Minor fixes for flake8
Added testing of the output for the Bio-PEPA command-line test.
Added output of the timeseries for the Bio-PEPA command-line tool. Failing test at the moment because it does not output the time column.
Added time to the output timeseries when running a timeseries for Bio-PEPA models. This now means all tests pass.
Small refactoring moving the 'get_time_grid' method inside the Configuration class. I'm not sure why it was ever not in there in the first place.
Added command-line options for setting the timing configurations for timeseries (of Bio-PEPA models for now) and a test that they are being explored.
Added a test fixture for exceptional cases. This is mostly to allow for full test coverage, but does have the benefit of checking that we do fail in some way when we have something that is incorrect.
Added a test for stochastic simulation of Bio-PEPA models. Do not yet have a stochastic simulator so of course the test fails
Updated the command-line runner so that it now records both the output and the error output. This means we are now properly checking in the cases of expected error that the correct error message is printed
Removed a TODO comment regarding reduction of expressions which was no longer relevant.
Updated the test for the stochastic solution to Bio-PEPA to be a simpler model. Since this test fixture is set up, we should be able to use it for mutliple models easily because it compares the ODE solution to the SSA solution so there is not expected values to set up.
A first crack at implementing stochastic simulation for Bio-PEPA models. It currently has the model hard coded, however the actual algorithm has the simulation model extracted, so the idea is that all we need to do now is generate a simulation model from an arbitrary Bio-PEPA model. There is some cleaning up to do first however, in particular the aggregation of the solutions is a horrible hack at the moment and probably won't allow for confidence intervals and the like which would be nice.
Made Bio-PEPA stochastic simulation a bit more generic by allowing the averaging of arbitrary time courses (which have the same column names and time grids of course).
Further generalisation to the Bio-PEPA stochastic simulation solver. We are now actually generating the actions and such from the model itself. Still a little tidying up work to do in particular the time course column names are hard-coded.
Now take the stochastic simulation of Bio-PEPA models takes the species names from the model for the time course so it should be more general, just need more tests.
Updated the Bio-PEPA stochastic simulator test to use multiple models. We are failing on one of the ones I have added.
One model for the stochastic simulation was failing simply because it reached a deadlock and that is completely reasonable for the simple model. Have not yet worked out what to do in this situation, but I now at least report it (via an exception) and I have removed this model from the stochastic simulation test.
Added a configuration option to ignore deadlock for the simulation of Bio-PEPA models. This now allows our stochastic simulation test to pass. We are now only really left to properly compute the remainder of the time course rather than simply filling out the final row.