dummy commit

.github/workflows/conda-tests.yml

@@ -48,6 +48,7 @@ jobs:
           echo "Creating Conda Environment from environment.yml"
           conda env create -f environment.yml
           conda activate tdc-conda-env
+          python run_tests.py tdc.test.test_model_server.TestModelServer.testscVI 
           python run_tests.py
           yapf --style=google -r -d tdc
           conda deactivate

tdc/model_server/model_loaders/scvi.py

@@ -0,0 +1,10 @@
+
+class scVILoader:
+
+    def __init__(self):
+        pass
+
+    def load(self):
+        """load scVI model
+        calling download_scvi() and any other helper functions
+        """

tdc/model_server/models/scvi.py

@@ -0,0 +1,20 @@
+
+class scVI:
+    """class to load and perform inference w/ scvi
+
+    adding any additional utils from scvi that facilitate inference / data processing
+    """
+
+    def __init__(self):
+        import scvi
+        pass
+
+    def forward(self, **kwargs):
+        """
+        loads self.model if needed
+        calls inference on these arguments
+        """
+
+    def load(self):
+        """import the model loader
+        -> then, LOAD the MODEL CLASS and return it and also save it into self.model"""

tdc/model_server/tdc_hf.py

@@ -14,7 +14,7 @@
     'CYP3A4_Veith-AttentiveFP',
 ]
 
-model_hub = ["Geneformer", "scGPT"]
+model_hub = ["Geneformer", "scGPT", "scVI"]
 
 
 class tdc_hf_interface:
@@ -66,6 +66,9 @@ def load(self):
             AutoModel.register(ScGPTConfig, ScGPTModel)
             model = AutoModel.from_pretrained("tdc/scGPT")
             return model
+        elif self.model_name == "scVI":
+            # import scVI model and return the model class
+            pass
         raise Exception("Not implemented yet!")
 
     def load_deeppurpose(self, save_path):

tdc/test/test_model_server.py

@@ -31,6 +31,19 @@ def setUp(self):
         print(os.getcwd())
         self.resource = cellxgene_census.CensusResource()
 
+    def testscVI(self):
+        from tdc.multi_pred.anndata_dataset import DataLoader
+        from tdc import tdc_hf_interface
+        # run scvi test
+        adata = DataLoader("cellxgene_sample_small",
+                    "./data",
+                    dataset_names=["cellxgene_sample_small"],
+                    no_convert=True).adata
+        # run scVI on a single sample
+        scvi = tdc_hf_interface("scVI")
+        model = scvi.load()  # this line can cause segmentation fault
+        pass
+
     def testscGPT(self):
         from tdc.multi_pred.anndata_dataset import DataLoader
         from tdc import tdc_hf_interface