Merge pull request #25 from htz1992213/main

upgrade lint and test checks

docs/source/conf.py

@@ -1,4 +1,4 @@
-# Configuration file for the Sphinx documentation builder.
+"""Configuration file for the Sphinx documentation builder."""
 #
 # This file only contains a selection of the most common options. For a full
 # list see the documentation:
@@ -10,10 +10,10 @@
 # add these directories to sys.path here. If the directory is relative to the
 # documentation root, use os.path.abspath to make it absolute, like shown here.
 #
+from __future__ import annotations
+
 import os
 import sys
-import sphinx_rtd_theme, sphinx_autodoc_typehints
-from typing import List
 
 sys.path.insert(0, os.path.abspath("../../mdgo"))
 
@@ -55,7 +55,7 @@
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
 # This pattern also affects html_static_path and html_extra_path.
-exclude_patterns: List[str] = []
+exclude_patterns: list[str] = []
 
 
 # -- Options for HTML output -------------------------------------------------

mdgo/__init__.py

@@ -1,10 +1,10 @@
-# coding: utf-8
 # Copyright (c) Tingzheng Hou.
 # Distributed under the terms of the MIT License.
 
-"""
-This package contains core modules and classes molecular dynamics simulation setup and analysis.
-"""
+"""This package contains core modules and classes molecular dynamics simulation setup and analysis."""
+
+from __future__ import annotations
+
 __author__ = "Mdgo Development Team"
 __email__ = "tingzheng_hou@berkeley.edu"
 __maintainer__ = "Tingzheng Hou"

mdgo/conductivity.py

@@ -1,19 +1,21 @@
-# coding: utf-8
 # Copyright (c) Tingzheng Hou.
 # Distributed under the terms of the MIT License.
 
-"""
-This module implements functions to calculate the ionic conductivity.
-"""
-from typing import Union
+"""This module implements functions to calculate the ionic conductivity."""
+
+from __future__ import annotations
+
+from typing import TYPE_CHECKING
 
 import numpy as np
-from tqdm.auto import tqdm
 from scipy import stats
-from MDAnalysis import Universe, AtomGroup
+from tqdm.auto import tqdm
 
 from mdgo.msd import msd_fft
 
+if TYPE_CHECKING:
+    from MDAnalysis import AtomGroup, Universe
+
 __author__ = "Kara Fong, Tingzheng Hou"
 __version__ = "0.3.0"
 __maintainer__ = "Tingzheng Hou"
@@ -26,10 +28,10 @@ def calc_cond_msd(
     anions: AtomGroup,
     cations: AtomGroup,
     run_start: int,
-    cation_charge: Union[int, float] = 1,
-    anion_charge: Union[int, float] = -1,
+    cation_charge: float = 1,
+    anion_charge: float = -1,
 ) -> np.ndarray:
-    """Calculates the conductivity "mean square displacement" over time
+    """Calculates the conductivity "mean square displacement" over time.
 
     Note:
        Coordinates must be unwrapped (in dcd file when creating MDAnalysis Universe)
@@ -51,15 +53,14 @@ def calc_cond_msd(
     anion_list = anions.split("residue")
     # compute sum over all charges and positions
     qr = []
-    for ts in tqdm(u.trajectory[run_start:]):
+    for _ts in tqdm(u.trajectory[run_start:]):
         qr_temp = np.zeros(3)
         for anion in anion_list:
             qr_temp += anion.center_of_mass() * anion_charge
         for cation in cation_list:
             qr_temp += cation.center_of_mass() * cation_charge
         qr.append(qr_temp)
-    msd = msd_fft(np.array(qr))
-    return msd
+    return msd_fft(np.array(qr))
 
 
 def get_beta(
@@ -127,14 +128,14 @@ def choose_msd_fitting_region(
 def conductivity_calculator(
     time_array: np.ndarray,
     cond_array: np.ndarray,
-    v: Union[int, float],
+    v: float,
     name: str,
     start: int,
     end: int,
-    T: Union[int, float],
+    T: float,
     units: str = "real",
 ) -> float:
-    """Calculates the overall conductivity of the system
+    """Calculates the overall conductivity of the system.
 
     Args:
         time_array: times at which position data was collected in the simulation