Minor update formatting of a comment.
Added another test for top rate in which there are two components which cooperate over an action and both perform it at rate T (they of course then cooperate further with an additional component). This test is failing and I have not yet even added in the expected answers
Added a TODO comment detailing a further passive rate test that I should add
Added more of the expected results to the TestTopRatePassiveCoop test, still failing because of other missing expected results.
Now implemented multiplications which involve a passive rate. This allows us to calculate the rates for our test TestTopRatePassiveCoop. I have also filled in all the expected results for that test which is now passing.
Removed a couple of blank lines in the test file in order to satisfy make lint
Added a new test for apparent rate calculation when there is a choice (caused by running two processin parallel) between cooperating with a process which performs the given activity with an active rate and one which does so with a passive rate.
Added a simple test to evaluate an expression containing a name-expression when we do not give it an environment. This simply increases the code coverage by a single line, but is a good line to test.
Removed the generic visit method of the Visitor, since it is never actually used. One can always just call the 'visit' method on the entity yourself.
Updated one Bio-PEPA test, such that the remove rate laws expression visitor now visits a NumExpression which increases our code coverage.
Removed code that was duplicated in pepapot.py and test_pepapot.py, specifically relating to obtaining an environment mapping constant names to values from a list of constant definitions.
Added a test to check the ApplyExpression convenience class methods for creating binary operator expressions work as expected.
Added another test to make sure we do raise an error upon an unknown function expression.
Added a very simple test to check that the base expression visitor does not fold over. We are not quite checking that it does indeed visit all of the sub-expressions and I suppose we should but to do so we would need to override the visit methods which would kind of defeat the purpose (although we could call them from the overridden methods).
When I refactored the builder functionality of parsed components into a visitor, I forgot to remove the 'get_builder' methods from each of the parsed component classes. Since these were not being used they were missing from the test coverage. Removing them an obvious win.
Added a Bio-PEPA test which actually uses a modifier (+), which increased our code coverage by a simple two lines.
Noticed a small bug in the top rate definition of multiplication in that if it is multiplied by zero the answer should of course be zero.
Added a test for all the TopRate arithmetic we should need for calculating apparent rates.
Propertly evaluate the fMA rate law where the stoichiometry is not one.
Added a simple Bio-PEPA test with a stoiciometry of 2, which uses fMA. We now have 100% test coverage