Release 0.30.0 #2622
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Release 0.30.0 #2622
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SUNContext for `x_pos_tmp_` wasn't updated after copying. Hopefully fixes AMICI-dev#2607.
) During PEtab parameter mapping, fill in fixed parameter values for initial values if requested. So far, this was only done for other parameters. Update documentation for amici/petab/parameter_mapping.py Fixes AMICI-dev#2610.
* add jax serialisation * doc * bad ruff * bad ruff
* add jax serialisation * doc * no compilation for jax * bad ruff * Update ExampleJaxPEtab.ipynb * bad ruff * Update ExampleJaxPEtab.ipynb
* refactor * correct doc * remove PK * fix tests * fix notebook * fix parameter ids * fix jax test * fix notebook * reviews * fixup
* mark jax experimental * add JAX import warning to pyest.ini
) * disentangle sim & preeq * disentangle sim & preeq * run preequilibration once * fix symlink * separate default dirs for jax/cpp, honour model dir/name * fix notebook * fix path SNAFU * fix models without preequilibration * fix tests * fixup * fix doc typehints * fix notebook * fix output dict construction * fix notebook
* disentangle sim & preeq * disentangle sim & preeq * run preequilibration once * fix symlink * separate default dirs for jax/cpp, honour model dir/name * fix notebook * fix path SNAFU * fix models without preequilibration * fix tests * fixup * fix doc typehints * fix notebook * implement jax-based reinitialisation * add more defaults & doc * fix state ids * fix template * Update model.py * breaking jax release * add jax runner to petab testsuite & fix * fix notebook * refactor petab test cases * fix parameter unscaling * fixups * refactor & simplify * fixup * fix notebook * fixup * Update petab.py
Codecov ReportAttention: Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## master #2622 +/- ##
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- Coverage 77.63% 77.17% -0.47%
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Files 329 332 +3
Lines 21708 22957 +1249
Branches 1477 1477
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+ Hits 16853 17717 +864
- Misses 4844 5229 +385
Partials 11 11
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* Tests: Skip llh test for Isensee_JCB2018 Until it has been decided which model/dataset is the correct one, and the expected llh is updated accordingly. See Benchmarking-Initiative/Benchmark-Models-PEtab#253 * fix broken pytest invocation
FFroehlich
approved these changes
Dec 10, 2024
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