Use Rich library in the CLI (#47)

* Use Rich library in the CLI

* Improve reporting capabilities

Co-authored-by: Felipe S. S. Schneider <[email protected]>

INSTALL.rst

@@ -14,11 +14,13 @@ The package, together with the above dependencies, can be installed from
 
    pip install overreact
 
-Optionally, extra functionality is provided by
-`thermo <https://github.com/CalebBell/thermo>`_::
+Optionally, extra functionality is provided such as a command-line interface
+and solvent properties::
 
-    pip install 'overreact[thermo]'
+    pip install 'overreact[cli,solvents]'
 
-This last line installs thermo  as well. thermo is used to calculate the
-dynamic viscosity of solvents in the context of the
+This last line installs `Rich <https://github.com/willmcgugan/rich>`_
+and `thermo <https://github.com/CalebBell/thermo>`_ as well.
+Rich is used in the command-line interface, and thermo is used
+to calculate the dynamic viscosity of solvents in the context of the
 :doc:`tutorials/collins-kimball` for diffusion-limited reactions.

overreact/misc.py

@@ -448,6 +448,8 @@ def _get_chemical(
 ):
     """Wrap `thermo.Chemical`.
 
+    This function is used for obtaining property values and requires the `thermo` package.
+
     All parameters are passed to `thermo.Chemical` and the returned object is
     returned.
 

overreact/rates.py

@@ -13,7 +13,7 @@
 def liquid_viscosity(id, temperature=298.15, pressure=constants.atm):
     """Dynamic viscosity of a solvent.
 
-    This function uses the `thermo` package.
+    This function requires the `thermo` package for obtaining property values.
 
     Parameters
     ----------

requirements.txt

@@ -1,5 +1,6 @@
-cclib==1.6.3
+cclib>=1.6.3
 scipy>=1.4.0
 matplotlib>=2.1.1
 pytest>=5.2.1
+rich>=9.2.0
 thermo>=0.1.39

setup.py

@@ -8,13 +8,13 @@
 setup(
     name="overreact",
     version=open("VERSION").read().strip(),
-    description="A Python package for constructing microkinetic models",
+    description="Construct precise chemical microkinetic models from first principles",
     author="Felipe Silveira de Souza Schneider",
     author_email="[email protected]",
     url="https://github.com/schneiderfelipe/overreact",
     packages=find_packages(),
     entry_points={"console_scripts": ["overreact = overreact.cli:main"]},
     install_requires=["cclib>=1.6.3", "scipy>=1.4.0"],
-    extras_require={"thermo": ["thermo>=0.1.39"]},
-    tests_require=["pytest>=5.2.1"],
+    extras_require={"cli": ["rich>=9.2.0"], "solvents": ["thermo>=0.1.39"],},
+    tests_require=["matplotlib>=2.1.1", "pytest>=5.2.1"],
 )

tests/test_thermo_gas.py

@@ -1,6 +1,6 @@
 #!/usr/bin/env python3
 
-"""Tests for gas phase using the thermo module."""
+"""Tests for gas phase using the `thermo` module."""
 
 import numpy as np
 import pytest

tests/test_thermo_solv.py

@@ -1,6 +1,6 @@
 #!/usr/bin/env python3
 
-"""Tests for solvation using the thermo module."""
+"""Tests for solvation using the `thermo` module."""
 
 import pytest