M3Drop 0.4.47__py3-none-any.whl → 0.4.49__py3-none-any.whl

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/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/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.dist-info → m3drop-0.4.49.dist-info}/METADATA

@@ -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-0.4.49.dist-info/RECORD

@@ -0,0 +1,14 @@
+m3Drop/ControlDeviceCPU.py,sha256=8P-hxd4thc2wSeon73b9rz3clIGkE3x0cEE82RiGFds,8880
+m3Drop/ControlDeviceGPU.py,sha256=4nzPtgyV0RsEOeezwCVJ7oyDOsp9-dRVLczlduUocpU,9143
+m3Drop/CoreCPU.py,sha256=csRg5TLQx1Sup7k3lDJm9OO5Oe5-1aC3u_6ldE_GIX8,18679
+m3Drop/CoreGPU.py,sha256=6LToLuWyHxX_7sC2z0Xnvy_qqgmpew5DmnCV0PxmTZQ,19785
+m3Drop/DiagnosticsCPU.py,sha256=l0Imkh3F3zo4ovihUjx7cYWYgzPdztWCN1hcBFO43nY,12943
+m3Drop/DiagnosticsGPU.py,sha256=bsatHyHszgbufneeJvFvHBTLzDuY006nP2yHPHs8s7M,14389
+m3Drop/NormalizationCPU.py,sha256=DmqvjcpHwkNZicEb2GBqTDBVyvtBeUSLmFRwRFDk0ms,7458
+m3Drop/NormalizationGPU.py,sha256=Kl5QvR4HCSgooUOf97-nu53J6wf3apdNvc3BFlTFiEM,7264
+m3Drop/__init__.py,sha256=W_TQ9P8_7Tdsa6kDZ6IJKT0FMkX_JFvBqiP821CZIrk,2180
+m3drop-0.4.49.dist-info/licenses/LICENSE,sha256=44Iqpp8Fc10Xzd5T7cT9UhO31Qftk3gBiCjtpwilP_k,1074
+m3drop-0.4.49.dist-info/METADATA,sha256=aUj_G6pHzrSKr70GwbOptvcAP7HCGviG8hYjq6OiqMk,5248
+m3drop-0.4.49.dist-info/WHEEL,sha256=wUyA8OaulRlbfwMtmQsvNngGrxQHAvkKcvRmdizlJi0,92
+m3drop-0.4.49.dist-info/top_level.txt,sha256=AEULFEFIgFtAwS-KBlIFoYXrqczX_rwqrEcdK46GIrA,7
+m3drop-0.4.49.dist-info/RECORD,,

m3drop-0.4.47.dist-info/RECORD

@@ -1,14 +0,0 @@
-m3Drop/ControlDeviceCPU.py,sha256=8P-hxd4thc2wSeon73b9rz3clIGkE3x0cEE82RiGFds,8880
-m3Drop/ControlDeviceGPU.py,sha256=4nzPtgyV0RsEOeezwCVJ7oyDOsp9-dRVLczlduUocpU,9143
-m3Drop/CoreCPU.py,sha256=csRg5TLQx1Sup7k3lDJm9OO5Oe5-1aC3u_6ldE_GIX8,18679
-m3Drop/CoreGPU.py,sha256=6LToLuWyHxX_7sC2z0Xnvy_qqgmpew5DmnCV0PxmTZQ,19785
-m3Drop/DiagnosticsCPU.py,sha256=l0Imkh3F3zo4ovihUjx7cYWYgzPdztWCN1hcBFO43nY,12943
-m3Drop/DiagnosticsGPU.py,sha256=z5BMOZNo_ruMBaDWJIE6zWhMUtf2ItY5Vcgu4N9lbok,14321
-m3Drop/NormalizationCPU.py,sha256=Mm8VzWDu-NONbp-ngAt4PLjCKAGc7gJZKf-Yd-U95r0,7255
-m3Drop/NormalizationGPU.py,sha256=1XRDZhNVkIbQMv_ggNoNEnIxRMY1NHDjOtOq4QGVRwY,7011
-m3Drop/__init__.py,sha256=W_TQ9P8_7Tdsa6kDZ6IJKT0FMkX_JFvBqiP821CZIrk,2180
-m3drop-0.4.47.dist-info/licenses/LICENSE,sha256=44Iqpp8Fc10Xzd5T7cT9UhO31Qftk3gBiCjtpwilP_k,1074
-m3drop-0.4.47.dist-info/METADATA,sha256=z1THnYFMNjSObhg-QIGn61c1-lyqlXZiyAtcSLfE-fc,5248
-m3drop-0.4.47.dist-info/WHEEL,sha256=wUyA8OaulRlbfwMtmQsvNngGrxQHAvkKcvRmdizlJi0,92
-m3drop-0.4.47.dist-info/top_level.txt,sha256=AEULFEFIgFtAwS-KBlIFoYXrqczX_rwqrEcdK46GIrA,7
-m3drop-0.4.47.dist-info/RECORD,,