Petab

Library:

* Fix handling of empty columns for residual calculation (PEtab-dev/PEtab392)
* Allow optional fixing of fixed parameters in parameter mapping (PEtab-dev/PEtab399)
* Fix function to flatten out time-point specific overrides (PEtab-dev/PEtab404)
* Add function to create a problem yaml file (PEtab-dev/PEtab398)
* Allow merging of multiple parameter files (PEtab-dev/PEtab407)

Documentation:

* In README, add to the overview table the coverage for the supporting tools,
and links and usage examples (various commits)
* Show README on readthedocs documentation front page (PEtab-dev/PEtab400)
* Correct description of observable and noise formulas (PEtab-dev/PEtab401)
* Update documentation on optional visualization values (PEtab-dev/PEtab405, PEtab-dev/PEtab419)

Visualization:

* Fix sorting problem (PEtab-dev/PEtab396)
* More generously handle optional values (PEtab-dev/PEtab405, PEtab-dev/PEtab419)
* Create dataset id also for simulation dataframe (PEtab-dev/PEtab408)
* Extend test suite for visualization (PEtab-dev/PEtab418)

Library:

* New create empty observable function (issue 386) (PEtab-dev/PEtab387)
* Deprecate petab.sbml.globalize_parameters (PEtab-dev/PEtab381)
* Fix computing log10 likelihood (PEtab-dev/PEtab380)
* Documentation update and typehints for visualization (PEtab-dev/PEtab372)
* Ordered result of `petab.get_output_parameters`
* Fix missing argument to parameters.create_parameter_df

Documentation:
* Add overview of supported PEtab feature in toolboxes
* Add contribution guide
* Fix optional values in documentation (PEtab-dev/PEtab378)

Library:

* Fixes / updates in functions for computing llh and chi2
* Allow and require output parameters defined in observable table to be defined in parameter table
* Fix merge_preeq_and_sim_pars_condition which incorrectly assumed lists
instead of dicts
* Update parameter mapping to deal with species and compartments in
condition table
* Removed `petab.migrations.sbml_observables_to_table`

For converting older PEtab files to observable table format, use one of the
previous releases

* Visualization:
* Fix various issues with get_data_to_plot
* Fixed various issues with expected presence of optional columns

File format:

* Updated documentation
* Observables table in YAML file now mandatory in schema (was implicitly
mandatory before, as observable table was required already)

Library:
* petablint:
* Fix: allow specifying observables file via CLI (Closes PEtab-dev/PEtab302)
* Fix: nominalValue is optional unless estimated!=1 anywhere (Fixes PEtab-dev/PEtab303)
* Fix: handle undefined observables more gracefully (Closes PEtab-dev/PEtab300) (PEtab-dev/PEtab351)
* Parameter mapping:
* Fix / refactor parameter mapping (breaking change) (PEtab-dev/PEtab344)
(now performing parameter value and scale mapping together)
* check optional measurement cols in mapping (PEtab-dev/PEtab350)
* allow calculating llhs (PEtab-dev/PEtab349), chi2 values (PEtab-dev/PEtab348) and residuals (PEtab-dev/PEtab345)
* Visualization
* Basic Scatterplots & lot of bar plot fixes (PEtab-dev/PEtab270)
* Fix incorrect length of bool `bool_preequ` when subsetting with ind_meas
(Closes PEtab-dev/PEtab322)
* make libcombine optional (PEtab-dev/PEtab338)

Library:

* Extensions and fixes for the visualization functions (PEtab-dev/PEtab255, PEtab-dev/PEtab262)
* Allow to extract fixed|free and scaled|non-scaled parameters (PEtab-dev/PEtab256, PEtab-dev/PEtab268, PEtab-dev/PEtab273)
* Various fixes (esp. PEtab-dev/PEtab264)
* Add function to get observable ids (PEtab-dev/PEtab269)
* Improve documentation (esp. PEtab-dev/PEtab289)
* Set default column for simulation results to 'simulation'
* Add support for COMBINE archives (PEtab-dev/PEtab271)
* Fix sbml observables to table
* Improve prior and dataframe tests (PEtab-dev/PEtab285, PEtab-dev/PEtab286, PEtab-dev/PEtab297)
* Add function to get parameter table with all default values (PEtab-dev/PEtab288)
* Move tests to github actions (PEtab-dev/PEtab281)
* Check for valid identifiers
* Fix handling of empty values in dataframes
* Allow to get numeric values in parameter mappings in scaled form (PEtab-dev/PEtab308)

Library:

* Fix parameter mapping: include output parameters not present in SBML model
* Fix missing `petab/petab_schema.yaml` in source distribution
* Let get_placeholders return an (ordered) list of placeholders
* Deprecate `petab.problem.from_folder` and related functions
(obsolete after introducing more flexible YAML files for grouping tables
and models)