Release 0.26.3 #2525
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Release 0.26.3 #2525
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Use the provided overall cmake configuration from SuiteSparse instead of using `make` wrappers for subprojects. Properly install the SuiteSparse libraries which makes finding their cmake configuration easier for downstream packages.
Removes most protected data members from `ReturnData`, in particular sundials objects. Makes the code slightly easier to follow and we won't have to worry about managing SUNContext outside of runAmiciSimulation with sundials>=6.0. Also saves some unnecessary copying of various data. Closes AMICI-dev#2348
) * Move mutable Model members to ModelStateDerived * Move ModelState::spl_ to ModelStateDerived Closes AMICI-dev#2504
* AmiVector -> std::vector * Wrap it with an NVector only when need in SteadystateProblem Avoids SUNContext issues when copying Model
…I-dev#2507) * Refactor ModelDimension and initialization of ModelStateDerived * Move some other model dimensions from the Model constructor to ModelDimensions * Perform more initialization of ModelStateDerived inside its constructor * dJydy_dense_ -> ModelStateDerived
* cmake_minimum_required(VERSION 3.22) as in sundials * regenerate * ..
* don't build more than necessary (no shared libs) * don't include suitesparse installation directory in sdist
Use petab.v1. Closes AMICI-dev#2509.
Only expose to where they are required.
…2515) Also build SUNDIALS and SuiteSparse in debug mode when `ENABLE_AMICI_DEBUGGING=TRUE`.
... when using `--no-build-isolation`.
Previously, we had to build the different SuiteSparse subprojects separately. Meanwhile, we can do that together. This is more concise, and saves a some extra cmake configuration runs, leading to faster package installation.
... and get rid of the URLs in pyproject.toml that aren't allowed on PyPI
* Make it consistent that SUNLinSolWrapper always holds the associated matrix * Always use SUNMatrixWrapper instead of raw SUNMatrix objects * Implement declared but missing move assignment This makes it a bit easier to finally address AMICI-dev#1164.
* Fix gradient checks. Previously, failing test would not have been reported (see AMICI-dev#2511). Quite some tests are now skipped, but better to test some than none... To be re-enabled later. * Sort test cases to avoid issues with pytest-xdist. * Refactor Requires ICB-DCM/fiddy#37
Codecov ReportAttention: Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## master #2525 +/- ##
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+ Coverage 77.68% 77.93% +0.25%
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Files 324 323 -1
Lines 20945 20915 -30
Branches 1456 1446 -10
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+ Hits 16271 16300 +29
+ Misses 4671 4612 -59
Partials 3 3
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It seems, the documentation didn't demonstrate how to plot measurements together with the model outputs yet.
Use SUNLinSolWrapper. Get rid of subclasses. Simplify. Closes AMICI-dev#1164. We should also be able to get rid of the remaining data members, but that's for another time...
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FFroehlich
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Oct 3, 2024
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Let's have another release after #2521 ✔️ and #2523 ✔️ , but before #2513.
This will also fix currently failing GHA workflows on
master(via #2522).