changelog.md

Changelog

(changes-0_7_4)=

🚀 0.7.4 (Unreleased)

✨ Features

👌 Minor Improvements:

🩹 Bug fixes

📚 Documentation

🗑️ Deprecations (due in 0.9.0)

🗑️❌ Deprecated functionality removed in this release

🚧 Maintenance

(changes-0_7_3)=

🚀 0.7.3 (2024-08-25)

✨ Features

• ✨ Add official Python 3.12 support (#1437)
• ✨ Add support for pfid megacomplex (#1510)
• ✨ Add official numpy 2 support (#1520, #1503)

🩹 Bug fixes

• 🩹 Fix ordering bug in MatrixProvider class (#1512)
• 🩹 Fix AttributeError validating bad DOAS user definition (#1513)
• 🩹 Fix error with xarray==2024.7.0 due to breaking change in applied deprecation (#1458)

🚧 Maintenance

-🧹🚇 Remove asv benchmarks and binder integration (#1511)

(changes-0_7_2)=

🚀 0.7.2 (2023-12-07)

✨ Features

• ✨ Official numpy 1.26 support (#1374)

🚧 Maintenance

• 🧹 Remove unused dependency: 'rich' (#1345)

(changes-0_7_1)=

🚀 0.7.1 (2023-07-28)

✨ Features

• ✨ Python 3.11 support (#1161)

🩹 Bug fixes

• 🩹 Fix coherent artifact clp label duplication (#1292)

(changes-0_7_0)=

🚀 0.7.0 (2023-03-27)

💥 BREAKING CHANGE

• 💥🚧 Dropped support for Python 3.8 and 3.9 and only support 3.10 (#1135)

✨ Features

• ✨ Add optimization history to result and iteration column to parameter history (#1134)
• ♻️ Complete refactor of model and parameter packages using attrs (#1135)
• ♻️ Move index dependent calculation to megacomplexes for speed-up (#1175)
• ✨ Add PreProcessingPipeline (#1256, #1263)

👌 Minor Improvements:

• 👌🎨 Wrap model section in result markdown in details tag for notebooks (#1098)
• 👌 Allow more natural column names in pandas parameters file reading (#1174)
• ✨ Integrate plugin system into Project (#1229)
• 👌 Make yaml the default plugin when passing a folder to save_result and load_result (#1230)
• ✨ Allow usage of subfolders in project API for parameters, models and data (#1232)
• ✨ Allow import of xarray objects in project API import_data (#1235)
• 🩹 Add number_of_clps to result and correct degrees_of_freedom calculation (#1249)
• 👌 Improve Project API data handling (#1257)
• 🗑️ Deprecate Result.number_of_parameters in favor of Result.number_of_free_parameters (#1262)
• 👌Improve reporting of standard error in case of non_negative constraint in the parameter (#1320)

🩹 Bug fixes

• 🩹 Fix result data overwritten when using multiple dataset_groups (#1147)
• 🩹 Fix for normalization issue described in #1157 (multi-gaussian irfs and multiple time ranges (streak))
• 🩹 Fix for crash described in #1183 when doing an optimization using more than 30 datasets (#1184)
• 🩹 Fix pretty_format_numerical for negative values (#1192)
• 🩹 Fix yaml result saving with relative paths (#1199)
• 🩹 Fix model markdown render for items without label (#1213)
• 🩹 Fix wrong file loading due to partial filename matching in Project (#1212)
• 🩹 Fix Project.import_data path resolving for different script and cwd (#1214)
• 👌 Refine project API (#1240)
• 🩹📚 Fix search in docs (#1268)

📚 Documentation

• 📚 Update quickstart guide to use Project API (#1241)

🗑️ Deprecations (due in 0.8.0)

• <model_file>.clp_area_penalties -> <model_file>.clp_penalties
• glotaran.ParameterGroup -> glotaran.Parameters
• Command Line Interface (removed without replacement) (#1228)
• Project.generate_model (removed without replacement)
• Project.generate_parameters (removed without replacement)
• glotaran.project.Result.number_of_data_points -> glotaran.project.Result.number_of_residuals
• glotaran.project.Result.number_of_parameters -> glotaran.project.Result.number_of_free_parameters

🗑️❌ Deprecated functionality removed in this release

• glotaran.project.Scheme(..., non_negative_least_squares=...)
• glotaran.project.Scheme(..., group=...)
• glotaran.project.Scheme(..., group_tolerance=...)
• <model_file>.non-negative-least-squares: true
• <model_file>.non-negative-least-squares: false
• glotaran.parameter.ParameterGroup.to_csv(file_name=parameters.csv)

🚧 Maintenance

• 🚇🩹 Fix wrong comparison in pr_benchmark workflow (#1097)
• 🔧 Set sourcery-ai target python version to 3.8 (#1095)
• 🚇🩹🔧 Fix manifest check (#1099)
• ♻️ Refactor: optimization (#1060)
• ♻️🚇 Use GITHUB_OUTPUT instead of set-output in github actions (#1166, #1177)
• 🚧 Add pinned version of odfpy to requirements_dev.txt (#1164)
• ♻️ Use validation action and validation as a git submodule (#1165)
• 🧹 Upgrade syntax to py310 using pyupgrade (#1162)
• 🧹 Remove unused 'type: ignore' (#1168)
• 🚧 Raise minimum dependency version to releases that support py310 (#1170)
• 🔧 Make mypy and doc string linters opt out instead of opt in (#1173)

(changes-0_6_0)=

🚀 0.6.0 (2022-06-06)

✨ 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)
• 🚧🔧 Add 'extras' and 'full' extras_require installation options (#1089)

🩹 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)

(changes-0_5_1)=

🚀 0.5.1 (2021-12-31)

🩹 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

(changes-0_5_0)=

🚀 0.5.0 (2021-12-01)

✨ 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)

🗑️ Deprecations (due in 0.7.0)

• 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)

(changes-0_4_2)=

🚀 0.4.2 (2021-12-31)

🩹 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 -> new)
• 🚇 Refine test_result_consistency (#936).

(changes-0_4_1)=

🚀 0.4.1 (2021-09-07)

✨ 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)

(changes-0_4_0)=

🚀 0.4.0 (2021-06-25)

✨ 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)

🗑️ Deprecations (due in 0.6.0)

• 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, ...)

(changes-0_3_3)=

🚀 0.3.3 (2021-03-18)

• 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)

(changes-0_3_2)=

🚀 0.3.2 (2021-02-28)

• Re-release of version 0.3.1 due to packaging issue

(changes-0_3_1)=

🚀 0.3.1 (2021-02-28)

• 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)

(changes-0_3_0)=

🚀 0.3.0 (2021-02-11)

• Significant code refactor with small API changes to parameter relation specification (see docs)
• Replaced lmfit with scipy.optimize

(changes-0_2_0)=

🚀 0.2.0 (2020-12-02)

• Large refactor with significant improvements but also small API changes (see docs)
• Removed doas plugin

(changes-0_1_0)=

🚀 0.1.0 (2020-07-14)

• Package was renamed to pyglotaran on PyPi

(changes-0_0_8)=

🚀 0.0.8 (2018-08-07)

• Changed nan_policiy to omit

(changes-0_0_7)=

🚀 0.0.7 (2018-08-07)

• Added support for multiple shapes per compartment.

(changes-0_0_6)=

🚀 0.0.6 (2018-08-07)

• First release on PyPI, support for Windows installs added.
• Pre-Alpha Development

🎉 Initial Commit (2016-05-09)

• Development on what would become pyglotaran started.