PEtab changelog

2021-03-19

NOTE: The original PEtab format + petab package repository has been split up (PEtab-dev/PEtab#476). This repository now only contains the PEtab specifications and general information on PEtab. The Python package is now available at https://github.com/PEtab-dev/libpetab-python/.

  • Removed python-package-related files (#518)

  • Doc: Add editorial board (#511)

  • Doc: Update tutorial references (#497)

  • Doc: Add description of PEtab development process (#507)

  • Update tutorial.rst (#512)

  • Update how-to-cite (Closes #432) (#509)

0.2 series

0.2.0

  • Specify how PEtab functionality can be expanded through extensions.

  • YAML files are now required for the specification of PEtab problems.

0.1 series

0.1.14

  • Fix sampling of priors in parameterScale (#492)

  • Clarify documentation of parameterScale priors

  • Improvements in petab.simulate (#479):

    • Fix default noise distributions

    • Add option for non-negative synthetic data

0.1.13

  • Fix for pandas 1.2.0 – use get_handle instead of get_filepath_or_buffer

  • Fix erroneous petab_test_suite symlink (all #493)

0.1.12

  • Documentation update:

    • Added SBML2Julia to list of tools supporting PEtab

    • Extended PEtab introduction

    • Tutorial for creating PEtab files

  • Minor fix: Default argument for optional ‘model’ parameter in petab.lint.check_condition_df` (#477)

0.1.11

  • Function for generating synthetic data (#472)

  • Minor documentation updates (#470)

0.1.10

  • Fixed deployment setup, no further changes.*

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)

0.1.7

Documentation:

  • Update coverage and links of supporting tools

  • Update explanatory figure

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)

0.0.2

Bugfix release

  • Fix petablint error

  • Fix minor issues in petab.visualize

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