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Release 0.4.0 #201

Merged
merged 21 commits into from
Oct 9, 2019
Merged

Release 0.4.0 #201

merged 21 commits into from
Oct 9, 2019

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dweindl
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@dweindl dweindl commented Oct 9, 2019

  • 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.

dweindl and others added 21 commits June 18, 2019 13:28
…ptimization result file and write to TSV file
git subrepo clone (merge) --branch=v0.10.10 --force git@github.com:ICB-DCM/AMICI.git deps/AMICI

subrepo:
  subdir:   "deps/AMICI"
  merged:   "b39a39f8"
upstream:
  origin:   "git@github.com:ICB-DCM/AMICI.git"
  branch:   "v0.10.10"
  commit:   "b39a39f8"
git-subrepo:
  version:  "0.4.0"
  origin:   "https://github.com/ingydotnet/git-subrepo"
  commit:   "5d6aba9"

Update AMICI requirement
* Add parPE logo

* Add github social logo
…B-DCM/AMICI.git deps/AMICI

subrepo:
  subdir:   "deps/AMICI"
  merged:   "8875a646"
upstream:
  origin:   "git@github.com:ICB-DCM/AMICI.git"
  branch:   "v0.10.12"
  commit:   "8875a646"
git-subrepo:
  version:  "0.4.0"
  origin:   "https://github.com/ingydotnet/git-subrepo"
  commit:   "5d6aba9"
subrepo:
  subdir:   "deps/AMICI"
  merged:   "9e7f2ff1"
upstream:
  origin:   "git@github.com:ICB-DCM/AMICI.git"
  branch:   "develop"
  commit:   "9e7f2ff1"
git-subrepo:
  version:  "0.4.0"
  origin:   "https://github.com/ingydotnet/git-subrepo"
  commit:   "5d6aba9"
* 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

Details:
* Add basic Dockerfile adapted from ci image

* Cleanup image, allow mpi as root in docker, update deprecated apt options

* Disable valgrind on docker build

* Basic charliecloud example doc

* Add Snakemake config file schema and validate

* Add documentation stub on using snakemake optimization workflow

* cleanup

* Update base image to Ubuntu19

* Update install_parpe.sh

* Fix >2 arguments to run_in_venv.sh

* Add snakemake as parPE python package requirement

* Add example for optimizing a PEtab model using the parPE docker image and charliecloud
Closes #197

* git subrepo pull (merge) --branch=v0.10.13 deps/AMICI

subrepo:
  subdir:   "deps/AMICI"
  merged:   "76162dfc"
upstream:
  origin:   "git@github.com:ICB-DCM/AMICI.git"
  branch:   "v0.10.13"
  commit:   "76162dfc"
git-subrepo:
  version:  "0.4.0"
  origin:   "https://github.com/ingydotnet/git-subrepo"
  commit:   "5d6aba9"

* Update python package AMICI requirement
@dweindl dweindl merged commit 96d889a into master Oct 9, 2019
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