Remove torch scatter dep

.github/workflows/test.yml

@@ -28,7 +28,6 @@ jobs:
       - name: Install dependencies
         run: |
           pip install torch==2.2.1 --index-url https://download.pytorch.org/whl/cpu
-          pip install torch-scatter -f https://data.pyg.org/whl/torch-2.2.1+cpu.html
           uv pip install .[test] --system
 
       - name: Run Tests

README.md

@@ -15,15 +15,7 @@ The aim of `aviary` is to contain multiple models for materials discovery under
 
 ## Installation
 
-Aviary requires [`torch-scatter`](https://github.com/rusty1s/pytorch_scatter). `pip install` it with
-
-```sh
-pip install torch-scatter -f https://data.pyg.org/whl/torch-2.2.1+cpu.html
-```
-
-Make sure you replace `2.2.1` with your actual `torch.__version__` (`python -c 'import torch; print(torch.__version__)'`) and `cpu` with your CUDA version if applicable.
-
-Then install `aviary` from source with
+Users can install `aviary` from source with
 
 ```sh
 pip install -U git+https://github.com/CompRhys/aviary

aviary/cgcnn/model.py

@@ -6,10 +6,10 @@
 import torch.nn.functional as F
 from pymatgen.util.due import Doi, due
 from torch import LongTensor, Tensor, nn
-from torch_scatter import scatter_add, scatter_mean
 
 from aviary.core import BaseModelClass
 from aviary.networks import SimpleNetwork
+from aviary.scatter import scatter_reduce
 
 if TYPE_CHECKING:
     from collections.abc import Sequence
@@ -114,7 +114,7 @@ def forward(
         """
         atom_fea = self.node_nn(atom_fea, nbr_fea, self_idx, nbr_idx)
 
-        crys_fea = scatter_mean(atom_fea, crystal_atom_idx, dim=0)
+        crys_fea = scatter_reduce(atom_fea, crystal_atom_idx, dim=0, reduce="mean")
 
         # NOTE required to match the reference implementation
         crys_fea = nn.functional.softplus(crys_fea)
@@ -236,7 +236,7 @@ def forward(
 
         # take the elementwise product of the filter and core
         nbr_msg = filter_fea * core_fea
-        nbr_summed = scatter_add(nbr_msg, self_idx, dim=0)
+        nbr_summed = scatter_reduce(nbr_msg, self_idx, dim=0, reduce="sum")
 
         nbr_summed = self.bn2(nbr_summed)
         return self.softplus2(atom_in_fea + nbr_summed)

aviary/scatter.py

@@ -0,0 +1,76 @@
+import torch
+
+
+def scatter_reduce(src, index, dim=-1, dim_size=None, reduce="sum"):
+    """Performs a scatter-reduce operation on the input tensor.
+
+    This function scatters the elements from the source tensor (src) into a new tensor
+    of shape determined by dim_size along the specified dimension (dim), using the
+    given reduction method. It's compatible with autograd for gradient computation.
+
+    NOTE this function was written by Claude 3.5 Sonnet.
+
+    Args:
+        src (torch.Tensor): The source tensor.
+        index (torch.Tensor): The indices of elements to scatter. Must be 1D or have
+            the same number of dimensions as src.
+        dim (int, optional): The axis along which to index. Defaults to -1.
+        dim_size (int, optional): The size of the output tensor's dimension `dim`.
+            If None, it's inferred as index.max().item() + 1. Defaults to None.
+        reduce (str, optional): The reduction operation to perform.
+            Options: "sum", "mean", "amax", "max", "amin", "min", "prod".
+            Defaults to "sum".
+
+    Returns:
+        torch.Tensor: The output tensor after the scatter-reduce operation.
+
+    Raises:
+        ValueError: If an unsupported reduction method is specified.
+        RuntimeError: If index and src tensors are incompatible.
+
+    Example:
+        >>> src = torch.tensor([1.0, 2.0, 3.0, 4.0, 5.0])
+        >>> index = torch.tensor([0, 1, 0, 1, 2])
+        >>> scatter_reduce(src, index, dim=0, reduce="sum")
+        tensor([4., 6., 5.])
+    """
+    if dim_size is None:
+        dim_size = index.max().item() + 1
+
+    # Prepare the output tensor shape
+    shape = list(src.shape)
+    shape[dim] = dim_size
+
+    # Ensure index has the same number of dimensions as src
+    if index.dim() != src.dim():
+        if index.dim() != 1:
+            raise RuntimeError(
+                "Index tensor must be 1D or have the same number of dimensions "
+                f"as src tensor. {index.shape=} != {src.shape=}"
+            )
+        # Expand index to match src dimensions
+        repeat_shape = [1] * src.dim()
+        repeat_shape[dim] = src.size(dim)
+        index = index.view(-1, *[1] * (src.dim() - 1)).expand_as(src)
+
+    # Perform scatter_reduce operation
+    if reduce in ["sum", "mean"]:
+        out = torch.zeros(shape, dtype=src.dtype, device=src.device)
+        out = out.scatter_add(dim, index, src)
+        if reduce == "mean":
+            count = torch.zeros(shape, dtype=src.dtype, device=src.device)
+            count = count.scatter_add(dim, index, torch.ones_like(src))
+            out = out / (count + (count == 0).float())  # avoid division by zero
+    elif reduce in ["amax", "max"]:
+        out = torch.full(shape, float("-inf"), dtype=src.dtype, device=src.device)
+        out = torch.max(out, out.scatter(dim, index, src))
+    elif reduce in ["amin", "min"]:
+        out = torch.full(shape, float("inf"), dtype=src.dtype, device=src.device)
+        out = torch.min(out, out.scatter(dim, index, src))
+    elif reduce == "prod":
+        out = torch.ones(shape, dtype=src.dtype, device=src.device)
+        out = out.scatter(dim, index, src, reduce="multiply")
+    else:
+        raise ValueError(f"Unsupported reduction method: {reduce}")
+
+    return out

aviary/segments.py

@@ -4,9 +4,9 @@
 
 import torch
 from torch import LongTensor, Tensor, nn
-from torch_scatter import scatter_add, scatter_max
 
 from aviary.networks import SimpleNetwork
+from aviary.scatter import scatter_reduce
 
 if TYPE_CHECKING:
     from collections.abc import Sequence
@@ -38,12 +38,12 @@ def forward(self, x: Tensor, index: Tensor) -> Tensor:
         """
         gate = self.gate_nn(x)
 
-        gate -= scatter_max(gate, index, dim=0)[0][index]
+        gate -= scatter_reduce(gate, index, dim=0, reduce="amax")[index]
         gate = gate.exp()
-        gate /= scatter_add(gate, index, dim=0)[index] + 1e-10
+        gate /= scatter_reduce(gate, index, dim=0, reduce="sum")[index] + 1e-10
 
         x = self.message_nn(x)
-        return scatter_add(gate * x, index, dim=0)
+        return scatter_reduce(gate * x, index, dim=0, reduce="sum")
 
     def __repr__(self) -> str:
         gate_nn, message_nn = self.gate_nn, self.message_nn
@@ -78,12 +78,12 @@ def forward(self, x: Tensor, index: Tensor, weights: Tensor) -> Tensor:
         """
         gate = self.gate_nn(x)
 
-        gate -= scatter_max(gate, index, dim=0)[0][index]
+        gate -= scatter_reduce(gate, index, dim=0, reduce="amax")[index]
         gate = (weights**self.pow) * gate.exp()
-        gate /= scatter_add(gate, index, dim=0)[index] + 1e-10
+        gate /= scatter_reduce(gate, index, dim=0, reduce="sum")[index] + 1e-10
 
         x = self.message_nn(x)
-        return scatter_add(gate * x, index, dim=0)
+        return scatter_reduce(gate * x, index, dim=0, reduce="sum")
 
     def __repr__(self) -> str:
         pow, gate_nn, message_nn = float(self.pow), self.gate_nn, self.message_nn

aviary/wren/model.py

@@ -6,10 +6,10 @@
 import torch.nn.functional as F
 from pymatgen.util.due import Doi, due
 from torch import LongTensor, Tensor, nn
-from torch_scatter import scatter_mean
 
 from aviary.core import BaseModelClass
 from aviary.networks import ResidualNetwork, SimpleNetwork
+from aviary.scatter import scatter_reduce
 from aviary.segments import MessageLayer, WeightedAttentionPooling
 
 if TYPE_CHECKING:
@@ -261,7 +261,9 @@ def forward(
             for attnhead in self.cry_pool
         ]
 
-        return scatter_mean(torch.mean(torch.stack(head_fea), dim=0), aug_cry_idx, dim=0)
+        return scatter_reduce(
+            torch.mean(torch.stack(head_fea), dim=0), aug_cry_idx, dim=0, reduce="mean"
+        )
 
     def __repr__(self) -> str:
         return (

examples/notebooks/Roost.ipynb

@@ -12,7 +12,6 @@
     "\n",
     "print(f\"{TORCH_VERSION=}\")\n",
     "\n",
-    "!pip install torch-scatter -f https://data.pyg.org/whl/torch-{TORCH_VERSION}.html\n",
     "!pip install -U git+https://github.com/CompRhys/aviary.git  # install aviary\n",
     "!wget -O taata.json.gz https://figshare.com/ndownloader/files/34423997"
    ]

examples/notebooks/Wren.ipynb

@@ -12,7 +12,6 @@
     "\n",
     "print(f\"{TORCH_VERSION=}\")\n",
     "\n",
-    "!pip install torch-scatter -f https://data.pyg.org/whl/torch-{TORCH_VERSION}.html\n",
     "!pip install -U git+https://github.com/CompRhys/aviary.git  # install aviary\n",
     "!wget -O taata.json.gz https://figshare.com/ndownloader/files/34423997"
    ]

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "aviary"
-version = "1.0.0"
+version = "1.1.0"
 description = "A collection of machine learning models for materials discovery"
 authors = [{ name = "Rhys Goodall", email = "[email protected]" }]
 readme = "README.md"
@@ -27,7 +27,6 @@ classifiers = [
   "Operating System :: OS Independent",
   "Programming Language :: Python :: 3.10",
   "Programming Language :: Python :: 3.11",
-  "Programming Language :: Python :: 3.8",
   "Programming Language :: Python :: 3.9",
   "Topic :: Scientific/Engineering :: Artificial Intelligence",
   "Topic :: Scientific/Engineering :: Chemistry",
@@ -42,7 +41,6 @@ dependencies = [
   "scikit_learn",
   "tensorboard",
   "torch",
-  "torch_scatter",
   "tqdm",
   "wandb",
 ]
@@ -114,6 +112,7 @@ ignore = [
   "D105",  # Missing docstring in magic method
   "D205",  # 1 blank line required between summary line and description
   "E731",  # Do not assign a lambda expression, use a def
+  "ISC001",
   "PD901", # pandas-df-variable-name
   "PLR",   # pylint refactor
   "PT006", # pytest-parametrize-names-wrong-type