Use Rich library in the CLI

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_core.py

@@ -159,31 +159,25 @@ def test_private_functions_work():
     assert list(core._unparse_reactions([(((1, "A"),), ((1, "B"),), True)])) == [
         "A -> B"
     ]
-    assert (
-        list(
-            core._unparse_reactions(
-                [
-                    (((2, "A"),), ((3, "B"),), True),
-                    (((1, "A"),), ((2, "C"),), True),
-                    (((50, "A"),), ((1, "D"),), True),
-                ]
-            )
+    assert list(
+        core._unparse_reactions(
+            [
+                (((2, "A"),), ((3, "B"),), True),
+                (((1, "A"),), ((2, "C"),), True),
+                (((50, "A"),), ((1, "D"),), True),
+            ]
         )
-        == ["2 A -> 3 B", "A -> 2 C", "50 A -> D"]
-    )
-    assert (
-        list(
-            core._unparse_reactions(
-                [
-                    (((1, "E"), (1, "S")), ((1, "ES"),), True),
-                    (((1, "ES"),), ((1, "E"), (1, "S")), True),
-                    (((1, "ES"),), ((1, "ES‡"),), False),
-                    (((1, "ES‡"),), ((1, "E"), (1, "P")), False),
-                ]
-            )
+    ) == ["2 A -> 3 B", "A -> 2 C", "50 A -> D"]
+    assert list(
+        core._unparse_reactions(
+            [
+                (((1, "E"), (1, "S")), ((1, "ES"),), True),
+                (((1, "ES"),), ((1, "E"), (1, "S")), True),
+                (((1, "ES"),), ((1, "ES‡"),), False),
+                (((1, "ES‡"),), ((1, "E"), (1, "P")), False),
+            ]
         )
-        == ["E + S -> ES", "ES -> E + S", "ES -> ES‡", "ES‡ -> E + P"]
-    )
+    ) == ["E + S -> ES", "ES -> E + S", "ES -> ES‡", "ES‡ -> E + P"]
 
     assert list(
         core._unparse_reactions(

tests/test_rates.py

@@ -165,27 +165,21 @@ def test_liquid_viscosities_are_correct():
 
 def test_conversion_of_rate_constants_work():
     """Ensure converting reaction rate constants work."""
-    assert (
-        rates.convert_rate_constant(
-            12345e5,
-            "cm3 mol-1 s-1",
-            "l mol-1 s-1",
-            molecularity=2,
-            temperature=[200, 298.15, 300, 400],
-        )
-        == pytest.approx(12345e8)
-    )
+    assert rates.convert_rate_constant(
+        12345e5,
+        "cm3 mol-1 s-1",
+        "l mol-1 s-1",
+        molecularity=2,
+        temperature=[200, 298.15, 300, 400],
+    ) == pytest.approx(12345e8)
 
-    assert (
-        rates.convert_rate_constant(
-            12345e10,
-            "cm3 particle-1 s-1",
-            "atm-1 s-1",
-            molecularity=2,
-            temperature=[200, 298.15, 300, 400],
-        )
-        == pytest.approx(13.63e-23 * 12345e10 * np.array([200, 298.15, 300, 400]), 1e-3)
-    )
+    assert rates.convert_rate_constant(
+        12345e10,
+        "cm3 particle-1 s-1",
+        "atm-1 s-1",
+        molecularity=2,
+        temperature=[200, 298.15, 300, 400],
+    ) == pytest.approx(13.63e-23 * 12345e10 * np.array([200, 298.15, 300, 400]), 1e-3)
 
 
 def test_conversion_rates_know_about_reaction_order():