Fix validation when some cells or genes are unexpessed (#82)

Author: jkanche

CHANGELOG.md

@@ -1,6 +1,6 @@
 # Changelog
 
-## Version 0.5.3 - 0.5.4
+## Version 0.5.3 - 0.5.5
 
 - 'config'  is renamed to 'context_or_config' to accept both TileDB's context or config objects. This supports in-memory TileDB contexts from [Phil](https://github.com/hanslovsky) [[#79](https://github.com/TileOme/cellarr/pull/79)].
 - Fixes the condition for path to assay groups.

src/cellarr/CellArrDataset.py

@@ -29,6 +29,7 @@
 
 from functools import lru_cache
 from typing import List, Optional, Sequence, Union
+from warnings import warn
 
 import pandas as pd
 import tiledb
@@ -173,12 +174,26 @@ def __init__(
 
     def _validate(self):
         num_cells = self._cell_metadata_tdb.nonempty_domain()[0][1]
-        num_rows = self._gene_annotation_tdb.nonempty_domain()[0][1]
+        num_feats = self._gene_annotation_tdb.nonempty_domain()[0][1]
 
         for mname, muri in self._matrix_tdb.items():
             dom = muri.nonempty_domain()
-            if dom[0][1] != num_cells or dom[1][1] != num_rows:
-                raise RuntimeError(f"Matrix {mname} has incorrect dimensions")
+            if dom[0][1] != num_cells:
+                warn(
+                    f"Matrix {mname} has fewer cells than expected - some cells may not have any gene expression.",
+                    UserWarning,
+                )
+                if dom[0][1] > num_cells:
+                    raise RuntimeError(f"Matrix {mname} has more cells than expected.")
+
+            if dom[1][1] != num_feats:
+                warn(
+                    f"Matrix {mname} has fewer genes than expected - some genes may not be expressed in any cells.",
+                    UserWarning,
+                )
+
+                if dom[1][1] > num_feats:
+                    raise RuntimeError(f"Matrix {mname} has more genes than expected.")
 
     def __del__(self):
         self._gene_annotation_tdb.close()