Release 0.18.0 #2115
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Release 0.18.0 #2115
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* re-fix sbml exception * Handle windows TemporaryDirectory cleanup failures * Fix windows PermissionError * remove unused import * Revert "re-fix sbml exception" This reverts commit ac596be. * Revert "remove unused import" This reverts commit 5007143. * fix spline sensitivity test with no parameters * Fix some sphinx issues * Fix some sphinx issues * Fix sphinx issues with TYPE_CHECKING * Doxygen doc * Temporary: Run sonar scanner before tests * cleanup .. * Revert "cleanup" This reverts commit ae0969a. * Cleanup * fix name * snakecase * improve C++ docstrings * cpp cleanup * case * .. * fixup doxygen * snakecase * typehints/case/.. * rename * simplify * exceptions * duplicated docs * private * rename; swig ignore * snake, shadow * simplify * adjust tolerances for spline tests * Revert "Temporary: Run sonar scanner before tests" This reverts commit 77478ac. * Add test stub * Check ctor arguments * fix regression * fix floating point splines * draft of example notebook * remove leftover code Co-authored-by: Daniel Weindl <[email protected]> * fix (maybe) signedness error on CI * test unit-tests * fix typo * switch to all float? * fix typo in header too * fix float division * split tests * fix finite differences * fix private * make spline exact on nodes * one more test spline * remove python syntax * derivatives are given/computed in linear space This is debatable, especially for boundary conditions like natural, but it should be the behaviour of the python code * test for logarithmic spline * approx tests * temporarily disable python tests * fix extrapolation for all BCs * use and check noExtrapolation * extrapolation tests * fix periodic bc in test * fix derivative computation for periodic bc * fix missing include for AmiException * fix missing commas * bugfix * fix sensitivity computation for fd * test sensitivity (simplest case) * remove unused variables * fix loop variable type * add atol in test * fix botched merge * more tests * <= instead of < in testing * forgot derivatives * fix precomputed sensitivities * relax tolerances * fix sensitivities computation for logarithmic splines * relax tolerances * fix evaluation points for test * relax tolerances * fix loop * small fixes * remove symlinks * move python files * post merge fixes * add discard_annotations to import_model_sbml * fix small merge mistakes * regenerate test models * Fix missing return * -Werror in debug mode * fix NameError: name 'SBMLException' is not defined * const * final value tests * fix comments * remove copy&paste leftover * make some more methods public * compute final values explicitly * fix coefficients_extrapolate indexing * more fixes for extrapolation sensitivity * remove unused variables * missing namespace * notebook to sphinx doc * fic horner form * rewrite python tests * add more C++ tests * python spline evaluation tests * update notebook * fix for when slopes are specified * specify constant flag * change ode_export to de_export * fix duplicated test name * try fixing sensitivity of final state with zero derivative and linear extrapolation * fix final value sensitivity inf in logscale * sensitivity with respect to plist * bugfix (C++ indexing is 0-based) * Spline example notebooks * remove leftover long output in notebook * Fixing typos in notebooks and adding symlink for docs * fix typo in spline C++ docstrings * add spline notebooks to documentation * Expensive tests only for merges to master * Remove redundant class - fixes SBML suite? * nb kernel * nb kernel * merge_group * cmake * ignore-glob * .. * .. * fo the minimal amount of work in notebooks when running in a Github action * split slow/fast spline tests * more relaxed tolerances on windows * try pip install in notebook * compute groundtruth only once per call to check_splines_full * add fides package to example notebook * precompute data for spline test * fix path * split pip pypesto and fide * use single core engine on github actions * even less work on Github actions * even less work whe running Github actions * fix unused folder argument * fix a possible edge case * fix problem with unique folders * maybe windows does not like long paths * Update python/sdist/amici/sbml_utils.py Co-authored-by: Daniel Weindl <[email protected]> * Update python/sdist/amici/sbml_utils.py Co-authored-by: Daniel Weindl <[email protected]> * Update python/sdist/amici/sbml_utils.py Co-authored-by: Daniel Weindl <[email protected]> * Update python/sdist/amici/sbml_utils.py Co-authored-by: Daniel Weindl <[email protected]> * Update src/splinefunctions.cpp Co-authored-by: Daniel Weindl <[email protected]> * Update python/sdist/amici/sbml_utils.py Co-authored-by: Daniel Weindl <[email protected]> * Update python/sdist/amici/sbml_utils.py Co-authored-by: Daniel Weindl <[email protected]> * Update python/sdist/amici/sbml_utils.py Co-authored-by: Daniel Weindl <[email protected]> * Update python/sdist/amici/sbml_utils.py Co-authored-by: Daniel Weindl <[email protected]> * Update python/sdist/amici/sbml_utils.py Co-authored-by: Daniel Weindl <[email protected]> * Update include/amici/abstract_model.h Co-authored-by: Daniel Weindl <[email protected]> * small changes * Update include/amici/abstract_model.h Co-authored-by: Daniel Weindl <[email protected]> * Update python/tests/splines_utils.py Co-authored-by: Daniel Weindl <[email protected]> * fix uuid * add python type hints * t_extrapolate * more docstrings * more type hints * more type hints * Update python/sdist/amici/sbml_utils.py Co-authored-by: Daniel Weindl <[email protected]> * mkdtemp * Update python/sdist/amici/sbml_utils.py Co-authored-by: Daniel Weindl <[email protected]> * docstring * docstrings * how to recompute precomputed results for spline tests * Update python/examples/example_splines/ExampleSplines.ipynb Co-authored-by: Daniel Weindl <[email protected]> * Update python/examples/example_splines/ExampleSplines.ipynb Co-authored-by: Daniel Weindl <[email protected]> * notebook suggestions * move spline plotting to library * add a more informative error when there are no converged starts in CI * splines in observables * No hack? * address Fabian's comments * finishing touches for assigning splines to species * more expressive argument names in splines.py * real-world spline examples using species assignment * fix non-refactored bits * update example notebook * more interesting errors * upgrade sympy? * dwdw needs the spline * revert debug changes * try more starts in github * Binder: update compilers * Revert "Binder: update compilers" This reverts commit 18b6210. * py311? * timeout=600 * Revert "py311?" This reverts commit 3e539db. * Revert "timeout=600" This reverts commit 4302eff. * DBG artifacts * Revert "DBG artifacts" This reverts commit 3c898bc. * conservation laws / assignment rules * notebook update * fix doc? * Revert "dwdw needs the spline" This reverts commit 4bef57a. * increase multistarts for swameye * Fix deprecation * Fix deprecation * remove assert * format * cleanup * cleanup * Apply suggestions from code review * Revert "Fix deprecation" This reverts commit 9eedc54. * Increase timeout --------- Co-authored-by: Lorenzo Contento <[email protected]> Co-authored-by: Daniel Weindl <[email protected]> Co-authored-by: Daniel Weindl <[email protected]>
Runs black, fixes line endings, ...
* pre-commit: sort imports / update contrib doc * sort imports * fix circular import
…ests (#2084) Fixes incorrect sensitivities for models with events with state-dependent trigger functions. Add three new event test cases and do some cleanup. Closes #2086 Co-authored-by: Paul Stapor <[email protected]>
I can't find any valid SBML model that has anything other than speciesReferences in listOfProducts/Reactants.
We have too many definitions of time ...
* add more swig ignores * Update amici.i * Update amici.i * Update amici.i * -s * 2304 * keep asserts * Update amici.i * Revert "2304" This reverts commit 2948382. * Revert "keep asserts" This reverts commit 3aa213b. * Revert "-s" This reverts commit 731cfc2. --------- Co-authored-by: Daniel Weindl <[email protected]>
* Test new PEtab model abstraction * Update .github/workflows/test_petab_test_suite.yml * Run v2.0.0 test suite * pysb models * .. * .. * .. * .. * libpetab-python.git@model_pysb * generalize fixed parameters * .. * .. * .. * .. * cleanup * cleanup * add support for species reinitialization in pysb * fixup preequilibration * fixup preequilibration pysb * fixup pysb import * prevent warnings? * move resolve mapping to petab lib, adapt to updated api * fix error message * fixup condition checks * suppress model warnings * fixup export issues * cleanup * fixup * fixup compartment * simplify * Fix NameError: name 'sbml_model' is not defined * ? * make pattern matching exact so we only assign single species * Update petab_import_pysb.py * .. * Revert ".." This reverts commit 02a4f24. * .. * deps * .. * Update test_benchmark_collection_models.yml * branch * Fix matplotlib conflict > The conflict is caused by: > The user requested matplotlib==3.5.3 > petab[vis] 0.2.0 depends on matplotlib>=3.6.0; extra == "vis" * merge? * e * .. * - libpetab-python.git@model_pysb * doc,cleanup * fix model name / dir * fixup, cleanup * cleanup; fixup merge * .. * pypi * pysb * .. * deps * pypi-petab * reqs --------- Co-authored-by: Fabian Fröhlich <[email protected]>
Only changing SWIG_EXECUTABLE will lead to inconsistent settings. Need to unset version and directory, so FindSWIG will try to set them according to SWIG_EXECUTABLE.
Fixes issues with paths containing blanks: `sh: line 1: C:/Program: No such file or directory` https://github.com/AMICI-dev/AMICI/actions/runs/5054632314/jobs/9069784824?pr=2104
Let CMake's FindBLAS try to find BLAS libraries in case the user didn't provide any other information via environment variables. Relates to #2103
... as this fails too often.
Fixes: `/home/runner/work/AMICI/AMICI/documentation/example_errors.ipynb:2262: WARNING: undefined label: /example_errors.ipynb#unsuccessful_factorization` Link was working until recently. Not sure what changed.
…forward sensitivities (#2108)
Codecov Report
Additional details and impacted files@@ Coverage Diff @@
## master #2115 +/- ##
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+ Coverage 75.56% 76.49% +0.92%
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Files 76 81 +5
Lines 13126 14857 +1731
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+ Hits 9919 11365 +1446
- Misses 3207 3492 +285
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let's wait for #2097, sorry missed submitting the review |
* Warn if ASA is used in combination with events. Co-authored-by: Fabian Fröhlich <[email protected]>
... except for one.
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SonarCloud Quality Gate failed. |
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