SBML import: Undeclared identifier error when using parameters with initial assignments in observables #2150
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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. 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.
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. 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.
dweindl
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Feb 23, 2024
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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…2304) 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 #2150.
dweindl
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Feb 27, 2024
…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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Related to #2145
The problem is again the way initial assignments are handled. Parameter symbols are replaced by the initial assignment expression, but not everywhere. Observable expressions still contain the parameter symbols that have been removed elsewhere.
The best would be not eliminating those parameter symbols, and instead handling them as static expressions (as proposed in #1269).
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