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Upgrade SUNDIALS to 7.1.1 #2513

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merged 37 commits into from
Oct 7, 2024
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@dweindl dweindl commented Sep 27, 2024

We've been lagging behind SUNDIALS development. This updates the SUNDIALS library from v5.8.0 to v7.1.1.

Note:

The majority of changes inside amici are related to the introduction of SUNContext, 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 #1565

@dweindl dweindl self-assigned this Sep 27, 2024
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codecov bot commented Sep 27, 2024

Codecov Report

Attention: Patch coverage is 70.00000% with 3 lines in your changes missing coverage. Please review.

Project coverage is 77.84%. Comparing base (e89a1de) to head (878f01c).
Report is 1 commits behind head on develop.

Files with missing lines Patch % Lines
...rty/sundials/include/sundials/sundials_context.hpp 66.66% 2 Missing and 1 partial ⚠️
Additional details and impacted files

Impacted file tree graph

@@             Coverage Diff             @@
##           develop    #2513      +/-   ##
===========================================
+ Coverage    77.75%   77.84%   +0.08%     
===========================================
  Files          323      325       +2     
  Lines        20915    21048     +133     
  Branches      1446     1472      +26     
===========================================
+ Hits         16262    16384     +122     
+ Misses        4650     4637      -13     
- Partials         3       27      +24     
Flag Coverage Δ
cpp 73.55% <70.00%> (+0.06%) ⬆️
cpp_python 34.03% <70.00%> (-0.11%) ⬇️
petab 37.04% <70.00%> (+0.37%) ⬆️
python 72.39% <70.00%> (+0.07%) ⬆️

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

Files with missing lines Coverage Δ
...ndials/include/sundials/sundials_convertibleto.hpp 100.00% <100.00%> (ø)
include/amici/model_dae.h 75.00% <ø> (+2.27%) ⬆️
include/amici/model_state.h 76.85% <ø> (-23.15%) ⬇️
include/amici/rdata.h 100.00% <ø> (ø)
include/amici/serialization.h 96.83% <ø> (+0.02%) ⬆️
include/amici/solver.h 100.00% <ø> (ø)
include/amici/solver_cvodes.h 100.00% <ø> (ø)
include/amici/solver_idas.h 100.00% <ø> (ø)
include/amici/sundials_linsol_wrapper.h 100.00% <ø> (ø)
include/amici/sundials_matrix_wrapper.h 76.54% <ø> (ø)
... and 16 more

... and 1 file with indirect coverage changes

@dweindl dweindl mentioned this pull request Oct 1, 2024
@dweindl dweindl marked this pull request as ready for review October 1, 2024 15:04
@dweindl dweindl requested a review from a team as a code owner October 1, 2024 15:04
@dweindl dweindl marked this pull request as draft October 2, 2024 14:05
@dweindl dweindl mentioned this pull request Oct 3, 2024
@dweindl dweindl marked this pull request as ready for review October 3, 2024 19:08
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🙏

@dweindl dweindl merged commit cd56633 into AMICI-dev:develop Oct 7, 2024
19 of 20 checks passed
@dweindl dweindl deleted the update_sundials branch October 7, 2024 09:35
dweindl added a commit that referenced this pull request Oct 9, 2024
* We still need to create an NVector, even if it's empty.
* Don't pass nullptr as sunctx

Issue introduced in #2513. 

Closes #2534.
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2 participants