AmiciObjective/PEtab import: Fix plist #1493
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## develop #1493 +/- ##
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+ Coverage 82.69% 82.70% +0.01%
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ping @FFroehlich |
For further background, see ICB-DCM#1448. We don't have to compute the full gradient in every model simulation. Some entries might not be required because of fixed parameter or some condition-specific objective parameter mapping. The former was supported (however, not tested), the latter was not supported. Now both are tested an supported. There was no good way to communicate the fixed parameters to AmiciCalculator where ExpData.plist gets set. Passing this information is currently only possible through the parameter mapping, based on which the required sensitivities are determined. Therefore, in addition to the general parameter mapping, there is now a parameter mapping that accounts for the fixed parameters. Not sure what could be a more elegant way to handle that.
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…1509) Fixes a warning `RuntimeWarning: The following problem parameters were not used: {[...]} amici.petab.conditions.fill_in_parameters(` in case of fixed parameters. The warning was issued since #1493. This also fills in the fixed parameter values in the parameter mapping for the fixed parameters that was missing in #1493.
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Follow-up to ICB-DCM#1493 and ICB-DCM#1509, which only filled in PEtab-fixed parameters for simulation but not preequilibration in the parameter mapping. Adding Weber_BMC2015 to the PEtab tests, where this issue popped up.
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For further background, see #1448.
We don't have to compute the full gradient in every model simulation. Some entries might not be required because of fixed parameter or some condition-specific objective parameter mapping. The former was supported (however, not tested), the latter was not supported. Now both are tested an supported.
There was no good way to communicate the fixed parameters to AmiciCalculator where ExpData.plist gets set. Passing this information is currently only possible through the parameter mapping, based on which the required sensitivities are determined. Therefore, in addition to the general parameter mapping, there is now a parameter mapping that accounts for the fixed parameters. Not sure what could be a more elegant way to handle that.