spatialcore 0.2.0__tar.gz → 0.2.1__tar.gz

{spatialcore-0.2.0 → spatialcore-0.2.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: spatialcore
-Version: 0.2.0
+Version: 0.2.1
 Summary: Standardized spatial statistics tools for computational biology
 Author: SpatialCore Contributors
 License-Expression: Apache-2.0

{spatialcore-0.2.0 → spatialcore-0.2.1}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "spatialcore"
-version = "0.2.0"
+version = "0.2.1"
 description = "Standardized spatial statistics tools for computational biology"
 readme = "README.md"
 license = "Apache-2.0"

{spatialcore-0.2.0 → spatialcore-0.2.1}/src/spatialcore/__init__.py

@@ -5,7 +5,7 @@ A thin, robust wrapper around standard libraries to ensure Python and R users
 get the exact same result for the same biological question.
 """
 
-__version__ = "0.2.0"
+__version__ = "0.2.1"
 
 # Track which modules are available in this installation
 _available_modules: list[str] = []

{spatialcore-0.2.0 → spatialcore-0.2.1}/src/spatialcore/annotation/training.py

@@ -1243,8 +1243,8 @@ def subsample_balanced(
     max_cells_per_type : int, default 5000
         Maximum cells per cell type in output.
     min_cells_per_type : int, default 50
-        Cell types with fewer cells than this are kept entirely
-        (no subsampling applied).
+        Minimum cells required to keep a cell type. Types with fewer
+        cells are removed before balancing.
     source_column : str, optional, default "reference_source"
         Column identifying which reference each cell came from.
         Set to None to disable source-aware balancing (simple capping).
@@ -1387,8 +1387,41 @@ def subsample_balanced(
     else:
         cell_types = adata.obs[label_column].astype(str)
 
-    unique_types = cell_types.unique()
     type_counts = cell_types.value_counts()
+    if min_cells_per_type > 0:
+        low_count_types = type_counts[type_counts < min_cells_per_type].index.tolist()
+        if low_count_types:
+            n_removed = int(type_counts[type_counts < min_cells_per_type].sum())
+            logger.info(
+                f"\nFiltering low-count cell types (<{min_cells_per_type} cells) before balancing:"
+            )
+            logger.info(f"  Removing {len(low_count_types)} types, {n_removed:,} cells")
+            for ct in low_count_types[:10]:
+                logger.info(f"    {ct}: {type_counts[ct]} cells")
+            if len(low_count_types) > 10:
+                logger.info(f"    ... and {len(low_count_types) - 10} more types")
+
+            keep_mask = ~cell_types.isin(low_count_types)
+            adata = adata[keep_mask].copy()
+
+            if group_by_column is not None:
+                cell_types = adata.obs[group_by_column].astype(str)
+            else:
+                cell_types = adata.obs[label_column].astype(str)
+
+            if props:
+                dropped = sorted(set(props) & set(low_count_types))
+                if dropped:
+                    for ct in dropped:
+                        props.pop(ct, None)
+                    logger.warning(
+                        "Dropping target_proportions for low-count types: %s",
+                        ", ".join(dropped),
+                    )
+
+            type_counts = cell_types.value_counts()
+
+    unique_types = cell_types.unique()
     target_totals = _resolve_target_totals(
         type_counts=type_counts,
         min_cells_per_type=min_cells_per_type,

{spatialcore-0.2.0 → spatialcore-0.2.1}/src/spatialcore.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: spatialcore
-Version: 0.2.0
+Version: 0.2.1
 Summary: Standardized spatial statistics tools for computational biology
 Author: SpatialCore Contributors
 License-Expression: Apache-2.0