Merge branch 'main' into bgv1-dev-branch.

Includes the move of safe_pandas_concat to brainglobe-utils.

brainreg/core/utils/misc.py

@@ -2,8 +2,6 @@
 from argparse import Namespace
 from pathlib import PurePath
 
-import pandas as pd
-
 
 def get_arg_groups(args, parser):
     arg_groups = {}
@@ -26,28 +24,3 @@ def serialise(obj):
 def log_metadata(file_path, args):
     with open(file_path, "w") as f:
         json.dump(args, f, default=serialise)
-
-
-def safe_pandas_concat(df1: pd.DataFrame, df2: pd.DataFrame) -> pd.DataFrame:
-    """
-    Concatenate two DataFrames without relying on deprecated functionality
-    when one of the DataFrames is empty.
-
-    If df1 and df2 are non-empty, return the concatenation.
-    If df1 is empty and df2 is not, return a copy of df2.
-    If df1 is non-empty and df2 is, return a copy of df1.
-    If df1 and df2 are empty, return an empty DataFrame with the same column
-    names as df1.
-
-    :param df1: DataFrame to concatenate.
-    :param df2: DataFrame to concatenate.
-    :returns: DataFrame formed from concatenation of df1 and df2.
-    """
-    if df1.empty and df2.empty:
-        return pd.DataFrame(columns=df1.columns)
-    elif df1.empty:
-        return df2.copy()
-    elif df2.empty:
-        return df1.copy()
-    else:
-        return pd.concat([df1, df2], ignore_index=True)

brainreg/core/utils/volume.py

@@ -10,9 +10,7 @@
 import imio
 import numpy as np
 import pandas as pd
-from brainglobe_utils.pandas.misc import initialise_df
-
-from .misc import safe_pandas_concat
+from brainglobe_utils.pandas.misc import initialise_df, safe_pandas_concat
 
 
 class UnknownAtlasValue(Exception):

pyproject.toml

@@ -24,6 +24,7 @@ dependencies = [
     "brainglobe-utils",
     "fancylog",
     "imio",
+    "brainglobe-utils>=0.2.7",
     "numpy",
     "scikit-image",
 ]