Clean up benchmarks and docs

CONTRIBUTING.md

@@ -4,33 +4,33 @@
 
 The following is a set of guidelines for contributing to the Chemics Python package. Submitted code that does not conform to these guidelines will not be merged into the package. Feel free to propose changes to this document in a Pull Request or Issue.
 
-## Environment
+## Development environment
 
 Use the `environment.yml` file to create a conda environment for developing the Chemics package. See the comments in the file for more details.
 
-## Code style
+## Code style, linting, and formatting
 
-All code in the Chemics package should adhere to the style enforced by the [Flake8](https://pypi.org/project/flake8/) tool. This will ensure a consistent code format throughout the package and prevent syntax errors during development. For the Flake8 style settings, ignore the E501, W503, W605 errors and warnings.
+All Python code in the Chemics package should adhere to the [PEP 8](https://peps.python.org/pep-0008/) style guide. All linting and formatting should be implemented with [ruff](https://github.com/astral-sh/ruff). Configuration for ruff is defined in the pyproject.toml file.
 
 ## Docstrings
 
 All functions, classes, and other Python components should contain docstrings with syntax and best practices outlined by the [NumPy docstring guide](https://numpydoc.readthedocs.io/en/latest/format.html). Within the docstring, use the references section to list references used to develop that function or method. A simple example of how to use a function or class should be included in its docstring.
 
 ## Examples
 
-Along with an example in the docstring, please provide a complete example in Sphinx documentation. Simple examples should also be provided in the docstrings.
+Along with an example in the docstring, please provide a complete example in the Sphinx documentation. Simple examples should also be provided in the docstrings.
 
 ## Tests
 
-New code for the Chemics package must include associated tests in the `tests/` folder. The [pytest](https://docs.pytest.org/en/latest/) framework is used to execute the test files.
+New code for the Chemics package must include associated tests in the `tests/` folder. The [pytest](https://github.com/pytest-dev/pytest) framework is used to execute the test files.
 
 ## Changelog
 
 Don't forget to edit the changelog based on your contributions. Follow the style on the [Keep a Changelog](https://keepachangelog.com) website.
 
 ## Sphinx documentation
 
-New source code should be included in the [Sphinx documentation](http://www.sphinx-doc.org/en/stable/) located in the `docs/` folder.
+New source code along with examples should be documented in the [Sphinx documentation](http://www.sphinx-doc.org/en/stable/) located in the `docs/` folder.
 
 ## Creating a pull request
 

LICENSE.md

@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2023 Chemics
+Copyright (c) 2024 Chemics
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

README.md

@@ -12,29 +12,39 @@ $ pip install chemics
 
 ## Usage
 
-The example below imports the Chemics package and creates a `Gas` class to calculate the density of nitrogen gas at a pressure of 101,325 Pa and 773 K.
+The example below imports the Chemics package and uses the `Gas` class to calculate the density and viscosity of nitrogen gas at a temperature of 773 K and pressure of 101,325 Pa.
 
 ```python
 import chemics as cm
 
-gas = cm.Gas('N2')
-rho = gas.density(101325, 773)
+gas = cm.Gas("N2", 773)
+rho = gas.density()
+mu = gas.viscosity()
 
-print(rho)
-# This prints a value of 0.4416
+print("Nitrogen gas properties at 773 K and 101,325 Pa")
+print(f"density    {rho:.4f} kg/m³")
+print(f"viscosity  {mu:.2f} μP")
+```
+
+This prints the following:
+
+```
+Nitrogen gas properties at 773 K and 101,325 Pa
+density    0.4416 kg/m³
+viscosity  363.82 μP
 ```
 
 This example uses the `ChemicalEquation` class to get properties of the reactants and products from a given chemical equation.
 
 ```python
 import chemics as cm
 
-ce = cm.ChemicalEquation('2 HCl + 2 Na -> 2 NaCl + H2')
+ce = cm.ChemicalEquation("2 HCl + 2 Na -> 2 NaCl + H2")
 ce.is_balanced()
-# Returns True for balanced equation
+# This returns True for balanced equation
 
 ce.rct_properties
-# Returns a dataframe of the reactant properties
+# This returns a dataframe of the reactant properties
 #                HCl        Na
 # moles            2         2
 # species        HCl        Na

benchmarks.py

@@ -1,39 +1,48 @@
+"""
+Benchmarks.
+"""
+
 import time
 import chemics as cm
 
 
 def run_benchmarks():
     """
-    Run benchmarks for the Gas methods. Elapsed time for subsequent method
-    calls should be near zero compared to the initial method execution.
-    """
+    Run benchmarks for Gas methods.
 
-    gas = cm.Gas('CH4', 890.5, 120325)
+    Run benchmarks for Gas heat capacity, thermal conductivity, and viscosity
+    methods. Elapsed time for subsequent method calls should be near zero
+    compared to the initial method execution.
+    """
+    gas = cm.Gas("CH4", 890.5, 120325)
 
     for i in range(5):
         tic = time.perf_counter()
         cp = gas.heat_capacity()
         toc = time.perf_counter()
-        print(f'Run {i + 1}, Elapsed time {toc - tic:.4f} s, cp {cp:.4f}')
+        print(f"Run {i + 1}, Elapsed time {toc - tic:.4f} s, cp {cp:.4f}")
     print()
 
     for i in range(5):
         tic = time.perf_counter()
         k = gas.thermal_conductivity()
         toc = time.perf_counter()
-        print(f'Run {i + 1}, Elapsed time {toc - tic:.4f} s, k {k:.4f}')
+        print(f"Run {i + 1}, Elapsed time {toc - tic:.4f} s, k {k:.4f}")
     print()
 
     for i in range(5):
         tic = time.perf_counter()
         mu = gas.viscosity()
         toc = time.perf_counter()
-        print(f'Run {i + 1}, Elapsed time {toc - tic:.4f} s, mu {mu:.4f}')
+        print(f"Run {i + 1}, Elapsed time {toc - tic:.4f} s, mu {mu:.4f}")
 
 
 def main():
+    """
+    Run the benchmarks.
+    """
     run_benchmarks()
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     main()

docs/examples/gas_properties.rst

@@ -31,5 +31,3 @@ This prints the output shown below.
    heat capacity         31.24 J/(mol⋅K)
    thermal conductivity  0.054 W/(m⋅K)
    viscosity             363.82 microPoise (μP)
-
-Done.

docs/installation.rst

@@ -12,17 +12,27 @@ Install Chemics using the pip package manager:
 Usage
 =====
 
-The example below imports the chemics package and creates a ``Gas`` class to calculate the density of nitrogen gas at a pressure of 101,325 Pa and 773 K.
+The example below imports the Chemics package and uses the ``Gas`` class to calculate the density and viscosity of nitrogen gas at a temperature of 773 K and pressure of 101,325 Pa.
 
-.. code-block:: python
+.. testcode::
 
    import chemics as cm
 
-   gas = cm.Gas('N2')
-   rho = gas.density(101325, 773)
-   print(rho)
-   # This prints a value of 0.4416
+   gas = cm.Gas("N2", 773)
+   rho = gas.density()
+   mu = gas.viscosity()
+
+   print("Nitrogen gas properties at 773 K and 101,325 Pa")
+   print(f"density    {rho:.4f} kg/m³")
+   print(f"viscosity  {mu:.2f} μP")
+
+This prints the following:
+
+.. testoutput::
 
+   Nitrogen gas properties at 773 K and 101,325 Pa
+   density    0.4416 kg/m³
+   viscosity  363.82 μP
 
 This example uses the ``ChemicalEquation`` class to get properties of the reactants and products from a given chemical equation.
 
@@ -32,7 +42,7 @@ This example uses the ``ChemicalEquation`` class to get properties of the reacta
 
    ce = cm.ChemicalEquation('2 HCl + 2 Na -> 2 NaCl + H2')
    ce.is_balanced()
-   # The returns True for balanced equation
+   # This returns True for balanced equation
 
    ce.rct_properties
    # This returns a dataframe of the reactant properties