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AMICI-dev / AMICI

Advanced Multilanguage Interface to CVODES and IDAS
https://amici.readthedocs.io/
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PEtab: fix missing parameters in fill_in_parameters #2449

Closed dweindl closed 1 month ago

dweindl commented 1 month ago

Allows providing only a subset of parameter to simulate_petab. The missing parameters are taken from nominalValues in the parameter table.

Fixes https://github.com/AMICI-dev/AMICI/issues/2444. Nevertheless, exclude Lang_PLOSComputBiol2024 to save time.

codecov[bot] commented 1 month ago

Codecov Report

All modified and coverable lines are covered by tests :white_check_mark:

Project coverage is 77.64%. Comparing base (a63b016) to head (15ceecd).

Additional details and impacted files [![Impacted file tree graph](https://app.codecov.io/gh/AMICI-dev/AMICI/pull/2449/graphs/tree.svg?width=650&height=150&src=pr&token=1bt9lbspzk&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=AMICI-dev)](https://app.codecov.io/gh/AMICI-dev/AMICI/pull/2449?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=AMICI-dev) ```diff @@ Coverage Diff @@ ## develop #2449 +/- ## ======================================== Coverage 77.64% 77.64% ======================================== Files 324 324 Lines 20928 20930 +2 Branches 1464 1464 ======================================== + Hits 16249 16251 +2 Misses 4676 4676 Partials 3 3 ``` | [Flag](https://app.codecov.io/gh/AMICI-dev/AMICI/pull/2449/flags?src=pr&el=flags&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=AMICI-dev) | Coverage Δ | | |---|---|---| | [cpp](https://app.codecov.io/gh/AMICI-dev/AMICI/pull/2449/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=AMICI-dev) | `73.41% <0.00%> (-0.01%)` | :arrow_down: | | [cpp_python](https://app.codecov.io/gh/AMICI-dev/AMICI/pull/2449/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=AMICI-dev) | `34.10% <87.50%> (+0.01%)` | :arrow_up: | | [petab](https://app.codecov.io/gh/AMICI-dev/AMICI/pull/2449/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=AMICI-dev) | `36.66% <100.00%> (+<0.01%)` | :arrow_up: | | [python](https://app.codecov.io/gh/AMICI-dev/AMICI/pull/2449/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=AMICI-dev) | `72.19% <87.50%> (+0.01%)` | :arrow_up: | Flags with carried forward coverage won't be shown. [Click here](https://docs.codecov.io/docs/carryforward-flags?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=AMICI-dev#carryforward-flags-in-the-pull-request-comment) to find out more. | [Files](https://app.codecov.io/gh/AMICI-dev/AMICI/pull/2449?dropdown=coverage&src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=AMICI-dev) | Coverage Δ | | |---|---|---| | [python/sdist/amici/petab/simulations.py](https://app.codecov.io/gh/AMICI-dev/AMICI/pull/2449?src=pr&el=tree&filepath=python%2Fsdist%2Famici%2Fpetab%2Fsimulations.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=AMICI-dev#diff-cHl0aG9uL3NkaXN0L2FtaWNpL3BldGFiL3NpbXVsYXRpb25zLnB5) | `92.85% <100.00%> (+0.14%)` | :arrow_up: |