fix: preserve directory-relative output paths

run_batdetect.py

@@ -1,5 +0,0 @@
-"""Run batdetect2.command.main() from the command line."""
-from batdetect2.cli import detect
-
-if __name__ == "__main__":
-    detect()

src/batdetect2/cli/inference.py

@@ -84,6 +84,7 @@ def common_predict_options(func):
         "--format",
         "format_name",
         type=str,
+        default="batdetect2",
         help=(
             "Output format name used by the prediction writer. If omitted, "
             "the config default is used."
@@ -159,6 +160,7 @@ def _run_prediction(
     num_workers: int,
     format_name: str | None,
     detection_threshold: float | None,
+    audio_dir: Path | None = None,
 ) -> None:
     logger.info("Initiating prediction process...")
 
@@ -182,11 +184,13 @@ def _run_prediction(
         detection_threshold=detection_threshold,
     )
 
-    common_path = audio_files[0].parent if audio_files else None
+    if audio_dir is None:
+        audio_dir = audio_files[0].parent if audio_files else None
+
     api.save_predictions(
         predictions,
         path=output_path,
-        audio_dir=common_path,
+        audio_dir=audio_dir,
         format=format_name,
     )
 
@@ -235,6 +239,7 @@ def predict_directory_command(
         num_workers=num_workers,
         format_name=format_name,
         detection_threshold=detection_threshold,
+        audio_dir=audio_dir,
     )