Release 0.31.0 #2649

dweindl · 2025-02-18T11:08:28Z

No description provided.

Add RDataReporting::observables_likelihood for computing observables, likelihood and the respective sensitivities. Closes AMICI-dev#2625. Fixes allocating sllh despite SensitivityMethod::none.

* update diffrax, remove ts_init * fix petab simulate * Update pyproject.toml * Update pytest.ini

* add event check in equilibration, add test * Update test_jax.py * Update model.py * Update model.py * decrease integration tols * decrease integration tols * decrease integration tols * decrease integration tols * revert scaling factor, add ss event API * Update test_jax.py * Update ExampleJaxPEtab.ipynb * Update petab.py

Fixes AMICI-dev#2627. ReturnData.sllh was always NaN because it wasn't 0-initialized.

* pre-commit autoupdate * pre-commit autoupdate `pre-commit autoupdate` and fix/ignore pyupgrade issues.

Reduce parameter mapping time for Froehlich_CellSystems2018 by 88% (1774s -> 216s).

* fix vectorisation * decorators, preequilibration * add documentation * fix petab_simulate * fix notebook * update/fix doc? * fix rtd * fix docstring * Update python/sdist/amici/jax/petab.py Co-authored-by: Daniel Weindl <[email protected]> --------- Co-authored-by: Daniel Weindl <[email protected]>

* fix AMICI-dev#2642 * fixup * fixup * add issue as regression test * fix path

* first working implementation * bugfixes * vectorisation go brrrrr * add doc, workaround Zhao_QuantBiol2020 * fixup * fixup * fixup * fixup * Update ExampleJaxPEtab.ipynb * fix notebook * fix pysb * fixup * fixup petab 0006 jax * fix noise parameters * fixup noise model * fixup * fixup sigma * remove workaround * Apply suggestions from code review Co-authored-by: Daniel Weindl <[email protected]> * Update de_model.py * Update pytest.ini * Update de_model.py * Update pysb_import.py * fixup --------- Co-authored-by: Daniel Weindl <[email protected]>

Avoid repeated lookups. Saves just a few seconds for Froehlich_CellSystems2018, but better than nothing...

* LakrisenkoPat2024 * SmithMal2025

amici wants to avoid sundials' checkpointing, that's we set `steps` (the number of integration steps at which a checkpoint is created) for `CVodeAdjInit` to the maximum number of integration steps (`mxsteps`) for the forward problem. However, the checkpoint is created at step `steps`, not at step `steps + 1`. Therefore, if the forward integration takes exactly `mxsteps`, a checkpoint is still created. This is not a problem per se, but it may trigger segfaults under circumstances not fully understood (-> LLNL/sundials#49). Although unlikely, it still occasionally crashes long running optimizations. This change should make sure that checkpointing never occurs.

Update valgrind suppressions and fix `run-valgrind-py.sh` for arguments containing spaces.

…dev#2647) Due to LLNL/sundials#82, we can get exceptions from `CVodeSolver::getSens`, escaping `FinalStateStorer::~FinalStateStorer`, that will result in crashes. This is fixed here. The issue is semi-producible with [Boehm_JProteomeRes2014](https://github.com/Benchmarking-Initiative/Benchmark-Models-PEtab/tree/15b4f78aff1121870537ad3e1a6b902cb8f73930/Benchmark-Models/Boehm_JProteomeRes2014) with forward sensitivities: Program output: ``` 2025-02-17 14:44:33.988 - amici.swig_wrappers - DEBUG - [model1_data1][cvodes:CVode:WARNING] python/sdist/amici/ThirdParty/sundials/src/cvodes/cvodes.c:3482: Internal t = 0 and h = 0 are such that t + h = t on the next step. The solver will continue anyway. (99) 2025-02-17 14:44:33.988 - amici.swig_wrappers - DEBUG - [model1_data1][cvodes:CVodeGetDky:BAD_T] python/sdist/amici/ThirdParty/sundials/src/cvodes/cvodes.c:3783: Illegal value for t.t = 2.5 is not between tcur - hu = 0 and tcur = 0. (-25) 2025-02-17 14:44:33.988 - amici.swig_wrappers - DEBUG - [model1_data1][cvodes:CVodeGetDky:BAD_T] python/sdist/amici/ThirdParty/sundials/src/cvodes/cvodes.c:3783: Illegal value for t.t = 5 is not between tcur - hu = 0 and tcur = 0. (-25) 2025-02-17 14:44:33.988 - amici.swig_wrappers - DEBUG - [model1_data1][cvodes:CVode:ILL_INPUT] python/sdist/amici/ThirdParty/sundials/src/cvodes/cvodes.c:3328: Trouble interpolating at tout = 5. tout too far back in direction of integration (-22) 2025-02-17 14:44:33.988 - amici.swig_wrappers - ERROR - [model1_data1][FORWARD_FAILURE] AMICI forward simulation failed at t = 5: AMICI failed to integrate the forward problem terminate called after throwing an instance of 'amici::CvodeException' what(): CVODE routine CVodeGetSens failed with error code -25. Thread 1 "python" received signal SIGABRT, Aborted. ``` Stack trace: ``` AMICI-dev#10 0x00007ffff70811f1 in _Unwind_RaiseException (exc=0x6d5ff10) at ../../../src/libgcc/unwind.inc:136 AMICI-dev#11 0x00007ffff48bb384 in __cxxabiv1::__cxa_throw (obj=<optimized out>, tinfo=0x7fff5c6d6aa8 <typeinfo for amici::CvodeException>, dest=0x7fff5c5476c4 <amici::CvodeException::~CvodeException()>) at ../../../../src/libstdc++-v3/libsupc++/eh_throw.cc:93 AMICI-dev#12 0x00007fff5c5bdb64 in amici::CVodeSolver::getSens (this=0x6d130d0) at python/sdist/amici/src/solver_cvodes.cpp:663 AMICI-dev#13 0x00007fffbc5709e8 in amici::Solver::getStateSensitivity (this=0x6d130d0, t=2.5) at python/sdist/amici/src/solver.cpp:1340 AMICI-dev#14 0x00007fffbc570750 in amici::Solver::writeSolution (this=0x6d130d0, t=0x6d26db0, x=..., dx=..., sx=..., xQ=...) at python/sdist/amici/src/solver.cpp:1303 AMICI-dev#15 0x00007fffbc5d376d in amici::ForwardProblem::getSimulationState (this=0x6d26c90) at python/sdist/amici/src/forwardproblem.cpp:421 AMICI-dev#16 0x00007fffbc5d45df in amici::FinalStateStorer::~FinalStateStorer (this=0x7fffffffb308, __in_chrg=<optimized out>) at include/amici/forwardproblem.h:450 AMICI-dev#17 0x00007fffbc5d2285 in amici::ForwardProblem::workForwardProblem (this=0x6d26c90) at python/sdist/amici/src/forwardproblem.cpp:203 AMICI-dev#18 0x00007fffbc54fbf9 in amici::runAmiciSimulation (solver=..., edata=0x5078010, model=..., rethrow=false) at python/sdist/amici/src/amici.cpp:108 ```

codecov · 2025-02-18T11:37:02Z

Codecov Report

Attention: Patch coverage is 95.03817% with 13 lines in your changes missing coverage. Please review.

Project coverage is 77.30%. Comparing base (64bbd80) to head (bc350cf).
Report is 19 commits behind head on master.

Files with missing lines	Patch %	Lines
python/sdist/amici/pysb_import.py	85.18%	4 Missing ⚠️
python/sdist/amici/jax/petab.py	98.31%	2 Missing ⚠️
python/sdist/amici/petab/pysb_import.py	91.30%	2 Missing ⚠️
python/sdist/amici/sbml_utils.py	0.00%	2 Missing ⚠️
python/sdist/amici/splines.py	0.00%	2 Missing ⚠️
python/sdist/amici/jax/model.py	95.00%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##           master    #2649      +/-   ##
==========================================
+ Coverage   77.00%   77.30%   +0.29%     
==========================================
  Files         332      332              
  Lines       22970    23142     +172     
  Branches     1479     1480       +1     
==========================================
+ Hits        17688    17889     +201     
+ Misses       5271     5242      -29     
  Partials       11       11

Flag	Coverage Δ
cpp	`76.44% <75.50%> (+2.50%)`	⬆️
cpp_python	`33.38% <23.29%> (-0.11%)`	⬇️
petab	`39.40% <88.30%> (+0.50%)`	⬆️
python	`72.36% <81.60%> (+0.28%)`	⬆️

Flags with carried forward coverage won't be shown. Click here to find out more.

Files with missing lines	Coverage Δ
include/amici/rdata.h	`100.00% <ø> (ø)`
python/sdist/amici/_codegen/model_class.py	`100.00% <100.00%> (ø)`
python/sdist/amici/constants.py	`100.00% <100.00%> (ø)`
python/sdist/amici/cxxcodeprinter.py	`92.17% <100.00%> (ø)`
python/sdist/amici/de_model.py	`90.30% <100.00%> (+0.14%)`	⬆️
python/sdist/amici/de_model_components.py	`89.61% <100.00%> (+0.42%)`	⬆️
python/sdist/amici/import_utils.py	`89.36% <100.00%> (ø)`
python/sdist/amici/jax/ode_export.py	`96.87% <100.00%> (ø)`
python/sdist/amici/logging.py	`79.76% <ø> (ø)`
python/sdist/amici/numpy.py	`83.33% <100.00%> (ø)`
... and 13 more

... and 4 files with indirect coverage changes

dweindl and others added 18 commits December 16, 2024 11:19

Add RDataReporting::observables_likelihood (AMICI-dev#2627)

3206fce

Add RDataReporting::observables_likelihood for computing observables, likelihood and the respective sensitivities. Closes AMICI-dev#2625. Fixes allocating sllh despite SensitivityMethod::none.

remove eqx.debug.nan, fixes 2629 (AMICI-dev#2630)

4522522

update diffrax & jaxlib (AMICI-dev#2632)

3d73624

* update diffrax, remove ts_init * fix petab simulate * Update pyproject.toml * Update pytest.ini

Fix RDataReporting::observables_likelihood (AMICI-dev#2633)

92a530b

Fixes AMICI-dev#2627. ReturnData.sllh was always NaN because it wasn't 0-initialized.

pre-commit autoupdate (AMICI-dev#2635)

57f5ed5

* pre-commit autoupdate * pre-commit autoupdate `pre-commit autoupdate` and fix/ignore pyupgrade issues.

Faster parameter mapping (AMICI-dev#2638)

923b8f4

Reduce parameter mapping time for Froehlich_CellSystems2018 by 88% (1774s -> 216s).

fix AMICI-dev#2642 (AMICI-dev#2643)

c9f698d

* fix AMICI-dev#2642 * fixup * fixup * add issue as regression test * fix path

PEtab parameter mapping: minor speedup (AMICI-dev#2640)

65f2ab7

Avoid repeated lookups. Saves just a few seconds for Froehlich_CellSystems2018, but better than nothing...

Update references (AMICI-dev#2634)

ff9e7af

* LakrisenkoPat2024 * SmithMal2025

Fix CVodeGetSensDky error message (AMICI-dev#2644)

66552d7

Update valgrind suppressions (AMICI-dev#2646)

8366b87

Update valgrind suppressions and fix `run-valgrind-py.sh` for arguments containing spaces.

Merge branch 'master' into develop

ce9a785

Bump version; update changelog

bc350cf

dweindl marked this pull request as ready for review February 18, 2025 13:20

dweindl requested a review from a team as a code owner February 18, 2025 13:20

FFroehlich approved these changes Feb 18, 2025

View reviewed changes

dweindl merged commit f742e48 into AMICI-dev:master Feb 18, 2025
34 checks passed

dweindl deleted the release_0.31.0 branch February 18, 2025 17:41

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Release 0.31.0 #2649

Release 0.31.0 #2649

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Release 0.31.0 #2649

Release 0.31.0 #2649

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