Updating synchronous dynamics #6
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In the previous implementation, the calls were being made against `proc` which is the Process which doesn't implement that function. It seems to need to be accessed through the dynamics on this process which resolves an Attribute Error which prevent tests from running. Additionally, the function was previously passed `t` which is the current time step of the simulation but as events are generated from the dynamics on a per-process basis, it needs to be passed the process instead to retrieve the correct set of results. 83 unit tests pass
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Continuous integration tests against addons:
apt:
packages:
- libhdf5-serial-dev(copied this from here https://github.com/h5py/h5py/blob/master/.travis.yml#L8-L11 so I don't 100% know if its relevant) but I don't know enough of how travis CI python tests work to confirm any of this |
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On 09/03/2021 14:20, Ryan Delaney wrote:
A friend currently taking the GD5302 was having some trouble getting
some examples using SynchronousDynamics to work from the book and asked
if I could take a look. I've tried to update synchronous dynamics to
match the implementation given in the Epidemic Modelling book and it
seems to work successfully on my machine (but will need to wait for
continuous integration tests to prove that).
I've updated the calls for |perElementEventDistribution| and
|fixedRateEventDistribution| to be called against the dynamics of a
process instead of the process directly and to pass them the process
used to determine the events instead of the current time step. This
seems to resolve the attribute errors currently occurring in unit tests
and begins to produce successful results for simple models. 83/83 unit
tests pass.
That's brilliant -- thanks! I'll be spending today working on this and
other bits for epydemic.
(You actually found something that the automated tests should have
caught. We mainly use StochasticDynamics, so when we refactored the
Process code we caught all the changes there and somehow didn't catch
them in the synchronous version. There *should* be a test that makes
sure both versions work on the same code....)
While I don't fully understand everything about how this library works,
it seems like a fascinating project and look forward to seeing the
future developments on it.
Glad it's of interest.
Cheers,
…--
-- Simon
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A friend currently taking the GD5302 was having some trouble getting some examples using SynchronousDynamics to work from the book and asked if I could take a look. I've tried to update synchronous dynamics to match the implementation given in the Epidemic Modelling book and it seems to work successfully on my machine (but will need to wait for continuous integration tests to prove that).
I've updated the calls for
perElementEventDistributionandfixedRateEventDistributionto be called against the dynamics of a process instead of the process directly and to pass them the process used to determine the events instead of the current time step. This seems to resolve the attribute errors currently occurring in unit tests and begins to produce successful results for simple models. 83/83 unit tests pass.While I don't fully understand everything about how this library works, it seems like a fascinating project and look forward to seeing the future developments on it.