From 5ce6459d636317c0553c1cfd4945a9d72a977034 Mon Sep 17 00:00:00 2001
From: Kevin Sitek <sitek.kevin@gmail.com>
Date: Fri, 11 Sep 2026 15:38:20 -0500
Subject: [PATCH 1/2] Added option to skip referencing if dataset already
 referenced

---
 ffrprep/ffrprep_cli.py    | 10 ++++++++--
 ffrprep/preproc.py        |  3 ++-
 ffrprep/tests/test_cli.py | 14 ++++++++++++++
 3 files changed, 24 insertions(+), 3 deletions(-)

diff --git a/ffrprep/ffrprep_cli.py b/ffrprep/ffrprep_cli.py
index b9bd3db..1ce50c5 100644
--- a/ffrprep/ffrprep_cli.py
+++ b/ffrprep/ffrprep_cli.py
@@ -1561,8 +1561,10 @@ def get_parser():
         help=(
             "Reference channel(s) for re-referencing. Provide space-separated "
             "channel names (e.g. --ref_channels M1 M2). Use 'average' for "
-            "average reference. Comma-separated single-argument styles are "
-            "also accepted for backward compatibility (e.g. 'M1,M2')."
+            "average reference, or 'skip' if the data is already referenced "
+            "and should not be re-referenced. Comma-separated single-argument "
+            "styles are also accepted for backward compatibility (e.g. "
+            "'M1,M2')."
         ),
         nargs="+",
         type=str,
@@ -1813,6 +1815,8 @@ def parse_ref_channels(ref_str):
         # Already a sequence; ensure items are stripped and handle
         # comma-separated tokens inside any element for backward
         # compatibility (e.g. ['M1,M2'] -> ['M1','M2']).
+        if len(ref_str) == 1 and isinstance(ref_str[0], str) and ref_str[0].strip().lower() == "skip":
+            return []  # Data is already referenced; do not re-reference
         out = []
         for item in ref_str:
             if isinstance(item, str) and "," in item:
@@ -1824,6 +1828,8 @@ def parse_ref_channels(ref_str):
     s = str(ref_str)
     if s.lower() == "average":
         return None  # Average reference
+    if s.lower() == "skip":
+        return []  # Data is already referenced; do not re-reference
     if "," in s:
         # Split and strip whitespace around channel names
         return [c.strip() for c in s.split(",") if c.strip()]
diff --git a/ffrprep/preproc.py b/ffrprep/preproc.py
index 9b521df..65bc329 100644
--- a/ffrprep/preproc.py
+++ b/ffrprep/preproc.py
@@ -587,7 +587,8 @@ def reference_data(eeg_data=None, ref_channels=None):
         Channels to be used as reference. If more than one channel
         in list, the average of the channels in `ref_channels` will
         be used as the reference. If `None`, all channels will be
-        averaged as the reference.
+        averaged as the reference. If an empty list, the data is
+        marked as already referenced and is not modified.
         Default = None.
 
     Returns
diff --git a/ffrprep/tests/test_cli.py b/ffrprep/tests/test_cli.py
index 892ca57..1977ad4 100644
--- a/ffrprep/tests/test_cli.py
+++ b/ffrprep/tests/test_cli.py
@@ -235,6 +235,20 @@ def test_parse_ref_channels_empty_string():
     assert parse_ref_channels("") is None
 
 
+def test_parse_ref_channels_skip():
+    """'skip' normalizes to [] (data already referenced; do not modify)."""
+    assert parse_ref_channels("skip") == []
+    assert parse_ref_channels("SKIP") == []
+    assert parse_ref_channels("Skip") == []
+
+
+def test_parse_ref_channels_skip_from_argparse_list():
+    """--ref_channels uses nargs='+', so real CLI usage always passes a
+    list (e.g. ['skip']) rather than a bare string."""
+    assert parse_ref_channels(["skip"]) == []
+    assert parse_ref_channels(["SKIP"]) == []
+
+
 # ---------------------------------------------------------------------------
 # run_ffrprep — mocked end-to-end behavior
 # ---------------------------------------------------------------------------

From f2d3592e2cf81ec6c9ed0a2b065223cb669cfeb1 Mon Sep 17 00:00:00 2001
From: Kevin Sitek <sitek.kevin@gmail.com>
Date: Fri, 11 Sep 2026 15:42:38 -0500
Subject: [PATCH 2/2] Fixed 'average' referencing which turned into literal
 string inside list

---
 ffrprep/ffrprep_cli.py    | 2 ++
 ffrprep/tests/test_cli.py | 7 +++++++
 2 files changed, 9 insertions(+)

diff --git a/ffrprep/ffrprep_cli.py b/ffrprep/ffrprep_cli.py
index 1ce50c5..c64c2cb 100644
--- a/ffrprep/ffrprep_cli.py
+++ b/ffrprep/ffrprep_cli.py
@@ -1817,6 +1817,8 @@ def parse_ref_channels(ref_str):
         # compatibility (e.g. ['M1,M2'] -> ['M1','M2']).
         if len(ref_str) == 1 and isinstance(ref_str[0], str) and ref_str[0].strip().lower() == "skip":
             return []  # Data is already referenced; do not re-reference
+        if len(ref_str) == 1 and isinstance(ref_str[0], str) and ref_str[0].strip().lower() == "average":
+            return None  # Average reference
         out = []
         for item in ref_str:
             if isinstance(item, str) and "," in item:
diff --git a/ffrprep/tests/test_cli.py b/ffrprep/tests/test_cli.py
index 1977ad4..abec3d3 100644
--- a/ffrprep/tests/test_cli.py
+++ b/ffrprep/tests/test_cli.py
@@ -220,6 +220,13 @@ def test_parse_ref_channels_average():
     assert parse_ref_channels("Average") is None
 
 
+def test_parse_ref_channels_average_from_argparse_list():
+    """--ref_channels uses nargs='+', so real CLI usage always passes a
+    list (e.g. ['average']) rather than a bare string."""
+    assert parse_ref_channels(["average"]) is None
+    assert parse_ref_channels(["AVERAGE"]) is None
+
+
 def test_parse_ref_channels_single():
     assert parse_ref_channels("Cz") == "Cz"
     assert parse_ref_channels("TP9") == "TP9"