restore support for species references #1358
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dweindl
approved these changes
Dec 9, 2020
Codecov Report
@@ Coverage Diff @@
## develop #1358 +/- ##
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+ Coverage 79.32% 79.46% +0.14%
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Files 62 62
Lines 10620 10782 +162
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+ Hits 8424 8568 +144
- Misses 2196 2214 +18
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FFroehlich
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Dec 15, 2020
* Fix: Don't require code context for call stack (fixes #1347) (#1348) * Fix Intel compiler warnings (#1349) 'type qualifier on return type is meaningless' Closes #1346 * Avoid segfault in CVODES CVAdataStore (#1351) Does not fix the root cause of occassional segfaults, but turns them into exceptions / integration failues. * CI: Move windows tests from TravisCI to GitHub Actions (#1354) Closes #1350 Removes obsolete .travis.yml * Fix cxxcode import for SymPy 1.6 (#1356) * Piecewise to heaviside (#1352) * 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 (#1358) * restore support for species references * fixup and improve error message * extend support for sbml functions (#1357) * 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 (#1361) * 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 warnings and treat as error (#1362) * 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 (#1360) * 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]> * version bump * fix some code smells to trigger GHA builds again? * update docker to 20.04 * pin breathe Co-authored-by: Daniel Weindl <[email protected]> Co-authored-by: Lorenzo Contento <[email protected]> Co-authored-by: Paul Stapor <[email protected]> Co-authored-by: dilpath <[email protected]>
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