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Release 0.2.4 #596
Release 0.2.4 #596
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* fix nlopt test by ignorance * make more readable
* added ensembles as sets of parameter vectors * add predictions for ensembles * add convenience functionality to ensembles and predictions (condense_to_arrays, compute_summary) * add documentation in conversion reactionn otebook, rerun notebook * add some convenience functionality for predictions from petab models * add visualization for parameter identifiability through ensembles Co-authored-by: Dilan Pathirana <59329744+dilpath@users.noreply.github.com>
* updated python script with not yet finished integration of cma-es optimizer * updated python script with not yet finished integration of cma-es optimizer * updated python script with not yet finished integration of cma-es optimizer * updated python script with not yet finished integration of cma-es optimizer * updated python script with not yet finished integration of cma-es optimizer * updated python script with not yet finished integration of cma-es optimizer * updated python script with not yet finished integration of cma-es optimizer * updated python script with not yet finished integration of cma-es optimizer * integration of cma-es optimizer * updated version * updated version * Update setup.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * updated version * updated version * updated version * updated version * updated version * updated version * updated version * updated version * updated version * updated version * not yet finished implementation of scipys differential evolution optimizer * not yet finished implementation of scipys differential evolution optimizer * not yet finished implementation of scipys differential evolution optimizer * updated version * updated version * uppdated version * uppdated version * updated version * updated version * updated version * updated version * updated version * updated version of travis.yml * updated version of travis.yml * more changes in optimizer.py * incorporation of two remarks in the file optimizer.py * first try to solve indentation error in optimizer.py * first try to solve indentation error in optimizer.py * fix docs * integrated scipy_differential_evolution_optimizer * updated scipy_differential_evolution_optimizer * integrated scipy_differential_evolution_optimizer * integrated scipy_differential_evolution_optimizer Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> Co-authored-by: yannikschaelte <yannik.schaelte@gmail.com> Co-authored-by: LeonardSchmiester <leonard.schmiester@helmholtz-muenchen.de> Co-authored-by: Paul Stapor <paul.stapor@helmholtz-muenchen.de>
Co-authored-by: Paul Stapor <paul.stapor@helmholtz-muenchen.de>
* fix ensemble identifiability plot if one or more categories are empty * add dimension reduction functionality via umap and pca * add visualizations for dimension reduction * rewrite reader and wrtier functions for ensembles and predictions to have an easier was to save ensemble predictions later one * add covariance matrix analysis code * add mltools to installation, as used for tests * make flake8 happy Co-authored-by: Dilan Pathirana <59329744+dilpath@users.noreply.github.com>
* added history saving and reading * updated read * test store history * test store history * pep8 standard * included hdf5_storage.ipynb * updated notebook * updated notebook * brought other history classes up to date with develop * added storge hdf5 notebook to example.rst * added storgae_hdf5 to toctree * updated docstring * removed history comment * added Hdf5History to tests * pep8 standard * remove TODOs and cleanup instance checks Co-authored-by: MerktSimon <simon.merkt@uni-bonn.de> Co-authored-by: FFroehlich <fabian@schaluck.com>
* fixup in chunk sizing and handng over of parameter mappings, fixes a bug which may yield to incorrect predictions if using of chunk size * allow passing on of umap parameters tothe umap routines * make user-defined fields of amici return data available to postprocessors Co-authored-by: Dilan Pathirana <59329744+dilpath@users.noreply.github.com>
* added MPIPoolEngine * updated to pep8 standard * Update pypesto/engine/mpi_pool.py Co-authored-by: Daniel Weindl <dweindl@users.noreply.github.com> * updated mpi pool engine * fixed init * Update pypesto/engine/mpi_pool.py Co-authored-by: Daniel Weindl <dweindl@users.noreply.github.com> * added example and a test * pep8 standard * added slurm example * Update doc/example/exampleBatchFile.slurm Co-authored-by: Daniel Weindl <dweindl@users.noreply.github.com> * first cleanup * added docstring and subprocess * small fix * changed test * changed test * pep8 standard * subprocess.run added * subprocess.run added * updated test * added terminal command to docstring of MPIPool * slight changes * updated to pep8 standard * added mpi4py installation * mpi4py installation in github workflow * added mpi4py to setup * mpi4py workflow installation II * mpi4py workflow installation III * mpi4py workflow installation IV * fixed typo * fixed typo II * Update pypesto/engine/mpi_pool.py Co-authored-by: Daniel Weindl <dweindl@users.noreply.github.com> * implemented suggestions * corrected os error * pep8 standard * used subprocess instead of os * flake8 standard * changed ci_push * Update ci_push.yml * Update test_optimize.py * Update test_optimize.py * Update example_MPIPool.py * Update test_optimize.py * Update test/optimize/test_optimize.py Co-authored-by: Daniel Weindl <dweindl@users.noreply.github.com> * Update test/optimize/test_optimize.py Co-authored-by: Daniel Weindl <dweindl@users.noreply.github.com> * Update test_optimize.py * Update example_MPIPool.py * removed MPEngine from example * Update test_optimize.py * Update test_optimize.py * Update example_MPIPool.py * added objective function to problem * pep8 standard * Dummy commit * Update test_optimize.py * Update test_optimize.py * Update pypesto/engine/mpi_pool.py Co-authored-by: Daniel Weindl <dweindl@users.noreply.github.com> * Update mpi_pool.py * Update mpi_pool.py Co-authored-by: Daniel Weindl <dweindl@users.noreply.github.com>
Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com>
* change gha to pr + master push * change to python 3.9 * rm ci_push * back to 3.8 until 3.9 fixed
Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> Co-authored-by: Fabian Fröhlich <fabian@schaluck.com>
* simplify doc build; add tox * fix tests * remove doc dep * fix typo * various fixes * more fixes * fix * try * test * reset * add pre-commit hooks, update contribution guide * apply pre-commits * fixup * fix quality test deps * remove restore-keys as not really hierarchical * tidy up pip deps * fix executables * address reviewer comments
* Added ProfileStorage test * Pep8 Standard * Added Profile/Sampling reader and writer to pypesto.store init * Added StorageSample Test * Pep8 Standard * Added suggestions. * Added suggestions. * Added suggestions II
* test * test * test * test * test * fix ipopt * quote github dep * fixup * add flaky rep * edit cache keys * add pre-commit test * test * simplify * fixup * optimize still weird * test separation * test * converge * fix mpi test * fix flake8
* Added read/write function for whole result. * Update pypesto/store/save_to_hdf5.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * Update pypesto/store/save_to_hdf5.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * Update test/base/test_store.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * Added suggestions * Added suggestions * Removed residues of AdaptiveParallelTemperingSampler * pep8 standard * add requirements-dev.txt (was .gitignored) Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> Co-authored-by: yannikschaelte <yannik.schaelte@gmail.com>
* fix slow waterfall plots * Update ci.yml Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com>
* fix ignored offset_y * fix indent * increase timeouts Co-authored-by: Paul Stapor <paul.stapor@helmholtz-muenchen.de>
* Calculate MCMC parameter/prediction CIs * Create ensembles from samples * Calculate and plot prediction uncertainties from ensembles * Customize output timepoints of AMICI objective * Parallelize ensemble predictions, with automatic batching Co-authored-by: Dilan Pathirana <59329744+dilpath@users.noreply.github.com> Co-authored-by: MerktSimon <simon.merkt@uni-bonn.de> Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com>
* update for fides 0.3.0 and make hybrid happ new default * fixup * reenable passing of None * fixup * increase timeouts * fix required fides * add better warning messages * adress review
* update changelog * update changelog * fix style Co-authored-by: Fabian Fröhlich <fabian_froehlich@hms.harvard.edu>
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👍
* update changelog * update changelog * fix style * Fix missing commits in changelog * fix rst Co-authored-by: Fabian Fröhlich <fabian_froehlich@hms.harvard.edu>
Codecov Report
@@ Coverage Diff @@
## main #596 +/- ##
===========================================
- Coverage 89.76% 34.96% -54.81%
===========================================
Files 78 91 +13
Lines 4632 5732 +1100
===========================================
- Hits 4158 2004 -2154
- Misses 474 3728 +3254
Continue to review full report at Codecov.
|
Ensembles/Sampling:
definition, parallelize ensemble predictions (Feature MCMC prediction confidence intervals - close #458 #490)
Optimization:
AMICI:
guess_steadystate
(More user-friendly default behaviour of AmiciObjective.guess_steadystate #562, Fix incorrect handling of AmiciObjective.guess_steadystate #582)Storage:
Engines:
Visualization:
CI:
Minor fixes (release notes Fix releasenotes closes #555 #558, nlop tests Fix nlopt optimization test by ignoring it #559, close files Close file descriptors of temporary files #495,
visualization waterfall plot start indices fix #554, deployment Deploy to pypi on publishing release #560, AMICI deepcopy Fixing test flakiness #570, flakiness Fixing test flakiness #570,
respect user-provided offsets Don't ignore user provided offset_y #576, update to SWIG 4 Update swig (minor) #591)