v0.6.0

[jsnel]

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

👌 Minor Improvements:

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

🩹 Bug fixes

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

📚 Documentation

• 🎨 Add new logo (🎨 Add new logo #1083, 🎨 Add new logo to readme #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 (🔧 Improve packaging tooling #923)
• 🔧🚇 Exclude test files from duplication checks on sonarcloud (🔧🚇 Exclude test files from duplication checks on sonarcloud #959)
• 🔧🚇 Only run check-manifest on the CI (🔧🚇 Only run check-maifest on the CI #967)
• 🚇👌 Exclude dependabot push CI runs ( 🚇👌 Exclude dependabot push CI runs #978)
• 🚇👌 Exclude sourcery AI push CI runs (🚇👌 Exclude sourcery AI push CI runs #1014)
• 👌📚🚇 Auto remove notebook written data when building docs (👌📚🚇 Auto remove notebook written data when building docs #1019)
• 👌🚇 Change integration tests to use self managed examples action (👌🚇 Change integration tests to use self managed examples action #1034)
• 🚇🧹 Exclude pre-commit bot branch from CI runs on push (🚇🧹 Exclude pre-commit bot branch from CI runs on push #1085)

New Contributors

• @patrickhaetti made their first contribution in ✨ Add parameter IO support for more formats supported by pandas #896

Full Changelog: v0.5.1...v0.6.0

---

This discussion was created from the release v0.6.0.