enable ruff and npy rules (#1998)

Signed-off-by: Jinzhe Zeng <[email protected]>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

pyproject.toml

@@ -140,6 +140,8 @@ select = [
     "I", # isort
     "UP", # pyupgrade
     "C4", # flake8-comprehensions
+    "RUF", # ruff
+    "NPY", # numpy
 ]
 ignore = [
     "E501", # line too long

reacnetgenerator/__init__.py

@@ -21,7 +21,7 @@
 
 from ._version import __version__
 
-mpl.use("svg")  # noqa
+mpl.use("svg")
 
 from .reacnetgen import ReacNetGenerator
 

reacnetgenerator/_detect.py

@@ -29,7 +29,7 @@
 from abc import ABCMeta, abstractmethod
 from collections import defaultdict
 from enum import Enum, auto
-from typing import Optional, Tuple
+from typing import ClassVar, Optional, Tuple
 
 import numpy as np
 
@@ -59,7 +59,7 @@ class _Detect(SharedRNGData, metaclass=ABCMeta):
         The ReacNetGenerator class.
     """
 
-    subclasses = {}
+    subclasses: ClassVar[dict] = {}
 
     # type hints
     # TODO: we need a better way to communicate with parameters
@@ -223,7 +223,7 @@ def _readNfunc(self, f):
                     else:
                         iscompleted = True
                         stepaindex = index
-                    N = [int(s) for s in line.split() if s.isdigit()][0]
+                    N = next(int(s) for s in line.split() if s.isdigit())
                     atomtype = np.zeros(N, dtype=int)
             else:
                 s = line.split()

tests/test_reacnetgen.py

@@ -132,9 +132,8 @@ def test_benchmark_hmm(self, benchmark, reacnetgen_param):
         hmmclass = _HMMFilter(reacnetgen)
         if hmmclass.runHMM:
             hmmclass._initHMM()
-        index = np.sort(
-            np.random.choice(hmmclass.step, hmmclass.step // 2, replace=False)
-        )
+        rng = np.random.default_rng()
+        index = np.sort(rng.choice(hmmclass.step, hmmclass.step // 2, replace=False))
         compressed_bytes = [
             listtobytes((5, 6)),
             listtobytes(((5, 6, 1),)),