Release 0.4.0

[dweindl]

• Update AMICI to 0.10.13
• Setup docker image for use with charliecloud (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 (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 CLI option to show supported optimizers #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 Document HDF5 output file format #175)
• Add worfklow figure
• Add ../doc/petab_model_import.md describing PEtab model import (Closes Document / add example for PEtab import and setup  #168)
• Pass H5File as const&, not as Id which will implicitely call H5File which requires HDF5 mutex locking.
• Extend, split, update steadystate example notebooks (Extend, split, update steadystate example notebooks #171)
• Ensure hdf5 mutex lock when using AMICI hdf5 helper functions (Closes Segfaults during HDF5 access with parallel optimization runs due to parallel HDF5 access #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 (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 Improve gradient checker #80)
• Reenable CERES parameter_tolerance option
• PEtab: Add support for non-constant parameter overrides in condition table (Closes PEtab: Add support for non-constant parameter overrides in condition table #158); support non-gaussian noise
• Use HDF5 C++ interface; cleanup.