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PEtab changelog

0.1 series

0.1.26

0.1.25

Full Changelog: https://github.com/PEtab-dev/libpetab-python/compare/v0.1.24...v0.1.25

0.1.24

  • Added method to generate condition-specific SBML models by @dweindl in PEtab-dev#108
  • GHA: Regular package installation instead of -e by @dweindl in PEtab-dev#106
  • Fixed unclosed file warnings by @dilpath in PEtab-dev#107

Full Changelog: https://github.com/PEtab-dev/libpetab-python/compare/v0.1.23...v0.1.24

0.1.23

... and other changes by @plakrisenko, @dweindl

Full Changelog: https://github.com/PEtab-dev/libpetab-python/compare/v0.1.22...v0.1.23

0.1.22

  • Allow zero bounds for log parameters by @FFroehlich in PEtab-dev#83
  • Adapt to Matplotlib 3.5 by @dweindl in PEtab-dev#86
  • Allow specifying file format for visualization by @dweindl in PEtab-dev#85
  • Visualization: Don't mess with rcParams by @dweindl in PEtab-dev#90
  • Linter: Check condition IDs are unique by @dweindl in PEtab-dev#92
  • Add support for pathlib for reading PEtab tables by @dweindl, @dilpath in PEtab-dev#93, PEtab-dev#91
  • Run tests also on Python 3.10 by @dweindl in PEtab-dev#88
  • Fix remote file retrieval on Windows @dweindl, @dilpath in PEtab-dev#91
  • Fix test suite for Windows @dweindl, @dilpath in PEtab-dev#91

Full Changelog: https://github.com/PEtab-dev/libpetab-python/compare/v0.1.21...v0.1.22

0.1.21

  • PEtab spec compliance: measurements must now be not null, and numeric (#76)
    • Users who relied on null measurements for simulation/plotting are recommended to store these dummy simulation-only measurements in an additional file, separate to real measurements used for calibration
  • Improve Unicode support (#79, fixes #77)
  • Convenience methods to scale or unscale a parameter vector (#78)

0.1.20

  • Visualization: plot additional simulation points (not only at measurements) (#62), bugfix (#68)
  • Documentation: visualization, observables, simulation, Sphinx fixes (#67)
  • Lint: ensure valid parameter IDs in observable and noise parameters (#69)
  • Convenience method for quick export of a PEtab problem to files (#71)

0.1.19

  • Visualization: refactoring (#58) including various bug fixes
  • Validation: Fixed detection of missing observable/noise parameter overrides (#64)
  • Optional relative paths in generated YAML (#57)

0.1.18

  • Fixed various documentation issues
  • Parameter mapping: Added option to ignore time-point specific noiseParameters (#51)

0.1.17

  • Updated package URL
  • Fixed noise formula check (#49)
  • Fixed override check and add noise formula check (#48)
  • Fixed timepoint override check (#47)

0.1.16

Update python version for pypi deployment, no further changes

0.1.15

NOTE: The original PEtab format + petab package repository has been split up (PEtab-dev#41). This repository now only contains the petab Python package. The PEtab specifications and related information are available at https://github.com/PEtab-dev/PEtab.

0.1.14

  • Fix sampling of priors in parameterScale (PEtab-dev/PEtab#492)
  • Clarify documentation of parameterScale priors
  • Improvements in petab.simulate (PEtab-dev/PEtab#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 PEtab-dev/PEtab#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`` (PEtab-dev/PEtab#477)

0.1.11

0.1.10

  • Fixed deployment setup, no further changes.*

0.1.9

Library:

0.1.8

Library:

Documentation:

Visualization:

0.1.7

Documentation:

  • Update coverage and links of supporting tools
  • Update explanatory figure

0.1.6

Library:

Documentation:

Visualization:

0.1.5

Library:

Documentation:

  • Add overview of supported PEtab feature in toolboxes
  • Add contribution guide
  • Fix optional values in documentation (PEtab-dev/PEtab#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:

0.1.2

Library:

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 (PEtab-dev/PEtab#244) (moves observableTransformation and noiseModel from the measurement table to the observables table)
  • Allow initial concentrations / sizes in condition table (PEtab-dev/PEtab#238)
  • Fixes and clarifications in the format documentation
  • Changes in prior columns of the parameter table (PEtab-dev/PEtab#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/PEtab#228)
  • Added unit tests and additional format validation steps
  • Optional parallelization of parameter mapping (PEtab-dev/PEtab#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 (PEtab-dev/PEtab#169)
  • Define YAML schema for grouping PEtab files, also allowing for more complex combinations of files (PEtab-dev/PEtab#183)

Library:

  • Refactor library. Reorganize petab.core functions.
  • Fix visualization w/o condition names PEtab-dev/PEtab#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:

0.0.0a16 and earlier

See git history