Ecosyste.ms: Timeline
Browse the timeline of events for every public repo on GitHub. Data updated hourly from GH Archive.
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
## [](https://sonarcloud.io/dashboard?id=...
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...
dweindl opened 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.
codecov[bot] created a comment on a pull request on AMICI-dev/AMICI
## [Codecov](https://app.codecov.io/gh/AMICI-dev/AMICI/pull/2556?dropdown=coverage&src=pr&el=h1&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=AMICI-dev...
codecov[bot] created a comment on a pull request on AMICI-dev/AMICI
## [Codecov](https://app.codecov.io/gh/AMICI-dev/AMICI/pull/2555?dropdown=coverage&src=pr&el=h1&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=AMICI-dev...