Merge branch 'dev' into thesis_augmented_gnn

Author: aditya0by0

README.md

@@ -13,7 +13,12 @@ To install this repository, download it and run
 pip install .
 ```
 
-The dependencies `torch`, `torch_geometric` and `torch-sparse` cannot be installed automatically.
+or install it directly with
+```bash
+pip install git+https://github.com/ChEB-AI/python-chebai-graph.git
+```
+
+The dependencies `torch`, `torch_geometric` and `torch_scatter` cannot be installed automatically.
 
 Use the following command:
 
@@ -22,8 +27,8 @@ pip install torch torch_scatter torch_geometric -f https://data.pyg.org/whl/torc
 ```
 
 Replace:
-- `${TORCH}` with your installed PyTorch version (e.g., `2.6.0`)
-- `${CUDA}` with e.g. `cpu`, `cu118`, or `cu121` depending on your system and CUDA version
+- `${TORCH}` with a PyTorch version (e.g., `2.8.0`; for later versions, check first if they are compatible with torch_scatter and [torch_geometric](https://pytorch-geometric.readthedocs.io/en/latest/install/installation.html))
+- `${CUDA}` with `cpu`, `cu118`, `cu121` (or other, depending on your system and CUDA version)
 
 If you already have `torch` installed, make sure that `torch_scatter` and `torch_geometric` are compatible with your
 PyTorch version and are installed with the same CUDA version.

chebai_graph/preprocessing/datasets/chebi.py

@@ -117,6 +117,7 @@ def _setup_properties(self) -> None:
         idents = [row["ident"] for row in raw_data]
         features = [row["features"] for row in raw_data]
 
+        # use vectorized version of encode function, apply only if value is present
         def enc_if_not_none(encode, value):
             return (
                 [encode(v) for v in value]

pyproject.toml

@@ -7,16 +7,23 @@ authors = [
 ]
 dependencies = [
     "chebai",
-    "descriptastorus"
+    "descriptastorus",
+    # below packages need to manually installed as mentioned in readme
+    # torch-geometric
+    # torch_scatter
 ]
 requires-python = ">=3.8"
 
 
 [project.optional-dependencies]
 dev = [
     "tox",
+]
+
+linters = [
+    "isort",
     "pre-commit",
-    "black"
+    "black",
 ]
 
 [build-system]