Fix Rule-handling in PEtab import #1753
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@@ Coverage Diff @@
## develop #1753 +/- ##
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- Coverage 73.59% 65.82% -7.77%
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Files 71 30 -41
Lines 12053 4337 -7716
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- Hits 8870 2855 -6015
+ Misses 3183 1482 -1701
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@dweindl Thanks for the work on the issue. As I understand this fixes the rate rule issue. Would it be possible to merge this in develop? |
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@matthiaskoenig : Will try to do this week. Needs a new https://github.com/PEtab-dev/libpetab-python release first. |
RateRules were previously ignored.
| value = get_species_initial( | ||
| petab_problem.sbml_model.getSpecies(species_id) | ||
| ) | ||
| element = petab_problem.sbml_model.getElementBySId(element_id) |
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hmm this doesn't account for InitialAssignments right? (was already the case for species before, but I am not sure thats correct in the first place)
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Yes, you are right. Good catch. Should add a test case.
| @@ -86,7 +86,8 @@ def get_fixed_parameters( | |||
| # remove overridden parameters (`object`-type columns) | |||
| fixed_parameters = [p for p in fixed_parameters | |||
| if condition_df[p].dtype != 'O' | |||
| and sbml_model.getParameter(p) is not None] | |||
| and sbml_model.getParameter(p) is not None | |||
| and sbml_model.getRuleByVariable(p) is None] | |||
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uuuuh, so what happens with rules here that don't have a RateRule qualifier?
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This is about whether these parameters should be considered as AMICI-constant-parameters. Any parameters that are rule targets cannot be constants. Or am I missing something?
Co-authored-by: Fabian Fröhlich <fabian_froehlich@hms.harvard.edu>
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SonarCloud Quality Gate failed. |
@matthiaskoenig : now available on pypi - |
RateRules-targets in the condition table were previously ignored.
Closes #1750
Also fixes a bug where InitialAssignments were not honored for elements that occurred as column in the condition table and were set to
NaN(i.e. "use model value").