Release 0.4.1 #1235
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Release 0.4.1 #1235
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* Extended scatter search documentation * Changed `get_default_ess_options` to default to fides for local optimization instead of no local optimizer * Added a wrapper for fides to forward walltime and function evaluation limits
Fixes
```
test/sample/test_sample.py: 542 warnings
pyPESTO/pypesto/sample/geweke_test.py:202: DeprecationWarning: Conversion of an array with ndim > 0 to a scalar is deprecated, and will error in future. Ensure you extract a single element from your array before performing this operation. (Deprecated NumPy 1.25.)
alpha2[idxs[i]] = alpha2[idxs[i]] / (
```
Fixes #1207
#1218) …ptions: maxfun * Use the correct option for setting the maximum number of function evaluations for each scipy optimizer. Closes #970 Note that this changes the default settings for some optimizers for which `maxfun` has so far been ignored. * Reenable tests for scipy `trust-constr` and `dogleg` optimizers, closes #613
The recent flake8 fails with `pypesto/objective/amici/amici.py:624:33: B026 Star-arg unpacking after a keyword argument is strongly discouraged, because it only works when the keyword parameter is declared after all parameters supplied by the unpacked sequence, and this change of ordering can surprise and mislead readers.` Fixed here.
* Closes #1164. Error due to amici not being able to compute initial jacobian paired with scipy bad error handling. Happens max 1:1e3 times. Therefore currently rerun the test. * Decrease flake to 2 for random encounters, and additionally add checked startpoints.
and some other formatting issues. Co-authored-by: Paul Jonas Jost <[email protected]>
* documentation * typehints * simplify Co-authored-by: Paul Jonas Jost <[email protected]>
…ts.py (#1223) And remove redundant / contradictory types from docstrings
* Updated Citation * Update README.md Co-authored-by: Daniel Weindl <[email protected]> --------- Co-authored-by: Daniel Weindl <[email protected]>
…_polynomial` (#1226) There seems to be an indexing error in `pypesto.profile.profile_next_guess.get_reg_polynomial`, resulting in too few points being used for extrapolating parameter trajectories. In the second case, not only too few, but also not the most recent parameter values are used. Closes #1224
* Warnings for scipy and laplace prior. * Returned develop changes. * Update pypesto/optimize/optimizer.py Co-authored-by: Daniel Weindl <[email protected]> --------- Co-authored-by: Daniel Weindl <[email protected]>
* Updated docstring on history module * Apply suggestions from code review Co-authored-by: Daniel Weindl <[email protected]> * Updated references --------- Co-authored-by: Daniel Weindl <[email protected]>
* Updated docstring for engine module. * Removed unnecessary import * Apply suggestions from code review Co-authored-by: Daniel Weindl <[email protected]> --------- Co-authored-by: Daniel Weindl <[email protected]>
* Julia caching more efficient. * Continue cachin tox and cache * Permission only to julia job. * moved caching before dependecie installation * explicitly load PyCall, since it seems to not be installed correctly. * Added Julia to all extra options. * Caching Pythin before julia installation due to conflicts arising with PyCall.
Codecov ReportAttention:
❗ Your organization needs to install the Codecov GitHub app to enable full functionality. Additional details and impacted files@@ Coverage Diff @@
## main #1235 +/- ##
==========================================
+ Coverage 84.10% 84.19% +0.08%
==========================================
Files 148 148
Lines 11799 11865 +66
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+ Hits 9924 9990 +66
Misses 1875 1875 ☔ View full report in Codecov by Sentry. |
Fixes a bug where `Ensemble.from_optimization_endpoints` would raise `TypeError: 'NoneType' object is not subscriptable` when processing the result of an optimization that failed at the initial point.
* Renaming and update CODEOWNERS Updated CODEOWNERS with the nonlinear monotone stuff. Renamed the examples everywhere * Update example.rst --------- Co-authored-by: Paul Jonas Jost <[email protected]>
* Update Changelog and Version. * Update Changelog. * Add another codeownership change --------- Co-authored-by: Doresic <[email protected]> Co-authored-by: Doresic <[email protected]>
PaulJonasJost
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dweindl,
FFroehlich,
m-philipps,
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burn_in_by_sequential_geweke#1217, Fix flake8 warning #1219)Hdf5History.from_history()#1211)pypesto.profile.profile_next_guess.get_reg_polynomial(Fix incorrect indexing in `pypesto.profile.profile_next_guess.get_reg… #1226)