parPE 0.5.0

What's Changed

Features

• Updated AMICI to v0.29.0 which comes with many new features and bug fixes (by @dweindl in #412)
• Added support for support for forward sensitivities (by @dweindl in #393)
• Use amici default options in generated HDF5 input files (by @dweindl in #392, #406)
• Set python package version via setuptools_scm (by @dweindl in #395)
• PEtab import: option to ignore initialization prior (by @dweindl in #402)
• Added scaffold for objective function / gradient evaluation with JSON I/O (by @dweindl in #400)

Fixes

• Fixed data race in aggregateLikelihood (by @dweindl in #411)
• PEtab pipeline:
  • Fixed potentially incorrect initial state from condition table (by @dweindl in #408)
  • Fail on problems using priors (they aren't supported and never have been) (by @dweindl in #384)
  • Only compute sensitivities with respect to optimized parameters (by @dweindl in #394)
  • HDF5 generation: Don't write obsolete sens_ind (by @dweindl in #407)
• Reduced clang warnings (by @dweindl in #397)

Full Changelog: v0.4.10...v0.5.0

parPE 0.4.10

What's Changed

• Updated AMICI to v0.20.0 by @dweindl in #378
• Replaced pthreads by C++ thread/mutex/condition by @dweindl in #363
• Added minibatch documentation to RTD by @dweindl in #375
• Dockerfile now uses Ubuntu22.04 and clang by default by @dweindl in #376 #374
• Added CITATION.cff by @dweindl in #379
• setup.py -> pyproject.toml by @dweindl in #381

Full Changelog: v0.4.9...v0.4.10

parPE 0.4.9

What's Changed

• Improved hierarchical optimization preprocessing by @dweindl in #366
• Updated AMICI to v0.11.23 by @dweindl in #369
• Added --flatten to parpe_petab_to_hdf5 as workaround for timepoint-specific output parameters by @dweindl
• Enabled ninja-based builds by @dweindl

Full Changelog: v0.4.8...v0.4.9

parPE 0.4.8

What's Changed

• Updated AMICI to v0.11.19 (#357)
• Documentation of mini-batch optimizers (#355)
• Docker image now comes with fides optimizer (#356)
• Docker image can now be imported by singularity (#289)
• Added option to specify maximum number of threads for multi-start optimization (#361)

New dependency: Boost.Thread

Full Changelog: v0.4.7...v0.4.8

parPE 0.4.7

• Updated AMICI to v0.11.18
• Fix PEtab import: HDF5 generation for state reinitialization with estimated initial conditions (#344)
• Fix race condition with parallel HDF5 calls with some HDF5 versions (#345)

parPE 0.4.6

• New optimizer ttps://github.com/dweindl/fides-cpp (C++ rewrite of https://github.com/fides-dev/fides) (#340)
• Updated to AMICI 0.11.17
• Updated DLIB optimizer interface (#337)
• Updated build scripts
• Fixed issues with C++17 compatibility of Intel Compiler (#334)
• ...

parPE 0.4.5

• Update to AMICI 0.11.13 (#321)
• Enable state-wise reinitialization for PEtab import (#306)
• Fix random test failures for MPI simulator runs
• Improved gradient-check (#315, #320, #314)
• CMake: Find MPI (#318)
• Update to Ceres 2.0.0 (#316)
• Create proper CMake package configuration (#313)
• Upgrade Ipopt and find via pkgconfig (#310)
• Don't replace INF timepoints by 1e8 during HDF5 generation
• Update and fix snakemake workflow
• Update documentation (#323, #322)
• Various smaller fixed
• Cleanup

parPE 0.4.4

• 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

parPE 0.4.3

Library

• Update to current PEtab
• Save more metadata in simulator result file (#259)
• More informative output for hierarchical optimization (Closes #210) (#255)
• Update to AMICI v0.10.21 and petab 0.1.7 (#261)
• Fix: Handle paths with blanks in build scripts (Fixes #246)
• Remove old example models lucarelli and raia (Closes #215)
• Misc fixups
• Cleanup build system, e.g. replace redundant CMake option BUILD_TESTS by auto-provided BUILD_TESTING

Documentation

• Update documentation, now created with sphinx/breeze/exhale and available at https://readthedocs.org/projects/parpe/ (#249) (#251)

CI

• Use Github actions instead of shippable (#256)
• Set up sonarcloud for static code analysis (#254)
• Various fixes (#258) (#236)
• Better integration of google tests in ctest using gtest_discover_tests. Raise CMake requirement. (#253)
• Run PEtab test suite (#244)
• Run python package tests via CTest
• Tests with steadystate example to pytest

parPE 0.4.2

• Improve parallel scaling by better message handling
• Remove unreliable auto-detection of launch via mpi launcher, use --mpi instead
• Allow setting integration retries / tolerance relaxation via environment variables PARPE_NUM_SIMULATION_TRIALS and PARPE_INTEGRATION_TOLERANCE_RELAXATION_FACTOR
• CMake: enable use of PACKAGE_ROOT
• Minor fixes