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AMICI-dev / AMICI

Advanced Multilanguage Interface to CVODES and IDAS
https://amici.readthedocs.io/
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Allow subselection of state variables for steady-state simulations #2387

Closed dweindl closed 3 months ago

dweindl commented 4 months ago

Allow subselection of state variables for convergence check during steady-state simulations via Model.set_steadystate_mask([1, 0, ..., 1]) (positve value: check; non-positive: don't check).

Closes #2368

codecov[bot] commented 4 months ago

Codecov Report

Attention: Patch coverage is 82.35294% with 6 lines in your changes are missing coverage. Please review.

Project coverage is 77.62%. Comparing base (e8493cf) to head (137af9d).

Additional details and impacted files [![Impacted file tree graph](https://app.codecov.io/gh/AMICI-dev/AMICI/pull/2387/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/2387?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 #2387 +/- ## ======================================== Coverage 77.61% 77.62% ======================================== Files 324 324 Lines 20895 20925 +30 Branches 1458 1464 +6 ======================================== + Hits 16218 16243 +25 - Misses 4674 4679 +5 Partials 3 3 ``` | [Flag](https://app.codecov.io/gh/AMICI-dev/AMICI/pull/2387/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/2387/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=AMICI-dev) | `73.40% <82.35%> (+0.01%)` | :arrow_up: | | [cpp_python](https://app.codecov.io/gh/AMICI-dev/AMICI/pull/2387/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=AMICI-dev) | `34.16% <17.64%> (-0.04%)` | :arrow_down: | | [petab](https://app.codecov.io/gh/AMICI-dev/AMICI/pull/2387/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=AMICI-dev) | `36.74% <21.21%> (-0.04%)` | :arrow_down: | | [python](https://app.codecov.io/gh/AMICI-dev/AMICI/pull/2387/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=AMICI-dev) | `72.16% <70.58%> (+<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/2387?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 | | |---|---|---| | [include/amici/model.h](https://app.codecov.io/gh/AMICI-dev/AMICI/pull/2387?src=pr&el=tree&filepath=include%2Famici%2Fmodel.h&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=AMICI-dev#diff-aW5jbHVkZS9hbWljaS9tb2RlbC5o) | `78.26% <100.00%> (+4.57%)` | :arrow_up: | | [include/amici/serialization.h](https://app.codecov.io/gh/AMICI-dev/AMICI/pull/2387?src=pr&el=tree&filepath=include%2Famici%2Fserialization.h&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=AMICI-dev#diff-aW5jbHVkZS9hbWljaS9zZXJpYWxpemF0aW9uLmg=) | `96.80% <100.00%> (+0.01%)` | :arrow_up: | | [include/amici/steadystateproblem.h](https://app.codecov.io/gh/AMICI-dev/AMICI/pull/2387?src=pr&el=tree&filepath=include%2Famici%2Fsteadystateproblem.h&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=AMICI-dev#diff-aW5jbHVkZS9hbWljaS9zdGVhZHlzdGF0ZXByb2JsZW0uaA==) | `100.00% <ø> (ø)` | | | [include/amici/vector.h](https://app.codecov.io/gh/AMICI-dev/AMICI/pull/2387?src=pr&el=tree&filepath=include%2Famici%2Fvector.h&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=AMICI-dev#diff-aW5jbHVkZS9hbWljaS92ZWN0b3IuaA==) | `83.33% <ø> (ø)` | | | [python/sdist/amici/swig\_wrappers.py](https://app.codecov.io/gh/AMICI-dev/AMICI/pull/2387?src=pr&el=tree&filepath=python%2Fsdist%2Famici%2Fswig_wrappers.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=AMICI-dev#diff-cHl0aG9uL3NkaXN0L2FtaWNpL3N3aWdfd3JhcHBlcnMucHk=) | `92.94% <ø> (ø)` | | | [src/steadystateproblem.cpp](https://app.codecov.io/gh/AMICI-dev/AMICI/pull/2387?src=pr&el=tree&filepath=src%2Fsteadystateproblem.cpp&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=AMICI-dev#diff-c3JjL3N0ZWFkeXN0YXRlcHJvYmxlbS5jcHA=) | `83.92% <100.00%> (+0.36%)` | :arrow_up: | | [src/hdf5.cpp](https://app.codecov.io/gh/AMICI-dev/AMICI/pull/2387?src=pr&el=tree&filepath=src%2Fhdf5.cpp&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=AMICI-dev#diff-c3JjL2hkZjUuY3Bw) | `89.60% <25.00%> (-0.39%)` | :arrow_down: | | [src/model.cpp](https://app.codecov.io/gh/AMICI-dev/AMICI/pull/2387?src=pr&el=tree&filepath=src%2Fmodel.cpp&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=AMICI-dev#diff-c3JjL21vZGVsLmNwcA==) | `83.94% <75.00%> (-0.08%)` | :arrow_down: | ... and [1 file with indirect coverage changes](https://app.codecov.io/gh/AMICI-dev/AMICI/pull/2387/indirect-changes?src=pr&el=tree-more&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=AMICI-dev)