ngiab-data-preprocess 4.2.2__py3-none-any.whl → 4.3.0__py3-none-any.whl

data_processing/create_realization.py

@@ -3,15 +3,15 @@ import logging
 import multiprocessing
 import shutil
 import sqlite3
-from collections import defaultdict
 from datetime import datetime
 from pathlib import Path
+from typing import Dict, Optional
 
 import pandas
 import requests
 import s3fs
 import xarray as xr
-from dask.distributed import Client, LocalCluster
+from data_processing.dask_utils import temp_cluster
 from data_processing.file_paths import file_paths
 from data_processing.gpkg_utils import (
     GeoPackage,
@@ -25,7 +25,8 @@ from tqdm.rich import tqdm
 logger = logging.getLogger(__name__)
 
 
-def get_approximate_gw_storage(paths: file_paths, start_date: datetime):
+@temp_cluster
+def get_approximate_gw_storage(paths: file_paths, start_date: datetime) -> Dict[str, int]:
     # get the gw levels from the NWM output on a given start date
     # this kind of works in place of warmstates for now
     year = start_date.strftime("%Y")
@@ -35,17 +36,10 @@ def get_approximate_gw_storage(paths: file_paths, start_date: datetime):
     fs = s3fs.S3FileSystem(anon=True)
     nc_url = f"s3://noaa-nwm-retrospective-3-0-pds/CONUS/netcdf/GWOUT/{year}/{formatted_dt}.GWOUT_DOMAIN1"
 
-    # make sure there's a dask cluster running
-    try:
-        client = Client.current()
-    except ValueError:
-        cluster = LocalCluster()
-        client = Client(cluster)
-
     with fs.open(nc_url) as file_obj:
-        ds = xr.open_dataset(file_obj)
+        ds = xr.open_dataset(file_obj)  # type: ignore
 
-        water_levels = dict()
+        water_levels: Dict[str, int] = dict()
         for cat, feature in tqdm(cat_to_feature.items()):
             # this value is in CM, we need meters to match max_gw_depth
             # xarray says it's in mm, with 0.1 scale factor. calling .values doesn't apply the scale
@@ -114,13 +108,13 @@ def make_noahowp_config(
                     lon=divide_conf_df.loc[divide, "longitude"],
                     terrain_slope=divide_conf_df.loc[divide, "mean.slope_1km"],
                     azimuth=divide_conf_df.loc[divide, "circ_mean.aspect"],
-                    ISLTYP=int(divide_conf_df.loc[divide, "mode.ISLTYP"]),
-                    IVGTYP=int(divide_conf_df.loc[divide, "mode.IVGTYP"]),
+                    ISLTYP=int(divide_conf_df.loc[divide, "mode.ISLTYP"]),  # type: ignore
+                    IVGTYP=int(divide_conf_df.loc[divide, "mode.IVGTYP"]),  # type: ignore
                 )
             )
 
 
-def get_model_attributes_modspatialite(hydrofabric: Path):
+def get_model_attributes_modspatialite(hydrofabric: Path) -> pandas.DataFrame:
     # modspatialite is faster than pyproj but can't be added as a pip dependency
     # This incantation took a while
     with GeoPackage(hydrofabric) as conn:
@@ -151,7 +145,7 @@ def get_model_attributes_modspatialite(hydrofabric: Path):
     return divide_conf_df
 
 
-def get_model_attributes_pyproj(hydrofabric: Path):
+def get_model_attributes_pyproj(hydrofabric: Path) -> pandas.DataFrame:
     # if modspatialite is not available, use pyproj
     with sqlite3.connect(hydrofabric) as conn:
         sql = """
@@ -185,7 +179,7 @@ def get_model_attributes_pyproj(hydrofabric: Path):
     return divide_conf_df
 
 
-def get_model_attributes(hydrofabric: Path):
+def get_model_attributes(hydrofabric: Path) -> pandas.DataFrame:
     try:
         with GeoPackage(hydrofabric) as conn:
             conf_df = pandas.read_sql_query(
@@ -259,7 +253,7 @@ def make_em_config(
 
 def configure_troute(
     cat_id: str, config_dir: Path, start_time: datetime, end_time: datetime
-) -> int:
+) -> None:
     with open(file_paths.template_troute_config, "r") as file:
         troute_template = file.read()
     time_step_size = 300
@@ -316,7 +310,7 @@ def create_realization(
     start_time: datetime,
     end_time: datetime,
     use_nwm_gw: bool = False,
-    gage_id: str = None,
+    gage_id: Optional[str] = None,
 ):
     paths = file_paths(cat_id)
 
@@ -354,12 +348,12 @@ def create_realization(
     create_partitions(paths)
 
 
-def create_partitions(paths: Path, num_partitions: int = None) -> None:
+def create_partitions(paths: file_paths, num_partitions: Optional[int] = None) -> None:
     if num_partitions is None:
         num_partitions = multiprocessing.cpu_count()
 
     cat_to_nex_pairs = get_cat_to_nex_flowpairs(hydrofabric=paths.geopackage_path)
-    nexus = defaultdict(list)
+    # nexus = defaultdict(list)
 
     # for cat, nex in cat_to_nex_pairs:
     #     nexus[nex].append(cat)

data_processing/dask_utils.py

@@ -0,0 +1,92 @@
+import logging
+
+from dask.distributed import Client
+
+logger = logging.getLogger(__name__)
+
+
+def shutdown_cluster():
+    try:
+        client = Client.current()
+        client.shutdown()
+    except ValueError:
+        logger.debug("No cluster found to shutdown")
+
+
+def no_cluster(func):
+    """
+    Decorator that ensures the wrapped function runs with no active Dask cluster.
+
+    This decorator attempts to shut down any existing Dask cluster before
+    executing the wrapped function. If no cluster is found, it logs a debug message
+    and continues execution.
+
+    Parameters:
+        func: The function to be executed without a Dask cluster
+
+    Returns:
+        wrapper: The wrapped function that will be executed without a Dask cluster
+    """
+
+    def wrapper(*args, **kwargs):
+        shutdown_cluster()
+        result = func(*args, **kwargs)
+        return result
+
+    return wrapper
+
+
+def use_cluster(func):
+    """
+    Decorator that ensures the wrapped function has access to a Dask cluster.
+
+    If a Dask cluster is already running, it uses the existing one.
+    If no cluster is available, it creates a new one before executing the function.
+    The cluster remains active after the function completes.
+
+    Parameters:
+        func: The function to be executed with a Dask cluster
+
+    Returns:
+        wrapper: The wrapped function with access to a Dask cluster
+    """
+
+    def wrapper(*args, **kwargs):
+        try:
+            client = Client.current()
+        except ValueError:
+            client = Client()
+        result = func(*args, **kwargs)
+        return result
+
+    return wrapper
+
+
+def temp_cluster(func):
+    """
+    Decorator that provides a temporary Dask cluster for the wrapped function.
+
+    If a Dask cluster is already running, it uses the existing one and leaves it running.
+    If no cluster exists, it creates a temporary one and shuts it down after
+    the function completes.
+
+    Parameters:
+        func: The function to be executed with a Dask cluster
+
+    Returns:
+        wrapper: The wrapped function with access to a Dask cluster
+    """
+
+    def wrapper(*args, **kwargs):
+        cluster_was_running = True
+        try:
+            client = Client.current()
+        except ValueError:
+            cluster_was_running = False
+            client = Client()
+        result = func(*args, **kwargs)
+        if not cluster_was_running:
+            client.shutdown()
+        return result
+
+    return wrapper

data_processing/dataset_utils.py

@@ -1,19 +1,22 @@
 import logging
 import os
+from datetime import datetime
 from pathlib import Path
-from typing import Tuple, Union
+from typing import List, Literal, Optional, Tuple, Union
 
 import geopandas as gpd
 import numpy as np
 import xarray as xr
-from dask.distributed import Client,  progress
-import datetime
+from xarray.core.types import InterpOptions
+from dask.distributed import Client, progress, Future
+from data_processing.dask_utils import use_cluster
 
 logger = logging.getLogger(__name__)
 
 # known ngen variable names
 # https://github.com/CIROH-UA/ngen/blob/4fb5bb68dc397298bca470dfec94db2c1dcb42fe/include/forcing/AorcForcing.hpp#L77
 
+
 def validate_dataset_format(dataset: xr.Dataset) -> None:
     """
     Validate the format of the dataset.
@@ -41,8 +44,9 @@ def validate_dataset_format(dataset: xr.Dataset) -> None:
     if "name" not in dataset.attrs:
         raise ValueError("Dataset must have a name attribute to identify it")
 
+
 def validate_time_range(dataset: xr.Dataset, start_time: str, end_time: str) -> Tuple[str, str]:
-    '''
+    """
     Ensure that all selected times are in the passed dataset.
 
     Parameters
@@ -60,7 +64,7 @@ def validate_time_range(dataset: xr.Dataset, start_time: str, end_time: str) ->
         start_time, or if not available, earliest available timestep in dataset.
     str
         end_time, or if not available, latest available timestep in dataset.
-    '''
+    """
     end_time_in_dataset = dataset.time.isel(time=-1).values
     start_time_in_dataset = dataset.time.isel(time=0).values
     if np.datetime64(start_time) < start_time_in_dataset:
@@ -77,7 +81,10 @@ def validate_time_range(dataset: xr.Dataset, start_time: str, end_time: str) ->
 
 
 def clip_dataset_to_bounds(
-    dataset: xr.Dataset, bounds: Tuple[float, float, float, float], start_time: str, end_time: str
+    dataset: xr.Dataset,
+    bounds: Tuple[float, float, float, float] | np.ndarray[tuple[int], np.dtype[np.float64]],
+    start_time: str,
+    end_time: str,
 ) -> xr.Dataset:
     """
     Clip the dataset to specified geographical bounds.
@@ -86,14 +93,14 @@ def clip_dataset_to_bounds(
     ----------
     dataset : xr.Dataset
         Dataset to be clipped.
-    bounds : tuple[float, float, float, float]
-        Corners of bounding box. bounds[0] is x_min, bounds[1] is y_min, 
+    bounds : tuple[float, float, float, float] | np.ndarray[tuple[int], np.dtype[np.float64]]
+        Corners of bounding box. bounds[0] is x_min, bounds[1] is y_min,
         bounds[2] is x_max, bounds[3] is y_max.
     start_time : str
         Desired start time in YYYY/MM/DD HH:MM:SS format.
     end_time : str
         Desired end time in YYYY/MM/DD HH:MM:SS format.
-    
+
     Returns
     -------
     xr.Dataset
@@ -110,33 +117,103 @@ def clip_dataset_to_bounds(
     return dataset
 
 
-def save_to_cache(stores: xr.Dataset, cached_nc_path: Path) -> xr.Dataset:
-    """Compute the store and save it to a cached netCDF file. This is not required but will save time and bandwidth."""
-    logger.info("Downloading and caching forcing data, this may take a while")
+def interpolate_nan_values(
+    dataset: xr.Dataset,
+    variables: Optional[List[str]] = None,
+    dim: str = "time",
+    method: InterpOptions = "nearest",
+    fill_value: str = "extrapolate",
+) -> None:
+    """
+    Interpolates NaN values in specified (or all numeric time-dependent)
+    variables of an xarray.Dataset. Operates inplace on the dataset.
 
-    if not cached_nc_path.parent.exists():
-        cached_nc_path.parent.mkdir(parents=True)
+    Parameters
+    ----------
+    dataset : xr.Dataset
+        The input dataset.
+    variables : Optional[List[str]], optional
+        A list of variable names to process. If None (default),
+        all numeric variables containing the specified dimension will be processed.
+    dim : str, optional
+        The dimension along which to interpolate (default is "time").
+    method : str, optional
+        Interpolation method to use (e.g., "linear", "nearest", "cubic").
+        Default is "nearest".
+    fill_value : str, optional
+        Method for filling NaNs at the start/end of the series after interpolation.
+        Set to "extrapolate" to fill with the nearest valid value when using 'nearest' or 'linear'.
+        Default is "extrapolate".
+    """
+    for name, var in dataset.data_vars.items():
+        # if the variable is non-numeric, skip
+        if not np.issubdtype(var.dtype, np.number):
+            continue
+        # if there are no NANs, skip
+        if not var.isnull().any().compute():
+            continue
+
+        dataset[name] = var.interpolate_na(
+            dim=dim,
+            method=method,
+            fill_value=fill_value if method in ["nearest", "linear"] else None,
+        )
 
-    # sort of terrible work around for half downloaded files
-    temp_path = cached_nc_path.with_suffix(".downloading.nc")
-    if os.path.exists(temp_path):
-        os.remove(temp_path)
 
-    ## Cast every single variable to float32 to save space to save a lot of memory issues later
-    ## easier to do it now in this slow download step than later in the steps without dask
-    for var in stores.data_vars: 
-        stores[var] = stores[var].astype("float32")
+@use_cluster
+def save_dataset(
+    ds_to_save: xr.Dataset,
+    target_path: Path,
+    engine: Literal["netcdf4", "scipy", "h5netcdf"] = "h5netcdf",
+):
+    """
+    Helper function to compute and save an xarray.Dataset to a NetCDF file.
+    Uses a temporary file and rename for atomicity.
+    """
+    if not target_path.parent.exists():
+        target_path.parent.mkdir(parents=True, exist_ok=True)
+
+    temp_file_path = target_path.with_name(target_path.name + ".saving.nc")
+    if temp_file_path.exists():
+        os.remove(temp_file_path)
 
     client = Client.current()
-    future = client.compute(stores.to_netcdf(temp_path, compute=False))
-    # Display progress bar
+    future: Future = client.compute(
+        ds_to_save.to_netcdf(temp_file_path, engine=engine, compute=False)
+    )  # type: ignore
+    logger.debug(
+        f"NetCDF write task submitted to Dask. Waiting for completion to {temp_file_path}..."
+    )
     progress(future)
     future.result()
+    os.rename(str(temp_file_path), str(target_path))
+    logger.info(f"Successfully saved data to: {target_path}")
+
+
+@use_cluster
+def save_to_cache(
+    stores: xr.Dataset, cached_nc_path: Path, interpolate_nans: bool = True
+) -> xr.Dataset:
+    """
+    Compute the store and save it to a cached netCDF file. This is not required but will save time and bandwidth.
+    """
+    logger.info(f"Processing dataset for caching. Final cache target: {cached_nc_path}")
 
-    os.rename(temp_path, cached_nc_path)
+    # lasily cast all numbers to f32
+    for name, var in stores.data_vars.items():
+        if np.issubdtype(var.dtype, np.number):
+            stores[name] = var.astype("float32", casting="same_kind")
 
-    data = xr.open_mfdataset(cached_nc_path, parallel=True, engine="h5netcdf")
-    return data
+    # save dataset locally before manipulating it
+    save_dataset(stores, cached_nc_path)
+    stores = xr.open_mfdataset(cached_nc_path, parallel=True, engine="h5netcdf")
+
+    if interpolate_nans:
+        interpolate_nan_values(dataset=stores)
+        save_dataset(stores, cached_nc_path)
+        stores = xr.open_mfdataset(cached_nc_path, parallel=True, engine="h5netcdf")
+
+    return stores
 
 
 def check_local_cache(
@@ -144,9 +221,8 @@ def check_local_cache(
     start_time: str,
     end_time: str,
     gdf: gpd.GeoDataFrame,
-    remote_dataset: xr.Dataset
+    remote_dataset: xr.Dataset,
 ) -> Union[xr.Dataset, None]:
-
     merged_data = None
 
     if not os.path.exists(cached_nc_path):
@@ -155,9 +231,7 @@ def check_local_cache(
 
     logger.info("Found cached nc file")
     # open the cached file and check that the time range is correct
-    cached_data = xr.open_mfdataset(
-        cached_nc_path, parallel=True, engine="h5netcdf"
-    )
+    cached_data = xr.open_mfdataset(cached_nc_path, parallel=True, engine="h5netcdf")
 
     if "name" not in cached_data.attrs or "name" not in remote_dataset.attrs:
         logger.warning("No name attribute found to compare datasets")
@@ -166,9 +240,9 @@ def check_local_cache(
         logger.warning("Cached data from different source, .name attr doesn't match")
         return
 
-    range_in_cache = cached_data.time[0].values <= np.datetime64(
-        start_time
-    ) and cached_data.time[-1].values >= np.datetime64(end_time)
+    range_in_cache = cached_data.time[0].values <= np.datetime64(start_time) and cached_data.time[
+        -1
+    ].values >= np.datetime64(end_time)
 
     if not range_in_cache:
         # the cache does not contain the desired time range
@@ -186,10 +260,8 @@ def check_local_cache(
     if range_in_cache:
         logger.info("Time range is within cached data")
         logger.debug(f"Opened cached nc file: [{cached_nc_path}]")
-        merged_data = clip_dataset_to_bounds(
-            cached_data, gdf.total_bounds, start_time, end_time
-        )
-        logger.debug("Clipped stores")        
+        merged_data = clip_dataset_to_bounds(cached_data, gdf.total_bounds, start_time, end_time)
+        logger.debug("Clipped stores")
 
     return merged_data
 
@@ -197,16 +269,27 @@ def check_local_cache(
 def save_and_clip_dataset(
     dataset: xr.Dataset,
     gdf: gpd.GeoDataFrame,
-    start_time: datetime.datetime,
-    end_time: datetime.datetime,
+    start_time: datetime,
+    end_time: datetime,
     cache_location: Path,
 ) -> xr.Dataset:
     """convenience function clip the remote dataset, and either load from cache or save to cache if it's not present"""
     gdf = gdf.to_crs(dataset.crs)
 
-    cached_data = check_local_cache(cache_location, start_time, end_time, gdf, dataset)
+    cached_data = check_local_cache(
+        cache_location,
+        start_time,  # type: ignore
+        end_time,  # type: ignore
+        gdf,
+        dataset,
+    )
 
     if not cached_data:
-        clipped_data = clip_dataset_to_bounds(dataset, gdf.total_bounds, start_time, end_time)
+        clipped_data = clip_dataset_to_bounds(
+            dataset,
+            gdf.total_bounds,
+            start_time,  # type: ignore
+            end_time,  # type: ignore
+        )
         cached_data = save_to_cache(clipped_data, cache_location)
-    return cached_data
+    return cached_data

data_processing/datasets.py

@@ -1,35 +1,31 @@
 import logging
+from typing import Optional
 
 import s3fs
-from data_processing.s3fs_utils import S3ParallelFileSystem
 import xarray as xr
-from dask.distributed import Client, LocalCluster
+from data_processing.dask_utils import use_cluster
 from data_processing.dataset_utils import validate_dataset_format
-
+from data_processing.s3fs_utils import S3ParallelFileSystem
 
 logger = logging.getLogger(__name__)
 
 
-def load_v3_retrospective_zarr(forcing_vars: list[str] = None) -> xr.Dataset:
+@use_cluster
+def load_v3_retrospective_zarr(forcing_vars: Optional[list[str]] = None) -> xr.Dataset:
     """Load zarr datasets from S3 within the specified time range."""
     # if a LocalCluster is not already running, start one
     if not forcing_vars:
         forcing_vars = ["lwdown", "precip", "psfc", "q2d", "swdown", "t2d", "u2d", "v2d"]
-    try:
-        client = Client.current()
-    except ValueError:
-        cluster = LocalCluster()
-        client = Client(cluster)
+
     s3_urls = [
-        f"s3://noaa-nwm-retrospective-3-0-pds/CONUS/zarr/forcing/{var}.zarr"
-        for var in forcing_vars
+        f"s3://noaa-nwm-retrospective-3-0-pds/CONUS/zarr/forcing/{var}.zarr" for var in forcing_vars
     ]
     # default cache is readahead which is detrimental to performance in this case
     fs = S3ParallelFileSystem(anon=True, default_cache_type="none")  # default_block_size
     s3_stores = [s3fs.S3Map(url, s3=fs) for url in s3_urls]
     # the cache option here just holds accessed data in memory to prevent s3 being queried multiple times
     # most of the data is read once and written to disk but some of the coordinate data is read multiple times
-    dataset = xr.open_mfdataset(s3_stores, parallel=True, engine="zarr", cache=True)
+    dataset = xr.open_mfdataset(s3_stores, parallel=True, engine="zarr", cache=True)  # type: ignore
 
     # set the crs attribute to conform with the format
     esri_pe_string = dataset.crs.esri_pe_string
@@ -54,7 +50,8 @@ def load_v3_retrospective_zarr(forcing_vars: list[str] = None) -> xr.Dataset:
     return dataset
 
 
-def load_aorc_zarr(start_year: int = None, end_year: int = None) -> xr.Dataset:
+@use_cluster
+def load_aorc_zarr(start_year: Optional[int] = None, end_year: Optional[int] = None) -> xr.Dataset:
     """Load the aorc zarr dataset from S3."""
     if not start_year or not end_year:
         logger.warning("No start or end year provided, defaulting to 1979-2023")
@@ -63,11 +60,6 @@ def load_aorc_zarr(start_year: int = None, end_year: int = None) -> xr.Dataset:
         start_year = 1979
     if not end_year:
         end_year = 2023
-    try:
-        client = Client.current()
-    except ValueError:
-        cluster = LocalCluster()
-        client = Client(cluster)
 
     logger.info(f"Loading AORC zarr datasets from {start_year} to {end_year}")
     estimated_time_s = ((end_year - start_year) * 2.5) + 3.5
@@ -75,9 +67,9 @@ def load_aorc_zarr(start_year: int = None, end_year: int = None) -> xr.Dataset:
     logger.info(f"This should take roughly {estimated_time_s} seconds")
     fs = S3ParallelFileSystem(anon=True, default_cache_type="none")
     s3_url = "s3://noaa-nws-aorc-v1-1-1km/"
-    urls = [f"{s3_url}{i}.zarr" for i in range(start_year, end_year+1)]
+    urls = [f"{s3_url}{i}.zarr" for i in range(start_year, end_year + 1)]
     filestores = [s3fs.S3Map(url, s3=fs) for url in urls]
-    dataset = xr.open_mfdataset(filestores, parallel=True, engine="zarr", cache=True)
+    dataset = xr.open_mfdataset(filestores, parallel=True, engine="zarr", cache=True)  # type: ignore
     dataset.attrs["crs"] = "+proj=longlat +datum=WGS84 +no_defs"
     dataset.attrs["name"] = "aorc_1km_zarr"
     # rename latitude and longitude to x and y
@@ -87,32 +79,29 @@ def load_aorc_zarr(start_year: int = None, end_year: int = None) -> xr.Dataset:
     return dataset
 
 
+@use_cluster
 def load_swe_zarr() -> xr.Dataset:
     """Load the swe zarr dataset from S3."""
-    s3_urls = [
-        f"s3://noaa-nwm-retrospective-3-0-pds/CONUS/zarr/ldasout.zarr"
-    ]
+    s3_urls = ["s3://noaa-nwm-retrospective-3-0-pds/CONUS/zarr/ldasout.zarr"]
     # default cache is readahead which is detrimental to performance in this case
     fs = S3ParallelFileSystem(anon=True, default_cache_type="none")  # default_block_size
     s3_stores = [s3fs.S3Map(url, s3=fs) for url in s3_urls]
     # the cache option here just holds accessed data in memory to prevent s3 being queried multiple times
     # most of the data is read once and written to disk but some of the coordinate data is read multiple times
-    dataset = xr.open_mfdataset(s3_stores, parallel=True, engine="zarr", cache=True)
-    
+    dataset = xr.open_mfdataset(s3_stores, parallel=True, engine="zarr", cache=True)  # type: ignore
+
     # set the crs attribute to conform with the format
     esri_pe_string = dataset.crs.esri_pe_string
     dataset = dataset.drop_vars(["crs"])
     dataset.attrs["crs"] = esri_pe_string
     # drop everything except SNEQV
     vars_to_drop = list(dataset.data_vars)
-    vars_to_drop.remove('SNEQV')
+    vars_to_drop.remove("SNEQV")
     dataset = dataset.drop_vars(vars_to_drop)
     dataset.attrs["name"] = "v3_swe_zarr"
 
     # rename the data vars to work with ngen
-    variables = {
-        "SNEQV": "swe"
-    }
+    variables = {"SNEQV": "swe"}
     dataset = dataset.rename_vars(variables)
 
     validate_dataset_format(dataset)

data_processing/file_paths.py

@@ -1,11 +1,13 @@
 from pathlib import Path
-
+from typing import Optional
+from datetime import datetime
 
 class file_paths:
     """
     This class contains all of the file paths used in the data processing
     workflow.
     """
+
     config_file = Path("~/.ngiab/preprocessor").expanduser()
     hydrofabric_dir = Path("~/.ngiab/hydrofabric/v2.2").expanduser()
     hydrofabric_download_log = Path("~/.ngiab/hydrofabric/v2.2/download_log.json").expanduser()
@@ -31,7 +33,7 @@ class file_paths:
     template_em_config = data_sources / "em-catchment-template.yml"
     template_em_model_config = data_sources / "em-config.yml"
 
-    def __init__(self, folder_name: str = None, output_dir: Path = None):
+    def __init__(self, folder_name: Optional[str] = None, output_dir: Optional[Path] = None):
         """
         Initialize the file_paths class with a the name of the output subfolder.
         OR the path to the output folder you want to use.
@@ -53,7 +55,7 @@ class file_paths:
         self.cache_dir.mkdir(parents=True, exist_ok=True)
 
     @classmethod
-    def get_working_dir(cls) -> Path:
+    def get_working_dir(cls) -> Path | None:
         try:
             with open(cls.config_file, "r") as f:
                 return Path(f.readline().strip()).expanduser()
@@ -67,9 +69,7 @@ class file_paths:
 
     @classmethod
     def root_output_dir(cls) -> Path:
-        if cls.get_working_dir() is not None:
-            return cls.get_working_dir()
-        return Path(__file__).parent.parent.parent / "output"
+        return cls.get_working_dir() or Path(__file__).parent.parent.parent / "output"
 
     @property
     def subset_dir(self) -> Path:
@@ -102,7 +102,7 @@ class file_paths:
     def append_cli_command(self, command: list[str]) -> None:
         current_time = datetime.now().strftime("%Y-%m-%d %H:%M:%S")
         command_string = " ".join(command)
-        history_file  = self.metadata_dir / "cli_commands_history.txt"
+        history_file = self.metadata_dir / "cli_commands_history.txt"
         if not history_file.parent.exists():
             history_file.parent.mkdir(parents=True, exist_ok=True)
         with open(self.metadata_dir / "cli_commands_history.txt", "a") as f: