AMICI: High-Performance Sensitivity Analysis for Large Ordinary Differential Equation Models

New features:

• Checking condition number when computing sensitivities via Newton by @FFroehlich in https://github.com/AMICI-dev/AMICI/pull/1730
• Removed SPBCG solver by @FFroehlich in https://github.com/AMICI-dev/AMICI/pull/1729
• Added Newton step convergence checks to steadystate solver by @FFroehlich in https://github.com/AMICI-dev/AMICI/pull/1737
• Removed legacy options/members amioption.newton_preeq and `Solver::r… by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1744
• Added ReturnData::cpu_time_total to track total time spent in runAmiciSimulation by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1743
• SBML import: Alternative algorithm for identifying conservation laws by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1748
• Use amici.AmiciVersionError to indicate version mismatch by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1764

Performance:

• Optional parallel computation of derivatives during model import by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1740
• Sparsify jacobian by @FFroehlich in https://github.com/AMICI-dev/AMICI/pull/1766
• Speedup for models with conservation laws by @FFroehlich in https://github.com/AMICI-dev/AMICI/pull/1765
• Speedup conservation law computation by @FFroehlich in https://github.com/AMICI-dev/AMICI/pull/1754
• Exploit stoichiometric matrix in pysb import by @FFroehlich in https://github.com/AMICI-dev/AMICI/pull/1761
• Speedup edata construction from petab problems by @FFroehlich in https://github.com/AMICI-dev/AMICI/pull/1746

Fixes:

• Fixed get_model_settings that would to setting incorrect initial states and initial state sensitivities for models with parameter-dependent initial states by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1751
• Use correct tolerances for convergence check in Newton solver by @FFroehlich in https://github.com/AMICI-dev/AMICI/pull/1728
• Harmonized convergence checks by @FFroehlich in https://github.com/AMICI-dev/AMICI/pull/1731
• Made sundials' KLU_INDEXTYPE match actual klu index type by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1733
• Fixed Model::setStateIsNonNegative logic that would raise exceptions in cases where it shouldn't by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1736
• Fixed undefined reference to dladdr by @kristianmeyerr in https://github.com/AMICI-dev/AMICI/pull/1738
• Fixed HDF5 OSX intermediate group creation errors by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1741
• Fixed recent cmake-based build issues due to changed sundials library directory by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1756
• Updated Windows installation instructions by @paulflang in https://github.com/AMICI-dev/AMICI/pull/1763

... and other contributions by @FFroehlich, @dweindl

Full Changelog: https://github.com/AMICI-dev/AMICI/compare/v0.11.26...v0.11.27