Extend, split, update steadystate example notebooks #171
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dweindl
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Oct 9, 2019
Release 0.4.0 * Enabled [Zenodo](https://zenodo.org/) integration * Update AMICI to 0.10.13 * Setup docker image for use with charliecloud (#182) * Cleanup misc/generateHDF5DataFileFromText.py, remove obsolete warning * Formatting * Update reference; add funding section to README * Add parPE logo (#195) * Show only interesting lines from /proc/self/status * Update FAQ * Disable building tests by default * CLI option to show supported optimizers (Closes #169) * Enable CLI starting point index selection for OptimizationApplication * Add script to read final parameter vectors from parPE (multi-start) optimization result file and write to TSV file * Add AMICI version and script invocation to generated hdf5 file * Add gradient check to snakefile * Fix: Ensure rdata->numstepsB has elements before access (segfault with forward sensitivities) * Fix parameter indexing for generating example data * Add doc/README.md * Document HDF5 output file format (Closes #175) * Add worfklow figure * Add ../doc/petab_model_import.md describing PEtab model import (Closes #168) * Pass H5File as const&, not as Id which will implicitely call H5File which requires HDF5 mutex locking. * Extend, split, update steadystate example notebooks (#171) * Ensure hdf5 mutex lock when using AMICI hdf5 helper functions (Closes #167) * Keep fixed parameters out of /parameters/parameterNames in HDF5 file, which should only contain optimization parameters * Update readme: Add coinhsl instructions * Fix HDF5 file generation after PEtab update: do not add AMICI fixed parameters to optmization parameters * Add scaffold for generation of LoadLeveler job files * Add snakemake scaffold for PEtab...analysis * Update PEtab parameter mapping to allow for condition specific scaling etc. * Update benchmark collection scripts, add Snakefile * Add basic data analysis Snakefile * Update plotting functions and example notebook * Use condition-specific parameter scales (#161) * Remove obsolete test files * Remove cpputest remnants * Update Ipopt install script to 3.12.12, cleanup * Remove work-around for non-threadsafe adjoints * Gradient check tolerance relative to objective function values to reduce number of test failures (Closes #80) * Reenable CERES parameter_tolerance option * PEtab: Add support for non-constant parameter overrides in condition table (Closes #158); support non-gaussian noise * Use HDF5 C++ interface; cleanup.
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