Cleanup

Author: cthoyt

requirements.txt

@@ -7,4 +7,5 @@ matplotlib
 tqdm
 networkx
 ninja
-jinja2
+jinja2
+class-resolver

setup.py

@@ -39,6 +39,7 @@
                 "networkx",
                 "ninja",
                 "jinja2",
+                "class-resolver",
             ],
         python_requires=">=3.7,<3.9",
         classifiers=[

torchdrug/layers/__init__.py

@@ -23,7 +23,7 @@
     "MessagePassingBase", "GraphConv", "GraphAttentionConv", "RelationalGraphConv", "GraphIsomorphismConv",
     "NeuralFingerprintConv", "ContinuousFilterConv", "MessagePassing", "ChebyshevConv",
     "DiffPool", "MinCutPool",
-    "MeanReadout", "SumReadout", "MaxReadout", "Softmax", "Set2Set", "Sort",
+    "MeanReadout", "SumReadout", "MaxReadout", "Softmax", "Set2Set", "Sort", "readout_resolver", "Readout",
     "ConditionalFlow",
     "NodeSampler", "EdgeSampler",
     "distribution", "functional",

torchdrug/models/chebnet.py

@@ -1,10 +1,12 @@
 from collections.abc import Sequence
 
 import torch
+from class_resolver import Hint
 from torch import nn
 
 from torchdrug import core, layers
 from torchdrug.core import Registry as R
+from torchdrug.layers import Readout, readout_resolver
 
 
 @R.register("models.ChebNet")
@@ -25,11 +27,11 @@ class ChebyshevConvolutionalNetwork(nn.Module, core.Configurable):
         batch_norm (bool, optional): apply batch normalization or not
         activation (str or function, optional): activation function
         concat_hidden (bool, optional): concat hidden representations from all layers as output
-        readout (str, optional): readout function. Available functions are ``sum`` and ``mean``.
+        readout: readout function. Available functions are ``sum`` and ``mean``.
     """
 
     def __init__(self, input_dim, hidden_dims, edge_input_dim=None, k=1, short_cut=False, batch_norm=False,
-                 activation="relu", concat_hidden=False, readout="sum"):
+                 activation="relu", concat_hidden=False, readout: Hint[Readout] = "sum"):
         super(ChebyshevConvolutionalNetwork, self).__init__()
 
         if not isinstance(hidden_dims, Sequence):
@@ -45,12 +47,7 @@ def __init__(self, input_dim, hidden_dims, edge_input_dim=None, k=1, short_cut=F
             self.layers.append(layers.ChebyshevConv(self.dims[i], self.dims[i + 1], edge_input_dim, k,
                                                     batch_norm, activation))
 
-        if readout == "sum":
-            self.readout = layers.SumReadout()
-        elif readout == "mean":
-            self.readout = layers.MeanReadout()
-        else:
-            raise ValueError("Unknown readout `%s`" % readout)
+        self.readout = readout_resolver.make(readout)
 
     def forward(self, graph, input, all_loss=None, metric=None):
         """

torchdrug/models/gat.py

@@ -1,10 +1,12 @@
 from collections.abc import Sequence
 
 import torch
+from class_resolver import Hint
 from torch import nn
 
 from torchdrug import core, layers
 from torchdrug.core import Registry as R
+from torchdrug.layers import Readout, readout_resolver
 
 
 @R.register("models.GAT")

torchdrug/models/gcn.py

@@ -5,8 +5,8 @@
 from torch import nn
 
 from torchdrug import core, layers
-from torchdrug.layers import readout_resolver, Readout
 from torchdrug.core import Registry as R
+from torchdrug.layers import Readout, readout_resolver
 
 
 @R.register("models.GCN")
@@ -99,11 +99,11 @@ class RelationalGraphConvolutionalNetwork(nn.Module, core.Configurable):
         batch_norm (bool, optional): apply batch normalization or not
         activation (str or function, optional): activation function
         concat_hidden (bool, optional): concat hidden representations from all layers as output
-        readout (str, optional): readout function. Available functions are ``sum``, ``mean``, and ``max``.
+        readout: readout function. Available functions are ``sum``, ``mean``, and ``max``.
     """
 
     def __init__(self, input_dim, hidden_dims, num_relation, edge_input_dim=None, short_cut=False, batch_norm=False,
-                 activation="relu", concat_hidden=False, readout="sum"):
+                 activation="relu", concat_hidden=False, readout: Hint[Readout] = "sum"):
         super(RelationalGraphConvolutionalNetwork, self).__init__()
 
         if not isinstance(hidden_dims, Sequence):
@@ -120,14 +120,7 @@ def __init__(self, input_dim, hidden_dims, num_relation, edge_input_dim=None, sh
             self.layers.append(layers.RelationalGraphConv(self.dims[i], self.dims[i + 1], num_relation, edge_input_dim,
                                                           batch_norm, activation))
 
-        if readout == "sum":
-            self.readout = layers.SumReadout()
-        elif readout == "mean":
-            self.readout = layers.MeanReadout()
-        elif readout == "max":
-            self.readout = layers.MaxReadout()
-        else:
-            raise ValueError("Unknown readout `%s`" % readout)
+        self.readout = readout_resolver.make(readout)
 
     def forward(self, graph, input, all_loss=None, metric=None):
         """

torchdrug/models/gin.py

@@ -1,10 +1,12 @@
 from collections.abc import Sequence
 
 import torch
+from class_resolver import Hint
 from torch import nn
 
 from torchdrug import core, layers
 from torchdrug.core import Registry as R
+from torchdrug.layers import Readout, readout_resolver
 
 
 @R.register("models.GIN")
@@ -26,12 +28,12 @@ class GraphIsomorphismNetwork(nn.Module, core.Configurable):
         batch_norm (bool, optional): apply batch normalization or not
         activation (str or function, optional): activation function
         concat_hidden (bool, optional): concat hidden representations from all layers as output
-        readout (str, optional): readout function. Available functions are ``sum``, ``mean``, and ``max``.
+        readout: readout function. Available functions are ``sum``, ``mean``, and ``max``.
     """
 
     def __init__(self, input_dim=None, hidden_dims=None, edge_input_dim=None, num_mlp_layer=2, eps=0, learn_eps=False,
                  short_cut=False, batch_norm=False, activation="relu", concat_hidden=False,
-                 readout="sum"):
+                 readout: Hint[Readout] = "sum"):
         super(GraphIsomorphismNetwork, self).__init__()
 
         if not isinstance(hidden_dims, Sequence):

torchdrug/models/neuralfp.py

@@ -1,11 +1,13 @@
 from collections.abc import Sequence
 
 import torch
+from class_resolver import Hint
 from torch import nn
 from torch.nn import functional as F
 
 from torchdrug import core, layers
 from torchdrug.core import Registry as R
+from torchdrug.layers import Readout, readout_resolver
 
 
 @R.register("models.NeuralFP")
@@ -25,11 +27,11 @@ class NeuralFingerprint(nn.Module, core.Configurable):
         batch_norm (bool, optional): apply batch normalization or not
         activation (str or function, optional): activation function
         concat_hidden (bool, optional): concat hidden representations from all layers as output
-        readout (str, optional): readout function. Available functions are ``sum`` and ``mean``.
+        readout: readout function. Available functions are ``sum``, ``mean``, and ``max``.
     """
 
     def __init__(self, input_dim, output_dim, hidden_dims, edge_input_dim=None, short_cut=False, batch_norm=False,
-                 activation="relu", concat_hidden=False, readout="sum"):
+                 activation="relu", concat_hidden=False, readout: Hint[Readout] = "sum"):
         super(NeuralFingerprint, self).__init__()
 
         if not isinstance(hidden_dims, Sequence):

torchdrug/models/schnet.py

@@ -1,10 +1,12 @@
 from collections.abc import Sequence
 
 import torch
+from class_resolver import Hint
 from torch import nn
 
 from torchdrug import core, layers
 from torchdrug.core import Registry as R
+from torchdrug.layers import Readout, readout_resolver
 
 
 @R.register("models.SchNet")
@@ -25,6 +27,7 @@ class SchNet(nn.Module, core.Configurable):
         batch_norm (bool, optional): apply batch normalization or not
         activation (str or function, optional): activation function
         concat_hidden (bool, optional): concat hidden representations from all layers as output
+        readout: readout function. Available functions are ``sum``, ``mean``, and ``max``.
     """
 
     def __init__(self, input_dim, hidden_dims, edge_input_dim=None, cutoff=5, num_gaussian=100, short_cut=True,

torchdrug/tasks/pretrain.py

@@ -1,13 +1,14 @@
 import copy
 
 import torch
+from class_resolver import Hint
 from torch import nn
 from torch.nn import functional as F
 from torch_scatter import scatter_max, scatter_min
 
 from torchdrug import core, tasks, layers
 from torchdrug.data import constant
-from torchdrug.layers import functional
+from torchdrug.layers import functional, readout_resolver, Readout
 from torchdrug.core import Registry as R
 
 
@@ -169,9 +170,10 @@ class ContextPrediction(tasks.Task, core.Configurable):
         r2 (int, optional): outer radius for context graphs
         readout (nn.Module, optional): readout function over context anchor nodes
         num_negative (int, optional): number of negative samples per positive sample
+        readout: readout function. Available functions are ``sum``, ``mean``, and ``max``.
     """
 
-    def __init__(self, model, context_model=None, k=5, r1=4, r2=7, readout="mean", num_negative=1):
+    def __init__(self, model, context_model=None, k=5, r1=4, r2=7, readout: Hint[Readout] = "mean", num_negative=1):
         super(ContextPrediction, self).__init__()
         self.model = model
         self.k = k
@@ -184,12 +186,8 @@ def __init__(self, model, context_model=None, k=5, r1=4, r2=7, readout="mean", n
             self.context_model = copy.deepcopy(model)
         else:
             self.context_model = context_model
-        if readout == "sum":
-            self.readout = layers.SumReadout()
-        elif readout == "mean":
-            self.readout = layers.MeanReadout()
-        else:
-            raise ValueError("Unknown readout `%s`" % readout)
+
+        self.readout = readout_resolver.make(readout)
 
     def substruct_and_context(self, graph):
         center_index = (torch.rand(len(graph), device=self.device) * graph.num_nodes).long()