CHANGELOG.md

PEtab changelog

2021-03-19

NOTE: The original PEtab format + petab package repository has been split up (#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