Pyglotaran

🩹 Bug fixes

- 🩹 Bugfix Use normalized initial_concentrations in result creation for decay megacomplex (927)
- 🩹 Fix save_result crashes on Windows if input data are on a different drive than result (931)

🚧 Maintenance

- 🚧 Forward port Improve result comparison workflow and v0.4 changelog (938)
- 🚧 Forward port of 936 test_result_consistency

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✨ Features

- ✨ Feature: Megacomplex Models (736)
- ✨ Feature: Full Models (747)
- ✨ Damped Oscillation Megacomplex (a.k.a. DOAS) (764)
- ✨ Add Dataset Groups (851)
- ✨ Performance improvements (in some cases up to 5x) (740)

👌 Minor Improvements:

- 👌 Add dimensions to megacomplex and dataset_descriptor (702)
- 👌 Improve ordering in k_matrix involved_compartments function (788)
- 👌 Improvements to application of clp_penalties (equal area) (801)
- ♻️ Refactor model.from_dict to parse megacomplex_type from dict and add simple_generator for testing (807)
- ♻️ Refactor model spec (836)
- ♻️ Refactor Result Saving (841)
- ✨ Use ruaml.yaml parser for roundtrip support (893)
- ♻️ Refactor Result and Scheme loading/initializing from files (903)
- ♻️ Several refactoring in `glotaran.Parameter` (910)
- 👌 Improved Reporting of Parameters (910, 914, 918)
- 👌 Scheme now excepts paths to model, parameter and data file without initializing them first (912)

🩹 Bug fixes

- 🩹 Fix/cli0.5 (765)
- 🩹 Fix compartment ordering randomization due to use of set (799)
- 🩹 Fix check_deprecations not showing deprecation warnings (775)
- 🩹 Fix and re-enable IRF Dispersion Test (786)
- 🩹 Fix coherent artifact crash for index dependent models 808
- 🩹 False positive model validation fail when combining multiple default megacomplexes (797)
- 🩹 Fix ParameterGroup repr when created with 'from_list' (827)
- 🩹 Fix for DOAS with reversed oscillations (negative rates) (839)
- 🩹 Fix parameter expression parsing (843)
- 🩹 Use a context manager when opening a nc dataset (848)
- 🚧 Disallow xarray versions breaking plotting in integration tests (900)
- 🩹 Fix 'dataset_groups' not shown in model markdown (906)

📚 Documentation

- 📚 Moved API documentation from User to Developer Docs (776)
- 📚 Add docs for the CLI (784)
- 📚 Fix deprecation in model used in quickstart notebook (834)

🩹 Bug fixes

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

🚧 Maintenance

- 🚇🚧 Updated 'gold standard' result comparison reference ([old](https://github.com/glotaran/pyglotaran-examples/commit/9b8591c668ad7383a908b853339966d5a5f7fe43) -> [new](https://github.com/glotaran/pyglotaran-examples/commit/fc5a5ca0c7fd8b224c85027b510a15717c696c7b))
- 🚇 Refine test_result_consistency (936).

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✨ 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)

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✨ 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)

🔌 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)

- 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)

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