Changelog

0.4.2 (2021-12-31)

🩹 Bug fixes

  • 🩹🚧 Backport of bugfix #927 discovered in PR #860 related to initial_concentration normalization when saving results (#935).

🚧 Maintenance

  • πŸš‡πŸš§ Updated β€˜gold standard’ result comparison reference (old -> new)

  • πŸš‡ Refine test_result_consistency #936

0.4.1 (2021-09-07)

✨ Features

  • Integration test result validation (#760)

🩹 Bug fixes

  • Fix unintended saving of sub-optimal parameters (0ece818, backport from #747)

  • Improve ordering in k_matrix involved_compartments function (#791)

0.4.0 (2021-06-25)

✨ Features

  • Add basic spectral model (#672)

  • Add Channel/Wavelength dependent shift parameter to irf. (#673)

  • Refactored Problem class into GroupedProblem and UngroupedProblem (#681)

  • Plugin system was rewritten (#600, #665)

  • Deprecation framework (#631)

  • Better notebook integration (#689)

🩹 Bug fixes

  • Fix excessive memory usage in _create_svd (#576)

  • Fix several issues with KineticImage model (#612)

  • Fix exception in sdt reader index calculation (#647)

  • Avoid crash in result markdown printing when optimization fails (#630)

  • ParameterNotFoundException doesn’t prepend β€˜.’ if path is empty (#688)

  • Ensure Parameter.label is str or None (#678)

  • Properly scale StdError of estimated parameters with RMSE (#704)

  • More robust covariance_matrix calculation (#706)

  • ParameterGroup.markdown() independent parametergroups of order (#592)

πŸ”Œ Plugins

  • ProjectIo β€˜folder’/’legacy’ plugin to save results (#620)

  • Model β€˜spectral-model’ (#672)

πŸ“š Documentation

  • User documentation is written in notebooks (#568)

  • Documentation on how to write a DataIo plugin (#600)

πŸ—‘οΈ Deprecations (due in 0.6.0)

  • glotaran.ParameterGroup -> glotaran.parameterParameterGroup

  • glotaran.read_model_from_yaml -> glotaran.io.load_model(..., format_name="yaml_str")

  • glotaran.read_model_from_yaml_file -> glotaran.io.load_model(..., format_name="yaml")

  • glotaran.read_parameters_from_csv_file -> glotaran.io.load_parameters(..., format_name="csv")

  • glotaran.read_parameters_from_yaml -> glotaran.io.load_parameters(..., format_name="yaml_str")

  • glotaran.read_parameters_from_yaml_file -> glotaran.io.load_parameters(..., format_name="yaml")

  • glotaran.io.read_data_file -> glotaran.io.load_dataset

  • result.save -> glotaran.io.save_result(result, ..., format_name="legacy")

  • result.get_dataset("<dataset_name>") -> result.data["<dataset_name>"]

  • glotaran.analysis.result -> glotaran.project.result

  • glotaran.analysis.scheme -> glotaran.project.scheme

  • model.simulate -> glotaran.analysis.simulation.simulate(model, ...)

0.3.3 (2021-03-18)

  • Force recalculation of SVD attributes in scheme._prepare_data (#597)

  • Remove unneeded check in spectral_penalties._get_area Fixes (#598)

  • Added python 3.9 support (#450)

0.3.2 (2021-02-28)

  • Re-release of version 0.3.1 due to packaging issue

0.3.1 (2021-02-28)

  • Added compatibility for numpy 1.20 and raised minimum required numpy version to 1.20 (#555)

  • Fixed excessive memory consumption in result creation due to full SVD computation (#574)

  • Added feature parameter history (#557)

  • Moved setup logic to setup.cfg (#560)

0.3.0 (2021-02-11)

  • Significant code refactor with small API changes to parameter relation specification (see docs)

  • Replaced lmfit with scipy.optimize

0.2.0 (2020-12-02)

  • Large refactor with significant improvements but also small API changes (see docs)

  • Removed doas plugin

0.1.0 (2020-07-14)

  • Package was renamed to pyglotaran on PyPi

0.0.8 (2018-08-07)

  • Changed nan_policiy to omit

0.0.7 (2018-08-07)

  • Added support for multiple shapes per compartment.

0.0.6 (2018-08-07)

  • First release on PyPI, support for Windows installs added.

  • Pre-Alpha Development