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Setup docker image for use with charliecloud #182

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merged 17 commits into from
Oct 8, 2019
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@dweindl dweindl commented May 31, 2019

  • Create Dockerfile for generating parPE docker image
  • Documentation and examples
  • Document Snakemake workflow for model import, optimization, ...
  • Add schema file for Snakemake config file

Closes #180

@dweindl dweindl changed the title [WIP] Setup docker image for use with charliecloud Setup docker image for use with charliecloud Oct 8, 2019
@dweindl dweindl merged commit 3fe186d into develop Oct 8, 2019
@dweindl dweindl deleted the feature_charlie branch October 9, 2019 20:31
@dweindl dweindl mentioned this pull request Oct 9, 2019
dweindl added a commit that referenced this pull request 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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