Feature cmaes #457
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Feature cmaes #457
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Release 0.2.0
yannikschaelte
requested review from
yannikschaelte,
jvanhoefer and
LeonardSchmiester
yannikschaelte
requested changes
Sep 8, 2020
Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com>
jvanhoefer
approved these changes
Sep 8, 2020
Codecov Report
@@ Coverage Diff @@
## develop #457 +/- ##
========================================
Coverage 91.06% 91.06%
========================================
Files 69 69
Lines 3971 3997 +26
========================================
+ Hits 3616 3640 +24
- Misses 355 357 +2
Continue to review full report at Codecov.
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yannikschaelte
approved these changes
Sep 9, 2020
LeonardSchmiester
approved these changes
Sep 14, 2020
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Complexity increasing per file
==============================
- test/test_optimize.py 1
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jvanhoefer
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Oct 5, 2020
* 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> * V 021 (#455) (#456) * 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> Co-authored-by: Jakob Vanhoefer <38346459+jvanhoefer@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: Fabian Fröhlich <fabian@schaluck.com> Co-authored-by: Paul Stapor <paul.stapor@helmholtz-muenchen.de> Co-authored-by: Thomas S. Ligon <tom@thomassligon.info> * Feature cmaes (#457) * 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 * updated version * updated version * updated version * updated version * updated version * fix flake8 Co-authored-by: Jakob Vanhoefer <38346459+jvanhoefer@users.noreply.github.com> Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> Co-authored-by: yannikschaelte <yannik.schaelte@gmail.com> * Plot convergence summary and update outdated notebook (#446) * update severely outdated example notebook * add convergence visualization * fix nans * fix flake * update docstring * use problem.get_reduced_vector * fix typehints + docstring * Update pypesto/visualize/optimizer_convergence.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * add to notebook, fix scale, add grad to vis test Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * fix type checks visualization reference points (#460) * fix for new amici release (#469) * fix for new amici release * update amici requirement * allow longer travis wait time Co-authored-by: yannikschaelte <yannik.schaelte@gmail.com> * fix arguments dlib (#466) (closes #465) * fix arguments ipopt * update docu minimize fct. * fix test_sbml_conversion.py Co-authored-by: Fabian Fröhlich <fabian@schaluck.com> * numpy based subindexing in amici_util (#462) * Update amici_util.py * add return doc * fixups * fix test * fix for non-unique par_opt_slice * reduce function complexity * add check for installation ipopt (#470) closes #468 Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> Co-authored-by: Fabian Fröhlich <fabian@schaluck.com> * check optional requirements amici/petab in PEtab import (#477) * add maxiter to Dlibs default options fixes #474 (#476) * add maxiter to Dlibs default options * Update pypesto/optimize/optimizer.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * fix flake8 Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * fix y_limits in waterfall plot for list of result objects (#475) * prepare v022 (#479) * prepare v022 * fix review suggestions * Fix merge conflicts (#481) * V 021 (#455) * 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> * fix flake8 Co-authored-by: Jakob Vanhoefer <38346459+jvanhoefer@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: Fabian Fröhlich <fabian@schaluck.com> Co-authored-by: Paul Stapor <paul.stapor@helmholtz-muenchen.de> Co-authored-by: Thomas S. Ligon <tom@thomassligon.info> 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> Co-authored-by: PhilippStaedter <42141163+PhilippStaedter@users.noreply.github.com> Co-authored-by: yannikschaelte <yannik.schaelte@gmail.com>
jvanhoefer
added a commit
that referenced
this pull request
Jan 18, 2021
* release v0.2.2 (#480) * 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> * V 021 (#455) (#456) * 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> Co-authored-by: Jakob Vanhoefer <38346459+jvanhoefer@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: Fabian Fröhlich <fabian@schaluck.com> Co-authored-by: Paul Stapor <paul.stapor@helmholtz-muenchen.de> Co-authored-by: Thomas S. Ligon <tom@thomassligon.info> * Feature cmaes (#457) * 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 * updated version * updated version * updated version * updated version * updated version * fix flake8 Co-authored-by: Jakob Vanhoefer <38346459+jvanhoefer@users.noreply.github.com> Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> Co-authored-by: yannikschaelte <yannik.schaelte@gmail.com> * Plot convergence summary and update outdated notebook (#446) * update severely outdated example notebook * add convergence visualization * fix nans * fix flake * update docstring * use problem.get_reduced_vector * fix typehints + docstring * Update pypesto/visualize/optimizer_convergence.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * add to notebook, fix scale, add grad to vis test Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * fix type checks visualization reference points (#460) * fix for new amici release (#469) * fix for new amici release * update amici requirement * allow longer travis wait time Co-authored-by: yannikschaelte <yannik.schaelte@gmail.com> * fix arguments dlib (#466) (closes #465) * fix arguments ipopt * update docu minimize fct. * fix test_sbml_conversion.py Co-authored-by: Fabian Fröhlich <fabian@schaluck.com> * numpy based subindexing in amici_util (#462) * Update amici_util.py * add return doc * fixups * fix test * fix for non-unique par_opt_slice * reduce function complexity * add check for installation ipopt (#470) closes #468 Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> Co-authored-by: Fabian Fröhlich <fabian@schaluck.com> * check optional requirements amici/petab in PEtab import (#477) * add maxiter to Dlibs default options fixes #474 (#476) * add maxiter to Dlibs default options * Update pypesto/optimize/optimizer.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * fix flake8 Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * fix y_limits in waterfall plot for list of result objects (#475) * prepare v022 (#479) * prepare v022 * fix review suggestions * Fix merge conflicts (#481) * V 021 (#455) * 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> * fix flake8 Co-authored-by: Jakob Vanhoefer <38346459+jvanhoefer@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: Fabian Fröhlich <fabian@schaluck.com> Co-authored-by: Paul Stapor <paul.stapor@helmholtz-muenchen.de> Co-authored-by: Thomas S. Ligon <tom@thomassligon.info> 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> Co-authored-by: PhilippStaedter <42141163+PhilippStaedter@users.noreply.github.com> Co-authored-by: yannikschaelte <yannik.schaelte@gmail.com> * fix dublicate * rerun github actions 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> Co-authored-by: PhilippStaedter <42141163+PhilippStaedter@users.noreply.github.com> Co-authored-by: yannikschaelte <yannik.schaelte@gmail.com>
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* saving visu spec * unnecessary imports removed Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com>
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Release 0.1.9 Library: * Allow URL as filenames for YAML files and SBML models (Closes #187) (#459) * Allow model time in observable formulas (#445) * Make float parsing from CSV round-trip (#444) * Validator: Error message for missing IDs, with line numbers. (#467) * Validator: Detect duplicated observable IDs (#446) * Some documentation and CI fixes / updates * Visualization: Add option to save visualization specification (#457) * Visualization: Column XValue not mandatory anymore (#429) * Visualization: Add sorting of indices of dataframes for the correct sorting of x-values (#430) * Visualization: Default value for the column x_label in vis_spec (#431)
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branch with integrated optimizer cma-es