From 37862091714fa7e1bee03248b4da527865c9689c Mon Sep 17 00:00:00 2001
From: Sean Freeman <sean.freeman@uah.edu>
Date: Wed, 13 Sep 2023 13:12:04 -0500
Subject: [PATCH 1/9] adding internal utils changes

---
 tobac/utils/internal/__init__.py              |   1 +
 .../general_internal.py}                      | 203 ++++++------------
 tobac/utils/internal/internal_consts.py       |   6 +
 tobac/utils/internal/iris_utils.py            | 156 ++++++++++++++
 tobac/utils/internal/xarray_utils.py          |  50 +++++
 5 files changed, 283 insertions(+), 133 deletions(-)
 create mode 100644 tobac/utils/internal/__init__.py
 rename tobac/utils/{internal.py => internal/general_internal.py} (78%)
 create mode 100644 tobac/utils/internal/internal_consts.py
 create mode 100644 tobac/utils/internal/iris_utils.py
 create mode 100644 tobac/utils/internal/xarray_utils.py

diff --git a/tobac/utils/internal/__init__.py b/tobac/utils/internal/__init__.py
new file mode 100644
index 00000000..463d824c
--- /dev/null
+++ b/tobac/utils/internal/__init__.py
@@ -0,0 +1 @@
+from .general_internal import *
diff --git a/tobac/utils/internal.py b/tobac/utils/internal/general_internal.py
similarity index 78%
rename from tobac/utils/internal.py
rename to tobac/utils/internal/general_internal.py
index 1354504f..271cccaa 100644
--- a/tobac/utils/internal.py
+++ b/tobac/utils/internal/general_internal.py
@@ -1,10 +1,25 @@
 """Internal tobac utilities
 """
+from __future__ import annotations
+
 import numpy as np
 import skimage.measure
 import xarray as xr
 import iris
+import iris.cube
+import pandas as pd
 import warnings
+from . import iris_utils
+from . import xarray_utils as xr_utils
+from typing import Union, Callable
+
+# list of common vertical coordinates to search for in various functions
+COMMON_VERT_COORDS: list[str] = [
+    "z",
+    "model_level_number",
+    "altitude",
+    "geopotential_height",
+]
 
 
 def _warn_auto_coordinate():
@@ -17,7 +32,7 @@ def _warn_auto_coordinate():
     )
 
 
-def get_label_props_in_dict(labels):
+def get_label_props_in_dict(labels: np.array) -> dict:
     """Function to get the label properties into a dictionary format.
 
     Parameters
@@ -40,7 +55,7 @@ def get_label_props_in_dict(labels):
     return region_properties_dict
 
 
-def get_indices_of_labels_from_reg_prop_dict(region_property_dict):
+def get_indices_of_labels_from_reg_prop_dict(region_property_dict: dict) -> tuple[dict]:
     """Function to get the x, y, and z indices (as well as point count) of all labeled regions.
     Parameters
     ----------
@@ -94,7 +109,7 @@ def get_indices_of_labels_from_reg_prop_dict(region_property_dict):
         return [curr_loc_indices, y_indices, x_indices]
 
 
-def iris_to_xarray(func):
+def iris_to_xarray(func: Callable) -> Callable:
     """Decorator that converts all input of a function that is in the form of
     Iris cubes into xarray DataArrays and converts all outputs with type
     xarray DataArrays back into Iris cubes.
@@ -160,7 +175,7 @@ def wrapper(*args, **kwargs):
     return wrapper
 
 
-def xarray_to_iris(func):
+def xarray_to_iris(func: Callable) -> Callable:
     """Decorator that converts all input of a function that is in the form of
     xarray DataArrays into Iris cubes and converts all outputs with type
     Iris cubes back into xarray DataArrays.
@@ -244,7 +259,7 @@ def wrapper(*args, **kwargs):
     return wrapper
 
 
-def irispandas_to_xarray(func):
+def irispandas_to_xarray(func: Callable) -> Callable:
     """Decorator that converts all input of a function that is in the form of
     Iris cubes/pandas Dataframes into xarray DataArrays/xarray Datasets and
     converts all outputs with the type xarray DataArray/xarray Dataset
@@ -324,7 +339,7 @@ def wrapper(*args, **kwargs):
     return wrapper
 
 
-def xarray_to_irispandas(func):
+def xarray_to_irispandas(func: Callable) -> Callable:
     """Decorator that converts all input of a function that is in the form of
     DataArrays/xarray Datasets into xarray Iris cubes/pandas Dataframes and
     converts all outputs with the type Iris cubes/pandas Dataframes back into
@@ -427,7 +442,7 @@ def wrapper(*args, **kwargs):
     return wrapper
 
 
-def njit_if_available(func, **kwargs):
+def njit_if_available(func: Callable, **kwargs) -> Callable:
     """Decorator to wrap a function with numba.njit if available.
     If numba isn't available, it just returns the function.
 
@@ -446,12 +461,15 @@ def njit_if_available(func, **kwargs):
         return func
 
 
-def find_vertical_axis_from_coord(variable_cube, vertical_coord=None):
+def find_vertical_axis_from_coord(
+    variable_cube: Union[iris.cube.Cube, xr.DataArray],
+    vertical_coord: Union[str, None] = None,
+) -> str:
     """Function to find the vertical coordinate in the iris cube
 
     Parameters
     ----------
-    variable_cube: iris.cube
+    variable_cube: iris.cube.Cube or xarray.DataArray
         Input variable cube, containing a vertical coordinate.
     vertical_coord: str
         Vertical coordinate name. If None, this function tries to auto-detect.
@@ -466,69 +484,21 @@ def find_vertical_axis_from_coord(variable_cube, vertical_coord=None):
     ValueError
         Raised if the vertical coordinate isn't found in the cube.
     """
-    list_vertical = [
-        "z",
-        "model_level_number",
-        "altitude",
-        "geopotential_height",
-    ]
 
     if vertical_coord == "auto":
         _warn_auto_coordinate()
 
     if isinstance(variable_cube, iris.cube.Cube):
-        list_coord_names = [coord.name() for coord in variable_cube.coords()]
-    elif isinstance(variable_cube, xr.Dataset) or isinstance(
-        variable_cube, xr.DataArray
-    ):
-        list_coord_names = variable_cube.coords
-
-    if vertical_coord is None or vertical_coord == "auto":
-        # find the intersection
-        all_vertical_axes = list(set(list_coord_names) & set(list_vertical))
-        if len(all_vertical_axes) >= 1:
-            return all_vertical_axes[0]
-        else:
-            raise ValueError(
-                "Cube lacks suitable automatic vertical coordinate (z, model_level_number, altitude, or geopotential_height)"
-            )
-    elif vertical_coord in list_coord_names:
-        return vertical_coord
-    else:
-        raise ValueError("Please specify vertical coordinate found in cube")
-
-
-def find_axis_from_coord(variable_cube, coord_name):
-    """Finds the axis number in an iris cube given a coordinate name.
-
-    Parameters
-    ----------
-    variable_cube: iris.cube
-        Input variable cube
-    coord_name: str
-        coordinate to look for
+        return iris_utils.find_vertical_axis_from_coord(variable_cube, vertical_coord)
+    if isinstance(variable_cube, xr.Dataset) or isinstance(variable_cube, xr.DataArray):
+        return xr_utils.find_vertical_axis_from_coord(variable_cube, vertical_coord)
 
-    Returns
-    -------
-    axis_number: int
-        the number of the axis of the given coordinate, or None if the coordinate
-        is not found in the cube or not a dimensional coordinate
-    """
-
-    list_coord_names = [coord.name() for coord in variable_cube.coords()]
-    all_matching_axes = list(set(list_coord_names) & set((coord_name,)))
-    if (
-        len(all_matching_axes) == 1
-        and len(variable_cube.coord_dims(all_matching_axes[0])) > 0
-    ):
-        return variable_cube.coord_dims(all_matching_axes[0])[0]
-    elif len(all_matching_axes) > 1:
-        raise ValueError("Too many axes matched.")
-    else:
-        return None
+    raise ValueError("variable_cube must be xr.DataArray or iris.cube.Cube")
 
 
-def find_dataframe_vertical_coord(variable_dataframe, vertical_coord=None):
+def find_dataframe_vertical_coord(
+    variable_dataframe: pd.DataFrame, vertical_coord: Union[str, None] = None
+) -> str:
     """Function to find the vertical coordinate in the iris cube
 
     Parameters
@@ -553,8 +523,9 @@ def find_dataframe_vertical_coord(variable_dataframe, vertical_coord=None):
         _warn_auto_coordinate()
 
     if vertical_coord is None or vertical_coord == "auto":
-        list_vertical = ["z", "model_level_number", "altitude", "geopotential_height"]
-        all_vertical_axes = list(set(variable_dataframe.columns) & set(list_vertical))
+        all_vertical_axes = list(
+            set(variable_dataframe.columns) & set(COMMON_VERT_COORDS)
+        )
         if len(all_vertical_axes) == 1:
             return all_vertical_axes[0]
         else:
@@ -568,7 +539,7 @@ def find_dataframe_vertical_coord(variable_dataframe, vertical_coord=None):
 
 
 @njit_if_available
-def calc_distance_coords(coords_1, coords_2):
+def calc_distance_coords(coords_1: np.array, coords_2: np.array) -> float:
     """Function to calculate the distance between cartesian
     coordinate set 1 and coordinate set 2.
     Parameters
@@ -595,13 +566,17 @@ def calc_distance_coords(coords_1, coords_2):
     return np.sqrt(np.sum(deltas**2))
 
 
-def find_hdim_axes_3D(field_in, vertical_coord=None, vertical_axis=None):
+def find_hdim_axes_3D(
+    field_in: Union[iris.cube.Cube, xr.DataArray],
+    vertical_coord: Union[str, None] = None,
+    vertical_axis: Union[int, None] = None,
+) -> tuple[int]:
     """Finds what the hdim axes are given a 3D (including z) or
     4D (including z and time) dataset.
 
     Parameters
     ----------
-    field_in: iris cube or xarray dataset
+    field_in: iris cube or xarray dataarray
         Input field, can be 3D or 4D
     vertical_coord: str
         The name of the vertical coord, or None, which will attempt to find
@@ -616,7 +591,6 @@ def find_hdim_axes_3D(field_in, vertical_coord=None, vertical_axis=None):
         The axes for hdim_1 and hdim_2
 
     """
-    from iris import cube as iris_cube
 
     if vertical_coord == "auto":
         _warn_auto_coordinate()
@@ -625,91 +599,54 @@ def find_hdim_axes_3D(field_in, vertical_coord=None, vertical_axis=None):
         if vertical_coord != "auto":
             raise ValueError("Cannot set both vertical_coord and vertical_axis.")
 
-    if type(field_in) is iris_cube.Cube:
-        return find_hdim_axes_3D_iris(field_in, vertical_coord, vertical_axis)
+    if type(field_in) is iris.cube.Cube:
+        return iris_utils.find_hdim_axes_3d(field_in, vertical_coord, vertical_axis)
     elif type(field_in) is xr.DataArray:
         raise NotImplementedError("Xarray find_hdim_axes_3D not implemented")
     else:
         raise ValueError("Unknown data type: " + type(field_in).__name__)
 
 
-def find_hdim_axes_3D_iris(field_in, vertical_coord=None, vertical_axis=None):
-    """Finds what the hdim axes are given a 3D (including z) or
-    4D (including z and time) dataset.
+def find_axis_from_coord(
+    variable_arr: Union[iris.cube.Cube, xr.DataArray], coord_name: str
+) -> int:
+    """Finds the axis number in an xarray or iris cube given a coordinate or dimension name.
 
     Parameters
     ----------
-    field_in: iris cube
-        Input field, can be 3D or 4D
-    vertical_coord: str or None
-        The name of the vertical coord, or None, which will attempt to find
-        the vertical coordinate name
-    vertical_axis: int or None
-        The axis number of the vertical coordinate, or None. Note
-        that only one of vertical_axis or vertical_coord can be set.
+    variable_arr: iris.cube.Cube or xarray.DataArray
+        Input variable cube
+    coord_name: str
+        coordinate or dimension to look for
 
     Returns
     -------
-    (hdim_1_axis, hdim_2_axis): (int, int)
-        The axes for hdim_1 and hdim_2
+    axis_number: int
+        the number of the axis of the given coordinate, or None if the coordinate
+        is not found in the variable or not a dimensional coordinate
     """
 
-    if vertical_coord == "auto":
-        _warn_auto_coordinate()
-
-    if vertical_coord is not None and vertical_axis is not None:
-        if vertical_coord != "auto":
-            raise ValueError("Cannot set both vertical_coord and vertical_axis.")
-
-    time_axis = find_axis_from_coord(field_in, "time")
-    if vertical_axis is not None:
-        vertical_coord_axis = vertical_axis
-        vert_coord_found = True
+    if isinstance(variable_arr, iris.cube.Cube):
+        return iris_utils.find_axis_from_coord(variable_arr, coord_name)
+    elif isinstance(variable_arr, xr.DataArray):
+        raise NotImplementedError(
+            "xarray version of find_axis_from_coord not implemented."
+        )
     else:
-        try:
-            vertical_axis = find_vertical_axis_from_coord(
-                field_in, vertical_coord=vertical_coord
-            )
-        except ValueError:
-            vert_coord_found = False
-        else:
-            vert_coord_found = True
-            ndim_vertical = field_in.coord_dims(vertical_axis)
-            if len(ndim_vertical) > 1:
-                raise ValueError(
-                    "please specify 1 dimensional vertical coordinate."
-                    " Current vertical coordinates: {0}".format(ndim_vertical)
-                )
-            if len(ndim_vertical) != 0:
-                vertical_coord_axis = ndim_vertical[0]
-            else:
-                # this means the vertical coordinate is an auxiliary coordinate of some kind.
-                vert_coord_found = False
-
-    if not vert_coord_found:
-        # if we don't have a vertical coordinate, and we are 3D or lower
-        # that is okay.
-        if (field_in.ndim == 3 and time_axis is not None) or field_in.ndim < 3:
-            vertical_coord_axis = None
-        else:
-            raise ValueError("No suitable vertical coordinate found")
-    # Once we know the vertical coordinate, we can resolve the
-    # horizontal coordinates
-
-    all_axes = np.arange(0, field_in.ndim)
-    output_vals = tuple(
-        all_axes[np.logical_not(np.isin(all_axes, [time_axis, vertical_coord_axis]))]
-    )
-    return output_vals
+        raise ValueError("variable_arr must be Iris Cube or Xarray DataArray")
 
 
 @irispandas_to_xarray
-def detect_latlon_coord_name(in_dataset, latitude_name=None, longitude_name=None):
+def detect_latlon_coord_name(
+    in_dataset: Union[xr.DataArray, iris.cube.Cube],
+    latitude_name: Union[str, None] = None,
+    longitude_name: Union[str, None] = None,
+) -> tuple[str]:
     """Function to detect the name of latitude/longitude coordinates
 
     Parameters
     ----------
-    in_dataset: iris.cube.Cube, xarray.Dataset, or xarray.Dataarray
+    in_dataset: iris.cube.Cube or xarray.DataArray
         Input dataset to detect names from
     latitude_name: str
         The name of the latitude coordinate. If None, tries to auto-detect.
diff --git a/tobac/utils/internal/internal_consts.py b/tobac/utils/internal/internal_consts.py
new file mode 100644
index 00000000..a3ec44f5
--- /dev/null
+++ b/tobac/utils/internal/internal_consts.py
@@ -0,0 +1,6 @@
+COMMON_VERT_COORDS: list[str] = [
+    "z",
+    "model_level_number",
+    "altitude",
+    "geopotential_height",
+]
diff --git a/tobac/utils/internal/iris_utils.py b/tobac/utils/internal/iris_utils.py
new file mode 100644
index 00000000..029061cb
--- /dev/null
+++ b/tobac/utils/internal/iris_utils.py
@@ -0,0 +1,156 @@
+"""Internal tobac utilities for iris cubes
+The goal will be to, ultimately, remove these when we sunset iris
+"""
+from __future__ import annotations
+
+from typing import Union
+
+import iris
+import iris.cube
+import numpy as np
+
+from . import general_internal as tb_utils_gi
+
+
+def find_axis_from_coord(
+    variable_cube: iris.cube.Cube, coord_name: str
+) -> Union[int, None]:
+    """Finds the axis number in an iris cube given a coordinate name.
+
+    Parameters
+    ----------
+    variable_cube: iris.cube
+        Input variable cube
+    coord_name: str
+        coordinate to look for
+
+    Returns
+    -------
+    axis_number: int
+        the number of the axis of the given coordinate, or None if the coordinate
+        is not found in the cube or not a dimensional coordinate
+    """
+
+    list_coord_names = [coord.name() for coord in variable_cube.coords()]
+    all_matching_axes = list(set(list_coord_names) & {coord_name})
+    if (
+        len(all_matching_axes) == 1
+        and len(variable_cube.coord_dims(all_matching_axes[0])) > 0
+    ):
+        return variable_cube.coord_dims(all_matching_axes[0])[0]
+    if len(all_matching_axes) > 1:
+        raise ValueError("Too many axes matched.")
+
+    return None
+
+
+def find_vertical_axis_from_coord(
+    variable_cube: iris.cube.Cube, vertical_coord: Union[str, None] = None
+) -> str:
+    """Function to find the vertical coordinate in the iris cube
+
+    Parameters
+    ----------
+    variable_cube: iris.cube
+        Input variable cube, containing a vertical coordinate.
+    vertical_coord: str
+        Vertical coordinate name. If None, this function tries to auto-detect.
+
+    Returns
+    -------
+    str
+        the vertical coordinate name
+
+    Raises
+    ------
+    ValueError
+        Raised if the vertical coordinate isn't found in the cube.
+    """
+
+    list_coord_names = [coord.name() for coord in variable_cube.coords()]
+
+    if vertical_coord is None or vertical_coord == "auto":
+        # find the intersection
+        all_vertical_axes = list(
+            set(list_coord_names) & set(tb_utils_gi.COMMON_VERT_COORDS)
+        )
+        if len(all_vertical_axes) >= 1:
+            return all_vertical_axes[0]
+        raise ValueError(
+            "Cube lacks suitable automatic vertical coordinate (z, model_level_number, altitude, "
+            "or geopotential_height)"
+        )
+    if vertical_coord in list_coord_names:
+        return vertical_coord
+    raise ValueError("Please specify vertical coordinate found in cube")
+
+
+def find_hdim_axes_3d(
+    field_in: iris.cube.Cube,
+    vertical_coord: Union[str, None] = None,
+    vertical_axis: Union[int, None] = None,
+) -> tuple[int]:
+    """Finds what the hdim axes are given a 3D (including z) or
+    4D (including z and time) dataset.
+
+    Parameters
+    ----------
+    field_in: iris cube
+        Input field, can be 3D or 4D
+    vertical_coord: str or None
+        The name of the vertical coord, or None, which will attempt to find
+        the vertical coordinate name
+    vertical_axis: int or None
+        The axis number of the vertical coordinate, or None. Note
+        that only one of vertical_axis or vertical_coord can be set.
+
+    Returns
+    -------
+    (hdim_1_axis, hdim_2_axis): (int, int)
+        The axes for hdim_1 and hdim_2
+    """
+
+    if vertical_coord is not None and vertical_axis is not None:
+        if vertical_coord != "auto":
+            raise ValueError("Cannot set both vertical_coord and vertical_axis.")
+
+    time_axis = find_axis_from_coord(field_in, "time")
+    if vertical_axis is not None:
+        vertical_coord_axis = vertical_axis
+        vert_coord_found = True
+    else:
+        try:
+            vertical_axis = find_vertical_axis_from_coord(
+                field_in, vertical_coord=vertical_coord
+            )
+        except ValueError:
+            vert_coord_found = False
+        else:
+            vert_coord_found = True
+            ndim_vertical = field_in.coord_dims(vertical_axis)
+            if len(ndim_vertical) > 1:
+                raise ValueError(
+                    "please specify 1 dimensional vertical coordinate."
+                    f" Current vertical coordinates: {ndim_vertical}"
+                )
+            if len(ndim_vertical) != 0:
+                vertical_coord_axis = ndim_vertical[0]
+            else:
+                # this means the vertical coordinate is an auxiliary coordinate of some kind.
+                vert_coord_found = False
+
+    if not vert_coord_found:
+        # if we don't have a vertical coordinate, and we are 3D or lower
+        # that is okay.
+        if (field_in.ndim == 3 and time_axis is not None) or field_in.ndim < 3:
+            vertical_coord_axis = None
+        else:
+            raise ValueError("No suitable vertical coordinate found")
+    # Once we know the vertical coordinate, we can resolve the
+    # horizontal coordinates
+
+    all_axes = np.arange(0, field_in.ndim)
+    output_vals = tuple(
+        all_axes[np.logical_not(np.isin(all_axes, [time_axis, vertical_coord_axis]))]
+    )
+    return output_vals
diff --git a/tobac/utils/internal/xarray_utils.py b/tobac/utils/internal/xarray_utils.py
new file mode 100644
index 00000000..641be123
--- /dev/null
+++ b/tobac/utils/internal/xarray_utils.py
@@ -0,0 +1,50 @@
+"""Internal tobac utilities for xarray datasets/dataarrays
+"""
+from __future__ import annotations
+
+
+from typing import Union
+import xarray as xr
+from . import general_internal as tb_utils_gi
+
+
+def find_vertical_axis_from_coord(
+    variable_cube: xr.DataArray,
+    vertical_coord: Union[str, None] = None,
+) -> str:
+    """Function to find the vertical coordinate in the iris cube
+
+    Parameters
+    ----------
+    variable_cube: iris.cube.Cube or xarray.DataArray
+        Input variable cube, containing a vertical coordinate.
+    vertical_coord: str
+        Vertical coordinate name. If None, this function tries to auto-detect.
+
+    Returns
+    -------
+    str
+        the vertical coordinate name
+
+    Raises
+    ------
+    ValueError
+        Raised if the vertical coordinate isn't found in the cube.
+    """
+
+    list_coord_names = variable_cube.coords
+
+    if vertical_coord is None or vertical_coord == "auto":
+        # find the intersection
+        all_vertical_axes = list(
+            set(list_coord_names) & set(tb_utils_gi.COMMON_VERT_COORDS)
+        )
+        if len(all_vertical_axes) >= 1:
+            return all_vertical_axes[0]
+        raise ValueError(
+            "Cube lacks suitable automatic vertical coordinate (z, model_level_number, "
+            "altitude, or geopotential_height)"
+        )
+    if vertical_coord in list_coord_names:
+        return vertical_coord
+    raise ValueError("Please specify vertical coordinate found in cube")

From e179280e02c1a5a4417fa0b4c6d47ef98d030699 Mon Sep 17 00:00:00 2001
From: Sean Freeman <sean.freeman@uah.edu>
Date: Tue, 19 Sep 2023 12:04:46 -0700
Subject: [PATCH 2/9] fixing packaging problems

---
 setup.py                | 2 +-
 tobac/utils/__init__.py | 5 ++++-
 tobac/utils/general.py  | 1 -
 3 files changed, 5 insertions(+), 3 deletions(-)

diff --git a/setup.py b/setup.py
index e01547e0..68b13c4d 100644
--- a/setup.py
+++ b/setup.py
@@ -86,7 +86,7 @@ def get_requirements(requirements_filename):
         "peter.marinescu@colostate.edu",
     ],
     license="BSD-3-Clause License",
-    packages=[PACKAGE_NAME, PACKAGE_NAME + ".utils"],
+    packages=[PACKAGE_NAME, PACKAGE_NAME + ".utils", PACKAGE_NAME + ".utils.internal"],
     install_requires=get_requirements("requirements.txt"),
     test_requires=["pytest"],
     zip_safe=False,
diff --git a/tobac/utils/__init__.py b/tobac/utils/__init__.py
index e8c077a2..52a1222a 100644
--- a/tobac/utils/__init__.py
+++ b/tobac/utils/__init__.py
@@ -18,4 +18,7 @@
     mask_features_surface,
     mask_cube_features,
 )
-from .internal import get_label_props_in_dict, get_indices_of_labels_from_reg_prop_dict
+from tobac.utils.internal import (
+    get_label_props_in_dict,
+    get_indices_of_labels_from_reg_prop_dict,
+)
diff --git a/tobac/utils/general.py b/tobac/utils/general.py
index 1146136d..2d2c5fd7 100644
--- a/tobac/utils/general.py
+++ b/tobac/utils/general.py
@@ -5,7 +5,6 @@
 import logging
 
 import pandas as pd
-
 from . import internal as internal_utils
 import numpy as np
 import sklearn

From 292a122edd3d9a6f80095ebbfedbd0db681c7b3a Mon Sep 17 00:00:00 2001
From: Sean Freeman <sean.freeman@uah.edu>
Date: Tue, 19 Sep 2023 13:22:39 -0700
Subject: [PATCH 3/9] cleaning up

---
 tobac/utils/__init__.py | 5 +----
 tobac/utils/general.py  | 1 +
 2 files changed, 2 insertions(+), 4 deletions(-)

diff --git a/tobac/utils/__init__.py b/tobac/utils/__init__.py
index b5fd2f5b..14e5773f 100644
--- a/tobac/utils/__init__.py
+++ b/tobac/utils/__init__.py
@@ -19,7 +19,4 @@
     mask_features_surface,
     mask_cube_features,
 )
-from tobac.utils.internal import (
-    get_label_props_in_dict,
-    get_indices_of_labels_from_reg_prop_dict,
-)
+from .internal import get_label_props_in_dict, get_indices_of_labels_from_reg_prop_dict
diff --git a/tobac/utils/general.py b/tobac/utils/general.py
index c08f2d98..7836a9c6 100644
--- a/tobac/utils/general.py
+++ b/tobac/utils/general.py
@@ -5,6 +5,7 @@
 import logging
 
 import pandas as pd
+
 from . import internal as internal_utils
 import numpy as np
 import sklearn

From f574ed7c1a79a3b90dfd3a73418dbc9185a183e5 Mon Sep 17 00:00:00 2001
From: Sean Freeman <sean.freeman@uah.edu>
Date: Tue, 19 Sep 2023 13:36:30 -0700
Subject: [PATCH 4/9] deleting non-used file

---
 tobac/utils/internal/internal_consts.py | 6 ------
 1 file changed, 6 deletions(-)
 delete mode 100644 tobac/utils/internal/internal_consts.py

diff --git a/tobac/utils/internal/internal_consts.py b/tobac/utils/internal/internal_consts.py
deleted file mode 100644
index a3ec44f5..00000000
--- a/tobac/utils/internal/internal_consts.py
+++ /dev/null
@@ -1,6 +0,0 @@
-COMMON_VERT_COORDS: list[str] = [
-    "z",
-    "model_level_number",
-    "altitude",
-    "geopotential_height",
-]

From bf2335e5f9144dbf0980642f5e456cf0bb0ed390 Mon Sep 17 00:00:00 2001
From: Sean Freeman <sean.freeman@uah.edu>
Date: Mon, 2 Oct 2023 10:14:17 -0500
Subject: [PATCH 5/9] adding build.os to rtd config

---
 .readthedocs.yml | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/.readthedocs.yml b/.readthedocs.yml
index 1fcc341c..adecddb6 100644
--- a/.readthedocs.yml
+++ b/.readthedocs.yml
@@ -1,5 +1,9 @@
 version: 2
 formats: all
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.11"
 python:
   version: 3
   install:

From 3c60e441e6d4c170032388cf111910b5b45ba684 Mon Sep 17 00:00:00 2001
From: Sean Freeman <sean.freeman@uah.edu>
Date: Tue, 3 Oct 2023 11:44:10 -0500
Subject: [PATCH 6/9] update readthedocs config

---
 .readthedocs.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/.readthedocs.yml b/.readthedocs.yml
index adecddb6..676445e1 100644
--- a/.readthedocs.yml
+++ b/.readthedocs.yml
@@ -5,6 +5,5 @@ build:
   tools:
     python: "3.11"
 python:
-  version: 3
   install:
     - requirements: doc/requirements.txt
\ No newline at end of file

From 18f322f5f155ca825c8440f99752e619524afc4b Mon Sep 17 00:00:00 2001
From: Sean Freeman <sean.freeman@uah.edu>
Date: Tue, 3 Oct 2023 12:25:38 -0500
Subject: [PATCH 7/9] switch to using typing.callable explicitly

---
 tobac/utils/internal/general_internal.py | 13 +++++++------
 1 file changed, 7 insertions(+), 6 deletions(-)

diff --git a/tobac/utils/internal/general_internal.py b/tobac/utils/internal/general_internal.py
index a9d3df3c..1da83ffd 100644
--- a/tobac/utils/internal/general_internal.py
+++ b/tobac/utils/internal/general_internal.py
@@ -11,7 +11,8 @@
 import warnings
 from . import iris_utils
 from . import xarray_utils as xr_utils
-from typing import Union, Callable
+from typing import Union
+import typing
 
 # list of common vertical coordinates to search for in various functions
 COMMON_VERT_COORDS: list[str] = [
@@ -109,7 +110,7 @@ def get_indices_of_labels_from_reg_prop_dict(region_property_dict: dict) -> tupl
         return [curr_loc_indices, y_indices, x_indices]
 
 
-def iris_to_xarray(func: Callable) -> Callable:
+def iris_to_xarray(func: typing.Callable) -> typing.Callable:
     """Decorator that converts all input of a function that is in the form of
     Iris cubes into xarray DataArrays and converts all outputs with type
     xarray DataArrays back into Iris cubes.
@@ -175,7 +176,7 @@ def wrapper(*args, **kwargs):
     return wrapper
 
 
-def xarray_to_iris(func: Callable) -> Callable:
+def xarray_to_iris(func: typing.Callable) -> typing.Callable:
     """Decorator that converts all input of a function that is in the form of
     xarray DataArrays into Iris cubes and converts all outputs with type
     Iris cubes back into xarray DataArrays.
@@ -259,7 +260,7 @@ def wrapper(*args, **kwargs):
     return wrapper
 
 
-def irispandas_to_xarray(func: Callable) -> Callable:
+def irispandas_to_xarray(func: typing.Callable) -> typing.Callable:
     """Decorator that converts all input of a function that is in the form of
     Iris cubes/pandas Dataframes into xarray DataArrays/xarray Datasets and
     converts all outputs with the type xarray DataArray/xarray Dataset
@@ -339,7 +340,7 @@ def wrapper(*args, **kwargs):
     return wrapper
 
 
-def xarray_to_irispandas(func: Callable) -> Callable:
+def xarray_to_irispandas(func: typing.Callable) -> typing.Callable:
     """Decorator that converts all input of a function that is in the form of
     DataArrays/xarray Datasets into xarray Iris cubes/pandas Dataframes and
     converts all outputs with the type Iris cubes/pandas Dataframes back into
@@ -442,7 +443,7 @@ def wrapper(*args, **kwargs):
     return wrapper
 
 
-def njit_if_available(func: Callable, **kwargs) -> Callable:
+def njit_if_available(func: typing.Callable, **kwargs) -> typing.Callable:
     """Decorator to wrap a function with numba.njit if available.
     If numba isn't available, it just returns the function.
 

From cf0e34313f0a0c7baefe7ae9ae073bc202481138 Mon Sep 17 00:00:00 2001
From: Sean Freeman <sean.freeman@uah.edu>
Date: Tue, 3 Oct 2023 12:33:28 -0500
Subject: [PATCH 8/9] revert typing changes, switch to 3.9 building of python

---
 .readthedocs.yml                         |  2 +-
 tobac/utils/internal/general_internal.py | 13 ++++++-------
 2 files changed, 7 insertions(+), 8 deletions(-)

diff --git a/.readthedocs.yml b/.readthedocs.yml
index 676445e1..96837528 100644
--- a/.readthedocs.yml
+++ b/.readthedocs.yml
@@ -3,7 +3,7 @@ formats: all
 build:
   os: ubuntu-22.04
   tools:
-    python: "3.11"
+    python: "3.9"
 python:
   install:
     - requirements: doc/requirements.txt
\ No newline at end of file
diff --git a/tobac/utils/internal/general_internal.py b/tobac/utils/internal/general_internal.py
index 1da83ffd..a9d3df3c 100644
--- a/tobac/utils/internal/general_internal.py
+++ b/tobac/utils/internal/general_internal.py
@@ -11,8 +11,7 @@
 import warnings
 from . import iris_utils
 from . import xarray_utils as xr_utils
-from typing import Union
-import typing
+from typing import Union, Callable
 
 # list of common vertical coordinates to search for in various functions
 COMMON_VERT_COORDS: list[str] = [
@@ -110,7 +109,7 @@ def get_indices_of_labels_from_reg_prop_dict(region_property_dict: dict) -> tupl
         return [curr_loc_indices, y_indices, x_indices]
 
 
-def iris_to_xarray(func: typing.Callable) -> typing.Callable:
+def iris_to_xarray(func: Callable) -> Callable:
     """Decorator that converts all input of a function that is in the form of
     Iris cubes into xarray DataArrays and converts all outputs with type
     xarray DataArrays back into Iris cubes.
@@ -176,7 +175,7 @@ def wrapper(*args, **kwargs):
     return wrapper
 
 
-def xarray_to_iris(func: typing.Callable) -> typing.Callable:
+def xarray_to_iris(func: Callable) -> Callable:
     """Decorator that converts all input of a function that is in the form of
     xarray DataArrays into Iris cubes and converts all outputs with type
     Iris cubes back into xarray DataArrays.
@@ -260,7 +259,7 @@ def wrapper(*args, **kwargs):
     return wrapper
 
 
-def irispandas_to_xarray(func: typing.Callable) -> typing.Callable:
+def irispandas_to_xarray(func: Callable) -> Callable:
     """Decorator that converts all input of a function that is in the form of
     Iris cubes/pandas Dataframes into xarray DataArrays/xarray Datasets and
     converts all outputs with the type xarray DataArray/xarray Dataset
@@ -340,7 +339,7 @@ def wrapper(*args, **kwargs):
     return wrapper
 
 
-def xarray_to_irispandas(func: typing.Callable) -> typing.Callable:
+def xarray_to_irispandas(func: Callable) -> Callable:
     """Decorator that converts all input of a function that is in the form of
     DataArrays/xarray Datasets into xarray Iris cubes/pandas Dataframes and
     converts all outputs with the type Iris cubes/pandas Dataframes back into
@@ -443,7 +442,7 @@ def wrapper(*args, **kwargs):
     return wrapper
 
 
-def njit_if_available(func: typing.Callable, **kwargs) -> typing.Callable:
+def njit_if_available(func: Callable, **kwargs) -> Callable:
     """Decorator to wrap a function with numba.njit if available.
     If numba isn't available, it just returns the function.
 

From 689e8622b793578fcad4a72f358f3dc9edd97783 Mon Sep 17 00:00:00 2001
From: Sean Freeman <sean.freeman@uah.edu>
Date: Wed, 8 Nov 2023 10:10:43 -0600
Subject: [PATCH 9/9] rename general_internal to basic

---
 tobac/utils/internal/__init__.py                       | 2 +-
 tobac/utils/internal/{general_internal.py => basic.py} | 0
 tobac/utils/internal/iris_utils.py                     | 2 +-
 tobac/utils/internal/xarray_utils.py                   | 2 +-
 4 files changed, 3 insertions(+), 3 deletions(-)
 rename tobac/utils/internal/{general_internal.py => basic.py} (100%)

diff --git a/tobac/utils/internal/__init__.py b/tobac/utils/internal/__init__.py
index 463d824c..da0f2b60 100644
--- a/tobac/utils/internal/__init__.py
+++ b/tobac/utils/internal/__init__.py
@@ -1 +1 @@
-from .general_internal import *
+from .basic import *
diff --git a/tobac/utils/internal/general_internal.py b/tobac/utils/internal/basic.py
similarity index 100%
rename from tobac/utils/internal/general_internal.py
rename to tobac/utils/internal/basic.py
diff --git a/tobac/utils/internal/iris_utils.py b/tobac/utils/internal/iris_utils.py
index 029061cb..36561799 100644
--- a/tobac/utils/internal/iris_utils.py
+++ b/tobac/utils/internal/iris_utils.py
@@ -9,7 +9,7 @@
 import iris.cube
 import numpy as np
 
-from . import general_internal as tb_utils_gi
+from . import basic as tb_utils_gi
 
 
 def find_axis_from_coord(
diff --git a/tobac/utils/internal/xarray_utils.py b/tobac/utils/internal/xarray_utils.py
index 641be123..6d37dacc 100644
--- a/tobac/utils/internal/xarray_utils.py
+++ b/tobac/utils/internal/xarray_utils.py
@@ -5,7 +5,7 @@
 
 from typing import Union
 import xarray as xr
-from . import general_internal as tb_utils_gi
+from . import basic as tb_utils_gi
 
 
 def find_vertical_axis_from_coord(