Ecosyste.ms: Timeline
Browse the timeline of events for every public repo on GitHub. Data updated hourly from GH Archive.
dweindl closed an issue on AMICI-dev/AMICI
SBML import: Incorrect processing of piecewise/Heaviside function
[Beer_MolBioSystems2014](https://github.com/Benchmarking-Initiative/Benchmark-Models-PEtab/tree/v2024.10.15/Benchmark-Models/Beer_MolBioSystems2014) has an assignment rule containing `piecewise`. T...
dweindl closed an issue on AMICI-dev/AMICI
model name "model" leads to cmake failures
model name "model" is default for pysb, leads to clash in cmake target names (see error below). Not sure whether we should not permit models named "model" or add a prefix to the cmake target. ...
dweindl closed an issue on AMICI-dev/AMICI
Refactor: move Model::state_ initalization to ModelState ctor
Move `Model::state_` initalization to `ModelState` ctor where it belongs.
dweindl closed an issue on AMICI-dev/AMICI
SBML test suite fails since sundials upgrade
https://github.com/AMICI-dev/AMICI/actions/runs/11212756053 > [OTHER] AMICI simulation failed: CVODE routine CVodeInit failed with error code -22. > Error: [rank 0][/home/runner/work/AMICI/AM...
dweindl closed an issue on AMICI-dev/AMICI
Install `amici[vis]` for binder
Currently, some notebooks fail to run on binder, because matplotlib and seaborn are missing. Amici needs to be installed with `vis` extras.
dweindl pushed 29 commits to master AMICI-dev/AMICI
- Upgrade SUNDIALS to 7.1.1 (#2513) We've been lagging behind SUNDIALS development. This updates the SUNDIALS library ... cd56633
- Install `amici[vis]` for binder (#2528) Closes #2526. 12420c3
- Fix initialization of Model::simulation_parameters_::pscale (#2530) pscale was set on moved-from object simulation_p... 539de29
- Pin sphinx<8 / update sphinx config for sphinx8 (#2532) Some dependency lifted there sphinx<8 requirement, but this ... 2784887
- Fix AmiVector::nvec_ for size 0 (#2535) * We still need to create an NVector, even if it's empty. * Don't pass null... e59e415
- Fix SBML test IDs (#2536) Make sure the printed test IDs correspond to actual test IDs, so they can be copy/pasted t... 2f70528
- CI: Re-enable benchmark model gradient checks / prettify gradient check output (#2524) * Make the result more inform... 6261491
- Refactor symbolic event processing (#2538) Extract some neutral changes from #1539 to reduce the diff there and avoi... b7a3e91
- Refactor: move Model::state_ initalization to ModelState ctor (#2533) Move `Model::state_` initalization to `ModelSt... f5533ba
- CMake: Set policies for CMake 3.31 (#2539) ... and remove some unnecessary stuff. ca01930
- Fix duplicated log messages (#2542) We need to remove the default error handler, otherwise sundials error message wi... 919de0e
- Add simulation status AMICI_FIRST_QRHSFUNC_ERR (#2541) was missing. d5123a5
- Optimize includes (#2543) * Remove unnecessary includes * Reduce public linking interface 4973321
- Update CMake export config (#2540) * We don't need to find SuiteSparse - sundials takes care of that * Fixes some i... ee2e0d2
- Doc: Add missing command in python_installation.rst (#2544) 09755d4
- Update benchmark problem name Fiedler_BMC->Fiedler_BMCSystBiol2016 2c957c8
- Fix pysb branch (#2548) Previous branch no longer exists. Now on master (https://github.com/pysb/pysb/commit/8be8263... d4bb0ce
- CMake: Don't attempt to create alias target if target of the same name already exists Fixes #2546. 9f821d9
- Fix `_collect_heaviside_roots` for `sympy.Heaviside` arguments Since https://github.com/AMICI-dev/AMICI/commit/b7a3e... c8778e5
- Fix capturing SUNDIALS warnings after 7.1.1 upgrade (#2551) Disable SUNDIALS's warning-handling through `SUNLogger`.... 8253a97
- and 9 more ...
dweindl closed an issue on AMICI-dev/AMICI
Upgrade sundials
Upgrade to the most recent [SUNDIALS release](https://github.com/LLNL/sundials/releases) 5.8
dweindl pushed 1 commit to develop AMICI-dev/AMICI
- Update references (#2518) * BarthelKun2024 * ArmisteadHoe2024 7f863cf
dweindl pushed 1 commit to develop AMICI-dev/AMICI
- Fix crashes when errors occur at output timepoints (#2555) Fixes a bug that lead to program termination if a root-af... 9f56266
dweindl closed a pull request on AMICI-dev/AMICI
Fix crashes when errors occur at output timepoints
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 th...
dweindl opened an issue on AMICI-dev/AMICI
Rate limit for inf/nan warnings
In some cases, there can be several thousands of Inf/Nan warnings during a single simulation for the same quantities. It would be convenient, if one could tell amici to not print/store them more th...
dweindl created a review comment on a pull request on AMICI-dev/AMICI
Wait, ExpData is not sufficient, we need to check the model timepoints
dweindl pushed 1 commit to develop AMICI-dev/AMICI
- Fix dangling pointer in SolverTest.SettersGettersWithSetup (#2556) Fixes a dangling pointer issue in SolverTest.Sett... fbe3840
dweindl pushed 1 commit to develop AMICI-dev/AMICI
- Fix dangling pointer in SolverTest.SettersGettersWithSetup (#2556) Fixes a dangling pointer issue in SolverTest.Sett... 3823880
dweindl closed a pull request on AMICI-dev/AMICI
Fix dangling pointer in SolverTest.SettersGettersWithSetup
Fixes a dangling pointer issue in SolverTest.SettersGettersWithSetup. The SUNContext was destroyed before the associated AmiVectors which resulted in invalid reads.
dweindl closed a pull request on AMICI-dev/AMICI
GHA: Ignore python3.13 failures for now
Until all dependencies work with Python3.13. pyarrow wheels are still missing.
github-merge-queue[bot] deleted a branch AMICI-dev/AMICI
gh-readonly-queue/develop/pr-2557-91054b3084890a0cf6c0ecab40d268b0db54d06c
github-merge-queue[bot] pushed 1 commit to develop AMICI-dev/AMICI
- GHA: Ignore python3.13 failures for now (#2557) Until all dependencies work with Python3.13. pyarrow wheels are stil... 40b496f
sonarcloud[bot] created a comment on a pull request on AMICI-dev/AMICI
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github-merge-queue[bot] created a branch on AMICI-dev/AMICI
gh-readonly-queue/develop/pr-2557-91054b3084890a0cf6c0ecab40d268b0db54d06c - Advanced Multilanguage Interface to CVODES and IDAS
FFroehlich pushed 2 commits to jax_export AMICI-dev/AMICI
codecov[bot] created a comment on a pull request on AMICI-dev/AMICI
## [Codecov](https://app.codecov.io/gh/AMICI-dev/AMICI/pull/2557?dropdown=coverage&src=pr&el=h1&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=AMICI-dev...
