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parPE 0.4.0
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@dweindl dweindl released this 09 Oct 21:24
· 296 commits to master since this release
v0.4.0
96d889a
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Learn about vigilant mode.
  • Enabled Zenodo 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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