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* Parameters plot, #418 (#425) * parameters plot, plotting a subset of parameters (#418) * "Variable used before assignment" fixed for parameters plot (#364) * Feature autocorrelation - close #251 (#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 <31767307+yannikschaelte@users.noreply.github.com> * docs * docs * grammar thingy * handle in get_data_to_plot in visu Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * fix display for least squares solver (#430) fix #429 * basic sanity checking for parameter fixing (#420) * basic sanity checking for parameter fixing * fixup type checks * fixup * fix typehints * fixup & refactor * update doc * fixup * Fix amici error output, fixes #427 (#428) * initial fix * add filter function * unify error and base initialization of return values * Profile options (#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 <31767307+yannikschaelte@users.noreply.github.com> * Prior Example, closes # 434 (#438) * Add notebook prior definition * fix sphinx * Update doc/example/prior_definition.ipynb Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * Update doc/example/prior_definition.ipynb Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * Update doc/example/prior_definition.ipynb Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * Update doc/example/prior_definition.ipynb Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * Update doc/example/prior_definition.ipynb Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * Update doc/example/prior_definition.ipynb Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * Update doc/example/prior_definition.ipynb Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * Update doc/example/prior_definition.ipynb Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * Update doc/example/prior_definition.ipynb Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * Improve notebook Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * Fix offset_y and scale_y in waterfal plot (#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 (#444) Co-authored-by: Thomas S. Ligon <tom@thomassligon.info> * Update priors.py (#448) * Fix optimization with priors (#452) * Update priors.py * Update priors.py * Fix PEtab import (Priors) (#454), closes #447 * bugfix + compliance to current PEtab version in prior import * resolve review + flake8 Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * prepare version 0.2.1 * Update doc/releasenotes.rst Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * Update doc/releasenotes.rst Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * Update doc/releasenotes.rst Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> Co-authored-by: Polina Lakrisenko <p.lakrisenko@gmail.com> Co-authored-by: Elba Raimúndez Alvarez <elba.raimundez@helmholtz-muenchen.de> Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> Co-authored-by: Fabian Fröhlich <fabian@schaluck.com> Co-authored-by: Paul Stapor <paul.stapor@helmholtz-muenchen.de> Co-authored-by: Thomas S. Ligon <tom@thomassligon.info>
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