qsiprep_dir --> output_dir

qsiprep/cli/workflow.py

@@ -67,7 +67,7 @@ def build_workflow(config_file, exec_mode, retval):
     build_log.log(25, f"\n{' ' * 9}".join(banner))
 
     # warn if older results exist: check for dataset_description.json in output folder
-    # msg = check_pipeline_version("QSIPrep", version, qsiprep_dir / "dataset_description.json")
+    # msg = check_pipeline_version("QSIPrep", version, output_dir / "dataset_description.json")
     # if msg is not None:
     #     build_log.warning(msg)
 

qsiprep/config.py

@@ -28,7 +28,7 @@
 This module implements the memory structures to keep a consistent, singleton config.
 Settings are passed across processes via filesystem, and a copy of the settings for
 each run and subject is left under
-``<qsiprep_dir>/sub-<participant_id>/log/<run_unique_id>/qsiprep.toml``.
+``<output_dir>/sub-<participant_id>/log/<run_unique_id>/qsiprep.toml``.
 Settings are stored using :abbr:`ToML (Tom's Markup Language)`.
 The module has a :py:func:`~qsiprep.config.to_filename` function to allow writing out
 the settings to hard disk in *ToML* format, which looks like:

qsiprep/tests/utils.py

@@ -88,10 +88,10 @@ def get_test_data_path():
     return os.path.abspath(os.path.join(os.path.dirname(__file__), "data") + os.path.sep)
 
 
-def check_generated_files(qsiprep_dir, output_list_file, optional_output_list_file):
+def check_generated_files(output_dir, output_list_file, optional_output_list_file):
     """Compare files generated by qsiprep with a list of expected files."""
-    found_files = sorted(glob(os.path.join(qsiprep_dir, "**/*"), recursive=True))
-    found_files = [os.path.relpath(f, qsiprep_dir) for f in found_files]
+    found_files = sorted(glob(os.path.join(output_dir, "**/*"), recursive=True))
+    found_files = [os.path.relpath(f, output_dir) for f in found_files]
 
     # Ignore figures
     found_files = sorted(list(set([f for f in found_files if "figures" not in f])))