From f4e003b84a57773ab51b6cdc0438f285264c50d4 Mon Sep 17 00:00:00 2001 From: Joshua Scarsbrook Date: Tue, 28 Jul 2026 00:06:52 +1000 Subject: [PATCH 1/2] Fix CLI output directory type --- brainles_preprocessing/cli.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/brainles_preprocessing/cli.py b/brainles_preprocessing/cli.py index 5490d51..2a8315b 100644 --- a/brainles_preprocessing/cli.py +++ b/brainles_preprocessing/cli.py @@ -59,7 +59,7 @@ def main( ), ], output_dir: Annotated[ - str | Path, + str, typer.Option( "-o", "--output_dir", From 6736cfa3cee8a34e38e943746dcb6d9641b1659c Mon Sep 17 00:00:00 2001 From: Joshua Scarsbrook Date: Sun, 2 Aug 2026 23:16:32 +1000 Subject: [PATCH 2/2] Use native Path type for CLI output directory --- brainles_preprocessing/cli.py | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/brainles_preprocessing/cli.py b/brainles_preprocessing/cli.py index 2a8315b..465075a 100644 --- a/brainles_preprocessing/cli.py +++ b/brainles_preprocessing/cli.py @@ -59,11 +59,15 @@ def main( ), ], output_dir: Annotated[ - str, + Path, typer.Option( "-o", "--output_dir", help="The path to the output directory", + exists=False, + file_okay=False, + dir_okay=True, + resolve_path=True, ), ], input_atlas: Annotated[ @@ -89,7 +93,6 @@ def main( Preprocess the input images according to the BraTS protocol. """ - output_dir = Path(output_dir) output_dir.mkdir(parents=True, exist_ok=True) # specify a normalizer