Changelogο
0.5.0 (2021-10-24)ο
β¨ Featuresο
β¨ Feature: Megacomplex Models (#736)
β¨ Feature: Full Models (#747)
β¨ Damped Oscillation Megacomplex (a.k.a. DOAS) (#764)
β¨ Add Dataset Groups (#851)
β¨ Performance improvements (in some cases up to 5x) (#740)
π Minor Improvements:ο
π Add dimensions to megacomplex and dataset_descriptor (#702)
π Improve ordering in k_matrix involved_compartments function (#788)
π Improvements to application of clp_penalties (equal area) (#801)
β»οΈ Refactor model.from_dict to parse megacomplex_type from dict and add simple_generator for testing (#807)
β»οΈ Refactor model spec (#836)
β»οΈ Refactor Result Saving (#841)
π©Ή Bug fixesο
π©Ή Fix/cli0.5 (#765)
π©Ή Fix compartment ordering randomization due to use of set (#799)
π©Ή Fix check_deprecations not showing deprecation warnings (#775)
π©Ή Fix and re-enable IRF Dispersion Test (#786)
π©Ή Fix coherent artifact crash for index dependent models #808
π©Ή False positive model validation fail when combining multiple default megacomplexes (#797)
π©Ή Fix ParameterGroup repr when created with βfrom_listβ (#827)
π©Ή Fix for DOAS with reversed oscillations (negative rates) (#839)
π©Ή Fix parameter expression parsing (#843)
π©Ή Use a context manager when opening a nc dataset (#848)
π Documentationο
π Moved API documentation from User to Developer Docs (#776)
π Add docs for the CLI (#784)
π Fix deprecation in model used in quickstart notebook (#834)
ποΈ Deprecations (due in 0.7.0)ο
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)
π§ Maintenanceο
π©Ή Fix Performance Regressions (between version) (#740)
π§ͺπ Add integration test result validation (#754)
π§ Add more QA tools for parts of glotaran (#739)
π§ Fix interrogate usage (#781)
π Speedup PR benchmark (#785)
0.4.0 (2021-06-25)ο
β¨ Featuresο
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)
π©Ή Bug fixesο
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 doesnβt prepend β.β 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)
π Pluginsο
ProjectIo
βfolderβ/βlegacyβ plugin to save results (#620)Model
βspectral-modelβ (#672)
π Documentationο
User documentation is written in notebooks (#568)
Documentation on how to write a
DataIo
plugin (#600)
ποΈ Deprecations (due in 0.6.0)ο
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)ο
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)ο
Re-release of version 0.3.1 due to packaging issue
0.3.1 (2021-02-28)ο
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)ο
Significant code refactor with small API changes to parameter relation specification (see docs)
Replaced lmfit with scipy.optimize
0.2.0 (2020-12-02)ο
Large refactor with significant improvements but also small API changes (see docs)
Removed doas plugin
0.1.0 (2020-07-14)ο
Package was renamed to
pyglotaran
on PyPi
0.0.8 (2018-08-07)ο
Changed
nan_policiy
toomit
0.0.7 (2018-08-07)ο
Added support for multiple shapes per compartment.
0.0.6 (2018-08-07)ο
First release on PyPI, support for Windows installs added.
Pre-Alpha Development