pyglotaran: a Python library for global and target analysis

pyglotaran 0.6.0 Release Notes

Triple code name release: "K.I.S.S." (keep it short and sweet), Keiko (first teaching release), Z.O.E. (happy birthday)

pyglotaran is a library commonly used for the analysis of time-resolved spectroscopy measurements in the study of energy transfer pathways in photosynthesis, or the characterization of energy transfer (in-)efficiencies in photovoltaic systems.

This is the first version of the software used in teaching, specifically the Photosynthesis and Energy 2022 course found here: ism200\PE2022

✨ Features

• ✨ Python 3.10 support (#977)
• ✨ Add simple decay megacomplexes (#860)
• ✨ Feature: Generators (#866)
• ✨ Project Class (#869)
• ✨ Add clp guidance megacomplex (#1029)

👌 Minor Improvements:

• 👌🎨 Add proper repr for DatasetMapping (#957)
• 👌 Add SavingOptions to save_result API (#966)
• ✨ Add parameter IO support for more formats supported by pandas (#896)
• 👌 Apply IRF shift in coherent artifact megacomplex (#992)
• 👌 Added IRF shift to result dataset (#994)
• 👌 Improve Result, Parameter and ParameterGroup markdown (#1012)
• 👌🧹 Add suffix to rate and lifetime and guard for missing datasets (#1022)
• ♻️ Move simulation to own module (#1041)
• ♻️ Move optimization to new module glotaran.optimization (#1047)
• 🩹 Fix missing installation of clp-guide megacomplex as plugin (#1066)

🩹 Bug fixes

• 🩹 Fix Crash in optimization_group_calculator_linked when using guidance spectra (#950)
• 🩹 ParameterGroup.get degrades full_label of nested Parameters with nesting over 2 (#1043)
• 🩹 Show validation problem if parameters are missing values (default: NaN) (#1076)

📚 Documentation

• 🎨 Add new logo (#1083, #1087)

🗑️ Deprecations (due in 0.8.0)

• glotaran.io.save_result(result, result_path, format_name='legacy') -> glotaran.io.save_result(result, Path(result_path) / 'result.yml')
• glotaran.analysis.simulation -> glotaran.simulation.simulation
• glotaran.analysis.optimize -> glotaran.optimization.optimize

🗑️❌ Deprecated functionality removed in this release

• glotaran.ParameterGroup -> glotaran.parameter.ParameterGroup
• 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.get_dataset("<dataset_name>") -> result.data["<dataset_name>"]
• glotaran.analysis.result -> glotaran.project.result
• glotaran.analysis.scheme -> glotaran.project.scheme

🚧 Maintenance

• 🔧 Improve packaging tooling (#923)
• 🔧🚇 Exclude test files from duplication checks on sonarcloud (#959)
• 🔧🚇 Only run check-manifest on the CI (#967)
• 🚇👌 Exclude dependabot push CI runs (#978)
• 🚇👌 Exclude sourcery AI push CI runs (#1014)
• 👌📚🚇 Auto remove notebook written data when building docs (#1019)
• 👌🚇 Change integration tests to use self managed examples action (#1034)
• 🚇🧹 Exclude pre-commit bot branch from CI runs on push (#1085)

New Contributors

• @patrickhaetti made their first contribution in https://github.com/glotaran/pyglotaran/pull/896

Full Changelog: https://github.com/glotaran/pyglotaran/compare/v0.5.1...v0.6.0