More work.

cubids/cubids.py

@@ -460,20 +460,17 @@ def change_filename(self, filepath, entities):
 
         Parameters
         ----------
-        filepath : str
-            Path prefix to a file in the affected key group change
-        entities : dictionary
-            A pybids dictionary of entities parsed from the new key
-            group name.
+        filepath : :obj:`str`
+            Path prefix to a file in the affected key group change.
+        entities : :obj:`dict`
+            A pybids dictionary of entities parsed from the new key group name.
 
         Notes
         -----
         This is the function I need to spend the most time on, since it has entities hardcoded.
         """
         exts = Path(filepath).suffixes
-        old_ext = ""
-        for ext in exts:
-            old_ext += ext
+        old_ext = "".join(exts)
 
         suffix = entities["suffix"]
         entity_file_keys = []
@@ -514,6 +511,7 @@ def change_filename(self, filepath, entities):
                 print("WARNING: DATATYPE CHANGE DETECETD")
         else:
             dtype = old
+
         new_path = str(self.path) + "/" + sub + "/" + ses + "/" + dtype + "/" + filename
 
         # add the scan path + new path to the lists of old, new filenames
@@ -825,7 +823,15 @@ def _purge_associations(self, scans):
             print("Not running any association removals")
 
     def get_nifti_associations(self, nifti):
-        """Get nifti associations."""
+        """Get nifti associations.
+
+        This uses globbing to find files with the same path and entities as the NIfTI,
+        but with a different extension and a suffix that at least starts with the same
+        suffix as the NIfTI.
+
+        For example, for *_asl.nii.gz, this will grab *_asl.json, *_aslcontext.tsv,
+        and *_asllabeling.jpg.
+        """
         # get all assocation files of a nifti image
         no_ext_file = str(nifti).split("/")[-1].split(".")[0]
         associations = []

pyproject.toml

@@ -21,16 +21,15 @@ classifiers = [
 license = {file = "LICENSE"}
 requires-python = ">=3.8"
 dependencies = [
-    "pyyaml",
-    "pybids",
-    "pandas",
-    "tqdm",
+    "datalad>=0.13.5,!=0.17.3,!=0.17.0,!=0.16.1",
+    "jinja2 < 3.1",
     "numpy",
+    "pandas",
+    "pybids",
+    "pyyaml",
     "scikit-learn",
-    "datalad>=0.13.5,!=0.17.3,!=0.17.0,!=0.16.1",
+    "tqdm",
     "wrapt<2,>=1.10",
-    "Sphinx",
-    "jinja2 < 3.1",
 ]
 dynamic = ["version"]
 
@@ -44,11 +43,11 @@ Paper = "https://doi.org/10.1016/j.neuroimage.2022.119609"
 doc = [
     "nbsphinx",
     "packaging",
+    "recommonmark",
     "sphinx >= 2.2",
     "sphinx-argparse",
-    "sphinx_rtd_theme",
     "sphinx_markdown_tables",
-    "recommonmark",
+    "sphinx_rtd_theme",
 ]
 tests = [
     "codespell",