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Published October 25, 2022 | Version v0.2.14
Software Open

pyPESTO - Parameter EStimation TOolbox for python

Authors/Creators

Description

  • Ensembles:
    • Save and load weights and sigmay (#876)
    • Define relative cutoff (#855)
  • PEtab:
    • Pass problem kwargs via petab importer (#874)
    • Use benchmark-models-petab instead of manual download (#915)
    • Use fake RData in in prediction_to_petab_measurement_df (#925)
  • Optimize:
    • Fides: Include message according to exitflag (#878)
  • Sampling:
    • Added Pymc v4 Sampler (#818, #944, #948)
  • Visualization:
    • Fix waterfall plot limits for non-offsetted log-plots (#891)
    • Plot unflattened model fit from flattened PEtab problems (#914)
    • Added the offset value to waterfall plot for better intuitive understanding (#910, #945)
    • Visualize parameter correlation (#888)
  • History and storage:
    • Fix history-result reconstruction mismatch (#902)
    • Move history to own module (#903)
    • Remove chi2, schi2 except for history convenience function (#904)
    • Clean up history hierarchy (#908)
    • Fix read_result with history (#907)
    • Improve hdf5 history file lock (#909, #921)
    • Fix message in check_overwrite (#894)
    • Deactivate automatic saving (#930, #932)
    • Allow problem=None in read_result_from_file (#936)
    • Remove superfluous get_or_create_group (#937)
    • Extract read_history_from_file from read_result_from_file (#939)
    • Select: use model ID in save postprocessor filename, by default (#943)
  • Select:
    • Clean up use of minimize_options in model problem (#918)
    • User-supplied method to produce pyPESTO problem (#884)
    • Report, and binary model ID post-processors (#900)
    • Move method.py functionalities to ui.py in petab_select (#919)
  • Objective and Result:
    • Julia objective (#927)
    • Fix set of keys to aggregate results in aggregated objective (#883)
    • Nicer OptimizeResult.summary (#895, #916, #935, #942, )
    • Fix disjoint IDs check in OptimizerResult.append (#922)
    • Fix OptimizeResult pickling (#953)
  • General:
    • Remove version from CITATION.cff (#887)
    • Fix CI and docs (#892, #893)
    • Literal typehints for mode (#899)
    • Fix pandas deprecation warning (#896)
    • Document NEP 29 (time-window based python support) (#905)
    • Fix get_for_key deprecation warning (#906)
    • Fix multiple warnings from existing AMICI model (#912)
    • Fix warning from AMICI fixed overrides (#912)
    • Fix flaky test CRFunModeHistoryTest.test_trace_all (#917)
    • Fix novel B024 ABC without abstract methods (#923)
    • Improve API docs and add overview notebook (#911)
    • Fix typos (#926)
    • Fix julia tests (#929, #933)
    • Fix flaky test_mpipoolengine (#938)
    • More informative test IDs in test_optimize (#940)
    • Speed-up import via lazy imports (#946)

Notes

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Files

ICB-DCM/pyPESTO-v0.2.14.zip

Files (4.4 MB)

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Additional details

Related works

Is supplement to
https://github.com/ICB-DCM/pyPESTO/tree/v0.2.14 (URL)