use ruff to lint codes

.pre-commit-config.yaml

@@ -21,11 +21,11 @@ repos:
     rev: 23.1.0
     hooks:
     -   id: black-jupyter
--   repo: https://github.com/PyCQA/isort
-    rev: 5.12.0
+-   repo: https://github.com/charliermarsh/ruff-pre-commit
+    rev: v0.0.252
     hooks:
-    - id: isort
-    files: \.py$
+    - id: ruff
+      args: ["--fix"]
 # numpydoc
 -   repo: https://github.com/Carreau/velin
     rev: 0.0.12

pyproject.toml

@@ -133,3 +133,35 @@ omit = ["*test*"]
 
 [tool.isort]
 profile = "black"
+
+[tool.ruff]
+target-version = "py37"
+
+select = [
+    "E", # errors
+    "F", # pyflakes
+    "D", # pydocstyle
+	"I", # isort
+    "UP", # pyupgrade
+]
+ignore = [
+    "E501", # line too long
+    "F401", # unused import
+    "F841", # local variable is assigned to but never used
+    "E741", # ambiguous variable name
+    "E402", # module level import not at top of file
+    "D413", # missing blank line after last section
+    "D416", # section name should end with a colon
+    "D203", # 1 blank line required before class docstring
+    "D107", # missing docstring in __init__
+    "D213", # multi-line docstring summary should start at the second line
+    "D100", # TODO: missing docstring in public module
+    "D101", # TODO: missing docstring in public class
+    "D102", # TODO: missing docstring in public method
+    "D103", # TODO: missing docstring in public function
+    "D104", # TODO: missing docstring in public package
+    "D105", # TODO: missing docstring in magic method
+    "D205", # 1 blank line required between summary line and description
+    "D401", # TODO: first line should be in imperative mood
+    "D404", # TODO: first word of the docstring should not be This
+]

reacnetgenerator/__init__.py

@@ -1,6 +1,6 @@
 # Copyright 2018-2022, East China Normal University
 """ReacNetGenerator is an automatic reaction network generator for
-reactive molecular dynamics simulation.[1]_
+reactive molecular dynamics simulation.[1]_.
 
 References
 ----------

reacnetgenerator/_detect.py

@@ -471,7 +471,7 @@ def _readstepfunc(self, item):
             s = line.split()
             if index > 1:
                 step_atoms.append(
-                    (index - 1, Atom(s[0], tuple((float(x) for x in s[1:4]))))
+                    (index - 1, Atom(s[0], tuple(float(x) for x in s[1:4])))
                 )
         _, step_atoms = zip(*sorted(step_atoms, key=operator.itemgetter(0)))
         step_atoms = Atoms(step_atoms)

reacnetgenerator/_draw.py

@@ -175,5 +175,5 @@ def _handlespecies(self, name):
         if species:
             logger.info("Species are:")
             for specname, n in showname.items():
-                logger.info("{} {}".format(n, specname))
+                logger.info(f"{n} {specname}")
         return species, showname

reacnetgenerator/_matrix.py

@@ -138,7 +138,7 @@ def _searchspecies(self, originspec, sortedreactions, species):
         for reaction, n_reaction in sortedreactions:
             ii = 1
             if originspec == reaction[1 - ii]:
-                if not reaction[ii] in species:
+                if reaction[ii] not in species:
                     searchedspecies.append((reaction[ii], (reaction, n_reaction)))
             if len(searchedspecies) >= self.n_searchspecies:
                 break

reacnetgenerator/_path.py

@@ -166,7 +166,7 @@ def _getatomroute(self, item):
         return moleculeroute, routestr
 
     def _printatomroute(self, atomeach, timeaxis=None):
-        """For analysis without HMM, we may not need to use np.unique"""
+        """For analysis without HMM, we may not need to use np.unique."""
         with WriteBuffer(
             open(
                 self.atomroutefilename

reacnetgenerator/_reachtml.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 # cython: linetrace=True
 # cython: language_level=3
 """Generate a web page to show the analysis report.
@@ -72,7 +71,8 @@ def _re(self, smi):
         like [H]C([H])[H]. However, OpenBabel will consider it as a methane molecule. So,
         you have to use [H][C]([H])[H], if you need to process some radicals.
 
-        Examples:
+        Examples
+        --------
         >>> self._re('C')
         [C]
         >>> self._re('[C]')

reacnetgenerator/_reaction.py

@@ -1,9 +1,6 @@
 # cython: language_level=3
 # cython: linetrace=True
-"""Reactions finder.
-
-
-"""
+"""Reactions finder."""
 from collections import Counter, defaultdict
 
 import numpy as np
@@ -84,9 +81,7 @@ def _filterspec(self, reaction):
         new_rightname = rightname - leftname
         if new_leftname and new_rightname:
             return "->".join(
-                (
-                    "+".join(sorted(side.elements()))
-                    for side in (new_leftname, new_rightname)
-                )
+                "+".join(sorted(side.elements()))
+                for side in (new_leftname, new_rightname)
             )
         return None

reacnetgenerator/commandline.py

@@ -206,5 +206,5 @@ def parm2cmd(pp: dict) -> List[str]:
         )
     for ii in ["nproc", "selectatoms", "stepinterval", "split", "maxspecies"]:
         if pp.get(ii, None):
-            commands.extend(("--{}".format(ii), str(pp[ii])))
+            commands.extend((f"--{ii}", str(pp[ii])))
     return commands

reacnetgenerator/gui.py

@@ -2,8 +2,7 @@
 # -*- coding: UTF-8 -*-
 # cython: language_level=3
 # cython: linetrace=True
-"""GUI version of ReacNetGenerator.
-"""
+"""GUI version of ReacNetGenerator."""
 import base64
 import os
 import tkinter as tk

reacnetgenerator/utils.py

@@ -530,7 +530,7 @@ def download_multifiles(urls: List[dict]) -> None:
     asyncio.run(gather_download_files(urls))
 
 
-def run_mp(nproc: int, **arg: Any) -> Iterable[Any]:
+def run_mp(nproc: int, **kwargs: Any) -> Iterable[Any]:
     """Process a file with multiple processors.
 
     Parameters
@@ -552,7 +552,7 @@ def run_mp(nproc: int, **arg: Any) -> Iterable[Any]:
     pool = Pool(nproc, maxtasksperchild=1000)
     semaphore = Semaphore(nproc * 150)
     try:
-        results = multiopen(pool=pool, semaphore=semaphore, **arg)
+        results = multiopen(pool=pool, semaphore=semaphore, **kwargs)
         for item in results:
             yield item
             semaphore.release()