π©Ή Use a context manager when opening a nc dataset #848
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avoid file locking when calling xarray.open_dataset
Sourcery Code Quality Reportβ Β Merging this PR will increase code quality in the affected files by 0.84%.
Here are some functions in these files that still need a tune-up:
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Benchmark is done. Checkout the benchmark result page. Benchmark diff v0.4.1 vs. mainParametrized benchmark signatures: BenchmarkOptimize.time_optimize(index_dependent, grouped, weight)Benchmark diff main vs. PRParametrized benchmark signatures: BenchmarkOptimize.time_optimize(index_dependent, grouped, weight) |
Codecov Report
@@ Coverage Diff @@
## main #848 +/- ##
=====================================
Coverage 84.9% 84.9%
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Files 77 77
Lines 4371 4372 +1
Branches 785 785
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+ Hits 3711 3712 +1
Misses 521 521
Partials 139 139
Continue to review full report at Codecov.
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s-weigand
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Oct 21, 2021
jsnel
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Oct 22, 2021
Adds new plot function to plot data and fitted traces for selected wavelengths. * β¨ Added 'plot_fit_overview' function to plot data and fit per wavelength β¨ Also added some convenience functions for data pre-processing * β¨ Added 'wavelength_range' parameter so the user can select data to plot * π§Ή Resticted DatasetConvertible objects to always be xr.Dataset * β»οΈ Factored out extraction of irf location to a seperate function * π Plotted fits and data are now shifted by the irf location * π§Ή Unified xarray typing style * πβ»οΈ Added 'dataset_name' argument, use 'load_dataset' to load result from file Ref.: glotaran/pyglotaran#848 * β»οΈ Refactored load_data and result_dataset_mapping to work with DataArray π result_dataset_mapping and thus also plot_data_and_fits and plot_fit_overview, no work with single file paths * β»οΈβ¨ Made 'plot_fit_overview' work properly with unevenly spaced wavelegths β»οΈ This required to remove the argument 'wavelength_range' and instead pass the wavelengths directly to 'plot_fit_overview' which gives the user more control. For convenience the function 'select_plot_wavelengths' was added, which provies the functionality of 'wavelength_range' * β»οΈ Moved 'plot_fit_overview' helper functions to plotting.utils 'maximum_coordinate_range' and 'add_unique_figure_legend' * β¨ Added figsize argument to plot_data_overview * π Reexport 'select_plot_wavelengths' from plotting.data for convenience * β¨ Added divide_by_scale parameter to divide data by dataset_scale This needs a feature added in pyglotaran 0.5.0, for older results it will show a warning. * π Made function name in 'select_plot_wavelengths' warning dynamic * π Added comments and docstrings to plot style code * π Made the ylabel of plots an argument and default to 'a.u.' * β»οΈ Addressed requested renaming and moving functions suited for this PR Ref: #39 (review) * β»οΈ Moved plot_concentrations to its own module with the same name
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avoid file locking when calling xarray.open_dataset
Checklist
Closes issues
closes #847