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parPE 0.4.4
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@dweindl dweindl released this 14 Oct 12:10
· 178 commits to master since this release
v0.4.4
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Learn about vigilant mode.
  • AMICI-related
    • Update to AMICI v0.11.2 (#295)
    • adjoint preequilibration
    • reduced memory requirements
    • Make proper use of amici::RDataReporting to avoid computing costly disregarded results (#296)
    • Add script / cmake target to update amici (Closes #288)
    • Handle AMICI failures more gracefully
    • Fix misc/rebuild_amici.sh in case of changed AMICI SWIG interface
  • Fix: HierarchicalOptimizationWrapper: Return full parameters and full gradient even if nothing computed analytically
  • Fix C++17 in CMakeLists template
  • Fix: Use absolute path in misc/setup_amici_model.sh
  • Fix PEtab import issues
  • Fix icpc option overriding warning (Closes #220)
  • Update example notebooks and run on github actions (#294)
  • Add CLI option to simulator to run simulations with nominal parameters (#293)
  • Various cleanup
    • #287, #285, #271, #270, #268, #267, and others
    • Remove obsolete parpeamici/steadystateSimulator.cpp
    • Remove outdated amiciHelper.py module for parsing AMICI source files
    • Remove all uses of std::tmpnam
  • Handle IpOpt reporting obj_value 0.0 in case of non-finite fval or gradient (#221)
  • Base image ubuntu:19.10 (EOL ubuntu:19.04)
  • adapt dataprovider and simulatio to df to third column in simulation condition table (#272)
  • Update gsllite (#269)
  • Fix petab import when online some measurements have preequilibrationCondition set
  • Add basic contribution guide
  • Fix race conditions in steadystate example (#265)
  • Cache sonar files on github actions
  • CI: No shallow clone for running sonarscanner
  • Remove obsolete and unreliabe functions parpe::launchedWithMpi and parpe::initMpiIfNeeded -- using MPI must be specified via CLI now
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