Update PURE mixture, mechanisms, and parameters

[murrayrm]

DRAFT PR. Putting this out so people can see the changes coming, but still working on a few things:

• Need to add an example of plot_all_species_containing
• May want to update the way attributes passed as a single string are handed (see below)
• Need to add user documentation for PURE and plotting changes

This PR makes a number changes to the way that PURE is implemented:

• There is now a single PURE mixture that uses parameters to turn on/off the use of machinery, resources, and fuel. This means that we don't need separate SimplePURE, EnergyPURE, etc. The old BasicPURE mixture is now just a call to PURE.
• Parameter values have been updated to come from documented sources (mainly SK07 = V. Sotiropoulos and Y. N. Kaznessis. "Synthetic Tetracycline-Inducible Regulatory Networks: Computer-Aided Design of Dynamic Phenotypes.", BMC Systems Biology 1, no. 1 (2007))

In addition, some changes that go beyond PURE were also implemented:

• There are now default mechanisms for all standard components. This means that you can create models without having to explicitly specific the mechanisms, as long as you are OK with the defaults.
• New plotting routines to generate plots containing a given species (plot_all_species_containing) or gene expression data (plot_gene_expression_data).
• Updated use of attributes to always pass a list (rather than a string). This addresses the issue pointed out by @zjuradoq in PR updated parameter processing #320. (Note: we might want to instead add a check for an attribute passed as a string and just create a list when we see it.)

Sample plot for plot_all_species_containing (from TBD):

Sample plot for plot_gene_expression_data (from gfp_expression.py):