• 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)
  • Unsupport pymc sampler until fixed (#944)
• 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)
• 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)

Codecov Report

Merging #879 (2782a0e) into main (488eca7) will decrease coverage by 3.73%. The diff coverage is 83.43%.

@@            Coverage Diff             @@
##             main     #879      +/-   ##
==========================================
- Coverage   88.57%   84.83%   -3.74%     
==========================================
  Files         106      109       +3     
  Lines        7543     7835     +292     
==========================================
- Hits         6681     6647      -34     
- Misses        862     1188     +326     

Impacted Files	Coverage Δ
pypesto/ensemble/dimension_reduction.py	30.30% <0.00%> (-50.26%)	:arrow_down:
pypesto/profile/profile.py	92.30% <ø> (ø)
pypesto/profile/validation_intervals.py	85.71% <ø> (ø)
pypesto/sample/sample.py	96.77% <ø> (ø)
pypesto/store/__init__.py	100.00% <ø> (ø)
pypesto/visualize/optimization_stats.py	87.23% <0.00%> (ø)
pypesto/select/postprocessors.py	41.17% <16.66%> (-58.83%)	:arrow_down:
pypesto/result/optimize.py	64.61% <23.80%> (-2.06%)	:arrow_down:
pypesto/optimize/optimizer.py	45.81% <28.26%> (-44.41%)	:arrow_down:
pypesto/visualize/parameters.py	84.55% <31.25%> (-8.18%)	:arrow_down:
... and 83 more

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