refactor initial subject IDs check and add more intermediate messages…

… for BIDS command

bagel/cli.py

@@ -202,8 +202,6 @@ def bids(
     check_overwrite(output, overwrite)
 
     jsonld = load_json(jsonld_path)
-    layout = BIDSLayout(bids_dir, validate=True)
-
     # Strip and store context to be added back later, since it's not part of
     # (and can't be easily added) to the existing data model
     context = {"@context": jsonld.pop("@context")}
@@ -217,21 +215,28 @@ def bids(
         pheno_subject.hasLabel: pheno_subject
         for pheno_subject in getattr(pheno_dataset, "hasSamples")
     }
-    bids_subject_list = ["sub-" + sub_id for sub_id in layout.get_subjects()]
 
+    # TODO: Revert to using Layout.get_subjects() to get BIDS subjects once pybids performance is improved
     butil.check_unique_bids_subjects(
         pheno_subjects=pheno_subject_dict.keys(),
-        bids_subjects=bids_subject_list,
+        bids_subjects=butil.get_bids_subjects_simple(bids_dir),
     )
 
     # Display validated input paths to user
     space = 32
     print(
-        "Parsing BIDS metadata to be merged with phenotypic annotations:\n"
+        "Initial checks of inputs passed:\n"
         f"   {'Phenotypic .jsonld to augment:' : <{space}} {jsonld_path}\n"
         f"   {'BIDS dataset directory:' : <{space}} {bids_dir}\n"
     )
 
+    print("Parsing and validating BIDS dataset. This may take a while...")
+    layout = BIDSLayout(bids_dir, validate=True)
+    print("BIDS parsing completed.\n")
+
+    print(
+        "Merging subject-level BIDS metadata with the phenotypic annotations...\n"
+    )
     for bids_sub_id in layout.get_subjects():
         pheno_subject = pheno_subject_dict.get(f"sub-{bids_sub_id}")
         session_list = []