Tags: stephanmg/AMICI
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Release 0.11.18 Merge pull request AMICI-dev#1531 from AMICI-dev/release_0.11.18
Release 0.11.17 Merge pull request AMICI-dev#1511 from AMICI-dev/release_0.11.17
Merge pull request AMICI-dev#1491 from AMICI-dev/release_0_11_16 Release 0.11.16
Release 0.11.15 Merge pull request AMICI-dev#1482 from AMICI-dev/release_0.11.15
Release 0.11.14 Merge pull request AMICI-dev#1466 from AMICI-dev/release_0.11.14
Release 0.11.13 (Merge pull request AMICI-dev#1431 from AMICI-dev/rel… …ease_0.11.13) Breaking changes: * AMICI requires Python>=3.7 * Updated package installation (PEP517/518): Creating source distributions requires https://github.com/pypa/build (AMICI-dev#1384) (but now handles all package building dependencies properly) Features: * More flexible state reinitialization (AMICI-dev#1417) Updated dependencies: * Upgrade to sundials 5.7.0 (AMICI-dev#1392) Fixes: * Python: account for heaviside functions in expressions (AMICI-dev#1382) * Python: allow loading of existing models in import_petab_problem (AMICI-dev#1383) * Python: Don't override user-provided compiler/linker flags (AMICI-dev#1389) * Python: PEtab import reinitialization fixes (AMICI-dev#1417) * Python: Fix PEtab observables for pysb models (AMICI-dev#1390) * Python: Substitute expressions in event condition expressions (AMICI-dev#1404) * Python: Unspecified initial states in PEtab conditions table default to SBML initial value (AMICI-dev#1397) * C++: Fix timepoint out of bounds access (AMICI-dev#1402) * C++: Fix exported CMake config (AMICI-dev#1388) * Fixed Dockerfile: add python3-venv (AMICI-dev#1398, AMICI-dev#1408) Other: * Slim exported swig interface (AMICI-dev#1425) * Updated documentation * Getting started tutorial (AMICI-dev#1423) * List supported SBML test tags (AMICI-dev#1428) * Add AMICI C++/Python/Matlab feature comparison (AMICI-dev#1409) * ... * Various minor CI improvements * ...
Merge pull request AMICI-dev#1381 from AMICI-dev/release_0_11_12 Release 0.11.12 Features: * Add expression IDs and names to generated models (AMICI-dev#1374) Fixes: * Raise minimum sympy version to 1.7.1 (Closes AMICI-dev#1367) * Fix species assignment rules in reactions (AMICI-dev#1372) * Fix id vector for DAEs (AMICI-dev#1376) Docs: * Update how-to-cite (AMICI-dev#1378)
Release 0.11.11 (AMICI-dev#1363) * Fix: Don't require code context for call stack (fixes AMICI-dev#1347) (AMICI-dev#1348) * Fix Intel compiler warnings (AMICI-dev#1349) 'type qualifier on return type is meaningless' Closes AMICI-dev#1346 * Avoid segfault in CVODES CVAdataStore (AMICI-dev#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 (AMICI-dev#1354) Closes AMICI-dev#1350 Removes obsolete .travis.yml * Fix cxxcode import for SymPy 1.6 (AMICI-dev#1356) * Piecewise to heaviside (AMICI-dev#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 <fabian@schaluck.com> * Update python/amici/ode_export.py Co-authored-by: Fabian Fröhlich <fabian@schaluck.com> * Update python/amici/ode_export.py Co-authored-by: Fabian Fröhlich <fabian@schaluck.com> * Update python/amici/ode_export.py Co-authored-by: Fabian Fröhlich <fabian@schaluck.com> * Update python/amici/ode_export.py Co-authored-by: Fabian Fröhlich <fabian@schaluck.com> * Update python/amici/sbml_import.py Co-authored-by: Fabian Fröhlich <fabian@schaluck.com> * 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 <dweindl@users.noreply.github.com> * document and simplify _collect_heaviside_roots * address review comments * reduce complexity * misplaced docstrings Co-authored-by: Fabian Fröhlich <fabian@schaluck.com> Co-authored-by: dilpath <dilan.private+github@outlook.com> Co-authored-by: Daniel Weindl <dweindl@users.noreply.github.com> * restore support for species references (AMICI-dev#1358) * restore support for species references * fixup and improve error message * extend support for sbml functions (AMICI-dev#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 (AMICI-dev#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 <fabian@schaluck.com> * CI: Show all compiler warnings and treat as error (AMICI-dev#1362) * CI: Show all compiler errors and treat as error Closes AMICI-dev#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 (AMICI-dev#1360) * Add support for different noise models for PySB import .. as already the case for SBML import. Closes AMICI-dev#1176 * Respect noise model selection for PySB-PEtab import (AMICI-dev#1339) * doc, import * Respect observable transformation for PySB-PEtab import (Fixes AMICI-dev#1339) * Set ODEModel._has_quadratic_nllh Co-authored-by: Fabian Fröhlich <fabian@schaluck.com> * version bump * fix some code smells to trigger GHA builds again? * update docker to 20.04 * pin breathe Co-authored-by: Daniel Weindl <dweindl@users.noreply.github.com> Co-authored-by: Lorenzo Contento <lcontento@users.noreply.github.com> Co-authored-by: Paul Stapor <paul.stapor@helmholtz-muenchen.de> Co-authored-by: dilpath <dilan.private+github@outlook.com>
Merge pull request AMICI-dev#1343 from AMICI-dev/release_0_11_10 Release 0.11.10
Merge pull request AMICI-dev#1340 from AMICI-dev/release_0_11_9 Release 0.11.9
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