Fix pandas FutureWarning (#144)

* Write safe concat function

* Use safe concat of dataframes

* Fix logic of safe concat method

* pre-commit pass

* Add unit test to aplease codecov overlords

* Update tests/tests/test_unit/test_misc.py

Co-authored-by: Alessandro Felder <[email protected]>

---------

Co-authored-by: Alessandro Felder <[email protected]>

src/brainreg/utils/misc.py

@@ -2,6 +2,8 @@
 from argparse import Namespace
 from pathlib import PurePath
 
+import pandas as pd
+
 
 def get_arg_groups(args, parser):
     arg_groups = {}
@@ -24,3 +26,28 @@ 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)

src/brainreg/utils/volume.py

@@ -12,6 +12,8 @@
 import pandas as pd
 from brainglobe_utils.pandas.misc import initialise_df
 
+from .misc import safe_pandas_concat
+
 
 class UnknownAtlasValue(Exception):
     pass
@@ -100,7 +102,7 @@ def add_structure_volume_to_df(
             "total_volume_mm3": [left_volume + right_volume],
         }
     )
-    df = pd.concat([df, df_new_row], ignore_index=True)
+    df = safe_pandas_concat(df, df_new_row)
     return df
 
 

tests/tests/test_unit/test_misc.py

@@ -0,0 +1,21 @@
+import pandas as pd
+from brainreg.utils.misc import safe_pandas_concat
+
+
+def test_safe_pandas_concat() -> None:
+    """
+    Test the following:
+    - Non-empty dataframes are concatenated as expected,
+    - When one dataframe is empty, the other is returned,
+    - When both dataframes are empty, an empty dataframe with
+    the corresponding columns is returned.
+    """
+    df1 = pd.DataFrame(data={"a": [1], "b": [2], "c": [3]})
+    df2 = pd.DataFrame(data={"a": [4], "b": [5], "c": [6]})
+    empty_df = pd.DataFrame(columns=["a", "b", "c"])
+    combined_df = pd.DataFrame(data={"a": [1, 4], "b": [2, 5], "c": [3, 6]})
+
+    assert combined_df.equals(safe_pandas_concat(df1, df2))
+    assert df1.equals(safe_pandas_concat(df1, empty_df))
+    assert df2.equals(safe_pandas_concat(empty_df, df2))
+    assert empty_df.equals(safe_pandas_concat(empty_df, empty_df))