Merge pull request #1 from compomics/pyproject

Project structure changes

.github/workflows/test.yml

@@ -0,0 +1,36 @@
+name: Tests
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.9", "3.10", "3.11"]
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python 3.8
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install ruff
+
+      - name: Run Ruff
+        run: ruff check --output-format=github .
+
+      # - name: Install package
+      #   run: pip install .
+
+      # - name: Test with pytest
+      #   run: |
+      #     pytest

.gitignore

@@ -1,5 +1,8 @@
 notebooks/_*.ipynb
 
+# vscode
+.vscode
+
 # jupyter
 MANIFEST
 build

molexpress/__init__.py

@@ -0,0 +1 @@
+__version__ = "0.1.0"

molexpress/datasets/encoders.py

@@ -1,78 +1,65 @@
+from __future__ import annotations
+
 import numpy as np
-from rdkit import Chem
 
+from molexpress import types
 from molexpress.datasets import featurizers
 from molexpress.ops import chem_ops
-from molexpress import types
-
 
-class MolecularGraphEncoder:
 
+class MolecularGraphEncoder:
     def __init__(
         self,
         atom_featurizers: list[featurizers.Featurizer],
         bond_featurizers: list[featurizers.Featurizer] = None,
-        self_loops: bool = False, 
+        self_loops: bool = False,
     ) -> None:
         self.node_encoder = MolecularNodeEncoder(atom_featurizers)
-        self.edge_encoder = MolecularEdgeEncoder(
-            bond_featurizers, self_loops=self_loops
-        )
-
-    def __call__(
-        self, 
-        molecule: types.Molecule | types.SMILES | types.InChI
-    ) -> np.ndarray:
+        self.edge_encoder = MolecularEdgeEncoder(bond_featurizers, self_loops=self_loops)
+
+    def __call__(self, molecule: types.Molecule | types.SMILES | types.InChI) -> np.ndarray:
         molecule = chem_ops.get_molecule(molecule)
         return {**self.node_encoder(molecule), **self.edge_encoder(molecule)}
 
     @staticmethod
     def _collate_fn(
-        data: list[tuple[types.MolecularGraph, np.ndarray]]
+        data: list[tuple[types.MolecularGraph, np.ndarray]],
     ) -> tuple[types.MolecularGraph, np.ndarray]:
-
-        """TODO: Not sure where to implement this collate function. 
+        """TODO: Not sure where to implement this collate function.
                  Temporarily putting it here.
 
         Procedure:
             Merges list of graphs into a single disjoint graph.
         """
 
-        x, y = list(zip(*data)) 
-
-        num_nodes = np.array([
-            graph['node_state'].shape[0] for graph in x
-        ])
-
+        x, y = list(zip(*data))
+
+        num_nodes = np.array([graph["node_state"].shape[0] for graph in x])
+
         disjoint_graph = {}
 
-        disjoint_graph['node_state'] = np.concatenate([
-            graph['node_state'] for graph in x
-        ])
+        disjoint_graph["node_state"] = np.concatenate([graph["node_state"] for graph in x])
 
-        if 'edge_state' in x[0]:
-            disjoint_graph['edge_state'] = np.concatenate([
-                graph['edge_state'] for graph in x
-            ])
+        if "edge_state" in x[0]:
+            disjoint_graph["edge_state"] = np.concatenate([graph["edge_state"] for graph in x])
 
-        edge_src = np.concatenate([graph['edge_src'] for graph in x])
-        edge_dst = np.concatenate([graph['edge_dst'] for graph in x])
-        num_edges = np.array([graph['edge_src'].shape[0] for graph in x])
-        indices = np.repeat(range(len(x)), num_edges) 
+        edge_src = np.concatenate([graph["edge_src"] for graph in x])
+        edge_dst = np.concatenate([graph["edge_dst"] for graph in x])
+        num_edges = np.array([graph["edge_src"].shape[0] for graph in x])
+        indices = np.repeat(range(len(x)), num_edges)
         edge_incr = np.concatenate([[0], num_nodes[:-1]])
         edge_incr = np.take_along_axis(edge_incr, indices, axis=0)
 
-        disjoint_graph['edge_src'] = edge_src + edge_incr
-        disjoint_graph['edge_dst'] = edge_dst + edge_incr 
-        disjoint_graph['graph_indicator'] = np.repeat(range(len(x)), num_nodes)
+        disjoint_graph["edge_src"] = edge_src + edge_incr
+        disjoint_graph["edge_dst"] = edge_dst + edge_incr
+        disjoint_graph["graph_indicator"] = np.repeat(range(len(x)), num_nodes)
 
         return disjoint_graph, np.stack(y)
 
 
 class Composer:
-
     """Wraps a list of featurizers.
-    
+
     While a Featurizer encodes an atom or bond based on a single property,
     the Composer encodes an atom or bond based on multiple properties.
 
@@ -84,64 +71,55 @@ class Composer:
     def __init__(self, featurizers: list[featurizers.Featurizer]) -> None:
         self.featurizers = featurizers
         assert all(
-            self.featurizers[0].output_dtype == f.output_dtype 
-            for f in self.featurizers
+            self.featurizers[0].output_dtype == f.output_dtype for f in self.featurizers
         ), "'dtype' of features need to be consistent."
 
     def __call__(self, inputs: types.Atom | types.Bond) -> np.ndarray:
         return np.concatenate([f(inputs) for f in self.featurizers])
-    
+
     @property
     def output_dim(self):
         return sum(f.output_dim for f in self.featurizers)
 
     @property
     def output_dtype(self):
         return self.featurizers[0].output_dtype
-
 
-class MolecularEdgeEncoder:
 
+class MolecularEdgeEncoder:
     def __init__(
-        self, 
-        featurizers: list[featurizers.Featurizer], 
-        self_loops: bool = False
+        self, featurizers: list[featurizers.Featurizer], self_loops: bool = False
     ) -> None:
-        self.featurizer = Composer(featurizers) 
+        self.featurizer = Composer(featurizers)
         self.self_loops = self_loops
         self.output_dim = self.featurizer.output_dim
         self.output_dtype = self.featurizer.output_dtype
 
     def __call__(self, molecule: types.Molecule) -> np.ndarray:
-
-        edge_src, edge_dst = chem_ops.get_adjacency(
-            molecule, self_loops=self.self_loops)
+        edge_src, edge_dst = chem_ops.get_adjacency(molecule, self_loops=self.self_loops)
 
         if self.featurizer is None:
-            return {'edge_src': edge_src, 'edge_dst': edge_dst}
+            return {"edge_src": edge_src, "edge_dst": edge_dst}
 
         if molecule.GetNumBonds() == 0:
             edge_state = np.zeros(
-                shape=(0, self.output_dim + int(self.self_loops)), 
+                shape=(0, self.output_dim + int(self.self_loops)),
                 dtype=self.output_dtype
             )
             return {
-                'edge_src': edge_src, 
-                'edge_dst': edge_dst, 
-                'edge_state': edge_state
+                "edge_src": edge_src,
+                "edge_dst": edge_dst,
+                "edge_state": edge_state,
             }
-        
+
         bond_encodings = []
 
         for i, j in zip(edge_src, edge_dst):
-
             bond = molecule.GetBondBetweenAtoms(int(i), int(j))
 
             if bond is None:
                 assert self.self_loops, "Found a bond to be None."
-                bond_encoding = np.zeros(
-                    self.output_dim + 1, dtype=self.output_dtype
-                )
+                bond_encoding = np.zeros(self.output_dim + 1, dtype=self.output_dtype)
                 bond_encoding[-1] = 1
             else:
                 bond_encoding = self.featurizer(bond)
@@ -151,23 +129,19 @@ def __call__(self, molecule: types.Molecule) -> np.ndarray:
             bond_encodings.append(bond_encoding)
 
         return {
-            'edge_src': edge_src, 
-            'edge_dst': edge_dst, 
-            'edge_state': np.stack(bond_encodings)
+            "edge_src": edge_src,
+            "edge_dst": edge_dst,
+            "edge_state": np.stack(bond_encodings),
         }
-
 
-class MolecularNodeEncoder:
 
+class MolecularNodeEncoder:
     def __init__(
-        self, 
-        featurizers: list[featurizers.Featurizer], 
+        self,
+        featurizers: list[featurizers.Featurizer],
     ) -> None:
-        self.featurizer = Composer(featurizers) 
+        self.featurizer = Composer(featurizers)
 
     def __call__(self, molecule: types.Molecule) -> np.ndarray:
-        node_encodings = np.stack([
-            self.featurizer(atom) for atom in molecule.GetAtoms()
-        ], axis=0)
-        return {'node_state': np.stack(node_encodings)}
-
+        node_encodings = np.stack([self.featurizer(atom) for atom in molecule.GetAtoms()], axis=0)
+        return {"node_state": np.stack(node_encodings)}