Don't eliminate parameters that are initial assignment targets (pt1) #2304
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## develop #2304 +/- ##
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dweindl
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Currently, parameters that are targets of initial assignments don't show up as parameters or expressions in the amici model. This is rather not what most users would expect. Therefore, treat all SBML parameters that are initial assignment targets and whose initial assignment does not evaluate to a number (for those that do, see AMICI-dev#2304) as amici expressions. Those static expressions will be handled more efficiently after AMICI-dev#2303. Related to AMICI-dev#2150.
Currently, parameters that are targets of initial assignments don't show up as parameters or expressions in the amici model. This is rather not what most users would expect. As a first step: treat all SBML parameters that are initial assignment targets and whose initial assignment evaluates to a number as amici parameters. Related to AMICI-dev#2150.
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Currently, parameters that are targets of initial assignments don't show up as parameters or expressions in the amici model. This is rather not what most users would expect. Therefore, treat all SBML parameters that are initial assignment targets and whose initial assignment does not evaluate to a number (for those that do, see AMICI-dev#2304) as amici expressions. Those static expressions will be handled more efficiently after AMICI-dev#2303. Related to AMICI-dev#2150.
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…2305) Currently, parameters that are targets of initial assignments don't show up as parameters or expressions in the amici model. This is rather not what most users would expect. Therefore, treat all SBML parameters that are initial assignment targets and whose initial assignment does not evaluate to a number (for those that do, see #2304) as amici expressions. Those static expressions will be handled more efficiently after #2303. Related to #2150. See also #2304.
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During PEtab import, parameters that are targets of initial assignments have so far not been turned into constant parameters, because they didn't exist in the amici model (see AMICI-dev#2304). Now that those parameters remain in the model, they should be turned into constant parameters, unless specified otherwise.
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Evaluate initial assignments to parameters to determine whether the targets are amici parameters or expressions. Related to AMICI-dev#2304.
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Evaluate initial assignments to parameters to determine whether the targets are amici parameters or expressions. Related to #2304. For example, it the initial assignment is `log(10)`, this should still be a parameter instead of an expression, but `sympy.log(10).is_Number` will be `False`.
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During PEtab import, parameters that are targets of initial assignments have so far not been turned into constant parameters, because they didn't exist in the amici model (see AMICI-dev#2304). Now that those parameters remain in the model, they should be turned into constant parameters, unless specified otherwise.
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…2345) During PEtab import, parameters that are targets of initial assignments have so far not been turned into constant parameters, because they didn't exist in the amici model (see #2304). Now that those parameters remain in the model, they should be turned into constant parameters, unless specified otherwise. Requires PEtab-dev/libpetab-python#248, otherwise PEtab parameter mapping will provide potentially incorrect values for those parameters.
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Currently, parameters that are targets of initial assignments don't show up as parameters or expressions in the amici model. This is rather not what most users would expect.
For example, previously:
SBML parameter with
value=2-> will result in an amici parameter with that nameSBML parameter with initial assignment
2-> will not result in an amici parameter with that nameAs a first step: treat all SBML parameters that are initial assignment targets and whose initial assignment evaluates to a number as amici parameters.
Related to #2150.