Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
* fix(CI) ignore multiple @param sections warning for the time being, fixes #504 (#505) * fix(CI) ignore multiple @param sections warning for the time being, fixes #504 * Update scripts/run-doxygen.sh Co-Authored-By: FFroehlich <[email protected]> * Feature state reduction using conservation laws (#492) * feature(python) implement computation of conservation laws for pysb models. * feature(core) separate nx_solver and nx_rdata * fix(tests) refresh pregenerated models + bugfixes * fix(matlab) fixes #491 * fix(tests) update and regenerate main.cpp * fix(tests) bugfixes * [WIP] commit current changes to update from head * feature(core) fix symbolic computations, regenerate pregenerated models, extend Model * fix(cpp) fix include for copy_n * fix(doc) add missing documentation * fix(matlab) fix compiler version string processing * fix(core) fix storage of x0 and sx0 post preequilibration/simulation * fix(cpp) fix typo * fix(CI) fix coverage generation * fix(python) fix model import for models that use sympy reserved names as component name * fix(python) fix conservation law computation for degradation rules with delete_molecules not set * feature(CI) add pysb model testcase with delete_molecules=True * Update include/amici/rdata.h Co-Authored-By: FFroehlich <[email protected]> * Update include/amici/vector.h Co-Authored-By: FFroehlich <[email protected]> * Update python/amici/ode_export.py Co-Authored-By: FFroehlich <[email protected]> * fix typo * Update python/amici/ode_export.py Co-Authored-By: FFroehlich <[email protected]> * fix typo * feature(CI) add additional pysb model tests * Update src/model.cpp Co-Authored-By: FFroehlich <[email protected]> * fix(doc) add more documentation to remove_typedefs * fix(doc) update comment and add some const specifiers * fix(python) fix raise exception when computing conservation laws involving muiltiple compartments * fix(CI) fix pysb SelfExporter cleanup and skip earm_1_3 example in python <=3.6 * fix(CI) fix module loading issues * feature(CI) add unittests for AmiVector(Array) * feature(python) move reversion of chainrule factor to cpp and reenable setInitialState(Sensitivities) for models with conservation laws * fix(cpp) remove deprecated code pieces * fix(cpp) refactor and fix user-specified x0 and sx0 * feature(CI) add additional tests for preequilibration models * fix(CI) fix coverage script * fix(CI) fix the coverage script for good * fix(cpp) fix incorrect sensitivities for preequilibration * feature(steadystate) use klu_refactor instead of always factoring de … (#513) * feature(steadystate) use klu_refactor instead of always factoring de novo, fixes #421 * fix(steadystate) remove erroneous bracket * Feauture automated deployment (#511) * feature(CI) bump version number * feature(CI) add script for automated deployment + travis configuration * fix(CI) readd comments to travis.yml * fix(CI) remove deprecated comments, hopefully fixes travis being stuck * fix(CI) fix indentation in travis.yml * Check positivity of sigmas from fsigmay (Closes #512). Free checking functions. Cleanup. * fix(python) Set parameter names when converting constant species to parameters * Reduce logsize (#521) * feature(CI) silence BNGL download (2.5k lines) * Create SlsMat wrapper so we don't need custom dtor, copyctr in Model (Closes #516) * Replace std::exchange (is C++14) * Get rid of newmat calls, make ctor explicit * Don't throw when (not) creating empty matrix * Fix doxygen doc * Show swig/modelname.template.i in IDE * Add Model::setAllStatesNonNegative() * Add option to check for finiteness of all Model::f* outputs (Closes #514) * Check if we have pysb before accessing pysb.core.Component * ode_export.py: don't create empty switch-cases during c++ code generation (closes #481) * Fix ExampleSteadystate notebook * Fix doxygen doc * Various bugfixes (#510) * fix(python) fix processing of conservation law construction with fixed initial conditions this cannot be tested yet as fixed initial conditions is not in the pysb master branch yet * fix(CI) extend ccpcheck to header files, fixes #503, fix all style/performance issues that came up * fix(CI) refactor SBML testsuite, fixes #502 * fix(python) implement check for unsupported functions * feature(python) add version string to compiled versions, fixes #509, * fix(core) bugfixes after ccpcheck changes * Update include/amici/model.h Co-Authored-By: FFroehlich <[email protected]> * fix(CI) change getAmiciVersion to getAmiciCommit and regenerate test models * fix(core) cleanup ExpData interface * feature(python) extend list of forbidden functions to include piecewise * fix(core) fixes edata interface * fix(CI) fix cppcheck issues * fix(core) fix dimension initialization in ExpData * fix(core) fix edata dimensions and piecewise function class * fix(doc) make stray variables in amici private and update documentation pdf * fix(steadystate) fix int fractions * fix(core) move sundials wrapper initializations to initializer list * fix(core) no = in initializer list * Fix include * Cleanup Model. Extract abstract methods. All implementations to cpp file. Cleanup include. Fix format and doc. * fix(Matlab) Add new source file to matlab source list * clang-format * fix(swig) Sneak in fix for Warning 401: Base class ignored * fix(core) Virtual dtor for abstract_model * ci(travis) Fold script section outputs * test * Feature better conservation laws (#520) * feature(python) we can and should implement conservation laws for monomers with only one species * feature(python) choose conservation laws such that the generated fill in is minimal * feature(python) finish work on fill-in minimization and refactor pysb_import such that public API is more evident * fix(doc) update documentation * fix(python) fix possible index computation, make ODEModel_from_pysb_importer public * fix(python) fix conservation law computation * fix(python) remove deprecated code, add some explanatory comments for future improvements * fix(doc) fix documentation, remove outdated pdf file * Update python/amici/pysb_import.py Co-Authored-By: FFroehlich <[email protected]> * Update python/amici/ode_export.py Co-Authored-By: FFroehlich <[email protected]> * fix(doc) remove return doc for function without return * fix(python) optimize get_appearance_counts * Better newton solver debugging and error messages (#527) * fix(steadystateproblem) extend ReturnData::newton_numsteps such that simulation does not overwrite newton results * fix(python) update newton_numsteps dimension * fix(steadystateproblem) better error propagation, fixes #508 * Update src/steadystateproblem.cpp Co-Authored-By: FFroehlich <[email protected]> * fix(steadystateproblem) replace int index with enum * feature(CI) split osx build into deploy and test mode * fix(CI) fix yml syntax * fix(CI) missed one space * fix(CI) extend nbconvert timeout and only run lcov when coverage is enabled * fix(python) fix codacy issues (#530)
- Loading branch information
1 parent
dce9bbc
commit cd7a15e