V 021 (ICB-DCM#455)

* Parameters plot, ICB-DCM#418 (ICB-DCM#425)

* parameters plot, plotting a subset of parameters (ICB-DCM#418)
* "Variable used before assignment" fixed for parameters plot (ICB-DCM#364)

* Feature autocorrelation - close ICB-DCM#251 (ICB-DCM#426)

* autocorrelation calculation by sokal

* docs

* notebook using ess

* added ess and ac in result

* created ess calculation

* rename variable

* docs

* fix

* remove print from test

* parameter index in 1d marginal plot

* added type

* added type

* docu

* flake8

* Update pypesto/sample/diagnostics.py

Co-authored-by: Yannik Schälte <[email protected]>

* docs

* docs

* grammar thingy

* handle in get_data_to_plot in visu

Co-authored-by: Yannik Schälte <[email protected]>

* fix display for least squares solver (ICB-DCM#430)

fix ICB-DCM#429

* basic sanity checking for parameter fixing (ICB-DCM#420)

* basic sanity checking for parameter fixing

* fixup type checks

* fixup

* fix typehints

* fixup & refactor

* update doc

* fixup

* Fix amici error output, fixes ICB-DCM#427 (ICB-DCM#428)

* initial fix

* add filter function

* unify error and base initialization of return values

* Profile options (ICB-DCM#419)

* change profile indexing to parameter indices instead of boolean indexing

* adapt also approximation and test to new profile api

Co-authored-by: Yannik Schälte <[email protected]>

* Prior Example, closes # 434 (ICB-DCM#438)

* Add notebook prior definition

* fix sphinx

* Update doc/example/prior_definition.ipynb

Co-authored-by: Yannik Schälte <[email protected]>

* Update doc/example/prior_definition.ipynb

Co-authored-by: Yannik Schälte <[email protected]>

* Update doc/example/prior_definition.ipynb

Co-authored-by: Yannik Schälte <[email protected]>

* Update doc/example/prior_definition.ipynb

Co-authored-by: Yannik Schälte <[email protected]>

* Update doc/example/prior_definition.ipynb

Co-authored-by: Yannik Schälte <[email protected]>

* Update doc/example/prior_definition.ipynb

Co-authored-by: Yannik Schälte <[email protected]>

* Update doc/example/prior_definition.ipynb

Co-authored-by: Yannik Schälte <[email protected]>

* Update doc/example/prior_definition.ipynb

Co-authored-by: Yannik Schälte <[email protected]>

* Update doc/example/prior_definition.ipynb

Co-authored-by: Yannik Schälte <[email protected]>

* Improve notebook

Co-authored-by: Yannik Schälte <[email protected]>

* Fix offset_y and scale_y in waterfal plot (ICB-DCM#441)

* Correct offset_y for waterfall plots of result lists

* enforce y_limits which show whole data when plotting result lists, if no explicit user input was given

* fix nans and infs, deal with possibly different number of optiimzation runs in different result objects

* fix 2 typos (ICB-DCM#444)

Co-authored-by: Thomas S. Ligon <[email protected]>

* Update priors.py (ICB-DCM#448)

* Fix optimization with priors (ICB-DCM#452)

* Update priors.py

* Update priors.py

* Fix PEtab import (Priors) (ICB-DCM#454), closes ICB-DCM#447

* bugfix + compliance to current PEtab version in prior import

* resolve review + flake8

Co-authored-by: Yannik Schälte <[email protected]>

* prepare version 0.2.1

* Update doc/releasenotes.rst

Co-authored-by: Yannik Schälte <[email protected]>

* Update doc/releasenotes.rst

Co-authored-by: Yannik Schälte <[email protected]>

* Update doc/releasenotes.rst

Co-authored-by: Yannik Schälte <[email protected]>

Co-authored-by: Polina Lakrisenko <[email protected]>
Co-authored-by: Elba Raimúndez Alvarez <[email protected]>
Co-authored-by: Yannik Schälte <[email protected]>
Co-authored-by: Fabian Fröhlich <[email protected]>
Co-authored-by: Paul Stapor <[email protected]>
Co-authored-by: Thomas S. Ligon <[email protected]>

Merge pull request ICB-DCM#416 from ICB-DCM/develop

Release 0.2.0

Merge pull request ICB-DCM#387 from ICB-DCM/develop

Release 0.1.0

Merge pull request ICB-DCM#305 from ICB-DCM/develop

Release 0.0.13

Merge pull request ICB-DCM#264 from ICB-DCM/develop

Release 0.0.12

Merge pull request ICB-DCM#229 from ICB-DCM/develop

Release 0.0.11

Merge pull request ICB-DCM#202 from ICB-DCM/develop

Release 0.0.10

Merge pull request ICB-DCM#187 from ICB-DCM/develop

Release 0.0.9

Merge pull request ICB-DCM#181 from ICB-DCM/develop

Release 0.0.8

Merge pull request ICB-DCM#161 from ICB-DCM/develop

Release 0.0.7