Data

Tools

Indexes

Applications

Experiments

Open Source Science

Recent Releases of parpe

parpe - parPE 0.7.0

What's Change

  • Updated amici to v0.31.0 by @dweindl in https://github.com/ICB-DCM/parPE/pull/420
  • Fixed an issue in the Dockerfile

Full Changelog: https://github.com/ICB-DCM/parPE/compare/v0.6.0...v0.7.0

- C++
Published by dweindl over 1 year ago

parpe - parPE 0.6.0

## What's Changed

  • Update container files by @dweindl in https://github.com/ICB-DCM/parPE/pull/414
    • activate parpe python environment by default
    • avoid unnecessary full rebuilds when modifying Dockerfile
  • Updated amici to v0.30.1 by @dweindl in https://github.com/ICB-DCM/parPE/pull/417
  • Fixed potential issues with MPI_Finalize being called from ~OptimizationApplication

Full Changelog: https://github.com/ICB-DCM/parPE/compare/v0.5.0...v0.6.0

- C++
Published by dweindl over 1 year ago

parpe - 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 https://github.com/ICB-DCM/parPE/pull/412)
  • Added support for support for forward sensitivities (by @dweindl in https://github.com/ICB-DCM/parPE/pull/393)
  • Use amici default options in generated HDF5 input files (by @dweindl in https://github.com/ICB-DCM/parPE/pull/392, https://github.com/ICB-DCM/parPE/pull/406)
  • Set python package version via setuptools_scm (by @dweindl in https://github.com/ICB-DCM/parPE/pull/395)
  • PEtab import: option to ignore initialization prior (by @dweindl in https://github.com/ICB-DCM/parPE/pull/402)
  • Added scaffold for objective function / gradient evaluation with JSON I/O (by @dweindl in https://github.com/ICB-DCM/parPE/pull/400)

Fixes

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

Full Changelog: https://github.com/ICB-DCM/parPE/compare/v0.4.10...v0.5.0

- C++
Published by dweindl over 1 year ago

parpe - parPE 0.4.10

What's Changed

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

Full Changelog: https://github.com/ICB-DCM/parPE/compare/v0.4.9...v0.4.10

- C++
Published by dweindl over 2 years ago

parpe - parPE 0.4.9

What's Changed

  • Improved hierarchical optimization preprocessing by @dweindl in https://github.com/ICB-DCM/parPE/pull/366
  • Updated AMICI to v0.11.23 by @dweindl in https://github.com/ICB-DCM/parPE/pull/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: https://github.com/ICB-DCM/parPE/compare/v0.4.8...v0.4.9

- C++
Published by dweindl over 4 years ago

parpe - 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: https://github.com/ICB-DCM/parPE/compare/v0.4.7...v0.4.8

- C++
Published by dweindl over 4 years ago

parpe - 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)

- C++
Published by dweindl almost 5 years ago

parpe - 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)
  • ...

- C++
Published by dweindl almost 5 years ago

parpe - 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

- C++
Published by dweindl about 5 years ago

parpe - 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/setupamicimodel.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

- C++
Published by dweindl over 5 years ago

parpe - 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 BUILDTESTS by auto-provided BUILDTESTING

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 gtestdiscovertests. Raise CMake requirement. (#253) * Run PEtab test suite (#244) * Run python package tests via CTest * Tests with steadystate example to pytest

- C++
Published by dweindl about 6 years ago

parpe - 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 PARPENUMSIMULATIONTRIALS and PARPEINTEGRATIONTOLERANCERELAXATION_FACTOR
  • CMake: enable use of PACKAGE_ROOT
  • Minor fixes

- C++
Published by dweindl over 6 years ago

parpe - parPE 0.4.1

  • 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)

- C++
Published by dweindl over 6 years ago

parpe - parPE 0.4.0

  • Enabled Zenodo integration
  • Update AMICI to 0.10.13
  • 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 (#195)
  • Show only interesting lines from /proc/self/status
  • Update FAQ
  • Disable building tests by default
  • CLI option to show supported optimizers (Closes #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 #175)
  • Add worfklow figure
  • Add ../doc/petabmodelimport.md describing PEtab model import (Closes #168)
  • Pass H5File as const&, not as Id which will implicitely call H5File which requires HDF5 mutex locking.
  • Extend, split, update steadystate example notebooks (#171)
  • Ensure hdf5 mutex lock when using AMICI hdf5 helper functions (Closes #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 (#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 #80)
  • Reenable CERES parameter_tolerance option
  • PEtab: Add support for non-constant parameter overrides in condition table (Closes #158); support non-gaussian noise
  • Use HDF5 C++ interface; cleanup.

- C++
Published by dweindl over 6 years ago

parpe - v0.3.2

Changes to previous version:

  • Extended and updates documentation
  • Extended and updates example notebooks
  • Fixed parallel HDF5 file access bugs
  • Fixed outdated paths

- C++
Published by dweindl almost 7 years ago

parpe - v0.3.1

  • PEtab: Add support for non-constant parameter overrides in condition table (Closes #158); support non-gaussian noise
  • Updated minibatch optimizer
  • Updated AMICI (now with sundials 4.xx)
  • Support for shared-memory parallel adjoint sensitivity analysis
  • Replace cpputest by googletest
  • Add tests
  • Various bugfixes
  • Refactoring, cleanup

- C++
Published by dweindl about 7 years ago

parpe - v0.3.0

Change pipeline to use PEtab data format.

Added support for preequilibration, replicates, numeric parameter overrides, fixed parameters.

Fixed various smaller issues. Cleanup. Documentation.

- C++
Published by dweindl about 7 years ago

parpe - parPE 0.2.0

  • Added mini-batch optimizer
  • ...
  • Updated AMICI to 0.8.2
  • Automated generation of example code (now requires AMICI Python package)
  • Major cleanup

- C++
Published by dweindl over 7 years ago