From 721e7288366200545c10fd9d9f860541a0a014e0 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Victor=20F=C3=A9rat?= <victor.ferat@live.Fr>
Date: Mon, 7 Aug 2023 19:01:32 +0200
Subject: [PATCH] Added deriv_root argument to CLI (#773)
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: Richard Höchenberger <richard.hoechenberger@gmail.com>
---
 docs/source/v1.5.md.inc    |  1 +
 mne_bids_pipeline/_main.py | 17 +++++++++++++++++
 2 files changed, 18 insertions(+)

diff --git a/docs/source/v1.5.md.inc b/docs/source/v1.5.md.inc
index 234232028..af661698d 100644
--- a/docs/source/v1.5.md.inc
+++ b/docs/source/v1.5.md.inc
@@ -2,6 +2,7 @@
 
 ### :new: New features & enhancements
 
+- Added `deriv_root` argument to CLI (#773 by @vferat)
 - Added support for annotating bad segments based on head movement velocity (#757 by @larsoner)
 - Added examples of T1 and FLASH BEM to website (#758 by @larsoner)
 - Added support for extended SSS (eSSS) in Maxwell filtering (#762 by @larsoner)
diff --git a/mne_bids_pipeline/_main.py b/mne_bids_pipeline/_main.py
index cd9ee1037..9489a2cca 100755
--- a/mne_bids_pipeline/_main.py
+++ b/mne_bids_pipeline/_main.py
@@ -59,6 +59,18 @@ def main():
         default=None,
         help="BIDS root directory of the data to process.",
     )
+    parser.add_argument(
+        "--deriv_root",
+        dest="deriv_root",
+        default=None,
+        help=dedent(
+            """\
+        The root of the derivatives directory
+        in which the pipeline will store the processing results.
+        If unspecified, this will be derivatives/mne-bids-pipeline
+        inside the BIDS root."""
+        ),
+    ),
     parser.add_argument(
         "--subject", dest="subject", default=None, help="The subject to process."
     )
@@ -115,6 +127,7 @@ def main():
         )
     steps = options.steps
     root_dir = options.root_dir
+    deriv_root = options.deriv_root
     subject, session = options.subject, options.session
     task, run = options.task, options.run
     n_jobs = options.n_jobs
@@ -148,6 +161,10 @@ def main():
     overrides = SimpleNamespace()
     if root_dir:
         overrides.bids_root = pathlib.Path(root_dir).expanduser().resolve(strict=True)
+    if deriv_root:
+        overrides.deriv_root = (
+            pathlib.Path(deriv_root).expanduser().resolve(strict=False)
+        )
     if subject:
         overrides.subjects = [subject]
     if session: