diff --git a/environment.yml b/environment.yml index 4295ed1b..9021c5bb 100644 --- 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 index 3a01b1cb..b37fddd8 100644 --- 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 index bb0062e1..8507b1e9 100644 --- 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]