Run simulations with json I/O #400
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Adds an executable to evaluate the objective function and its gradient based on parameters provided in a JSON file. The output will be written to another JSON file. This makes it easier to compare specific simulation results to some other tool.
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## What's Changed ### Features * Updated AMICI to v0.29.0 which comes with many new features and bug fixes (by @dweindl in #412) * Added support for support for forward sensitivities (by @dweindl in #393) * Use amici default options in generated HDF5 input files (by @dweindl in #392, #406) * Set python package version via setuptools_scm (by @dweindl in #395) * PEtab import: option to ignore initialization prior (by @dweindl in #402) * Added scaffold for objective function / gradient evaluation with JSON I/O (by @dweindl in #400) ### Fixes * Fixed data race in aggregateLikelihood (by @dweindl in #411) * PEtab pipeline: * Fixed potentially incorrect initial state from condition table (by @dweindl in #408) * Fail on problems using priors (they aren't supported and never have been) (by @dweindl in #384) * Only compute sensitivities with respect to optimized parameters (by @dweindl in #394) * HDF5 generation: Don't write obsolete sens_ind (by @dweindl in #407) * Reduced clang warnings (by @dweindl in #397) **Full Changelog**: v0.4.10...v0.5.0
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Adds an executable to evaluate the objective function and its gradient based on parameters provided in a JSON file. The output will be written to another JSON file. This makes it easier to compare specific simulation results to some other tool.