add model template

Author: quentinblampey

benchmark/domains/setup.py

@@ -0,0 +1,29 @@
+import numpy as np
+from anndata import AnnData
+
+VALID_MODEL_NAMES = ["STAGATE", "SEDR", "GraphST", "SpaceFlow"]
+
+
+class Model:
+    def __init__(self, model_name: str, hidden_dim: int) -> None:
+        super().__init__()
+        assert model_name in VALID_MODEL_NAMES
+
+        self.model_name = model_name
+        self.hidden_dim = hidden_dim
+
+        self.build_model()
+
+    def build_model(self) -> None:
+        raise NotImplementedError
+
+    def train(self) -> None:
+        raise NotImplementedError
+
+    def inference(adata: AnnData) -> np.ndarray:
+        raise NotImplementedError
+
+    def __call__(self, adata: AnnData) -> np.ndarray:
+        self.train()
+        adata.obsm[self.model_name] = self.inference(adata)
+        return adata.obsm[self.model_name]

benchmark/domains/__init__.py benchmark/model/__init__.py

@@ -1,6 +1,6 @@
 # Install
 
-## SEDR
+## SEDR (Quentin)
 
 [Github](https://github.com/JinmiaoChenLab/SEDR), [Docs](https://sedr.readthedocs.io/en/latest/Installation.html)
 
@@ -15,7 +15,7 @@ python setup.py build
 python setup.py.install
 ```
 
-## STAGATE
+## STAGATE (Quentin)
 
 [Github](https://github.com/QIFEIDKN/STAGATE_pyG), [Docs](https://stagate.readthedocs.io/en/latest/Installation_pyG.html)
 
@@ -30,7 +30,7 @@ python setup.py build
 python setup.py install
 ```
 
-## GraphST
+## GraphST ()
 
 [Github](https://github.com/JinmiaoChenLab/GraphST), [Docs](https://deepst-tutorials.readthedocs.io/en/latest/)
 
@@ -49,7 +49,7 @@ python setup.py build
 python setup.py install
 ```
 
-## SpaceFlow
+## SpaceFlow (Hakim)
 
 [Github](https://github.com/hongleir/SpaceFlow), Docs