Release 0.28.0 #2581
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Release 0.28.0 #2581
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…ndent sigmas (AMICI-dev#2562) Due to PEtab not allowing and observables in noiseFormula and AMICI not allowing state variables in sigma expressions, we are trying to replace any state variables by matching observables during PEtab import. However, if there were multiple observables with the same observableFormula, or one observableFormula was contained in another one, the substition of observableFormula for observableId could - depending on the ordering - result in noiseFormulas depending on other observables, which could lead to incorrect sensitivities due to AMICI-dev#2561. This change ensures that we are only using the observableId from the same row of the observable table as the noiseFormula. --------- Co-authored-by: Dilan Pathirana <[email protected]>
* Fix instance vs class attribute for step sizes * Only flatten problems where necessary
Set PYTHONFAULTHANDLER=1 for more output on crashes (AMICI-dev#2565). So far, this was only set for Ubuntu tests.
* Refactor tests/benchmark-models/test_benchmark_collection.sh into pytest cases * Unify with gradient checks in `tests/benchmark-models/test_petab_benchmark.py` * Test some additional benchmark problems For now, just consolidating the old tests. To be cleaned up further later on. Closes AMICI-dev#2510.
* Reference value wasn't found for Fiedler_BMCSystBiol2016, because it was recently renamed * Print all rows from gradient check results
Ignore warnings during macos pytest runs.
It looks like all our dependencies are now Python3.13-ready (https://github.com/AMICI-dev/AMICI/actions/runs/11753436377/job/32746292107), so we should require Python3.13 tests to pass.
…eSensitivityMode::integrationOnly` (AMICI-dev#2576) Fixes a bug that would result in disabling Newton's method for steady-state computation when steady-state sensitivity mode is set to `integrationOnly`, even if no senitivities are computed. This was because only the sensitivity method was checked, but not the sensitivity order. Fixes AMICI-dev#2575.
**Breaking change** Change the default mode for computing steady states and sensitivities at steady state to `integrationOnly` (from previously `integrateIfNewtonFails`). This is done for a more robust default behaviour. For example, the evaluation in https://doi.org/10.1371/journal.pone.0312148 shows that - at least for some models - Newton's method may easily lead to physically impossible solutions. To keep the previous behaviour, use: ```python amici_model.setSteadyStateComputationMode(amici.SteadyStateComputationMode.integrateIfNewtonFails) amici_model.setSteadyStateSensitivityMode(amici.SteadyStateSensitivityMode.integrateIfNewtonFails) ``` Closes AMICI-dev#2571.
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## master #2581 +/- ##
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+ Coverage 77.76% 78.00% +0.24%
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Files 325 325
Lines 21858 21852 -6
Branches 1473 1456 -17
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+ Hits 16997 17046 +49
+ Misses 4834 4795 -39
+ Partials 27 11 -16
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`amici.petab.conditions.fill_in_parameters` emits a warnings if parameters are supplied that don't occur in the parameter mapping. This is to point out potential issues with the parameter mapping. However, sometimes it's more convenient to silently ignore those extra parameters. Therefore, make this warning optional.
Update `fixes`, ignore test models.
When copying SUNDIALS objects, we need to make sure they have a valid `SUNContext` set. When copying `ModelStateDerived`, the `SUNContext` needs to be updated. Otherwise, dangling SUNContext pointers likely result in segfaults later on (AMICI-dev#2579). This was done only for a subset of objects. In particular the ones added only during AMICI-dev#2505 were missing, because of other changes happening in parallel. To make this less messy: Add `set_ctx(.)` functions all our sundials vector/matrix wrappers. Closes AMICI-dev#2579.
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FFroehlich
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