[TST, REF] Address pandas SettingWithCopyWarnings (#534)

* Address warning in ImagesToCoordinates.

* Address in validate_images_df.

* Raise exception on warning in tests.

nimare/tests/conftest.py

@@ -4,6 +4,7 @@
 
 import nibabel as nib
 import numpy as np
+import pandas as pd
 import pytest
 from nilearn.image import resample_img
 
@@ -12,6 +13,8 @@
 
 from ..utils import get_resource_path
 
+pd.options.mode.chained_assignment = "raise"
+
 
 @pytest.fixture(scope="session")
 def testdata_ibma(tmp_path_factory):

nimare/transforms.py

@@ -456,7 +456,7 @@ def transform(self, dataset):
 
             # specify original coordinates
             original_ids = set(old_coordinates_df["id"])
-            metadata[metadata["id"].isin(original_ids)]["coordinate_source"] = "original"
+            metadata.loc[metadata["id"].isin(original_ids), "coordinate_source"] = "original"
 
         # ensure z_stat is treated as float
         if "z_stat" in coordinates_df.columns:

nimare/utils.py

@@ -227,10 +227,12 @@ def validate_images_df(image_df):
         if not shared_path.endswith(op.sep):
             shared_path = op.dirname(shared_path) + op.sep
         LGR.info("Shared path detected: '{0}'".format(shared_path))
+        image_df_out = image_df.copy()  # To avoid SettingWithCopyWarning
         for abs_col in abs_cols:
-            image_df[abs_col + "__relative"] = image_df[abs_col].apply(
+            image_df_out[abs_col + "__relative"] = image_df[abs_col].apply(
                 lambda x: x.split(shared_path)[1] if isinstance(x, str) else x
             )
+        image_df = image_df_out
     return image_df