Fix readthedocs.yaml and update readme

README.md

@@ -22,7 +22,7 @@ PyCharge was developed to allow both novice and experienced users model a wide r
 - Moving dipoles can be modelled by specifying the dipole's origin position as a function of time.
 - Parallelized version of the dipole simulation method using [mpi4py](https://mpi4py.readthedocs.io/en/stable/) to enable the parallel execution of computationally demanding simulations on high performance computing environments to significantly improve run time.
 
-Our computational physics paper introducing the PyCharge package is available on [arXiv](https://arxiv.org/abs/2107.12437) and includes an extensive review of the rich physics that govern the coupled dipole simulations.
+Our research paper, published in [Computational Physics Communications](https://doi.org/10.1016/j.cpc.2022.108291) and available on [arXiv](https://arxiv.org/abs/2107.12437), introduces the PyCharge package and provides a comprehensive review of the rich physics that govern the coupled dipole simulations.
 
 ## Documentation
 
@@ -99,7 +99,7 @@ We welcome all bug reports and suggestions for future features and enhancements,
 If you are using PyCharge for research purposes, we kindly request that you cite the following paper:
 
 M. Filipovich and S. Hughes, [PyCharge: An open-source Python package for self-consistent electrodynamics
-simulations of Lorentz oscillators and moving point charges](https://arxiv.org/abs/2107.12437), arXiv:2107.12437.
+simulations of Lorentz oscillators and moving point charges](https://doi.org/10.1016/j.cpc.2022.108291), Comput. Phys. Commun. 274, 108291 (2022).
 
 ## License
 

docs/docs_requirements.txt

@@ -1,6 +1,6 @@
 mkdocs-material==7.1.5
 python-markdown-math==0.8
-mkdocstrings==0.15.1
+mkdocstrings-python==1.10.3
 numpy==1.20.3
 dill==0.3.3
 scipy==1.6.3

docs/index.md

@@ -16,7 +16,7 @@ PyCharge was developed to allow both novice and experienced users model a wide r
 - Moving dipoles can be modelled by specifying the dipole's origin position as a function of time.
 - Parallelized version of the dipole simulation method using [mpi4py](https://mpi4py.readthedocs.io/en/stable/) to enable the parallel execution of computationally demanding simulations on high performance computing environments to significantly improve run time.
 
-Our computational physics paper introducing the PyCharge package was published in [Computer Physics Communications](https://doi.org/10.1016/j.cpc.2022.108291) and is also available on [arXiv](https://arxiv.org/abs/2107.12437). The paper includes an extensive review of the rich physics that govern the coupled dipole simulations.
+Our research paper, published in [Computational Physics Communications](https://doi.org/10.1016/j.cpc.2022.108291) and available on [arXiv](https://arxiv.org/abs/2107.12437), introduces the PyCharge package and provides a comprehensive review of the rich physics that govern the coupled dipole simulations.
 
 ## Usage
 
@@ -76,7 +76,7 @@ We welcome all bug reports and suggestions for future features and enhancements,
 If you are using PyCharge for research purposes, we kindly request that you cite the following paper:
 
 M. Filipovich and S. Hughes, [PyCharge: An open-source Python package for self-consistent electrodynamics
-simulations of Lorentz oscillators and moving point charges](https://arxiv.org/abs/2107.12437), Comput. Phys. Commun. 274, 108291 (2022).
+simulations of Lorentz oscillators and moving point charges](https://doi.org/10.1016/j.cpc.2022.108291), Comput. Phys. Commun. 274, 108291 (2022).
 
 ## License
 

docs/javascripts/config.js

@@ -1,3 +1,7 @@
+/*
+ *   Copyright (c) 2024 
+ *   All rights reserved.
+ */
 window.MathJax = {
     tex: {
       inlineMath: [["\\(", "\\)"]],

examples/paper_figures/figure8.py

@@ -29,7 +29,7 @@ def scaled_total_energy(dipole1, dipole2):
                + 0.5*k*(dipole1.moment_disp[0])**2)
     energy2 = (0.5*dipole2.m_eff * dipole2.moment_vel[0]**2
                + 0.5*k*(dipole2.moment_disp[0])**2)
-    max_energy = max(max(energy1), max(energy2))
+    max_energy = max(max(energy1), max(energy2))  # pylint: disable=W3301
     return (energy1/max_energy, energy2/max_energy)
 
 

examples/paper_figures/figure9.py

@@ -29,7 +29,7 @@ def scaled_total_energy(dipole1, dipole2):
                + 0.5*k*(dipole1.moment_disp[0])**2)
     energy2 = (0.5*dipole2.m_eff * dipole2.moment_vel[0]**2
                + 0.5*k*(dipole2.moment_disp[0])**2)
-    max_energy = max(max(energy1), max(energy2))
+    max_energy = max(max(energy1), max(energy2))  # pylint: disable=W3301
     return (energy1/max_energy, energy2/max_energy)
 
 

pycharge/simulation.py

@@ -185,7 +185,7 @@ def calculate_E(
             E_y += E_field[1]
             E_z += E_field[2]
         if self.E_external is not None:  # Add external E field
-            E_field_external = self.E_external(t, x, y, z)
+            E_field_external = self.E_external(t, x, y, z)  # pylint: disable=E1102
             E_x += E_field_external[0]
             E_y += E_field_external[1]
             E_z += E_field_external[2]
@@ -236,7 +236,7 @@ def calculate_B(
             By += 1/(c*r_mag)*(rz*E_x-rx*E_z)
             Bz += 1/(c*r_mag)*(rx*E_y-ry*E_x)
         if self.B_external is not None:  # Add external B field
-            B_field_external = self.B_external(t, x, y, z)
+            B_field_external = self.B_external(t, x, y, z)  # pylint: disable=E1102
             Bx += B_field_external[0]
             By += B_field_external[1]
             Bz += B_field_external[2]
@@ -461,8 +461,8 @@ def run_mpi(
         """
         try:
             from mpi4py import MPI  # pylint: disable=import-outside-toplevel
-        except ImportError:
-            NotImplementedError('mpi4py package is not installed.')
+        except ImportError as exc:
+            raise NotImplementedError('mpi4py package is not installed.') from exc
         self._init_simulation(timesteps, dt, save_E)
         if file is not None and self._load(file):
             return

readthedocs.yaml

@@ -1,9 +1,15 @@
 version: 2
 
+# Optional: Specify build environment details
+build:
+  os: "ubuntu-22.04"
+  tools:
+    python: "3.7"
+
 python:
   version: 3.7
   install:
     - requirements: docs/docs_requirements.txt
 
 mkdocs:
-  configuration: mkdocs.yml
+  configuration: mkdocs.yml