Petab

Data format:

* Introduce observables table instead of SBML assignment rules for defining
observation model (PEtab-dev/PEtab244) (moves observableTransformation and noiseModel
from the measurement table to the observables table)
* Allow initial concentrations / sizes in condition table (PEtab-dev/PEtab238)
* Fixes and clarifications in the format documentation
* Changes in prior columns of the parameter table (PEtab-dev/PEtab222)
* Introduced separate version number of file format, this release being
version 1

Library:

* Adaptations to new file formats
* Various bugfixes and clean-up, especially in visualization and validator
* Parameter mapping changed to include all model parameters and not only
those differing from the ones defined inside the SBML model
* Introduced constants for all field names and string options, replacing
most string literals in the code (PEtab-dev/PEtab228)
* Added unit tests and additional format validation steps
* Optional parallelization of parameter mapping (PEtab-dev/PEtab205)
* Extended documentation (in-source and example Jupyter notebooks)

Bugfix release

* Fix `petablint` error
* Fix minor issues in `petab.visualize`

Data format:
* Update format and documentation with respect to data and parameter scales
(PEtab-dev/PEtab169)
* Define YAML schema for grouping PEtab files, also allowing for more complex
combinations of files (PEtab-dev/PEtab183)

Library:
* Refactor library. Reorganize `petab.core` functions.
* Fix visualization w/o condition names PEtab-dev/PEtab142
* Extend validator
* Removed deprecated functions petab.Problem.get_constant_parameters
and petab.sbml.constant_species_to_parameters
* Minor fixes and extensions

Data format: *No changes*

Library:
* Extended visualization support
* Add helper function and test case to deal with timepoint-specific parameters
flatten_timepoint_specific_output_overrides (PEtab-dev/PEtab128) (Closes PEtab-dev/PEtab125)
* Fix get_noise_distributions: so far we got 'normal' everywhere due to
wrong grouping (PEtab-dev/PEtab147)
* Fix create_parameter_df: Exclude rule targets (PEtab-dev/PEtab149)
* Verify condition table column names occur as model parameters
(Closes PEtab-dev/PEtab150) (PEtab-dev/PEtab151)
* More informative error messages in case of wrongly set observable and
noise parameters (Closes PEtab-dev/PEtab118) (PEtab-dev/PEtab155)
* Update doc for copasi import and github installation (PEtab-dev/PEtab158)
* Extend validator to check if all required parameters are present in
parameter table (Closes PEtab-dev/PEtab43) (PEtab-dev/PEtab159)
* Setup documentation for RTD (PEtab-dev/PEtab161)
* Handle None in petab.core.split_parameter_replacement_list (Closes PEtab-dev/PEtab121)
* Fix(lint) correct handling of optional columns. Check before access.
* Remove obsolete generate_experiment_id.py (Closes PEtab-dev/PEtab111) PEtab-dev/PEtab166

See git history