huggingface geneformer

mims-harvard · Oct 26, 2024 · 5f14c49 · 5f14c49
1 parent 08db3c4
commit 5f14c49
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Showing 3 changed files with 6 additions and 5 deletions.
diff --git a/environment.yml b/environment.yml
@@ -40,7 +40,7 @@ dependencies:
     - torchvision==0.16.1
     - transformers==4.43.4
     - yapf==0.40.2
-    - git+https://github.com/amva13/geneformer.git@main#egg=geneformer
+    - git+https://huggingface.co/ctheodoris/Geneformer.git@main#egg=geneformer
 
 variables:
   KMP_DUPLICATE_LIB_OK: "TRUE"
diff --git a/requirements.txt b/requirements.txt
@@ -23,4 +23,4 @@ tiledbsoma>=1.7.2,<2.0.0
 yapf>=0.40.2,<1.0.0
 
 # github packages
-git+https://github.com/amva13/geneformer.git@main#egg=geneformer
+git+https://huggingface.co/ctheodoris/Geneformer.git@main#egg=geneformer
diff --git a/tdc/test/test_model_server.py b/tdc/test/test_model_server.py
@@ -103,12 +103,13 @@ def testGeneformerTokenizer(self):
         geneformer = tdc_hf_interface("Geneformer")
         model = geneformer.load()
         tokenized_data = tokenizer.create_dataset(cells, metadata)
-        input_tensor = torch.tensor(tokenized_data)
-        input_tensor = torch.squeeze(input_tensor)
+        # input_tensor = torch.tensor(tokenized_data)
+        # input_tensor = torch.squeeze(input_tensor)
         try:
             out = model(tokenized_data)
         except Exception as e:
-            raise Exception("tensor shape is", input_tensor.shape, "exception was:", e)
+            # raise Exception("tensor shape is", input_tensor.shape, "exception was:", e)
+            raise Exception(e)
         # input_tensor = torch.tensor(cells)
         # input_tensor_squeezed = torch.squeeze(input_tensor)
         # x = input_tensor_squeezed.shape[0]