More flexible state reinitialization / PEtab import reinitialization fixes #1417
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Codecov Report
@@ Coverage Diff @@
## develop #1417 +/- ##
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- Coverage 79.07% 79.03% -0.05%
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Files 66 66
Lines 10061 10099 +38
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+ Hits 7956 7982 +26
- Misses 2105 2117 +12
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…ags for bwd-compat
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Feb 17, 2021
FFroehlich
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Feb 17, 2021
| @@ -409,6 +416,9 @@ void ConditionContext::applyCondition(const ExpData *edata, | |||
| "not match ExpData (%zd).", | |||
| model_->nk(), edata->fixedParameters.size()); | |||
| model_->setFixedParameters(edata->fixedParameters); | |||
| if(!edata->reinitializeFixedParameterInitialStates) | |||
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I am confused, don't we want to check for edata->reinitializeFixedParameterInitialStates here?
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The thing is, that if edata->reinitializeFixedParameterInitialStates == true, then this has been set on Model a couple of lines before. This will populate the index array in Model. If we would execute the next line, this would overwrite them with an empty array.
Not great, but keeps backward compatibility for the moment and still allow selective reinitialization. To be cleaned up soon.
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….13) Breaking changes: * AMICI requires Python>=3.7 * Updated package installation (PEP517/518): Creating source distributions requires https://github.com/pypa/build (#1384) (but now handles all package building dependencies properly) Features: * More flexible state reinitialization (#1417) Updated dependencies: * Upgrade to sundials 5.7.0 (#1392) Fixes: * Python: account for heaviside functions in expressions (#1382) * Python: allow loading of existing models in import_petab_problem (#1383) * Python: Don't override user-provided compiler/linker flags (#1389) * Python: PEtab import reinitialization fixes (#1417) * Python: Fix PEtab observables for pysb models (#1390) * Python: Substitute expressions in event condition expressions (#1404) * Python: Unspecified initial states in PEtab conditions table default to SBML initial value (#1397) * C++: Fix timepoint out of bounds access (#1402) * C++: Fix exported CMake config (#1388) * Fixed Dockerfile: add python3-venv (#1398, #1408) Other: * Slim exported swig interface (#1425) * Updated documentation * Getting started tutorial (#1423) * List supported SBML test tags (#1428) * Add AMICI C++/Python/Matlab feature comparison (#1409) * ... * Various minor CI improvements * ...
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Adds possibility to provide state indices for selective reinitialization based on fixed parameters.
The previous
ExpData::reinitializeFixedParameterInitialStatesis still there, but will be removed in an upcoming version.Addresses #1345, #1396, #1319
Supersedes #1344
Include new test cases from PEtab-dev/petab_test_suite#35