Fix ruff 0.16.0 errors (#42)

Author: PardhavMaradani

.github/ISSUE_TEMPLATE/bug_report.md

@@ -19,7 +19,6 @@ about: Create a report to help us improve
 import mdadash
 
 ...
-
 ```
 
 ## Current environment

docs/source/_static/README.md

@@ -8,7 +8,7 @@ so a file named "default.css" will overwrite the builtin "default.css".
 The path to this folder is set in the Sphinx `conf.py` file in the line:
 
 ```python
-html_static_path = ['_static']
+html_static_path = ["_static"]
 ```
 
 ## Examples of file to add to this directory

docs/source/_templates/README.md

@@ -8,7 +8,7 @@ so a file named "page.html" will overwrite the builtin "page.html".
 The path to this folder is set in the Sphinx `conf.py` file in the line:
 
 ```python
-templates_path = ['_templates']
+templates_path = ["_templates"]
 ```
 
 ## Examples of file to add to this directory

docs/source/conf.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 #
 # Configuration file for the Sphinx documentation builder.
 #

mdadash/backend/analyses/__init__.py

@@ -5,12 +5,12 @@
 from . import acf, com_distance, dssp, energies, janin, msd, ramachandran, rog
 
 __all__ = [
-    "energies",
+    "acf",
     "com_distance",
-    "rog",
     "dssp",
-    "ramachandran",
+    "energies",
     "janin",
     "msd",
-    "acf",
+    "ramachandran",
+    "rog",
 ]

mdadash/backend/analyses/acf.py

@@ -1,4 +1,5 @@
 import logging
+from typing import ClassVar
 
 import matplotlib.pyplot as plt
 import MDAnalysis as mda
@@ -25,7 +26,7 @@ class ACFAnalysis(WidgetBase):
         "Universe Configuration section in the Settings page."
     )
 
-    _inputs = [
+    _inputs: ClassVar = [
         {
             "attribute": "_run_mode",
             "name": "Run mode",

mdadash/backend/analyses/com_distance.py

@@ -4,6 +4,7 @@
 
 import logging
 from collections import deque
+from typing import ClassVar
 
 import matplotlib.pyplot as plt
 from IPython.display import display
@@ -25,7 +26,7 @@ class COMDistance(WidgetBase):
     name = "COMDistance"
     description = "Distance between two COMs"
 
-    _inputs = [
+    _inputs: ClassVar = [
         {
             "attribute": "selection1",
             "name": "Selection 1",
@@ -171,10 +172,7 @@ def on_input_change(self, attribute, _old_value, new_value):
             self._set_x_values()
         elif attribute == "custom_title":
             self._set_title()
-        elif attribute == "selection1":
-            self._update_selections()
-            reset_plot = True
-        elif attribute == "selection2":
+        elif attribute in ("selection1", "selection2"):
             self._update_selections()
             reset_plot = True
         elif attribute in ("periodic", "updating"):

mdadash/backend/analyses/dssp.py

@@ -1,5 +1,6 @@
 import logging
 from collections import deque
+from typing import ClassVar
 
 import matplotlib.pyplot as plt
 import numpy as np
@@ -18,7 +19,7 @@ class DSSPAnalysis(WidgetBase):
     name = "DSSP Analysis"
     description = "Secondary structure assignment of protein"
 
-    _inputs = [
+    _inputs: ClassVar = [
         {
             "attribute": "_run_frequency",
             "name": "Run frequency",

mdadash/backend/analyses/energies.py

@@ -4,6 +4,7 @@
 
 import logging
 from collections import deque
+from typing import ClassVar
 
 import matplotlib.pyplot as plt
 from IPython.display import display
@@ -20,7 +21,7 @@ class EnergyWidgetBase:
     data_key = ""
     y_label = "Energy ( kJ / mol )"
 
-    _inputs = [
+    _inputs: ClassVar = [
         {
             "attribute": "maxlen",
             "name": "Max values",
@@ -101,7 +102,7 @@ def on_input_change(self, attribute, _old_value, new_value):
 
     def run_every_frame(self):
         """every-frame run handler"""
-        ts = getattr(self, "u").trajectory.ts
+        ts = self.u.trajectory.ts  # pylint: disable=no-member
         if self.data_key not in ts.data:
             return  # pragma: no cover
         self.steps.append(ts.data["step"])

mdadash/backend/analyses/janin.py

@@ -3,6 +3,7 @@
 """
 
 import logging
+from typing import ClassVar
 
 import matplotlib.pyplot as plt
 from IPython.display import display
@@ -23,7 +24,7 @@ class JaninPlot(WidgetBase):
     name = "Janin Plot"
     description = "Dihedral angles analysis using Janin plot"
 
-    _inputs = [
+    _inputs: ClassVar = [
         {
             "attribute": "selection",
             "name": "Selection",