v0.4.0

pyglotaran 0.4.0 Release Notes

✨ 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 '.' 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)

🗑️ Deprecations

• 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, ...)

🔌 Plugins

• ProjectIo 'folder'/'legacy' plugin to save results (#620)
• Model 'spectral-model' (#672)

📚 Documentation

• User documentation is written in notebooks (#568)
• Documentation on how to write a DataIo plugin (#600)

v0.3.3

pyglotaran 0.3.3 Release Notes

pyglotaran is a Python library for global and target analysis of time-resolved spectroscopy data.

This is the latest and probably last patch on the v0.3 maintenance branch, as development for the next milestone is well underway on the main branch in the repository

Highlights

• Much faster when using equal area penalties
• Support for Python 3.9

Changelog

• 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)

Usage notice

This software package is made available as an early access release, to the advantage of the (scientific) community who wishes to make use of it before it has fully matured, but without any warranties. Please refer to the usage notice in the README.

For a modest collection of examples, see the pyglotaran_examples repository.
For examples on how to do plotting of results see the pyglotaran_extras repository.

Citing

If you use the pyglotaran package in an academic context, we would appreciate a citation. You can cite the software as:

Jörn Weißenborn, Joris Snellenburg, Sebastian Weigand, & Ivo H.M. van Stokkum. (2021, March 18). pyglotaran: a Python library for global and target analysis (Version v0.3.3). Zenodo. http://doi.org/10.5281/zenodo.4619635

v0.3.2

pyglotaran 0.3.2 Release Notes

The first release of pyglotaran ready for a wider audience was v0.3.0, this is the first proper patch release to follow, fixing some small but important issues.

Highlights

• Compatible with NumPy 1.20.
• Using less memory during optimization (during Result creation).
• Saved result datasets are smaller in size.

Changelog

• 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)
• Correction to setup.cfg to satisfy PyPI and version bump 0.3.1 -> 0.3.2

Version numbering

A glitch in the matrix resulted v0.3.1 having a visually unappealing front page on PyPI. To fix this, a new release had to be drafted which is identical to v0.3.1, other than a configuration file used in rendering said front page. For all intents and purposes both versions are the same, released on the same date, and thus share the same Highlights and Changelog (w.r.t v0.3.0)

Usage notice

This software package is made available as an early access release, to the advantage of the (scientific) community who wishes to make use of it before it has fully matured, but without any warranties. Please refer to the usage notice in the README.

For a modest collection of examples, see the pyglotaran_examples repository.
For examples on how to do plotting of results see the pyglotaran_extras repository.

v0.3.1

pyglotaran 0.3.1 Release Notes

The first release of pyglotaran ready for a wider audience was v0.3.0, this is the first patch release for that version, fixing some small but important issues.

Highlights

• Compatible with NumPy 1.20.
• Using less memory during optimization (during Result creation).
• Saved result datasets are smaller in size.

Changelog

• 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)

Usage notice

This software package is made available as an early access release, to the advantage of the (scientific) community who wishes to make use of it before it has fully matured, but without any warranties. Please refer to the usage notice in the README.

For a modest collection of examples, see the pyglotaran_examples repository.
For examples on how to do plotting of results see the pyglotaran_extras repository.

v0.3.0

pyglotaran 0.3.0 Release Notes

pyglotaran 0.3.0 is considered the first release ready for a wider audience, enjoy your glimpse into the future of global and target analysis!

Highlights

• Switched to internal optimization mechanism
• Introduced a new Schema and Problem class for greater control over optimization
• Parameter relations using custom expression now possible
• Simultaneous global and target analysis with multiple datasets now possible!

Usage notice

This software package is made available as an early access release, to the advantage of the (scientific) community who wishes to make use of it before it has fully matured, but without any warranties. Please refer to the usage notice in the README.

For a modest collection of examples, see the pyglotaran_examples repository.
For examples on how to do plotting of results see the pyglotaran_extras

pyglotaran 0.2.0 BusFactor++

Celebratory BusFactor++ release!

Future release of pyglotaran will include meatballs!

Consult readme before use.