Merge pull request PEtab-dev#454 from PEtab-dev/develop

Release 0.1.8

Merge pull request PEtab-dev#427 from PEtab-dev/develop

Release 0.1.7

Merge pull request PEtab-dev#423 from PEtab-dev/develop

Release 0.1.6

Merge pull request PEtab-dev#391 from PEtab-dev/release_0.1.5

Release 0.1.5

Library:

* New create empty observable function (issue 386) (PEtab-dev#387)
* Deprecate petab.sbml.globalize_parameters (PEtab-dev#381)
* Fix computing log10 likelihood (PEtab-dev#380)
* Documentation update and typehints for visualization  (PEtab-dev#372)
* 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#378)

Merge pull request PEtab-dev#370 from PEtab-dev/release_0.1.4

Release 0.1.4

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

Merge pull request PEtab-dev#357 from PEtab-dev/release_0.1.3

Release 0.1.3

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#302)
  * Fix: nominalValue is optional unless estimated!=1 anywhere (Fixes PEtab-dev#303)
  * Fix: handle undefined observables more gracefully (Closes PEtab-dev#300) (PEtab-dev#351)
* Parameter mapping: 
  * Fix / refactor parameter mapping (breaking change) (PEtab-dev#344)
    (now performing parameter value and scale mapping together)
  * check optional measurement cols in mapping (PEtab-dev#350)
* allow calculating llhs (PEtab-dev#349), chi2 values (PEtab-dev#348) and residuals (PEtab-dev#345)
* Visualization
  * Basic Scatterplots & lot of bar plot fixes (PEtab-dev#270)
  * Fix incorrect length of bool `bool_preequ` when subsetting with ind_meas 
    (Closes PEtab-dev#322)
* make libcombine optional (PEtab-dev#338)

Merge pull request PEtab-dev#311 from PEtab-dev/develop

Release 0.1.2

Merge pull request PEtab-dev#254 from ICB-DCM/release_0.1.1

Release 0.1.1

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)

Merge pull request PEtab-dev#248 from ICB-DCM/release_0.1.0

Release 0.1.0

Data format:

* Introduce observables table instead of SBML assignment rules for defining
  observation model (PEtab-dev#244) (moves observableTransformation and noiseModel
  from the measurement table to the observables table)
* Allow initial concentrations / sizes in condition table (PEtab-dev#238)
* Fixes and clarifications in the format documentation
* Changes in prior columns of the parameter table (PEtab-dev#222)
* 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#228)
* Added unit tests and additional format validation steps
* Optional parallelization of parameter mapping (PEtab-dev#205)
* Extended documentation (in-source and example Jupyter notebooks)

Merge pull request PEtab-dev#204 from ICB-DCM/release_0.0.2

Release 0.0.2

Bugfix release

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