PetabJL integration #1089
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PetabJL integration #1089
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…ough manual pickling works
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❗ Your organization is not using the GitHub App Integration. As a result you may experience degraded service beginning May 15th. Please install the Github App Integration for your organization. Read more. @@ Coverage Diff @@
## develop #1089 +/- ##
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- Coverage 88.16% 84.48% -3.69%
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Files 79 148 +69
Lines 5257 11593 +6336
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+ Hits 4635 9794 +5159
- Misses 622 1799 +1177
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sebapersson
suggested changes
Jun 30, 2023
yannikschaelte
approved these changes
Jul 20, 2023
pypesto/objective/julia/petabJl.py
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| hess = self.petab_jl_problem.computeHessian | ||
| x_names = np.asarray(self.petab_jl_problem.θ_estNames) | ||
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| # call the super super constructor |
dweindl
reviewed
Jul 28, 2023
Merged
PaulJonasJost
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Oct 2, 2023
* Use cloudpickle for pickling dynesty sampler (#1094) Cloudpickle handles ABC-derived classes properly, whereas the latest dill version on pypi (0.3.6) does not. Cloudpickle is already installed with pypesto, so there seems to be no need to get dill on top. * Restrict fval magnitude in waterfall with order_by_id (#1090) * restrict waterfall with order_by_id to fvals < 1e100 * add constant for parameters/waterfall plot maximum value * Add startpoint_method to Problem (#1093) It's not intuitive that `x_guesses` is part of `Problem`, but `startpoint_method`s are handled separately. See also discussion in #1017. This patch * adds `startpoint_method` to `Problem` * during PEtab import, sets `Problem.startpoint_method` based on the PEtab problem * deprecates `startpoint_method` arguments where also `Problem` is passed Closes #1035 * Small initialize fix (#1095) Censoring bounds should not be reinitialized when calculators are reinitialized. * Added Falco et al to bib. (#1100) * fix storage (#1099) * Hierarchical parameter plot fix (#1106) * Fix parameter plot If, in any case (because some inner optimization failed, simulation failed, or some other reason) and there is a`optimize_result`dictionary in `result.optmize_result.list` which doesn't contain the `INNER_PARAMETERS` key and its item, the parameter plot would fail at line 381. This is a fix to make it robust to this. If any of the `optimize_result` objects has a `INNER_PARAMETER` key, then the other ones will be filled with NaN values, and plotted. * Dilan review change Co-authored-by: Dilan Pathirana <[email protected]> * Update pypesto/visualize/parameters.py Co-authored-by: Daniel Weindl <[email protected]> * Add comments * Add comment Testing the quality check * Fix quality check error --------- Co-authored-by: Dilan Pathirana <[email protected]> Co-authored-by: Daniel Weindl <[email protected]> * Fix startpoint sampling for hierarchical optimization (#1105) * Fix startpoint sampling for hierarchical optimization See #1096 * fixed pars * fixup --------- Co-authored-by: Doresic <[email protected]> * PetabJL integration (#1089) * SingleCore engine works, multicore has problems with pickling even though manual pickling works * intermediate commit * Working tests. * small changes needs verification * created base test to check for integration into python. * Added julia module file for test * Added test for objective function evaluation * Added values for evaluation * Added installation of packages to Workflow. * Readded the Julia files that for some reason were deleted. * Removed PetabJL from default pypesto.petab import * Temporariy added amici as dependency. Needs to be taken care of appropriately. * Moved Importer to objective/julia * Deactivated precompilation in test * Integrated suggestions * add comments * add sundials to ci --------- Co-authored-by: Yannik Schälte <[email protected]> * Fix #1108 (#1109) * enable setting the y limits of a waterfall plot by using the y_limits argument * use default y limits for zoomed in starts * fix #1108 Co-authored-by: Paul Jonas Jost <[email protected]> * SacessOptimizer: retry reading, delay deleting (#1110) * delete temporary files only after *all* were read successfully * retry reading temp file upon error to work around potential filesystem latency issues * SacessOptimizer: Fix logging with multiprocessing (#1112) * SacessOptimizer: Fix logging with multiprocessing * Fix: `ValueError: setting an array element with a sequence.` * Other platform tests (#1113) * blind attempt mac * brew installs * try python 3.11 numba * try windows * fix cache * stuff * stuff * stuff * stuff * minimal test * add basic workflow test * Update .github/workflows/ci.yml Co-authored-by: Daniel Weindl <[email protected]> * close figures --------- Co-authored-by: Daniel Weindl <[email protected]> * SacessOptimizer: tmpdir option (#1115) SacessOptimizer: * Add option to pass a custom directory for temporary files * Make the default temporary file paths unique, to avoid name collisions when running multiple SacessOptimizer instances from within the same working directory * Notebook on differences (#1098) * Notebook on differences * simplify some parts; add some more details and visualizations * minor edit * add workflow comparison to docs * integrated suggestions * integrated suggestions 2 * fixup * removed personal info. changed nlop objective appropriatly --------- Co-authored-by: Yannik Schälte <[email protected]> Co-authored-by: Yannik Schaelte <[email protected]> * Documentation fixes (#1120) * document hierarchical optimization sources; add aesara+jax to objective docs * document origin of the mh + pt samplers * fix typo * fix typo * Update pypesto/sample/parallel_tempering.py Typo * streamline doc deps * update setup req versions * try cyipopt fix * test * tesT * test * fix test_visualize::test_optimization_scatter_with_x_None * test * fixup --------- Co-authored-by: Paul Jonas Jost <[email protected]> * update changelog+version * Changed Codeowners and contact to accomodate changes in personell (#1123) * Updated version and Changelog (#1122) * Updated version and Changelog * Updated Changelog * Update CHANGELOG.rst --------- Co-authored-by: Daniel Weindl <[email protected]> Co-authored-by: Maren Philipps <[email protected]> Co-authored-by: Doresic <[email protected]> Co-authored-by: Polina Lakrisenko <[email protected]> Co-authored-by: Dilan Pathirana <[email protected]> Co-authored-by: Yannik Schälte <[email protected]> Co-authored-by: Yannik Schaelte <[email protected]>
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Broaden the usability of the Julia objective with a PEtab_jl objective, that is meant to be used for integration of PEtab.jl
The objective has the option to precompile its module which speeds the multiprocessing optimization up (as otherwise the module which is the time consuming part will always have to be reloaded). Currently if I run the code manually it works fine (even exact same code as the tests) but when running the tests it fails to precompile. So the precompilation is turned off in the tests.