From abd4c934ae94d77b817257898d3fa62126ed524a Mon Sep 17 00:00:00 2001
From: maestroque <kikasgeorg@ece.auth.gr>
Date: Tue, 3 Sep 2024 17:39:07 +0300
Subject: [PATCH] Add auto mode for input files in CLI

---
 phys2denoise/cli/run.py  | 3 ++-
 phys2denoise/workflow.py | 2 +-
 2 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/phys2denoise/cli/run.py b/phys2denoise/cli/run.py
index ccaf7ab..71d34b4 100644
--- a/phys2denoise/cli/run.py
+++ b/phys2denoise/cli/run.py
@@ -69,7 +69,8 @@ def _get_parser():
         dest="mode",
         type=str,
         help="Format of the input physiological data. Options are: "
-        "physio or bids. Default is physio.",
+        "auto, physio or bids. Default is auto, which determines the input file mode automatically.",
+        default="auto",
     )
 
     # Important optional arguments
diff --git a/phys2denoise/workflow.py b/phys2denoise/workflow.py
index 0db25c7..2f3459c 100644
--- a/phys2denoise/workflow.py
+++ b/phys2denoise/workflow.py
@@ -77,7 +77,7 @@ def build(
     metrics,
     metric_args,
     metrics_to_export,
-    mode="physio",
+    mode="auto",
     fs=None,
     bids_parameters=dict(),
     bids_channel=None,