Fix install

.github/workflows/build.yml

@@ -30,18 +30,21 @@ jobs:
     - run: conda --version
     - run: which python
     - name: install conda dependenies
+      run: conda install scipy mpi4py h5py
+    - name: install torch
       env:
-        TORCH: "1.8"
-      run: conda install scipy mpi4py h5py pytorch==${TORCH} torchvision cpuonly -c pytorch -c conda-forge
+        TORCH: "1.8.0"
+        TORCH_VISION: "0.9.0"
+      run: pip install torch==${TORCH}+cpu torchvision==${TORCH_VISION}+cpu -f https://download.pytorch.org/whl/torch_stable.html
 
     - name: install torch geometric
       env:
         TORCH_GEO: "1.8.0"
       run: |
-        pip install --no-index torch-scatter -f https://pytorch-geometric.com/whl/torch-${TORCH_GEO}+cpu.html
-        pip install --no-index torch-sparse -f https://pytorch-geometric.com/whl/torch-${TORCH_GEO}+cpu.html
-        pip install --no-index torch-cluster -f https://pytorch-geometric.com/whl/torch-${TORCH_GEO}+cpu.html
-        pip install --no-index torch-spline-conv -f https://pytorch-geometric.com/whl/torch-${TORCH_GEO}+cpu.html
+        pip install torch-scatter -f https://pytorch-geometric.com/whl/torch-${TORCH_GEO}+cpu.html
+        pip install torch-sparse -f https://pytorch-geometric.com/whl/torch-${TORCH_GEO}+cpu.html
+        pip install torch-cluster -f https://pytorch-geometric.com/whl/torch-${TORCH_GEO}+cpu.html
+        pip install torch-spline-conv -f https://pytorch-geometric.com/whl/torch-${TORCH_GEO}+cpu.html
         pip install torch-geometric
 
     - name: Install the package

deeprank_gnn/DataSet.py

@@ -140,7 +140,7 @@ def __init__(self, root='./', database=None, transform=None, pre_transform=None,
         # and get fname and mol name from the index
         self.create_index_molecules()
 
-    def __len__(self):
+    def len(self):
         """Gets the length of the dataset
         Returns:
             int: number of complexes in the dataset
@@ -229,7 +229,7 @@ def check_edge_feature(self):
                     exit()
 
     def load_one_graph(self, fname, mol):
-        """Loads one graph 
+        """Loads one graph
 
         Args:
             fname (str): hdf5 file name

tests/test_nn.py

@@ -11,7 +11,7 @@
 class TestNeuralNet(unittest.TestCase):
 
     def setUp(self):
-        self.database = 'tests//hdf5/1ATN_residue.hdf5'
+        self.database = 'tests/hdf5/1ATN_residue.hdf5'
 
     def test_neural_net(self):
         NN = NeuralNet(self.database, GINet,