Changes to the python interface and the ability to set the seed of the RNG#17
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davidcsterratt wants to merge 83 commits into
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Changes to the python interface and the ability to set the seed of the RNG#17davidcsterratt wants to merge 83 commits into
davidcsterratt wants to merge 83 commits into
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This is because with my hack to py4j the die_on_exit method doesn't work because of the redirection of the stdout. In any case, this is probably a neater method.
* addVariableMap renamed to addVariable * setTransitionRate renamed to setTransitionRateOrVariable * setVariable removed, since setTransitionRateOrVariable does the job * addVariable(String label, float input) created * addVariable(Agent agent, String siteName, String linkName) removed
…atic model creation The model and simulation are separate concepts in SpatialKappa, but previously had reinitialised the simulation after changing a model. In this refactoring the model is only initialised using initialiseSim() and runForTime() or runUntilTime(). The interface is also made more similar to the IKappaModel.
… times Fix the issue by representing time as double rather than float. In addition, if the time between events dt is more than 12 orders of magnitude (i.e. 10^12) times smaller than the time t, throw an exception. This ensures that there are at least 13 bits available to represent dt, since the mantissa in a double has 53 bits, and log2(10^12) (the maxiumum ratio between t and dt) is approximately 40 bits. https://docs.oracle.com/javase/specs/jls/se7/html/jls-4.html#jls-4.2.3
The conversion of times to doubles didn't work for some situations, so this change creates a local time within a time step in runByTime2(), used in KappaNEURON. This reduces the likelihood of a precision error.
Conflicts: README.md
add jar file to fix python compilation
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There is quite a lot here, but the main change to the core is the Utils.setSeed() method. It would be great if this could be merged into your SpatialKappa fork