Release 0.14.0 #1898
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Release 0.14.0 #1898
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for SBML import. Does not currently work with PySB import. Also fixes some argument type issues. Co-authored-by: Daniel Weindl <[email protected]>
…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.
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.
Fixes some GHA warnings.
Older binaries are no longer available.
... and set `-Werror` for compiling models in debug mode.
Adds `operator==` for `amici::ExpData` and fixes issues for other `operator==` in case of NaNs in arrays. Closes #1880
Setuptools meanwhile requires listing data directories as subpackages. Fixes #1888.
Fixes #1890. Also: * use homebrew boost version * fix CMake logic for selecting a specific Python version.
Codecov Report
Additional details and impacted files@@ Coverage Diff @@
## master #1898 +/- ##
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+ Coverage 75.55% 75.78% +0.23%
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Files 74 75 +1
Lines 12877 12913 +36
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+ Hits 9729 9786 +57
+ Misses 3148 3127 -21
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v0.14.0 (2022-11-23)
Features:
Added optional functionality to apply C99 math optimization to generated C++ code
by @dweindl and @lcontento in Use SymPy simple floating-point optimizations #1377, Make sympy code optimizations optional #1878
Added option to treat fixed parameters as constants in PEtab import
by @dweindl in PEtab import: Add option for treating fixed parameters as constants #1877
Added equality operator for ExpData
by @dweindl in Add operator== for ExpData #1881
Updated base image for Dockerfile to Ubuntu 22.04/Python 3.10
by @dweindl in Dockerfile: Update base image to Ubuntu 22.04 #1896
Fixes:
Fixed deprecation warnings
by @dweindl in Fix pandas groupby deprecation warning #1873, Fix SetuptoolsDeprecationWarning #1893
Fixes/updates to GitHub actions
by @dweindl in GHA: update actions #1885, Fix SetuptoolsDeprecationWarning #1893, Doxygen 1.9.5 on RTD #1889, GHA: Pin python version for osx tests #1891
Added hdf5 search directories for arm64 architecture (M1/M2 macs)
by @Doresic in Add macos hdf5 header/library paths #1894
Fixed missing return in generated non-void functions
by @dweindl in Code-gen: Fix missing
returnin non-void-returning functions #1892Fixed import failure for pre-compiled models
by @dweindl in Fix
petab_import.import_model(..., compile=False)failure #1897Documentation:
by @dweindl in Update reference list #1874, Update reference list #1884
Full Changelog:
v0.13.0...v0.14.0