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Fix startpoint sampling for PEtab-derived problems with fixed parameters #1169

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merged 7 commits into from
Nov 3, 2023

Commits on Oct 31, 2023

  1. Fix startpoint sampling for PEtab-derived problems with fixed parameters

    Startpoint sampling for PetabImporter-derived problems didn't work correctly
    in case parameters were fixed in addition to those marked estimate=0 in the
    underlying PEtab problem.
    
    Fixing any parameters after the construction of the pypesto.Problem and the
    corresponding startpoint method would lead to errors in during startpoint
    sampling, because the list of fixed parameters was never updated.
    
    In order to fix that, we need to have the current pypesto.Problem available
    for startpoint sampling to get access to the fixed parameters.
    Accessing `pypesto.Problem` is not compatible with the current
    `FunctionStartpoints`, therefore we derive a new `PetabStartpoints` class
    from `CheckedStartpoints.sample`.
    dweindl committed Oct 31, 2023
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  2. test

    dweindl committed Oct 31, 2023
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  3. fixup

    dweindl committed Oct 31, 2023
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Commits on Nov 1, 2023

  1. Refactor PetabStartpoints

    dweindl committed Nov 1, 2023
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  2. all

    dweindl committed Nov 1, 2023
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Commits on Nov 3, 2023

  1. Update pypesto/petab/importer.py

    Co-authored-by: Fabian Fröhlich <fabian@schaluck.com>
    dweindl and FFroehlich authored Nov 3, 2023
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