlers from the main logger to the OpenDrift logger if not already added
-        
+
         # Create file handler to save log to file
         file_handler = logging.FileHandler(logfile_name)
         fmt = "%(asctime)s %(levelname)-7s %(name)s.%(module)s.%(funcName)s:%(lineno)d: %(message)s"
-        datefmt = '%Y-%m-%d %H:%M:%S'
+        datefmt = "%Y-%m-%d %H:%M:%S"
         formatter = logging.Formatter(fmt, datefmt)
         file_handler.setFormatter(formatter)
         logger.addHandler(file_handler)
@@ -49,7 +50,7 @@ def setup_logger(self, logfile_name: str) -> logging.Logger:
         stream_handler = logging.StreamHandler()
         stream_handler.setFormatter(formatter)
         logger.addHandler(stream_handler)
-        
+
         logger.info("Particle tracking manager simulation.")
         logger.info(f"Log filename: {logfile_name}")
         return logger

particle_tracking_manager/config_misc.py

@@ -2,14 +2,12 @@
 
 # Standard library imports
 import datetime
-import json
 import logging
 import pathlib
-from enum import Enum
-from typing import Any, Dict, Optional, Union
+
+from typing import Self
 
 # Third-party imports
-import xarray as xr
 from pydantic import (
     BaseModel,
     ConfigDict,
@@ -19,17 +17,17 @@
     field_validator,
     model_validator,
 )
-from pydantic.fields import FieldInfo
-from typing_extensions import Self
 
 # Local imports
-from .config_the_manager import TheManagerConfig, OutputFormatEnum
+from .config_the_manager import OutputFormatEnum, TheManagerConfig
+
 
 logger = logging.getLogger()
 
 
 class ParticleTrackingState(BaseModel):
     """Track simulation state."""
+
     has_run_setup: bool = False  # this may not be required for all models
     has_added_reader: bool = False
     has_run_seeding: bool = False
@@ -40,20 +38,25 @@ def generate_default_output_file() -> str:
     """Generate a default output file name based on the current date and time."""
     return f"output-results_{datetime.datetime.now():%Y-%m-%dT%H%M%SZ}"
 
+
 class SetupOutputFiles(BaseModel):
     """Handle all changes/work on output files.
-    
+
     This class runs first thing. Then logger setup.
     """
 
-    output_file: Optional[str] = Field(TheManagerConfig.model_json_schema()["properties"]["output_file"]["default"])
-    output_format: OutputFormatEnum = Field(TheManagerConfig.model_json_schema()["properties"]["output_format"]["default"])
+    output_file: str | None = Field(
+        TheManagerConfig.model_json_schema()["properties"]["output_file"]["default"]
+    )
+    output_format: OutputFormatEnum = Field(
+        TheManagerConfig.model_json_schema()["properties"]["output_format"]["default"]
+    )
 
     class Config:
         validate_default: bool = True
 
     @field_validator("output_file", mode="after")
-    def assign_output_file_if_needed(value: Optional[str]) -> str:
+    def assign_output_file_if_needed(value: str | None) -> str:
         """Assign a default output file name if not provided."""
         if value is None:
             return generate_default_output_file()
@@ -70,9 +73,13 @@ def add_output_file_extension(self) -> Self:
         """Add the appropriate file extension based on the output format."""
         if self.output_format is not None:
             if self.output_format == "netcdf":
-                self.output_file = str(pathlib.Path(self.output_file).with_suffix(".nc"))
+                self.output_file = str(
+                    pathlib.Path(self.output_file).with_suffix(".nc")
+                )
             elif self.output_format == "parquet":
-                self.output_file = str(pathlib.Path(self.output_file).with_suffix(".parquet"))
+                self.output_file = str(
+                    pathlib.Path(self.output_file).with_suffix(".parquet")
+                )
             else:
                 raise ValueError(f"output_format {self.output_format} not recognized.")
         return self