Pyglotaran

- `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)

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✨ Features

- ✨ Official numpy 1.26 support (1374)

🚧 Maintenance

- 🧹 Remove unused dependency: 'rich' (1345)

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✨ Features

- ✨ Python 3.11 support (1161)

🩹 Bug fixes

- 🩹 Fix coherent artifact clp label duplication (1292)

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- `glotaran.model.Model.model_dimension` -> `glotaran.project.Scheme.model_dimension`
- `glotaran.model.Model.global_dimension` -> `glotaran.project.Scheme.global_dimension`
- `<model_file>.type.kinetic-spectrum` -> `<model_file>.default_megacomplex.decay`
- `<model_file>.type.spectral-model` -> `<model_file>.default_megacomplex.spectral`
- `<model_file>.spectral_relations` -> `<model_file>.clp_relations`
- `<model_file>.spectral_relations.compartment` -> `<model_file>.clp_relations.source`
- `<model_file>.spectral_constraints` -> `<model_file>.clp_constraints`
- `<model_file>.spectral_constraints.compartment` -> `<model_file>.clp_constraints.target`
- `<model_file>.equal_area_penalties` -> `<model_file>.clp_area_penalties`
- `<model_file>.irf.center_dispersion` -> `<model_file>.irf.center_dispersion_coefficients`
- `<model_file>.irf.width_dispersion` -> `<model_file>.irf.width_dispersion_coefficients`
- `glotaran.project.Scheme(..., non_negative_least_squares=...)` -> `<model_file>dataset_groups.default.residual_function`
- `glotaran.project.Scheme(..., group=...)` -> `<model_file>dataset_groups.default.link_clp`
- `glotaran.project.Scheme(..., group_tolerance=...)` -> `glotaran.project.Scheme(..., clp_link_tolerance=...)`
- `<scheme_file>.maximum-number-function-evaluations` -> `<scheme_file>.maximum_number_function_evaluations`
- `<model_file>.non-negative-least-squares: true` -> `<model_file>dataset_groups.default.residual_function: non_negative_least_squares`
- `<model_file>.non-negative-least-squares: false` -> `<model_file>dataset_groups.default.residual_function: variable_projection`
- `glotaran.parameter.ParameterGroup.to_csv(file_name=parameters.csv)` -> `glotaran.io.save_parameters(parameters, file_name=parameters.csv)`

🚧 Maintenance

- 🩹 Fix Performance Regressions (between version) (740)
- 🧪🚇 Add integration test result validation (754)
- 🔧 Add more QA tools for parts of glotaran (739)
- 🔧 Fix interrogate usage (781)
- 🚇 Speedup PR benchmark (785)
- 🚇🩹 Use pinned versions of dependencies to run integration CI tests (892)
- 🧹 Move megacomplex integration tests from root level to megacomplexes (894)
- 🩹 Fix artifact download in pr_benchmark_reaction workflow (907)

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- `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, ...)`

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🩹 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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