Attempt to fix pytorch/anndata issue

inst/scripts/PredictScTourPseudotime.py

@@ -3,11 +3,10 @@
 import numpy as np
 import pandas as pd
 import torch
+import anndata
 from anndata import AnnData
 
 def PredictPseudotime(GEXfile, model_file, ptime_out_file, embedding_out_file):
-    torch.serialization.add_safe_globals([AnnData, "anndata._core.file_backing.AnnDataFileManager"])
-
     #read count data and variable genes
     adataObj = sc.read_10x_h5(GEXfile)
     adataObj.X = round(adataObj.X).astype(np.float32)
@@ -17,7 +16,7 @@ def PredictPseudotime(GEXfile, model_file, ptime_out_file, embedding_out_file):
         print('AnnData object is a csr matrix, converting to dense because scipy depreciated the .A shorthand')
         adataObj.X = adataObj.X.toarray()
 
-    with torch.serialization.add_safe_globals([AnnData]):
+    with torch.serialization.add_safe_globals([AnnData, anndata._core.file_backing.AnnDataFileManager]):
         checkpoint = torch.load(model_file, map_location=torch.device('cpu'))
     model_adata = checkpoint['adata']
 
@@ -31,7 +30,7 @@ def PredictPseudotime(GEXfile, model_file, ptime_out_file, embedding_out_file):
     #subset to genes found in the pretrained model.
     adataObj = adataObj[:, genes_in_model]
     #initalize a trainer and pull a previously saved model from model_file
-    with torch.serialization.safe_globals([AnnData, "anndata._core.file_backing.AnnDataFileManager"]):
+    with torch.serialization.safe_globals([AnnData, anndata._core.file_backing.AnnDataFileManager]):
         tnode = sct.predict.load_model(model_file)
     pred_t = sct.predict.predict_time(adata = adataObj, model = tnode)
     adataObj.obs['ptime'] = pred_t