Parameters plot, #418 #425
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## develop #425 +/- ##
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- Coverage 91.28% 91.15% -0.14%
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Files 68 68
Lines 3854 3865 +11
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+ Hits 3518 3523 +5
- Misses 336 342 +6
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paulstapor
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Jul 6, 2020
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| Parameters | ||
| ---------- | ||
| x_full: array_like, ndim=1 | ||
| The vector in dimension dim_full. | ||
| x_indices: | ||
| indices of x_full that should remain |
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Very good that you added that the full vector is meant! This can always be a little confusing...
| legends: Optional[Union[str, List[str]]] = None, | ||
| balance_alpha: bool = True, | ||
| start_indices: Optional[Union[int, Iterable[int]]] = None | ||
| ) -> matplotlib.axes.Axes: |
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Thanks for the proper type hints here and everywhere! 👍
pypesto/visualize/parameters.py
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| colors: list, or RGBA, optional | ||
| list of colors, or single color | ||
| colors: | ||
| list of RGBA colors, or single RGBA color | ||
| color or list of colors for plotting. If not set, clustering is done |
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I think the first part of this line is redundant. 🙃
| parameter_indices: | ||
| Specifies which parameters should be plotted. Allowed string values are | ||
| 'all' (both fixed and free parameters will be plotted) and | ||
| 'free_only' (only free parameters will be plotted) |
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Cool feature. Was using hacks in PESTO back then to have precisely this functionality...
test/visualize/test_visualize.py
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| reference=ref_point, | ||
| balance_alpha=False, | ||
| start_indices=(0, 1, 4)) | ||
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| visualize.parameters([result_1, result_2], | ||
| free_indices_only=True, | ||
| parameter_indices='all', |
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I think here it should be 'free_only'...
Would be good to us in the above example a list of indices, to also have the new functionality checked.
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Oh, you're right, thanks!
FFroehlich
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Jul 6, 2020
| def parameters( | ||
| results: Union[Result, Sequence[Result]], | ||
| ax: Optional[matplotlib.axes.Axes] = None, | ||
| parameter_indices: Union[str, Sequence[int]] = 'free_only', |
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Suggested change
| parameter_indices: Union[str, Sequence[int]] = 'free_only', | |
| parameter_indices: Union[Literal['all','free_only'], Sequence[int]] = 'free_only', |
Literal can be imported from typing, see https://www.python.org/dev/peps/pep-0586/.
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But only starting python 3.8, right?
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Looks like. Currently, pyPESTO is >=3.6. We could move to 3.8, but as long as e.g. anaconda still defaults to 3.7, I would not be too restrictive.
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Good point, probably shouldn't be changed yet to keep backwards compatibility.
LeonardSchmiester
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Jul 14, 2020
* prepare v0.2.0 (#417) * prepare v020 * Update doc/releasenotes.rst * limit pymc3 + arviz versions in setup.py * 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> 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: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com>
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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>
yannikschaelte
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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> 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>
yannikschaelte
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* 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>
jvanhoefer
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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> * 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>
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* 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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