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parPE 0.4.1
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@dweindl dweindl released this 13 Dec 14:19
· 284 commits to master since this release
v0.4.1
1ce7004
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Learn about vigilant mode.
  • Update AMICI and disentangle parallel AMICI output during optimization and simulation (#204)
  • Autodeploy to dockerhub using github action (#205)
  • Improvements minibatch (#206) (https://www.biorxiv.org/content/10.1101/859884v1)
  • implemented changes from supermuc with fixes in minibatch rescue interceptor and line search algorithm
  • Use PEtab parameter prior for starting point sampling (#194)

Minor:

  • Explicitly enable oversubscription since we are using OpenMPI
  • Disentangle parallel AMICI output during optimization (Closes #202)
  • Update list of references
  • Fix model naming
  • Fix docker MPI issues
    • due to lack of SYS_PTRACE permissions (disable Vader) (Closes #185)
    • Disable Infiniband for OpenMPI
    • enable tcp via loopback
  • Set RelWithDebInfo as default build type
  • Update AMICI to v0.10.16 and PEtab v0.0.0a17 (#209)
  • Disable saving states and observables during optimization, as the current format does not support varying number of timepoints and crashes
  • Allow creation of virtual environment in the absence of ensurepip
  • Fix uninitialized usage warnings
  • Add Zenodo badge (Closes #189)
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