Added a test for highlighting Bio-PEPA code, which currently fails because it is not yet implemented.
Added the Bio-PEPA lexer for syntax highlighting, all tests now passing.
Fixed keyword arguments for PEPA and Bio-PEPA syntax highlighting
Minor cosmetic fixups to allow 'make lint' to succeed.
Added a test to the simple bio-pepa base test base class which checks that we produce the correct reactions from a given Bio-PEPA model. It is currently failing for all models because I have not yet actually implemented that.
Begun the ability to convert the list of species definitions in a Bio-PEPA model into a list of reactions. So far only reactants works, but it means I have a working test for at least one simple Bio-PEPA model. The test works pretty well as the reactions are computed and then formatted, so when writing a test you only need to write down the expected reactions in a simple reaction syntax.
Added in the expected reactions for all of the simple Bio-PEPA test models. A lot of the tests still failing because we have not yet actually implemented the reactions well.
All tests passing for the expected reactions now.
Removed a spurious definition of a test Bio-PEPA model (as a string) from pepapot/pepapot.py
Just some minor tidying up for 'make lint'
Added a pylint configuration file and added pylint to the 'make lint' command. Generating quite a lot of messages at the moment, so I'm going to try and fix these.
Removed deprecated options from the pylint configuration file.
Some minor fixes for things that pylint is complaining about.
Minor refactor to avoid brining the 'output_conf' name into the global scope when running from the command-line.
A nothing class definition was changed to a 'namedtuple' because that's what it was.
Some more gentle refactoring thanks to pylint.
Some nice refactoring to reduce the number of variables within a method definition. I think it is now also a little more robust.
Another use of @staticmethod to provide a slightly more organised source code.
Further fairly gentle refactorings, this time I've used ParsedBioModel.get_reactions (which I changed from being the property ParsedBioModel.reactions) to implement expanding the rate laws.
Added a simple todo regarding the computation of 'actions' of a Bio-PEPA model for simulation and a set of 'reactions' which both do similar things.