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API for creating petab problems from scratch #220

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dweindl opened this issue Jul 25, 2023 · 0 comments
Open

API for creating petab problems from scratch #220

dweindl opened this issue Jul 25, 2023 · 0 comments
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dweindl commented Jul 25, 2023 •
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It would be nice to have some high-level API to create PEtab problems from scratch, instead of manually assembling the dataframes.

Something like

pp = petab.Problem()
pp.add_condition("conditionId", param1=2, param2=3)
pp.add_observable("observable1", formula="x1", ...)
pp.add_measurement(observable_id="observable1", time=2.5, measurement=1.337, noise_parameters=0.1, ...)
pp.add_parameter(parameter_id="p1", estimated=False, nominal_value=42)

Ideally also some API for dropping conditions / observables / measurements and potentially for modifying conditions / observables / measurements.
@dweindl dweindl self-assigned this Dec 4, 2024
dweindl added a commit to dweindl/libpetab-python that referenced this issue Dec 4, 2024
@dweindl
Functions for adding conditions/observables/parameter to Problem
4d5e790 
Will simplify writing test cases and interactively assembling petab problems.

To be extended.

Related to PEtab-dev#220.
@dweindl dweindl mentioned this issue Dec 4, 2024
Merged
dweindl added a commit to dweindl/libpetab-python that referenced this issue Dec 5, 2024
@dweindl
Functions for adding conditions/observables/parameter to Problem
dc20a0c 
Will simplify writing test cases and interactively assembling petab problems.

To be extended.

Related to PEtab-dev#220.
dweindl added a commit to dweindl/libpetab-python that referenced this issue Dec 6, 2024
@dweindl
Functions for adding conditions/observables/parameter to Problem
78e32c0 
Will simplify writing test cases and interactively assembling petab problems.

To be extended.

Related to PEtab-dev#220.
dweindl added a commit to dweindl/libpetab-python that referenced this issue Dec 6, 2024
@dweindl
Functions for adding conditions/observables/parameter to Problem
6b9bff5 
Will simplify writing test cases and interactively assembling petab problems.

To be extended.

Related to PEtab-dev#220.
dweindl added a commit that referenced this issue Dec 9, 2024
@dweindl
Functions for adding conditions/observables/parameter to Problem (#328)
9baf981 
Add functions for adding individual conditions/observables/parameter/measurements to Problem. This will simplify writing test cases and interactively assembling petab problems.

`petab.v2.Problem.add_*` will be added / updated to the new format separately.

Related to #220.
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