missed a couple of docstrings

Author: srivarra

pyproject.toml

@@ -104,6 +104,5 @@ ignore = [
   "D400", # first line should end with a period [Bug: doesn’t work with single-line docstrings]
   "D401", # First line should be in imperative mood; try rephrasing
 ]
-per-file-ignores."*/__init__.py" = ["F401"]
 per-file-ignores."tests/*" = ["D"]
 pydocstyle.convention = "numpy"

tests/preprocessing/resize_images_tests.py

@@ -132,7 +132,7 @@ def test_resize_volumes(self):
                     ),
                     ignore_index=True,
                 )
-            op_fname = f"im_c00{c}_z000_t005_p007_3.3-0.8-1.0.npy"
+            op_fname = "im_c00{c}_z000_t005_p007_3.3-0.8-1.0.npy".format(c=c)
             exp_meta_dict.append(
                 {
                     "time_idx": self.time_idx,
@@ -168,7 +168,7 @@ def test_resize_volumes(self):
         exp_meta_dict = []
         for c in channel_ids:
             for s in [0, 2]:
-                op_fname = f"im_c00{c}_z00{s}_t005_p007_3.3-0.8-1.0.npy"
+                op_fname = "im_c00{c}_z00{s}_t005_p007_3.3-0.8-1.0.npy".format(c=c, s=s)
                 exp_meta_dict.append(
                     {
                         "time_idx": self.time_idx,

viscy/data/combined.py

@@ -396,7 +396,20 @@ class CachedConcatDataModule(LightningDataModule):
 
     Concatenates multiple data modules with support for distributed
     sampling and caching optimizations for large-scale ML training.
-    # TODO: MANUAL_REVIEW - Verify caching behavior and memory usage
+
+    Parameters
+    ----------
+    data_modules : Sequence[LightningDataModule]
+        Data modules to concatenate.
+
+    Raises
+    ------
+    ValueError
+        If inconsistent number of workers or batch size across data modules.
+    NotImplementedError
+        If stage other than "fit" is requested.
+    ValueError
+        If patches per stack are inconsistent across data modules.
     """
 
     def __init__(self, data_modules: Sequence[LightningDataModule]):

viscy/data/hcs.py

@@ -3,8 +3,6 @@
 import os
 import re
 import tempfile
-
-# from collections.abc import Callable, Sequence
 from pathlib import Path
 from typing import Callable, Literal, Sequence
 
@@ -35,8 +33,15 @@ def _ensure_channel_list(str_or_seq: str | Sequence[str]) -> list[str]:
     """
     Ensure channel argument is a list of strings.
 
-    :param Union[str, Sequence[str]] str_or_seq: channel name or list of channel names
-    :return list[str]: list of channel names
+    Parameters
+    ----------
+    str_or_seq : str | Sequence[str]
+        Channel name or list of channel names
+
+    Returns
+    -------
+    list[str]
+        List of channel names
     """
     if isinstance(str_or_seq, str):
         return [str_or_seq]
@@ -81,10 +86,17 @@ def _search_int_in_str(pattern: str, file_name: str) -> str:
 def _collate_samples(batch: Sequence[Sample]) -> Sample:
     """Collate samples into a batch sample.
 
-    :param Sequence[Sample] batch: a sequence of dictionaries,
+    Parameters
+    ----------
+    batch : Sequence[Sample]
+        A sequence of dictionaries,
         where each key may point to a value of a single tensor or a list of tensors,
         as is the case with ``train_patches_per_stack > 1``.
-    :return Sample: Batch sample (dictionary of tensors)
+
+    Returns
+    -------
+    Sample
+        Batch sample (dictionary of tensors)
     """
     collated: Sample = {}
     for key in batch[0].keys():