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Release 0.2.4 #596

Merged
merged 31 commits into from
Mar 17, 2021
Merged

Release 0.2.4 #596

merged 31 commits into from
Mar 17, 2021

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yannikschaelte
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jvanhoefer and others added 30 commits January 20, 2021 13:37
* 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>
…ate (#562)

If supported, enable `guess_steadystate` by default. If not supported, disable by default. If requested but unsupported, raise.

Status quo was confusing to users, see e.g. #440

Co-authored-by: Fabian Fröhlich <fabian@schaluck.com>
indentation error / unreachable code
* 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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👍

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FFroehlich commented Mar 17, 2021

Couple of PRs seem to be missing in release notes: #561, #556, #572 (I think this was misassigned to #570), #589.

@yannikschaelte
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Thanks, #561 was missing, #556 is an issue (I guess #566 was meant), #572 misassigned, #589 missing. Fixed in #597.

* update changelog

* update changelog

* fix style

* Fix missing commits in changelog

* fix rst

Co-authored-by: Fabian Fröhlich <fabian_froehlich@hms.harvard.edu>
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Codecov Report

Merging #596 (2f31e0e) into main (a34608d) will decrease coverage by 54.80%.
The diff coverage is 25.74%.

Impacted file tree graph

@@             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     
Impacted Files Coverage Δ
pypesto/objective/aggregated.py 25.49% <0.00%> (-74.51%) ⬇️
pypesto/optimize/__init__.py 100.00% <ø> (ø)
pypesto/petab/importer.py 0.00% <0.00%> (-81.76%) ⬇️
pypesto/visualize/waterfall.py 14.63% <0.00%> (-79.20%) ⬇️
pypesto/store/save_to_hdf5.py 18.96% <6.25%> (-42.80%) ⬇️
pypesto/objective/amici.py 20.32% <6.81%> (-71.25%) ⬇️
pypesto/visualize/ensemble.py 10.16% <10.16%> (ø)
pypesto/visualize/misc.py 13.18% <11.11%> (-71.75%) ⬇️
pypesto/visualize/sampling.py 10.89% <12.42%> (-67.74%) ⬇️
pypesto/ensemble/ensemble.py 12.90% <12.90%> (ø)
... and 99 more

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@yannikschaelte yannikschaelte merged commit 625c419 into main Mar 17, 2021
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