immucellai2 2.1.30__tar.gz → 2.1.32__tar.gz

{immucellai2-2.1.30 → immucellai2-2.1.32}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: immucellai2
-Version: 2.1.30
+Version: 2.1.32
 Summary: A tool for immune cell type deconvolution
 Home-page: https://github.com/VyvyanYjm/ImmuCellAI2.0
 Author: YangJingmin

{immucellai2-2.1.30 → immucellai2-2.1.32}/immucellai2/Deconvolution.py

@@ -267,36 +267,33 @@ def MainRun(RunObject, seed=42, MultithreadModule = 'joblib'):
             RunObject.SampleList[sample_index], 
             RunObject.MAPorMLE 
         )) 
-    #EmceeParameterCopy = RunObject.EmceeParameter.mycopy() 
-    MultiprocessingReturnValue = [] 
+    MultiprocessingReturnValue = []
     if MultithreadModule == 'joblib':
-        try: 
-            results = joblib.Parallel(n_jobs=int(EnvironmentRun.ThreadNum), backend='loky',verbose=0)(joblib.delayed(ThreadRunEachSamples)(*arg) for arg in parameterlist) 
-        except: 
-            print('error occurs while paralleling') 
-        finally: 
-            del parameterlist 
-            print('finished all!') 
+       try:
+          MultiprocessingReturnValue = joblib.Parallel(n_jobs=int(EnvironmentRun.ThreadNum), backend='loky',verbose=0)(joblib.delayed(ThreadRunEachSamples)(*arg) for arg in parameterlist)
+       except:
+          print('error occurs while paralleling')
+       finally:
+          del parameterlist
+          print('finished all!')
     elif MultithreadModule == 'multiprocessing':
         with multiprocessing.Pool(processes=int(EnvironmentRun.ThreadNum)) as pool:
-            results = pool.starmap(
-                ThreadRunEachSamples, 
-                [(EmceeParameterCopy, 
-                  CelltypesReferenceMatrix, 
-                  RunObject.SamplesBulkRNAseqExpression[sample_index], 
-                  RunObject.SampleList[sample_index], 
-                  seed + sample_index, 
-                  RunObject.MAPorMLE
-                  ) for sample_index in range(nsamples)]
-            )   
+            try:
+                MultiprocessingReturnValue = pool.starmap(ThreadRunEachSamples, parameterlist)
+            except Exception as e:
+                print(f'Error occurs while paralleling: {e}')
+            finally:
+                pool.close()
+                pool.join()
+                print('Finished all!')
     MergedResultObject = MergeResultsForAllSample(
-        ThreadList=[MultiprocessesResult(
-            RunObject.SampleList[i], 
-            result, 
-            deepcopy(RunObject.CellType)
-        ) for i, result in enumerate(results)],
+        ThreadList = [MultiprocessesResult(
+            SampleName = RunObject.SampleList[Sampleii],
+            SamplingResult = MultiprocessingReturnValue[Sampleii],
+            CellType=deepcopy(RunObject.CellType),
+        )   for Sampleii in range(len(MultiprocessingReturnValue))],
         OtherParams=[deepcopy(RunObject.CellType), RunObject.FileCellTypeCategory]
-    ) 
+        ) 
     RecordTime.ShowCostTime()
     if os.path.exists("TempThread"): 
         os.system("rm -rf TempThread")

{immucellai2-2.1.30 → immucellai2-2.1.32}/immucellai2/myclasses.py

@@ -99,16 +99,10 @@ class CLASS_FOR_RUNRESULT(object):
             self.EmceeFunction2( McSamplingResultList[sampleii, :, :, :] )
       return  NewMcSamplingResultList
    def optimized_calculation(self, FlatSamplingResultOne, nCellType):
-      row_sums = FlatSamplingResultOne.sum(axis=1, keepdims=True)
-      row_sums_safe = row_sums + 1e-10 
-      if FlatSamplingResultOne.shape[1] == nCellType:
-         return FlatSamplingResultOne / row_sums_safe
-      elif FlatSamplingResultOne.shape[1] + 1 == nCellType:
-         normalized = FlatSamplingResultOne / row_sums_safe
-         last_col = 1 - normalized.sum(axis=1, keepdims=True)
-         return numpy.column_stack((normalized, last_col))
-      else:
-         raise ValueError(f"Dimension mismatch: input {FlatSamplingResultOne.shape[1]} columns, target {nCellType}columns")
+       if FlatSamplingResultOne.shape[1] == nCellType:
+           return FlatSamplingResultOne / FlatSamplingResultOne.sum(axis=1)[:, None]
+       elif FlatSamplingResultOne.shape[1] + 1 == nCellType:
+           return numpy.column_stack((FlatSamplingResultOne, 1 - FlatSamplingResultOne.sum(axis=1)))
    def EmceeFunction2(self, FlatSamplingResultList): 
       fshape = FlatSamplingResultList.shape
       nCellType = len(self.CellType)

{immucellai2-2.1.30 → immucellai2-2.1.32}/immucellai2.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: immucellai2
-Version: 2.1.30
+Version: 2.1.32
 Summary: A tool for immune cell type deconvolution
 Home-page: https://github.com/VyvyanYjm/ImmuCellAI2.0
 Author: YangJingmin

{immucellai2-2.1.30 → immucellai2-2.1.32}/setup.cfg

@@ -1,6 +1,6 @@
 [metadata]
 name = immucellai2
-version = 2.1.30
+version = 2.1.32
 author = YangJingmin
 author_email = yangjingmin2021@163.com
 description = A tool for immune cell type deconvolution