PEtab import: Add option for treating fixed parameters as constants #1877
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Makes the changes from #1810 optional, as sometimes users prefer more flexible models. The default is to treat non-estimated parameters in PEtab as constants in AMICI.
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Additional details and impacted files@@ Coverage Diff @@
## develop #1877 +/- ##
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+ Coverage 75.51% 75.82% +0.30%
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Files 74 74
Lines 12882 12895 +13
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+ Hits 9728 9777 +49
+ Misses 3154 3118 -36
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dweindl
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Oct 26, 2022
dweindl
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Oct 26, 2022
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* Fix pandas groupby deprecation warning (#1873) Fixes #1872 * Update reference list (#1874) * Code printing: Use SymPy C99 math optimizations (#1377) for SBML import. Does not currently work with PySB import. Also fixes some argument type issues. Co-authored-by: Daniel Weindl <daniel.weindl@helmholtz-muenchen.de> * PEtab import: Add option for treating fixed parameters as constants (#1877) Makes the changes from #1810 optional, as sometimes users prefer more flexible models. The default remains to treat non-estimated parameters in PEtab as constants in AMICI. Also adds a basic check for loading existing models during PEtab, to see if they are compatible to what was supposed to be imported. Only checks non-constant parameter IDs so far. * Make sympy code optimizations optional (#1878) Turns out that applying sympy optimizations as introduced in #1377 is potentially very costly. Therefore, they are disabled by default. They can be enabled by setting `AmiciCxxCodePrinter.optimizations` as shown in the test case. * Update reference list (#1884) * GHA: update actions (#1885) Fixes some GHA warnings. * Add macos hdf5 header/library paths (#1894) * Doxygen 1.9.5 on RTD (#1889) Older binaries are no longer available. * Code-gen: Fix missing `return` in non-void-returning functions (#1892) ... and set `-Werror` for compiling models in debug mode. * Add operator== for ExpData (#1881) Adds `operator==` for `amici::ExpData` and fixes issues for other `operator==` in case of NaNs in arrays. Closes #1880 * Fix SetuptoolsDeprecationWarning (#1893) Setuptools meanwhile requires listing data directories as subpackages. Fixes #1888. * Dockerfile: Update base image to Ubuntu 22.04 (#1896) * GHA: Pin python version for osx tests (#1891) Fixes #1890. Also: * use homebrew boost version * fix CMake logic for selecting a specific Python version. * Fix `petab_import.import_model(..., compile=False)` failure (#1897) Fixes a bug where amici would fail importing an extension that was never built. * bump version, update changelog * fix changelog * -Wno-error=deprecated-declarations Co-authored-by: Daniel Weindl <dweindl@users.noreply.github.com> Co-authored-by: Lorenzo Contento <lcontento@users.noreply.github.com> Co-authored-by: Daniel Weindl <daniel.weindl@helmholtz-muenchen.de> Co-authored-by: Doresic <85789271+Doresic@users.noreply.github.com>
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Makes the changes from #1810 optional, as sometimes users prefer more flexible models.
The default remains to treat non-estimated parameters in PEtab as constants in AMICI.
Also adds a basic check for loading existing models during PEtab, to see if they are compatible to what was supposed to be imported. Only checks non-constant parameter IDs so far.