Remove some old TODOs that are now solved

torchmd · Jan 26, 2024 · 9da5319 · 9da5319
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commit 9da5319
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Showing 2 changed files with 1 addition and 92 deletions.
diff --git a/torchmdnet/datasets/ani.py b/torchmdnet/datasets/ani.py
@@ -269,11 +269,6 @@ def get_atomref(self, max_z=100):
 
         return refs.view(-1, 1)
 
-    # Circumvent https://github.com/pyg-team/pytorch_geometric/issues/4567
-    # TODO remove when fixed
-    def process(self):
-        super().process()
-
 
 class ANI1XBase(ANIBase):
     @property
@@ -350,16 +345,6 @@ def sample_iter(self, mol_ids=False):
                     if data := self.filter_and_pre_transform(data):
                         yield data
 
-    # Circumvent https://github.com/pyg-team/pytorch_geometric/issues/4567
-    # TODO remove when fixed
-    def download(self):
-        super().download()
-
-    # Circumvent https://github.com/pyg-team/pytorch_geometric/issues/4567
-    # TODO remove when fixed
-    def process(self):
-        super().process()
-
 
 class ANI1CCX(ANI1XBase):
     __doc__ = ANIBase.__doc__
@@ -392,16 +377,6 @@ def sample_iter(self, mol_ids=False):
                     if data := self.filter_and_pre_transform(data):
                         yield data
 
-    # Circumvent https://github.com/pyg-team/pytorch_geometric/issues/4567
-    # TODO remove when fixed
-    def download(self):
-        super().download()
-
-    # Circumvent https://github.com/pyg-team/pytorch_geometric/issues/4567
-    # TODO remove when fixed
-    def process(self):
-        super().process()
-
 
 class ANI2X(ANIBase):
     __doc__ = ANIBase.__doc__
@@ -477,8 +452,3 @@ def get_atomref(self, max_z=100):
             refs[key] = val * self.HARTREE_TO_EV
 
         return refs.view(-1, 1)
-
-    # Circumvent https://github.com/pyg-team/pytorch_geometric/issues/4567
-    # TODO remove when fixed
-    def process(self):
-        super().process()
diff --git a/torchmdnet/datasets/comp6.py b/torchmdnet/datasets/comp6.py
@@ -223,17 +223,6 @@ def raw_url_name(self):
     def raw_file_names(self):
         return ["ani_md_bench.h5"]
 
-    # Circumvent https://github.com/pyg-team/pytorch_geometric/issues/4567
-    # TODO remove when fixed
-    def download(self):
-        super().download()
-
-    # Circumvent https://github.com/pyg-team/pytorch_geometric/issues/4567
-    # TODO remove when fixed
-    def process(self):
-        super().process()
-
-
 class DrugBank(COMP6Base):
     """
     DrugBank Benchmark. This benchmark is developed through a subsampling of the
@@ -249,16 +238,6 @@ class DrugBank(COMP6Base):
     def raw_file_names(self):
         return ["drugbank_testset.h5"]
 
-    # Circumvent https://github.com/pyg-team/pytorch_geometric/issues/4567
-    # TODO remove when fixed
-    def download(self):
-        super().download()
-
-    # Circumvent https://github.com/pyg-team/pytorch_geometric/issues/4567
-    # TODO remove when fixed
-    def process(self):
-        super().process()
-
 
 class GDB07to09(COMP6Base):
     """
@@ -275,16 +254,6 @@ class GDB07to09(COMP6Base):
     def raw_file_names(self):
         return ["gdb11_07_test500.h5", "gdb11_08_test500.h5", "gdb11_09_test500.h5"]
 
-    # Circumvent https://github.com/pyg-team/pytorch_geometric/issues/4567
-    # TODO remove when fixed
-    def download(self):
-        super().download()
-
-    # Circumvent https://github.com/pyg-team/pytorch_geometric/issues/4567
-    # TODO remove when fixed
-    def process(self):
-        super().process()
-
 
 class GDB10to13(COMP6Base):
     """
@@ -304,16 +273,6 @@ def raw_file_names(self):
             "gdb13_13_test1000.h5",
         ]
 
-    # Circumvent https://github.com/pyg-team/pytorch_geometric/issues/4567
-    # TODO remove when fixed
-    def download(self):
-        super().download()
-
-    # Circumvent https://github.com/pyg-team/pytorch_geometric/issues/4567
-    # TODO remove when fixed
-    def process(self):
-        super().process()
-
 
 class Tripeptides(COMP6Base):
     """
@@ -329,16 +288,6 @@ class Tripeptides(COMP6Base):
     def raw_file_names(self):
         return ["tripeptide_full.h5"]
 
-    # Circumvent https://github.com/pyg-team/pytorch_geometric/issues/4567
-    # TODO remove when fixed
-    def download(self):
-        super().download()
-
-    # Circumvent https://github.com/pyg-team/pytorch_geometric/issues/4567
-    # TODO remove when fixed
-    def process(self):
-        super().process()
-
 
 class S66X8(COMP6Base):
     """
@@ -362,16 +311,6 @@ def raw_url_name(self):
     def raw_file_names(self):
         return ["s66x8_wb97x6-31gd.h5"]
 
-    # Circumvent https://github.com/pyg-team/pytorch_geometric/issues/4567
-    # TODO remove when fixed
-    def download(self):
-        super().download()
-
-    # Circumvent https://github.com/pyg-team/pytorch_geometric/issues/4567
-    # TODO remove when fixed
-    def process(self):
-        super().process()
-
 
 class COMP6v1(Dataset):
     """
@@ -389,7 +328,7 @@ def __init__(
 
         self.subsets = [
             DS(root, transform, pre_transform, pre_filter)
-            for DS in (ANIMD, DrugBank, GDB07to09, GDB10to13, Tripeptides, S66X8)
+           for DS in (ANIMD, DrugBank, GDB07to09, GDB10to13, Tripeptides, S66X8)
         ]
 
         self.num_samples = sum(len(subset) for subset in self.subsets)