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It used to be that the module pysb.bng.generate_equations would return the equations when everything was available but if e.g. initial conditions were not available it would return an error. Now it si…
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MatchOnce is meaningless on concrete complexpatterns, so Initial should either force it to False or raise an exception if it's True. This was exposed through an equivalent bug in BNG which lead to PyS…
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If you run a model with no rules (for example, because you haven't invoked the macro or module functions that declare the rules yet, you get the following error. Ideally the function would check and t…
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current syntax for monomer declaration requires state sites arguments to be string:
Monomer('erbb', ['bf', 'bd', 'type'], {'type':['1','2','3','4']})
this makes function calls on monomers that are n…
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The pysb source gets installed in /usr/local/... where the user has no root access. When this happens the user cannot run any of the examples. A better choice would be to install it with pip in the us…
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Get documentation up on read the docs
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BNG reports certain rule-parsing errors by printing "ERROR: ..." to stdout. Currently we only look for BNG errors by examining stderr. We'll need to also parse stdout for "ERROR".
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If rate parameters are given a type descriptor (as a shortcut, this could even be automatic based on their names, e.g. myrate_kf) then it would be simpler to assign default values to them during rapid…
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Add some function(s) to generate synthetic data from a model.
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*\* the "No module named ode" error comes from this line in
pysb/pysundials_helpers.py:
```
from scipy.integrate.ode import IntegratorBase
```
*\* this line fails also if I attempt it in iPython…