PR addressing issues I raised recently

cubids/cli.py

@@ -261,7 +261,7 @@ def _parse_apply():
     )
     parser.add_argument(
         "edited_summary_tsv",
-        type=IsFile,
+        type=Path,
         action="store",
         help=(
             "path to the _summary.tsv that has been edited "
@@ -273,7 +273,7 @@ def _parse_apply():
     )
     parser.add_argument(
         "files_tsv",
-        type=IsFile,
+        type=Path,
         action="store",
         help=(
             "path to the _files.tsv that has been edited "
@@ -440,23 +440,26 @@ def _parse_copy_exemplars():
     )
     parser.add_argument(
         "exemplars_dir",
-        type=PathExists,
+        type=Path,
         action="store",
         help=(
-            "absolute path to the root of a BIDS dataset "
-            "containing one subject from each Acquisition Group. "
+            "name of the directory to create where to store exemplar dataset. "
+            "It will include one subject from each Acquisition Group. "
             "It should contain sub-X directories and "
             "dataset_description.json."
         ),
     )
     parser.add_argument(
         "exemplars_tsv",
-        type=IsFile,
+        type=Path,
         action="store",
         help=(
-            "absolute path to the .tsv file that lists one "
+            "path to the .tsv that lists one "
             "subject from each Acquisition Group "
-            "(*_AcqGrouping.tsv from the cubids-group output)"
+            "(*_AcqGrouping.tsv from the cubids-group output). "
+            "If the file is located in the code/CuBIDS "
+            "directory, then users can just pass the .tsv "
+            "filename instead of the full path "
         ),
     )
     parser.add_argument(
@@ -489,6 +492,12 @@ def _parse_copy_exemplars():
         action="store",
         help="Docker image tag or Singularity image file.",
     )
+    parser.add_argument(
+        "--force-unlock",
+        action="store_true",
+        default=False,
+        help="unlock dataset before adding nifti info ",
+    )
     return parser
 
 

cubids/cubids.py

@@ -416,7 +416,7 @@ def apply_tsv_changes(self, summary_tsv, files_tsv, new_prefix, raise_on_error=T
 
         full_cmd = "\n".join(merge_commands + move_ops)
         if full_cmd:
-            renames = new_prefix + "_full_cmd.sh"
+            renames = str(Path(self.path) / (new_prefix + "_full_cmd.sh"))
 
             # write full_cmd to a .sh file
             with open(renames, "w") as fo:
@@ -683,6 +683,10 @@ def copy_exemplars(self, exemplars_dir, exemplars_tsv, min_group_size):
                     exemplars_dir,
                 ]
             )
+        if "/" not in str(exemplars_tsv):
+            if not self.cubids_code_dir:
+                self.create_cubids_code_dir()
+            exemplars_tsv = self.path + "/code/CuBIDS/" + exemplars_tsv
 
         # load the exemplars tsv
         subs = pd.read_table(exemplars_tsv)