Pypesto

-------------------

* Model selection (397):
* Automated model selection with forward/backward/brute force methods and
AIC/AICc/BIC criteria
* Much functionality (methods, criteria, model space, problem
specification) via `PEtab Select <https://github.com/PEtab-dev/petab_select>`
* Plotting routines
* `Example notebook <https://github.com/ICB-DCM/pyPESTO/blob/main/doc/example/model_selection.ipynb>`
* Model calibration postprocessors
* Select first model that improves on predecessor model
* Use previous MLE as startpoint
* Tests

* AMICI:
* Maintain model settings when pickling for multiprocessing (747)

* General:
* Apply nbqa black and isort to auto-format all notebooks via
pre-commit hook (794)
* Apply black formatting via pre-commit hook (796)
* Require Python >= 3.8 (795)
* Fix various warnings (778)
* Minor fixes (792)

-------------------

* AMICI:
* Make AMICI objective report only what is being asked for (777)

* Optimization:
* (Breaking) Refactor startpoint generation with clear assignments;
allow checking gradients (769)
* (Breaking) Prioritize history vs optimize result (775)

* Storage:
* Fix loading empty history and result generation from multiple
histories (764)
* Fix autosave function for single-core (770)
* Fix potential autosave overwriting and typehints (772)
* Allow loading of partial results from history file (783)

* CI:
* Compile AMICI models without gradients in test suite (774)

* General:
* (Breaking) Create result sub-module; shift storage+result related
functionality (784)
* Fix finite difference constant mode (786)
* Refactor ensemble module (788)
* Introduce general C constants file (788)
* Apply isort for automatic imports formatting (785)
* Reduce run log output (789)
* Various minor fixes (765, 766, 768, 771)

------------------

* General:
* Automatically save results (749)
* Update all docstrings to numpy standard (750)
* Add Google Colab and nbviewer links to all notebooks for online
execution (758)
* Option to not save hess and sres in result (760)
* Set minimum supported python version to 3.7 (755)

* Visualization:
* Parameterize start index in optimized model fit (744)

------------------

* PEtab:
* Use correct measurement column name in `rdatas_to_simulation_df` (721)
* Visualize optimized model fit via PEtab problem (725)
* Un-ignore observable scaling tests (742)
* New function to plot model trajectory with custom time points (739)

* Optimization:
* OOD Refactor startpoint generation (732)
* Update to fides 0.6.0 (733)
* Correctly report FVAL vs CHI2 values in fides (741)

* Ensemble:
* Option for using weighted ensemble means (702)
* Default names and bounds for `Ensemble.from_sample` (730)

* Storage:
* Load optimization result from HDF5 history (726)

* General:
* Enable use of priors with least squares optimizers (745)
* Add temporary CITATION.cff file (734)
* Regular scheduled CI runs (754)
* Allow to not copy objective in problem (756)

* Fixes:
* Fix non-exported visualization in notebook (729)
* Mark some more tests as flaky (704)
* Fix minor data type and OOD issues in parameter and waterfall plots
(731)

------------------

* Finite Differences:
* Adaptive finite differences (671)
* Add helper function for checking gradients of objectives (690)
* Small bug fixes (711, 714)

* Storage:
* Store representation of the objective (669)
* Minor fixes in HDF5 history (679)
* HDF5 reader for ensemble predictions (681)
* Update storage demo jupyter notebook (699)
* Option to trim trace to be monotonically decreasing (705)

* General:
* Improved tests and bug fixes of validation intervals (676, 685)
* Add input file validation via PEtab linter for PEtab import (678)
* Remove default values from docstring (680)
* Minor fixes/improvements of ensembles (687, 688)
* Fix sorting of optimization values including `NaN` values (691)
* Specify axis limits for plotting (693)
* Minor fixes in visualization (696)
* Add installation option `all_optimizers` (695)
* Improve installation documentation (689)
* Update `pysb` and `BNG` version on GitHub Actions (697)
* Bug fix in steady state guesses (715)

------------------

* Objective:
* Basic finite differences (666)
* Fix factor 2 in res/fval values (619)

* Optimization:
* Sort optimization results when appending (668)
* Read optimizer result from HDF5 (previously only CSV) (663)

* Storage:
* Load ensemble from HDF5 (640)

* CI:
* Add flake8 checks as pre-commit hook (662)
* Add efficient biological conversion reaction test model (619)

* General:
* No automatic import of the predict module (657)
* Assert unique problem parameter names (665)
* Load ensemble from optimization result with and without history usage
(640)
* Calculate validation profile significance (658)
* Set pypesto screen logger to "INFO" by default (667)

* Minor fixes:
* Fix axis variable overwriting in `visualize.sampling_parameter_traces`
(665)