Switch shutil.copy2 to shutil.copyfile

Existing file permissions were copied alongside the file itself, causing issues with
overwrriting existing files even when in an temporary directory if user executing
script did not have the appropriate permissions.

This switches the `copy2` method used to `copyfile` which does not have this issue

Author: kaitj

scripts/fix_rbc_release_tr.py

@@ -244,7 +244,7 @@ def _restore_tr(resampled: Path, source: Path) -> None:
 def _patch_head_bold(head_bold: Path, native_bold: Path, work_dir: Path) -> Path:
     work_dir.mkdir(parents=True, exist_ok=True)
     patched = work_dir / head_bold.name
-    shutil.copy2(head_bold, patched)
+    shutil.copyfile(head_bold, patched)
     _restore_tr(patched, native_bold)
     return patched
 
@@ -394,11 +394,11 @@ def _export_metrics(
         zstd_dst = (
             out_func_dir / f"{stem_with_space}_reg-{reg_set}_desc-zstd_{metric}.nii.gz"
         )
-        shutil.copy2(srcs["sm6"], sm6_dst)
-        shutil.copy2(srcs["smZstd"], smzstd_dst)
+        shutil.copyfile(srcs["sm6"], sm6_dst)
+        shutil.copyfile(srcs["smZstd"], smzstd_dst)
         # ``zstd`` = z-scored raw (no smoothing); not in MetricsOutputs.
         zstd_src = compute_zscore(srcs["raw"], template_brain_mask)
-        shutil.copy2(zstd_src, zstd_dst)
+        shutil.copyfile(zstd_src, zstd_dst)
 
     for atl in atlases:
         base = f"{stem_no_space}_atlas-{atl}_space-{run.space}_reg-{reg_set}"
@@ -408,7 +408,7 @@ def _export_metrics(
         # Transpose to ``(T, n_rois)`` to match AFNI's ``.1D`` and the release.
         ts_arr = np.loadtxt(metrics.timeseries[atl])
         np.savetxt(ts_dst, ts_arr.T, delimiter="\t")
-        shutil.copy2(metrics.correlation_matrix[atl], pearson_dst)
+        shutil.copyfile(metrics.correlation_matrix[atl], pearson_dst)
         _compute_partial_correlation(ts_dst, partial_dst)
 
 
@@ -479,13 +479,13 @@ def _process_run(
                 f_low=bandpass[0],
                 f_high=bandpass[1],
             )
-            shutil.copy2(bp_result.regressed_bold, out_bold)
+            shutil.copyfile(bp_result.regressed_bold, out_bold)
             cleaned_bold = bp_result.regressed_bold
 
             bpf_reg = bandpass_regressor_file(
                 reg_file, tr=tr, f_low=bandpass[0], f_high=bandpass[1]
             )
-            shutil.copy2(bpf_reg, out_reg)
+            shutil.copyfile(bpf_reg, out_reg)
             LOG.info("  wrote reg-%s -> %s", reg_set, out_bold.name)
 
         if metrics_done: