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Release 0.4.4#297

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dweindl merged 51 commits intomasterICB-DCM/parPE:masterfrom developICB-DCM/parPE:developCopy head branch name to clipboardOct 14, 2020

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Commits

Commits on Apr 4, 2020

• Remove obsolete and unreliabe functions parpe::launchedWithMpi and parpe::initMpiIfNeeded

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Commits on Apr 5, 2020

• Cleanup parpe::AnalyticalParameterHdf5Reader::getOptimizationParameterIndices

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• CI: No shallow clone for running sonarscanner

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• Remove outdated docs dataFormatForHDF5generation.md

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• Remove obsolte codacy.yml codacy configuration

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• Cache sonar files on github actions

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• Fix race conditions in steadystate example (#265)

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• Add basic contribution guide

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• Fix petab import when online some measurements have preequilibrationCondition set

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• Cleanup (#267)

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• Verious cleanup (#268)

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• Update gsllite (#269)

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• Cleanup (#270)

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• Remove outdated example example_steadystate_parallel

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Commits on Apr 12, 2020

• Misc cleanup (#271)

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Commits on Apr 20, 2020

• adapt dataprovider and simulatio to df to third column in simulation condition table (#272)

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Commits on Apr 23, 2020

• git subrepo pull (merge) --branch=develop deps/AMICI

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Commits on Apr 24, 2020

• git subrepo commit (merge) deps/AMICI

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• git subrepo pull (merge) --branch=develop deps/AMICI (#275)

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• git subrepo commit (merge) deps/AMICI

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• Merge branch 'develop' into update_amici

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• Merge pull request #276 from ICB-DCM/update_amici

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Commits on Apr 25, 2020

• Base image ubuntu:19.10 (EOL ubuntu:19.04)

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Commits on Apr 28, 2020

• Update to AMICI 1b74f554795784074e8a1b6ee75bec3086f7203a (#282)

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Commits on May 13, 2020

• Update Amici v0.11 (#283)

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Commits on May 16, 2020

• Handle AMICI failures more gracefully

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• Handle IpOpt reporting obj_value 0.0 in case of non-finite fval or gradient (#221)

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Commits on Jun 15, 2020

• Update AMICI (> 0.11.1) (#286)

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• Misc cleanup (#285)

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• Remove outdated amiciHelper.py module for parsing AMICI source files

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• Remove obsolete parpeamici/steadystateSimulator.cpp

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Commits on Jun 16, 2020

• Various cleanup (#287)

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• Add script / cmake target to update amici (Closes #288)

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Commits on Jun 17, 2020

• Update AMICI: Fix steadystate sim (#290)

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Commits on Jun 22, 2020

• git subrepo clone --branch=develop --force [email protected]:ICB-DCM/AMICI.git deps/AMICI (#291)

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Commits on Jun 24, 2020

• Add CLI option to simulator to run simulations with nominal parameters (#293)

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• Remove all uses of std::tmpnam

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• Update example notebooks and run on github actions (#294)

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• Fix icpc option overriding warning (Closes #220)

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Commits on Jul 13, 2020

• Fix PEtab import issues

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Commits on Jul 14, 2020

• Fix misc/rebuild_amici.sh in case of changed AMICI SWIG interface

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• Fix segfault in case of empty amici::ReturnData::numsteps

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• Make proper use of amici::RDataReporting to avoid computing costly disregarded results (#296)

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Commits on Jul 16, 2020

• Fix: Use absolute path in misc/setup_amici_model.sh

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• Fix C++17 in CMakeLists template

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Commits on Jul 19, 2020

• Update to AMICI v0.11.2 (featuring adjoint preequilibration) (#295)

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Commits on Jul 21, 2020

• Fix: HierarchicalOptimizationWrapper: Return full parameters and full gradient even if nothing computed analytically

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Commits on Jul 27, 2020

• Fix: Don't access AMICI rdata->x with non-full reporting mode

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Commits on Oct 13, 2020

• CI: GHA: pull_request, workflow_dispatch

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• Doc: Use m2r from fork

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Commits on Oct 14, 2020

• CI: Replace deprecated GHA ::set-env and ::add-path

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