Merge pull request #2 from OpenDrugDiscovery/pre-commit

Added and run pre-commit hooks

.github/SECURITY.md

@@ -1,3 +1,3 @@
 # Security Policy
 
-Please report any security-related issues directly to [email protected]. 
+Please report any security-related issues directly to [email protected].

.github/workflows/pre-commit-ci.yml

@@ -0,0 +1,15 @@
+# Based on https://github.com/pre-commit/action
+name: pre-commit
+
+on:
+  pull_request:
+  push:
+    branches: [main]
+
+jobs:
+  pre-commit:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v3
+    - uses: actions/setup-python@v3
+    - uses: pre-commit/[email protected]

.gitignore

@@ -140,10 +140,9 @@ cache/
 *.hdf5
 nohup.out
 *.out
-*.crt 
+*.crt
 *.key
 *.dat
 *.xyz
 *.csv
 *.txt
-

.pre-commit-config.yaml

@@ -0,0 +1,26 @@
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.4.0
+    hooks:
+      - id: end-of-file-fixer
+      - id: trailing-whitespace
+      - id: check-yaml
+      - id: check-toml
+      - id: check-json
+      - id: check-merge-conflict
+      - id: requirements-txt-fixer
+      - id: detect-private-key
+  - repo: https://github.com/psf/black
+    rev: 23.3.0
+    hooks:
+      - id: black
+  - repo: https://github.com/pycqa/isort
+    rev: 5.12.0
+    hooks:
+      - id: isort
+        args: ["--profile", "black"]
+  - repo: https://github.com/charliermarsh/ruff-pre-commit
+    # Ruff version.
+    rev: 'v0.0.241'
+    hooks:
+      - id: ruff

env.yml

@@ -64,6 +64,6 @@ dependencies:
   - ruff
   - ipykernel
   - pydantic <= 2.0
-  
+
   - pip:
       - torch-nl

openqdc/datasets/ani.py

@@ -1,14 +1,15 @@
 import os
-import numpy as np
 from os.path import join as p_join
-from openqdc.utils.constants import MAX_ATOMIC_NUMBER
+
+import numpy as np
+
 from openqdc.datasets.base import BaseDataset, read_qc_archive_h5
+from openqdc.utils.constants import MAX_ATOMIC_NUMBER
 from openqdc.utils.io import get_local_cache
 
 
 class ANI1(BaseDataset):
-    __name__ = 'ani1'
-
+    __name__ = "ani1"
 
     # Energy in hartree, all zeros by default
     atomic_energies = np.zeros((MAX_ATOMIC_NUMBER,), dtype=np.float32)
@@ -21,29 +22,27 @@ class ANI1(BaseDataset):
         "ωB97x:6-31G(d) Energy",
     ]
 
-
     def __init__(self) -> None:
         super().__init__()
 
     @property
     def root(self):
-        return p_join(get_local_cache(), 'ani')
-    
+        return p_join(get_local_cache(), "ani")
+
     @property
     def preprocess_path(self):
-        path = p_join(self.root, 'preprocessed', self.__name__)
+        path = p_join(self.root, "preprocessed", self.__name__)
         os.makedirs(path, exist_ok=True)
         return path
-    
+
     def read_raw_entries(self):
-        raw_path = p_join(self.root, f'{self.__name__}.h5')
-        samples = read_qc_archive_h5(raw_path, self.__name__, self.energy_target_names, 
-                                     self.force_target_names)
+        raw_path = p_join(self.root, f"{self.__name__}.h5")
+        samples = read_qc_archive_h5(raw_path, self.__name__, self.energy_target_names, self.force_target_names)
         return samples
 
 
 class ANI1CCX(ANI1):
-    __name__ = 'ani1ccx'
+    __name__ = "ani1ccx"
 
     # Energy in hartree, all zeros by default
     atomic_energies = np.zeros((MAX_ATOMIC_NUMBER,), dtype=np.float32)
@@ -67,10 +66,10 @@ class ANI1CCX(ANI1):
 
     def __init__(self) -> None:
         super().__init__()
-    
+
 
 class ANI1X(ANI1):
-    __name__ = 'ani1x'
+    __name__ = "ani1x"
 
     # Energy in hartree, all zeros by default
     atomic_energies = np.zeros((MAX_ATOMIC_NUMBER,), dtype=np.float32)
@@ -94,10 +93,10 @@ class ANI1X(ANI1):
         "MP2:cc-pVQZ Correlation Energy",
         "MP2:cc-pVTZ Correlation Energy",
         "wB97x:6-31G(d) Total Energy",
-        "wB97x:def2-TZVPP Total Energy"
+        "wB97x:def2-TZVPP Total Energy",
     ]
 
-    force_target_names = [ 
+    force_target_names = [
         "wB97x:6-31G(d) Atomic Forces",
         "wB97x:def2-TZVPP Atomic Forces",
     ]
@@ -111,21 +110,21 @@ def __init__(self) -> None:
         super().__init__()
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     for data_class in [
-            ANI1, 
-            # ANI1CCX, 
-            # ANI1X
-        ]:
+        ANI1,
+        # ANI1CCX,
+        # ANI1X
+    ]:
         data = data_class()
         n = len(data)
 
         for i in np.random.choice(n, 3, replace=False):
             x = data[i]
-            print(x.name, x.subset, end=' ')
+            print(x.name, x.subset, end=" ")
             for k in x:
                 if x[k] is not None:
-                    print(k, x[k].shape, end=' ')
-                
+                    print(k, x[k].shape, end=" ")
+
             print()
-        exit()
+        exit()

openqdc/datasets/base.py

@@ -1,27 +1,34 @@
 import os
-import torch
-import numpy as np
-import pickle as pkl
-from tqdm import tqdm
 from os.path import join as p_join
+
+import numpy as np
+import torch
 from sklearn.utils import Bunch
-from openqdc.utils.io import get_local_cache, pull_locally, push_remote, load_hdf5_file, copy_exists
+from tqdm import tqdm
+
+from openqdc.utils.constants import NB_ATOMIC_FEATURES
+from openqdc.utils.io import (
+    copy_exists,
+    get_local_cache,
+    load_hdf5_file,
+    pull_locally,
+    push_remote,
+)
 from openqdc.utils.molecule import atom_table
-from openqdc.utils.constants import BOHR2ANG, MAX_ATOMIC_NUMBER, NB_ATOMIC_FEATURES
 
 
-def extract_entry(df, i, subset, energy_target_names, force_target_names=None): 
+def extract_entry(df, i, subset, energy_target_names, force_target_names=None):
     x = np.array([atom_table.GetAtomicNumber(s) for s in df["symbols"][i]])
     xs = np.stack((x, np.zeros_like(x)), axis=-1)
-    positions= df["geometry"][i].reshape((-1, 3))
-    energies= np.array([df[k][i] for k in energy_target_names])
-    
+    positions = df["geometry"][i].reshape((-1, 3))
+    energies = np.array([df[k][i] for k in energy_target_names])
+
     res = dict(
-        name= np.array([df["name"][i]]),
-        subset= np.array([subset]),     
-        energies= energies.reshape((1, -1)).astype(np.float32),
-        atomic_inputs = np.concatenate((xs, positions), axis=-1, dtype=np.float32),
-        n_atoms = np.array([x.shape[0]], dtype=np.int32),
+        name=np.array([df["name"][i]]),
+        subset=np.array([subset]),
+        energies=energies.reshape((1, -1)).astype(np.float32),
+        atomic_inputs=np.concatenate((xs, positions), axis=-1, dtype=np.float32),
+        n_atoms=np.array([x.shape[0]], dtype=np.int32),
     )
     if force_target_names is not None and len(force_target_names) > 0:
         forces = np.zeros((positions.shape[0], 3, len(force_target_names)), dtype=np.float32)
@@ -47,8 +54,7 @@ def read_qc_archive_h5(raw_path, subset, energy_target_names, force_target_names
     # print('\n'*3)
     # exit()
 
-    samples = [extract_entry(data_t, i, subset, energy_target_names, force_target_names) 
-               for i in tqdm(range(n))]
+    samples = [extract_entry(data_t, i, subset, energy_target_names, force_target_names) for i in tqdm(range(n))]
     return samples
 
 
@@ -71,45 +77,44 @@ def __init__(self) -> None:
     @property
     def root(self):
         return p_join(get_local_cache(), self.__name__)
-    
+
     @property
     def preprocess_path(self):
-        path = p_join(self.root, 'preprocessed')
+        path = p_join(self.root, "preprocessed")
         os.makedirs(path, exist_ok=True)
         return path
-    
+
     @property
     def data_keys(self):
         keys = list(self.data_types.keys())
         if len(self.__force_methods__) == 0:
             keys.remove("forces")
         return keys
-    
+
     @property
     def data_types(self):
         return {
-            "atomic_inputs": np.float32, 
-            "position_idx_range": np.int32, 
+            "atomic_inputs": np.float32,
+            "position_idx_range": np.int32,
             "energies": np.float32,
-            "forces": np.float32
+            "forces": np.float32,
         }
-    
+
     @property
     def data_shapes(self):
         return {
-            "atomic_inputs": (-1, NB_ATOMIC_FEATURES), 
-            "position_idx_range": (-1, 2), 
+            "atomic_inputs": (-1, NB_ATOMIC_FEATURES),
+            "position_idx_range": (-1, 2),
             "energies": (-1, len(self.energy_target_names)),
-            "forces": (-1, 3, len(self.force_target_names))
+            "forces": (-1, 3, len(self.force_target_names)),
         }
-    
+
     def read_raw_entries(self):
         raise NotImplementedError
-    
+
     def collate_list(self, list_entries):
         # concatenate entries
-        res = {key: np.concatenate([r[key] for r in list_entries if r is not None], axis=0) 
-               for key in list_entries[0]}
+        res = {key: np.concatenate([r[key] for r in list_entries if r is not None], axis=0) for key in list_entries[0]}
 
         csum = np.cumsum(res.pop("n_atoms"))
         x = np.zeros((csum.shape[0], 2), dtype=np.int32)
@@ -121,52 +126,48 @@ def save_preprocess(self, data_dict):
         # save memmaps
         for key in self.data_keys:
             local_path = p_join(self.preprocess_path, f"{key}.mmap")
-            out = np.memmap(local_path, 
-                            mode="w+", 
-                            dtype=data_dict[key].dtype, 
-                            shape=data_dict[key].shape)
+            out = np.memmap(local_path, mode="w+", dtype=data_dict[key].dtype, shape=data_dict[key].shape)
             out[:] = data_dict.pop(key)[:]
             out.flush()
             push_remote(local_path)
-            
+
         # save smiles and subset
         for key in ["name", "subset"]:
             local_path = p_join(self.preprocess_path, f"{key}.npz")
             uniques, inv_indices = np.unique(data_dict[key], return_inverse=True)
             with open(local_path, "wb") as f:
                 np.savez_compressed(f, uniques=uniques, inv_indices=inv_indices)
             push_remote(local_path)
-    
-    def read_preprocess(self): 
+
+    def read_preprocess(self):
         self.data = {}
         for key in self.data_keys:
             filename = p_join(self.preprocess_path, f"{key}.mmap")
             pull_locally(filename)
             self.data[key] = np.memmap(
-                filename, mode='r', 
+                filename,
+                mode="r",
                 dtype=self.data_types[key],
             ).reshape(self.data_shapes[key])
-            
+
         for key in self.data:
-            print(f'Loaded {key} with shape {self.data[key].shape}, dtype {self.data[key].dtype}')
+            print(f"Loaded {key} with shape {self.data[key].shape}, dtype {self.data[key].dtype}")
 
         for key in ["name", "subset"]:
             filename = p_join(self.preprocess_path, f"{key}.npz")
             pull_locally(filename)
             # with open(filename, "rb") as f:
             self.data[key] = np.load(open(filename, "rb"))
             for k in self.data[key]:
-                print(f'Loaded {key}_{k} with shape {self.data[key][k].shape}, dtype {self.data[key][k].dtype}')
+                print(f"Loaded {key}_{k} with shape {self.data[key][k].shape}, dtype {self.data[key][k].dtype}")
 
     def is_preprocessed(self):
-        predicats = [copy_exists(p_join(self.preprocess_path, f"{key}.mmap"))
-                     for key in self.data_keys]
-        predicats += [copy_exists(p_join(self.preprocess_path, f"{x}.npz"))
-                      for x in ["name", "subset"]]
+        predicats = [copy_exists(p_join(self.preprocess_path, f"{key}.mmap")) for key in self.data_keys]
+        predicats += [copy_exists(p_join(self.preprocess_path, f"{x}.npz")) for x in ["name", "subset"]]
         return all(predicats)
 
     def __len__(self):
-        return self.data['energies'].shape[0]
+        return self.data["energies"].shape[0]
 
     def __getitem__(self, idx: int):
         p_start, p_end = self.data["position_idx_range"][idx]
@@ -190,5 +191,5 @@ def __getitem__(self, idx: int):
             energies=energies,
             name=name,
             subset=subset,
-            forces=forces
+            forces=forces,
         )