Release 0.27.0 #2554
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Release 0.27.0 #2554
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We've been lagging behind SUNDIALS development. This updates the SUNDIALS library from v5.8.0 to [v7.1.1](https://sundials.readthedocs.io/en/latest/Changelog_link.html#changes-to-sundials-in-release-7-1-1). Note: * This includes the post-7.1.1 changes to `cmake/tpl/FindKLU.cmake` from LLNL/sundials#582 * This includes the post-7.1.1 changes to [`sundials/src/sunmatrix/sparse/sunmatrix_sparse.c:SUNMatScaleAddI_Sparse`](https://github.com/LLNL/sundials/blob/736369d543cb80956b1ba87377ffc0c8cf6b342b/src/sunmatrix/sparse/sunmatrix_sparse.c#L625C1-L694C2) from LLNL/sundials#584, fixing LLNL/sundials#581 The majority of changes inside amici are related to the introduction of [SUNContext](https://sundials.readthedocs.io/en/latest/sundials/SUNContext_link.html#the-suncontext-type), which is required for the construction of all SUNDIALS objects. Other trivial changes are related to renamed types and macros. Furthermore, the error handling strategy has changed. As a consequence, simulation error messages will look slightly different. Closes AMICI-dev#1565
…v#2530) pscale was set on moved-from object simulation_parameters instead of simulation_parameters_
Some dependency lifted there sphinx<8 requirement, but this leads to a number of issues with other dependencies. Therefore, require sphinx<8 for now. Anyways fix some upcoming issue with sphinx 8 when doc2path will return something path-like (see ICB-DCM/pyPESTO#1482).
* We still need to create an NVector, even if it's empty. * Don't pass nullptr as sunctx Issue introduced in AMICI-dev#2513. Closes AMICI-dev#2534.
Make sure the printed test IDs correspond to actual test IDs, so they can be copy/pasted to rerun. Previously this was not the case when running with pytest-xdist.
…ck output (AMICI-dev#2524) * Make the result more informative and more readable. * Re-enable some test problems, use stricter tolerances for some at least (AMICI-dev#2511) * More problem-specific settings
Extract some neutral changes from AMICI-dev#1539 to reduce the diff there and avoid conflicts.
…dev#2533) Move `Model::state_` initalization to `ModelState` ctor where it belongs. Closes AMICI-dev#2531.
... and remove some unnecessary stuff.
We need to remove the default error handler, otherwise sundials error message will be printed twice.
* Remove unnecessary includes * Reduce public linking interface
* We don't need to find SuiteSparse - sundials takes care of that * Fixes some issues when consuming the amici-exported CMake config * Set CMAKE_PREFIX_PATH when configuring models * Install system-wide libsuitesparse-dev to make sure it doesn't interfere with our vendored version
Previous branch no longer exists. Now on master (pysb/pysb@8be8263).
…e already exists Fixes AMICI-dev#2546.
Since AMICI-dev@b7a3e91, if dxdt was a sympy.Heaviside, it wasn't correctly processed, because only its arguments were checked. That means, root-finding would not be enabled for this discontinuity. This would happen if a Rule or KineticLaw is a plain Piecewise function (not embedded inside a more complex expression). Fixes AMICI-dev#2545. The bug was exposed only after the previous release, this did not affect any former amici releases.
Disable SUNDIALS's warning-handling through `SUNLogger`. Instead pipe everything both errors and warnings through the provided`SUNErrHandlerFn`. For details, see AMICI-dev#2550. Fixes AMICI-dev#2550. This also corrects the error message formatting - file path and line numbers for debug builds, but omitted in release builds - which was inverted before.
* update jax notebook * Apply suggestions from code review Co-authored-by: Daniel Weindl <[email protected]> --------- Co-authored-by: Daniel Weindl <[email protected]>
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Codecov ReportAttention: Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## master #2554 +/- ##
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+ Coverage 77.75% 77.93% +0.18%
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Files 323 325 +2
Lines 20915 21858 +943
Branches 1446 1473 +27
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+ Hits 16262 17035 +773
- Misses 4650 4796 +146
- Partials 3 27 +24
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* add 3.13 to test matrix * remove py3.9 leftover
Until all dependencies work with Python3.13. pyarrow wheels are still missing.
…#2556) Fixes a dangling pointer issue in SolverTest.SettersGettersWithSetup. The SUNContext was destroyed before the associated AmiVectors which resulted in invalid reads.
Fixes a bug that lead to program termination if a root-after-reinitialization error (potentially also others) occurred at an output timepoint, because an non-existing/invalid SimulationState for that timepoint was accessed. See AMICI-dev#2491 for further details. Fixes AMICI-dev#2491. Also avoid some unnecessary copying (during which previously the segfault occurred if this bug triggered in non-debug builds).
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FFroehlich
approved these changes
Oct 21, 2024
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