M3Drop 0.4.47__tar.gz → 0.4.49__tar.gz

{m3drop-0.4.47 → m3drop-0.4.49/M3Drop.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: M3Drop
-Version: 0.4.47
+Version: 0.4.49
 Summary: A Python implementation of the M3Drop single-cell RNA-seq analysis tool.
 Home-page: https://github.com/PragalvhaSharma/m3DropNew
 Author: Tallulah Andrews

{m3drop-0.4.47/M3Drop.egg-info → m3drop-0.4.49}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: M3Drop
-Version: 0.4.47
+Version: 0.4.49
 Summary: A Python implementation of the M3Drop single-cell RNA-seq analysis tool.
 Home-page: https://github.com/PragalvhaSharma/m3DropNew
 Author: Tallulah Andrews

{m3drop-0.4.47 → m3drop-0.4.49}/m3Drop/DiagnosticsGPU.py

@@ -231,7 +231,8 @@ def NBumiCheckFitFSGPU(
             p_is_chunk_gpu           # Output
         )
 
-        p_is_chunk_gpu = cp.nan_to_num(p_is_chunk_gpu, nan=0.0, posinf=1.0, neginf=0.0)
+        # [MEMORY FIX] Use copy=False to prevent doubling memory usage
+        cp.nan_to_num(p_is_chunk_gpu, copy=False, nan=0.0, posinf=1.0, neginf=0.0)
         
         row_ps_gpu += p_is_chunk_gpu.sum(axis=0)
         col_ps_gpu[current_row:end_row] = p_is_chunk_gpu.sum(axis=1)
@@ -275,7 +276,7 @@ def NBumiCompareModelsGPU(
         stats, 
         mask_filename=mask_filename,
         mode=mode, 
-        manual_target=manual_target,
+        manual_target=manual_target, 
         phase_label="Phase [1/3]",
         desc_label="Fitting Basic Model (Virtual)..."
     )

{m3drop-0.4.47 → m3drop-0.4.49}/m3Drop/NormalizationCPU.py

@@ -122,9 +122,17 @@ def NBumiPearsonResidualsCombinedCPU(
     adata_out_approx = anndata.AnnData(obs=adata_in.obs, var=filtered_var)
     adata_out_approx.write_h5ad(output_filename_approx, compression=None)
     
+    # --- CHUNK SIZE FIX ---
     # Calculate appropriate H5 storage chunks
     storage_chunk_rows = int(1_000_000_000 / (ng_filtered * 8)) 
-    if storage_chunk_rows < 1: storage_chunk_rows = 1
+    
+    # [CRITICAL FIX] Clamp chunk size to total rows (nc)
+    if storage_chunk_rows > nc: 
+        storage_chunk_rows = nc
+        
+    if storage_chunk_rows < 1: 
+        storage_chunk_rows = 1
+    # ----------------------
     
     # Open both files for writing simultaneously
     with h5py.File(output_filename_full, 'a') as f_full, h5py.File(output_filename_approx, 'a') as f_approx:

{m3drop-0.4.47 → m3drop-0.4.49}/m3Drop/NormalizationGPU.py

@@ -101,8 +101,17 @@ def NBumiPearsonResidualsCombinedGPU(
     adata_out_approx = anndata.AnnData(obs=adata_in.obs, var=filtered_var)
     adata_out_approx.write_h5ad(output_filename_approx, compression=None)
     
+    # --- CHUNK SIZE FIX ---
+    # Calculate rows needed to fill ~1GB
     storage_chunk_rows = int(1_000_000_000 / (ng_filtered * 8)) 
-    if storage_chunk_rows < 1: storage_chunk_rows = 1
+    
+    # [CRITICAL FIX] Clamp chunk size to total rows (nc)
+    if storage_chunk_rows > nc: 
+        storage_chunk_rows = nc
+        
+    if storage_chunk_rows < 1: 
+        storage_chunk_rows = 1
+    # ----------------------
     
     # Open both files for writing simultaneously
     with h5py.File(output_filename_full, 'a') as f_full, h5py.File(output_filename_approx, 'a') as f_approx:

{m3drop-0.4.47 → m3drop-0.4.49}/setup.py

@@ -5,7 +5,7 @@ with open("README.md", "r", encoding="utf-8") as fh:
 
 setuptools.setup(
     name="M3Drop",  # Name for pip (pip install M3Drop)
-    version="0.4.47",
+    version="0.4.49",
     author="Tallulah Andrews",
     author_email="tandrew6@uwo.ca",
     description="A Python implementation of the M3Drop single-cell RNA-seq analysis tool.",