Feature: (Soft) Require Solid Density for Substance.solid()

Various unrealistic behaviors were noticed for solids that resulted from their densities automatically being set to 1.

A simple example would be adding an arbitrary quantity, say 50 grams, of an arbitrary solid substance, say NaCl, to a container. The container would report a volume of 50 mL, but in reality NaCl has a density of around 2.17 g/mL, so the actual volume taken up by the salt would be ~23 mL.

To address these problems, both the Substance() constructor and Substance.solid() have been given an additional parameter, density, to allow for this value to be specified for both currently supported phases of matter (solids and liquids).

However, there are cases where a user may not know the density of a solid, or it may not be required for setting up their experiments (e.g. when the solid is in a very dilute solution, and the concentration in said solution need not be precise). To allow for these cases, Substance.solid() can still be called without providing a density. Doing so will trigger a warning for the user to inform them of the risks associated with not providing a density, which they can either choose to ignore or choose to address by providing a density.

As one might expect, the unit test code responsible for creating solids was refactored to provide solid densities. This broke some of the strict equalities present on many of the assert statements, so a number of these were adjusted to include a call to pytest.approx(). The two example files were also updated to include solid densities for Substance.solid().

Additional cleanup changes that were made to Substance:

Unused concentration attribute was removed.
Constructor argument value checking was improved - unsupported molecule types will now trigger a ValueError.
Constructor now requires a molecular weight and density, both of which must be positive (for now, the door for infinite density and molecular weight has been left open, but this may be removed if deemed appropriate).
Repeated code across Substance(), Substance.solid(), and Substance.liquid() was consolidated (the latter two functions simply call the constructor with the appropriate phase of matter).

Additional changes that were missed in previous features:

The two example files contained references to the functions Recipe.create_container() and Container.dilute(), both of which were removed in the Container rework feature pull request. These examples were updated to reflect the current state of the library.
The default enzyme density parameter was not removed from either the Config class or pyplate.yaml. The parameter has now been removed from both files.

ekwan / PyPlate

Feature: (Soft) Require Solid Density for Substance.solid() #34