PEtab changelog¶
0.1 series¶
0.1.9¶
Library:
- Allow URL as filenames for YAML files and SBML models (Closes #187) (#459)
- Allow model time in observable formulas (#445)
- Make float parsing from CSV round-trip (#444)
- Validator: Error message for missing IDs, with line numbers. (#467)
- Validator: Detect duplicated observable IDs (#446)
- Some documentation and CI fixes / updates
- Visualization: Add option to save visualization specification (#457)
- Visualization: Column XValue not mandatory anymore (#429)
- Visualization: Add sorting of indices of dataframes for the correct sorting of x-values (#430)
- Visualization: Default value for the column x_label in vis_spec (#431)
0.1.8¶
Library:
- Use
core.is_empty
to check for empty values (#434) - Move tests to python 3.8 (#435)
- Update to libcombine 0.2.6 (#437)
- Make float parsing from CSV round-trip (#444)
- Lint: Allow model time in observable formulas (#445)
- Lint: Detect duplicated observable ids (#446)
- Fix likelihood calculation with missing values (#451)
Documentation:
- Move format documentation to restructuredtext format (#452)
- Document all noise distributions and observable scales (#452)
- Fix documentation for prior distribution (#449)
Visualization:
- Make XValue column non-mandatory (#429)
- Apply correct condition sorting (#430)
- Apply correct default x label (#431)
0.1.6¶
Library:
- Fix handling of empty columns for residual calculation (#392)
- Allow optional fixing of fixed parameters in parameter mapping (#399)
- Fix function to flatten out time-point specific overrides (#404)
- Add function to create a problem yaml file (#398)
- Allow merging of multiple parameter files (#407)
Documentation:
- In README, add to the overview table the coverage for the supporting tools, and links and usage examples (various commits)
- Show REAMDE on readthedocs documentation front page (#400)
- Correct description of observable and noise formulas (#401)
- Update documentation on optional visualization values (#405, #419)
Visualization:
- Fix sorting problem (#396)
- More generously handle optional values (#405, #419)
- Create dataset id also for simulation dataframe (#408)
- Extend test suite for visualization (#418)
0.1.5¶
Library:
- New create empty observable function (issue 386) (#387)
- Deprecate petab.sbml.globalize_parameters (#381)
- Fix computing log10 likelihood (#380)
- Documentation update and typehints for visualization (#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 (#378)
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
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 #302)
- Fix: nominalValue is optional unless estimated!=1 anywhere (Fixes #303)
- Fix: handle undefined observables more gracefully (Closes #300) (#351)
- Parameter mapping:
- Fix / refactor parameter mapping (breaking change) (#344) (now performing parameter value and scale mapping together)
- check optional measurement cols in mapping (#350)
- allow calculating llhs (#349), chi2 values (#348) and residuals (#345)
- Visualization
- Basic Scatterplots & lot of bar plot fixes (#270)
- Fix incorrect length of bool
bool_preequ
when subsetting with ind_meas (Closes #322)
- make libcombine optional (#338)
0.1.2¶
Library:
- Extensions and fixes for the visualization functions (#255, #262)
- Allow to extract fixed|free and scaled|non-scaled parameters (#256, #268, #273)
- Various fixes (esp. #264)
- Add function to get observable ids (#269)
- Improve documentation (esp. #289)
- Set default column for simulation results to ‘simulation’
- Add support for COMBINE archives (#271)
- Fix sbml observables to table
- Improve prior and dataframe tests (#285, #286, #297)
- Add function to get parameter table with all default values (#288)
- Move tests to github actions (#281)
- Check for valid identifiers
- Fix handling of empty values in dataframes
- Allow to get numeric values in parameter mappings in scaled form (#308)
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)
0.1.0¶
Data format:
- Introduce observables table instead of SBML assignment rules for defining observation model (#244) (moves observableTransformation and noiseModel from the measurement table to the observables table)
- Allow initial concentrations / sizes in condition table (#238)
- Fixes and clarifications in the format documentation
- Changes in prior columns of the parameter table (#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 (#228)
- Added unit tests and additional format validation steps
- Optional parallelization of parameter mapping (#205)
- Extended documentation (in-source and example Jupyter notebooks)
0.0.1¶
Data format:
- Update format and documentation with respect to data and parameter scales (#169)
- Define YAML schema for grouping PEtab files, also allowing for more complex combinations of files (#183)
Library:
- Refactor library. Reorganize
petab.core
functions. - Fix visualization w/o condition names #142
- Extend validator
- Removed deprecated functions petab.Problem.get_constant_parameters and petab.sbml.constant_species_to_parameters
- Minor fixes and extensions
0.0 series¶
0.0.0a17¶
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 (#128) (Closes #125)
- Fix get_noise_distributions: so far we got ‘normal’ everywhere due to wrong grouping (#147)
- Fix create_parameter_df: Exclude rule targets (#149)
- Verify condition table column names occur as model parameters (Closes #150) (#151)
- More informative error messages in case of wrongly set observable and noise parameters (Closes #118) (#155)
- Update doc for copasi import and github installation (#158)
- Extend validator to check if all required parameters are present in parameter table (Closes #43) (#159)
- Setup documentation for RTD (#161)
- Handle None in petab.core.split_parameter_replacement_list (Closes #121)
- Fix(lint) correct handling of optional columns. Check before access.
- Remove obsolete generate_experiment_id.py (Closes #111) #166
0.0.0a16 and earlier¶
See git history