Ecosyste.ms: Timeline
Browse the timeline of events for every public repo on GitHub. Data updated hourly from GH Archive.
dweindl opened a draft pull request on AMICI-dev/AMICI
Refactor benchmark collection tests
* Refactor tests/benchmark-models/test_benchmark_collection.sh into pytest cases * Unify with gradient checks in `tests/benchmark-models/test_petab_benchmark.py` Closes #2510.
sonarcloud[bot] created a comment on a pull request on AMICI-dev/AMICI
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sonarcloud[bot] created a comment on a pull request on AMICI-dev/AMICI
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FFroehlich pushed 4 commits to jax_export AMICI-dev/AMICI
- Add missing simulation status codes (#2560) Closes #2559. a20447a
- PEtab import: Fix potentially incorrect sensitivities with state-dependent sigmas (#2562) Due to PEtab not allowing ... 9c603e1
- Fix benchmark collection gradient check (#2564) * Fix instance vs class attribute for step sizes * Only flatten pro... 56e6956
- Merge branch 'develop' into jax_export b84dbdb
dweindl created a comment on an issue on AMICI-dev/AMICI
> I would currently guess that this is related to some external changes (runner image, brew packages, ...) Different jobs from the same workflow: * https://github.com/dweindl/AMICI/actions/runs...
dweindl created a comment on an issue on AMICI-dev/AMICI
This happens already during import of the amici-extension. I would currently guess that this is related to some external changes (runner image, brew packages, ...) https://github.com/dweindl/AMI...
dweindl opened an issue on AMICI-dev/AMICI
Support for sympy expressions for observables and sigmas
`amici.sbml_import.SbmlImporter.sbml2amici` currently expects expressions for observables/sigmas/... as strings. I think it would be preferable to (additionally) allow sympy expressions there, bec...
dweindl pushed 1 commit to develop AMICI-dev/AMICI
- Fix benchmark collection gradient check (#2564) * Fix instance vs class attribute for step sizes * Only flatten pro... 56e6956
dweindl closed a pull request on AMICI-dev/AMICI
Fix benchmark collection gradient check
* Fix instance vs class attribute for step sizes * Only flatten problems where necessary
codecov[bot] created a comment on a pull request on AMICI-dev/AMICI
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dweindl opened an issue on AMICI-dev/AMICI
GHA: redundant testing in test_python_cplusplus.yml macos_cpp_py, macos_python
In `test_python_cplusplus.yml`, both macos_cpp_py and macos_python are running the same python tests for no apparent reason. We can save some time there.
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dweindl created a comment on an issue on AMICI-dev/AMICI
Another crash, now for `python/examples/example_splines_swameye//ExampleSplinesSwameye2003.ipynb` on Ubuntu: https://github.com/AMICI-dev/AMICI/actions/runs/11495925466/job/31996499560?pr=2563 :-/ ...
dweindl opened a pull request on AMICI-dev/AMICI
GHA: PYTHONFAULTHANDLER=1
Set PYTHONFAULTHANDLER=1 for more output on crashes (#2565). So far, this was only set for Ubuntu tests.
dweindl opened an issue on AMICI-dev/AMICI
scripts/run-python-tests.sh: line 22: 7262 Segmentation fault
`scripts/run-python-tests.sh: line 22: 7262 Segmentation fault: 11 pytest --ignore-glob=*petab* --ignore-glob=*test_splines.py --durations=10 $@` E.g. https://github.com/AMICI-dev/AMICI/action...
dweindl pushed 1 commit to develop AMICI-dev/AMICI
- PEtab import: Fix potentially incorrect sensitivities with state-dependent sigmas (#2562) Due to PEtab not allowing ... 9c603e1
dweindl closed a pull request on AMICI-dev/AMICI
PEtab import: Fix potentially incorrect sensitivities with state-depe…
…ndent sigmas Due to PEtab not allowing and observables in noiseFormula and AMICI not allowing state variables in sigma expressions, we are trying to replace any state variables by matching obse...
codecov[bot] created a comment on a pull request on AMICI-dev/AMICI
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dweindl pushed 1 commit to develop AMICI-dev/AMICI
- Add missing simulation status codes (#2560) Closes #2559. a20447a
codecov[bot] created a comment on a pull request on AMICI-dev/AMICI
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dweindl opened a draft pull request on AMICI-dev/AMICI
PEtab import: Fix potentially incorrect sensitivities with state-depe…
…ndent sigmas Due to PEtab not allowing and observables in noiseFormula and AMICI not allowing state variables in sigma expressions, we are trying to replace any state variables by matching obse...