Release 0.11.11 #1363
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Release 0.11.11 #1363
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'type qualifier on return type is meaningless' Closes #1346
Does not fix the root cause of occassional segfaults, but turns them into exceptions / integration failues.
Closes #1350 Removes obsolete .travis.yml
* parse piecewise into heaviside functions * Add Events as model quantity, parse Heavisides slightly differently * bugfix * rename symbols of root to h and switch order of functions to make sure h is known when dxdotdx_explicit is generated, to have the header file of h included * rename root symbols to HeavisideFunction_ to have things more indicative * tell AMICI about root, stau, and deltasx functions * heavisides without sensitivities should be working * need to change generation of stau to generration via inverse function theorem * compute stau via inverse function theorem * added functionality for deltasx, but segfaulting * bugfixing * remove debug output * get indentations right * Update python/amici/ode_export.py Co-authored-by: Fabian Fröhlich <[email protected]> * Update python/amici/ode_export.py Co-authored-by: Fabian Fröhlich <[email protected]> * Update python/amici/ode_export.py Co-authored-by: Fabian Fröhlich <[email protected]> * Update python/amici/ode_export.py Co-authored-by: Fabian Fröhlich <[email protected]> * Update python/amici/ode_export.py Co-authored-by: Fabian Fröhlich <[email protected]> * Update python/amici/sbml_import.py Co-authored-by: Fabian Fröhlich <[email protected]> * add a test for trajectories * fix sroot and test * cosmetic * add analytical expressions for sensitivities * add test for a complex condition * add test for many conditions * fix test * improve documentation * rename tests and refactor test for iterated piecewise, to check SBML piecewise logic a bit further * cleanup for code review * further cleanup * quarter way done with parsing heavisides into piecewise * fix logic parsing * monkeypatch sympy printer * enable more tests * implement denesting of piecewise * fix SBML nonsense * fix boolean triggers * simplify logic checks * fix code smells * add events to variable prototypes * cleanup * report details for skipped tests durin GHA run * better skip printing * resubstitution of non-optimized RHS into stau * add sensitivity tests * refactor tests * remove skipping display code * update test stats * Update python/amici/ode_export.py * Apply suggestions from code review Co-authored-by: Daniel Weindl <[email protected]> * document and simplify _collect_heaviside_roots * address review comments * reduce complexity * misplaced docstrings Co-authored-by: Fabian Fröhlich <[email protected]> Co-authored-by: dilpath <[email protected]> Co-authored-by: Daniel Weindl <[email protected]>
* restore support for species references * fixup and improve error message
* add more function mappings * fixup min/max * fix rem * add Mod to unsupported functions * more trigonometric functions * more functions, fix xref * fix xref with init assignment * extend unsupported functions * fix plus with empty arguments, update statistics * update test stats * fix stats
* Refactor: introduce import_utils.py To collect format-independent functions for model import. * add additional file to SBML Testsuite path check * Include new module in doc Co-authored-by: Fabian Fröhlich <[email protected]>
* CI: Show all compiler errors and treat as error Closes #1167 * Fix unused arguments * Fix deprecated-copy * Fix NVector (non-)const mess * Fix CMake deprecation warning * Fix doxygen * Fix some typos * Simplify / reduce number of const_casts
* Add support for different noise models for PySB import .. as already the case for SBML import. Closes #1176 * Respect noise model selection for PySB-PEtab import (#1339) * doc, import * Respect observable transformation for PySB-PEtab import (Fixes #1339) * Set ODEModel._has_quadratic_nllh Co-authored-by: Fabian Fröhlich <[email protected]>
Codecov Report
@@ Coverage Diff @@
## master #1363 +/- ##
==========================================
+ Coverage 78.46% 78.77% +0.31%
==========================================
Files 62 63 +1
Lines 9797 9933 +136
==========================================
+ Hits 7687 7825 +138
+ Misses 2110 2108 -2
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