Release 0.10.0 #271
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Release 0.10.0 #271
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* fix two regularly stochastically failing tests * add explanation * add scaled pdf norm * fix wrong branch * fix errors * fixup
* add scaled pdf norm * add tests for scaled pdf norm * update __init__s
* add first petab import draft * allow arbitrary prior distributions * extend gitignore, flake8 excludes * parameters: subclass dict directly instead of UserDict (possible in python 3, and to ensure compatibility with python 3.8 * add StochasticKernel to __init__ * add extras_require petab-amici * tidy up petab import; fix namings * add petab, amici to travis reqs * test * install amici dependencies * run petab notebook * adapt nb * add ScaledPDFNorm * create base PEtabImporter * cont * tidy up petab notebook * set "zero transition density" info to debug level * ignore amici_models * add tests for petab * fixup * fix minor errors * fix .travis.yml * update version and releasenotes for 0.10.0 * rerun petab notebook * add petab notebook to docs * address reviewer comments * fix typo * tidy up .gitignore * tidy up
yannikschaelte
requested review from
EmadAlamoudi,
elbaraim and
JanHasenauer
and removed request for
JanHasenauer
Codecov Report
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## master #271 +/- ##
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Coverage ? 83.48%
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Files ? 88
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Hits ? 4060
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EmadAlamoudi
approved these changes
Feb 19, 2020
* use develop branches of amici, petab * shorten travis times * fix future warnings * test * test * gridsearchcv: explicit arguments * test * test * test
* find last id of successful run in the database * address reviewer comments * address additional reviewer comments * flake8 fix Co-authored-by: Yannik Schälte <[email protected]>
* Feature listpopulationsize (#274) * Init ListPopulation ListPopulation provides user definded population sizes which are comitted using a list. It's implementation follows the ListEpsilon case. List must have as many entries as populations are to be run. * Add t argument to adapt_population_size We will need to configure smc class such that it passes t as an argument to the _adapt_population_size. Therefor all adapt_population_size function have to be given t as well. * Adapt smc.run to ListPopulation In order to use ListPopulation we need to break before the _prepare_next_iteration in the end. Also pass t to _adapt_population_size * Update populationstrategy.py * Pass argumentname for better readability * Rename class Class name should contain Size as well * Added test for ListPopulationSize Simple test for ListPopulationSize according to the test_ListEpsilon function. * Add get_config function in ListPopulationSize Added get_config class according to ListEpsilon.get_config() function * Reformat code Added t==t_max other code termination block. Did not add logger info because while loop would not have produced a logger info itself. * Modify documentation Changed Population values to PopulationSize values * Add empty line for doc parsing * Remove empty line * Remove assertions Assertions didnt work. Co-authored-by: Yannik Schälte <[email protected]> * fixup * add docstring * fix style; back-relocate prepare_next_iteration * update releasenotes Co-authored-by: nbungi <[email protected]>
This was referenced Feb 20, 2020
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throughout the 0.9 series).