Update.

aslprep/cli/parser.py

@@ -497,12 +497,13 @@ def _bids_filter(value):
         "world usage crucial for obtaining funding.",
     )
     g_other.add_argument(
-        "--sloppy",
-        dest="debug",
-        action="store_true",
-        default=False,
-        help="Use low-quality tools for speed - TESTING ONLY",
+        "--debug",
+        action="store",
+        nargs="+",
+        choices=config.DEBUG_MODES + ("all",),
+        help="Debug mode(s) to enable. 'all' is alias for all available modes.",
     )
+
     latest = check_latest()
     if latest is not None and currentv < latest:
         print(

aslprep/config.py

@@ -161,6 +161,11 @@
     pass
 
 
+# Debug modes are names that influence the exposure of internal details to
+# the user, either through additional derivatives or increased verbosity
+DEBUG_MODES = ("pdb",)
+
+
 class _Config:
     """An abstract class forbidding instantiation."""
 
@@ -322,6 +327,8 @@ class execution(_Config):
     """A path where anatomical derivatives are found to fast-track *sMRIPrep*."""
     bids_dir = None
     """An existing path to the dataset, which must be BIDS-compliant."""
+    bids_database_dir = None
+    """Path to the directory containing SQLite database indices for the input BIDS dataset."""
     bids_description_hash = None
     """Checksum (SHA256) of the ``dataset_description.json`` of the BIDS dataset."""
     bids_filters = None
@@ -375,6 +382,8 @@ class execution(_Config):
     _paths = (
         "anat_derivatives",
         "bids_dir",
+        "bids_database_dir",
+        "aslprep_dir",
         "fs_license_file",
         "fs_subjects_dir",
         "layout",
@@ -396,6 +405,9 @@ def init(cls):
             from bids.layout import BIDSLayout
             from bids.layout.index import BIDSLayoutIndexer
 
+            _db_path = cls.bids_database_dir or (cls.work_dir / cls.run_uuid / "bids_db")
+            _db_path.mkdir(exist_ok=True, parents=True)
+
             # Recommended after PyBIDS 12.1
             _indexer = BIDSLayoutIndexer(
                 validate=False,
@@ -412,8 +424,11 @@ def init(cls):
             )
             cls._layout = BIDSLayout(
                 str(cls.bids_dir),
+                database_path=_db_path,
+                reset_database=cls.bids_database_dir is None,
                 indexer=_indexer,
             )
+            cls.bids_database_dir = _db_path
 
         cls.layout = cls._layout
         if cls.bids_filters:
@@ -426,6 +441,9 @@ def init(cls):
                     for k, v in filters.items()
                 }
 
+        if "all" in cls.debug:
+            cls.debug = list(DEBUG_MODES)
+
 
 # These variables are not necessary anymore
 del _fs_license