Skip to content

Latest commit

 

History

History
225 lines (158 loc) · 9.07 KB

changelog.md

File metadata and controls

225 lines (158 loc) · 9.07 KB
Raw

Changelog

0.6.0 (Unreleased)

✨ Features

  • ✨ Add simple decay megacomplexes (#860)

👌 Minor Improvements:

🩹 Bug fixes

  • 🩹 Fix Crash in optimization_group_calculator_linked when using guidance spectra (#950)

📚 Documentation

🗑️ Deprecations (due in 0.8.0)

🚧 Maintenance

  • 🔧 Improve packaging tooling (#923) 🔧🚇 Exclude test files from duplication checks on sonarcloud (#959)

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

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)

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).

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)

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, ...)

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)

0.3.2 (2021-02-28)

  • Re-release of version 0.3.1 due to packaging issue

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)

0.3.0 (2021-02-11)

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

0.2.0 (2020-12-02)

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

0.1.0 (2020-07-14)

  • Package was renamed to pyglotaran on PyPi

0.0.8 (2018-08-07)

  • Changed nan_policiy to omit

0.0.7 (2018-08-07)

  • Added support for multiple shapes per compartment.

0.0.6 (2018-08-07)

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