release v0.1.3

Author: KiddoZhu

Diff for: conda/torchdrug/meta.yaml

@@ -1,21 +1,21 @@
 package:
   name: torchdrug
-  version: 0.1.2
+  version: 0.1.3
 
 source:
   path: ../..
 
 requirements:
   host:
-    - python >=3.7,<3.9
+    - python >=3.7,<3.10
     - pip
   run:
-    - python >=3.7,<3.9
+    - python >=3.7,<3.10
     - pytorch >=1.8.0
     - pytorch-scatter >=2.0.8
     - decorator
     - numpy >=1.11
-    - rdkit
+    - rdkit >=2020.09
     - matplotlib
     - tqdm
     - networkx

Diff for: setup.py

@@ -13,7 +13,7 @@
         long_description_content_type="text/markdown",
         url="https://torchdrug.ai/",
         author="TorchDrug Team",
-        version="0.1.2",
+        version="0.1.3",
         license="Apache-2.0",
         keywords=["deep-learning", "pytorch", "drug-discovery"],
         packages=setuptools.find_packages(),
@@ -24,23 +24,23 @@
                 "layers/functional/extension/*.cpp",
                 "layers/functional/extension/*.cu",
                 "utils/extension/*.cpp",
-                "utils/template/*.html"
-            ]},
+                "utils/template/*.html",
+            ]
+        },
         test_suite="nose.collector",
-        install_requires=
-            [
-                "torch>=1.8.0",
-                "torch-scatter>=2.0.8",
-                "decorator",
-                "numpy>=1.11",
-                "rdkit-pypi",
-                "matplotlib",
-                "tqdm",
-                "networkx",
-                "ninja",
-                "jinja2",
-            ],
-        python_requires=">=3.7,<3.9",
+        install_requires=[
+            "torch>=1.8.0",
+            "torch-scatter>=2.0.8",
+            "decorator",
+            "numpy>=1.11",
+            "rdkit-pypi>=2020.9",
+            "matplotlib",
+            "tqdm",
+            "networkx",
+            "ninja",
+            "jinja2",
+        ],
+        python_requires=">=3.7,<3.10",
         classifiers=[
             "Development Status :: 4 - Beta",
             'Intended Audience :: Developers',

Diff for: test/layers/test_conv.py

@@ -38,7 +38,7 @@ def test_graph_conv(self):
         adjacency /= adjacency.sum(dim=0, keepdim=True).sqrt() * adjacency.sum(dim=1, keepdim=True).sqrt()
         x = adjacency.t() @ self.input
         truth = conv.activation(conv.linear(x))
-        self.assertTrue(torch.allclose(result, truth, rtol=1e-4, atol=1e-7), "Incorrect graph convolution")
+        self.assertTrue(torch.allclose(result, truth, rtol=1e-2, atol=1e-3), "Incorrect graph convolution")
 
         num_head = 2
         conv = layers.GraphAttentionConv(self.input_dim, self.output_dim, num_head=num_head).cuda()
@@ -55,15 +55,15 @@ def test_graph_conv(self):
             outputs.append(output)
         truth = torch.cat(outputs, dim=-1)
         truth = conv.activation(truth)
-        self.assertTrue(torch.allclose(result, truth), "Incorrect graph attention convolution")
+        self.assertTrue(torch.allclose(result, truth, rtol=1e-2, atol=1e-3), "Incorrect graph attention convolution")
 
         eps = 1
         conv = layers.GraphIsomorphismConv(self.input_dim, self.output_dim, eps=eps).cuda()
         result = conv(self.graph, self.input)
         adjacency = self.graph.adjacency.to_dense().sum(dim=-1)
         x = (1 + eps) * self.input + adjacency.t() @ self.input
         truth = conv.activation(conv.mlp(x))
-        self.assertTrue(torch.allclose(result, truth, atol=1e-4, rtol=1e-7), "Incorrect graph isomorphism convolution")
+        self.assertTrue(torch.allclose(result, truth, rtol=1e-2, atol=1e-2), "Incorrect graph isomorphism convolution")
 
         conv = layers.RelationalGraphConv(self.input_dim, self.output_dim, self.num_relation).cuda()
         result = conv(self.graph, self.input)
@@ -72,7 +72,7 @@ def test_graph_conv(self):
         x = torch.einsum("htr, hd -> trd", adjacency, self.input)
         x = conv.linear(x.flatten(1)) + conv.self_loop(self.input)
         truth = conv.activation(x)
-        self.assertTrue(torch.allclose(result, truth, atol=1e-4, rtol=1e-7), "Incorrect relational graph convolution")
+        self.assertTrue(torch.allclose(result, truth, rtol=1e-2, atol=1e-3), "Incorrect relational graph convolution")
 
         conv = layers.ChebyshevConv(self.input_dim, self.output_dim, k=2).cuda()
         result = conv(self.graph, self.input)
@@ -83,7 +83,7 @@ def test_graph_conv(self):
         bases = [self.input, laplacian.t() @ self.input, (2 * laplacian.t() @ laplacian.t() - identity) @ self.input]
         x = conv.linear(torch.cat(bases, dim=-1))
         truth = conv.activation(x)
-        self.assertTrue(torch.allclose(result, truth, atol=1e-4, rtol=1e-7), "Incorrect chebyshev graph convolution")
+        self.assertTrue(torch.allclose(result, truth, rtol=1e-2, atol=1e-3), "Incorrect chebyshev graph convolution")
 
 
 if __name__ == "__main__":

Diff for: test/layers/test_pool.py

@@ -43,8 +43,8 @@ def test_pool(self):
             truth_adj = torch.einsum("bna, bnm, bmc -> bac", assignment, adjacency, assignment)
             index = torch.arange(self.output_node, device=truth.device)
             truth_adj[:, index, index] = 0
-            self.assertTrue(torch.allclose(result, truth), "Incorrect diffpool node feature")
-            self.assertTrue(torch.allclose(result_adj, truth_adj), "Incorrect diffpool adjacency")
+            self.assertTrue(torch.allclose(result, truth, rtol=1e-3, atol=1e-4), "Incorrect diffpool node feature")
+            self.assertTrue(torch.allclose(result_adj, truth_adj, rtol=1e-3, atol=1e-4), "Incorrect diffpool adjacency")
 
             graph = self.graph[0]
             rng_state = torch.get_rng_state()
@@ -60,8 +60,8 @@ def test_pool(self):
             truth_adj = torch.einsum("na, nm, mc -> ac", assignment, adjacency, assignment)
             index = torch.arange(self.output_node, device=truth.device)
             truth_adj[index, index] = 0
-            self.assertTrue(torch.allclose(result, truth), "Incorrect diffpool node feature")
-            self.assertTrue(torch.allclose(result_adj, truth_adj), "Incorrect diffpool adjacency")
+            self.assertTrue(torch.allclose(result, truth, rtol=1e-3, atol=1e-4), "Incorrect diffpool node feature")
+            self.assertTrue(torch.allclose(result_adj, truth_adj, rtol=1e-3, atol=1e-4), "Incorrect diffpool adjacency")
 
         pool = layers.MinCutPool(self.input_dim, self.output_node, self.feature_layer, self.pool_layer).cuda()
         all_loss = torch.tensor(0, dtype=torch.float32, device="cuda")
@@ -89,10 +89,10 @@ def test_pool(self):
         x = x - torch.eye(self.output_node, device=x.device) / (self.output_node ** 0.5)
         regularization = x.flatten(-2).norm(dim=-1).mean()
         truth_metric = {"normalized cut loss": cut_loss, "orthogonal regularization": regularization}
-        self.assertTrue(torch.allclose(result, truth), "Incorrect min cut pool feature")
-        self.assertTrue(torch.allclose(result_adj, truth_adj), "Incorrect min cut pool adjcency")
+        self.assertTrue(torch.allclose(result, truth, rtol=1e-3, atol=1e-4), "Incorrect min cut pool feature")
+        self.assertTrue(torch.allclose(result_adj, truth_adj, rtol=1e-3, atol=1e-4), "Incorrect min cut pool adjcency")
         for key in result_metric:
-            self.assertTrue(torch.allclose(result_metric[key], truth_metric[key], atol=1e-4, rtol=1e-7),
+            self.assertTrue(torch.allclose(result_metric[key], truth_metric[key], rtol=1e-3, atol=1e-4),
                             "Incorrect min cut pool metric")
 
 

Diff for: torchdrug/__init__.py

@@ -12,4 +12,4 @@
 handler.setFormatter(format)
 logger.addHandler(handler)
 
-__version__ = "0.1.2"
+__version__ = "0.1.3"

Diff for: torchdrug/utils/decorator.py

@@ -1,5 +1,6 @@
 import inspect
 import warnings
+import functools
 
 from decorator import decorator
 
@@ -100,14 +101,19 @@ def deprecated_alias(**alias):
     Handle argument alias for a function and output deprecated warnings.
     """
 
-    def wrapper(func, *args, **kwargs):
-        for key, value in alias.items():
-            if key in kwargs:
-                if value in kwargs:
-                    raise TypeError("%s() got values for both `%s` and `%s`" % (func.__name__, value, key))
-                warnings.warn("%s(): argument `%s` is deprecated in favor of `%s`" % (func.__name__, key, value))
-                kwargs[value] = kwargs.pop(key)
+    def decorate(func):
 
-        return func(*args, **kwargs)
+        @functools.wraps(func)
+        def wrapper(*args, **kwargs):
+            for key, value in alias.items():
+                if key in kwargs:
+                    if value in kwargs:
+                        raise TypeError("%s() got values for both `%s` and `%s`" % (func.__name__, value, key))
+                    warnings.warn("%s(): argument `%s` is deprecated in favor of `%s`" % (func.__name__, key, value))
+                    kwargs[value] = kwargs.pop(key)
 
-    return decorator(wrapper, kwsyntax=True)
+            return func(*args, **kwargs)
+
+        return wrapper
+
+    return decorate