tobac 1.5.0

[freemansw1]

Changelog

Enhancements for Users

• Feature detection and tracking in three dimensions is now supported #209
• Feature detection, segmentation, and tracking across periodic boundaries is now supported #259
• Transformation of feature detection points to allow segmentation on a new grid is now supported #242
• n_min_threshold in feature detection can now be set for each threshold level instead of uniformly for all thresholds #208
• Feature detection now has the option to only detect a feature if all previous thresholds have been met #283
• Unsegmented points can now have their marker value selected #285
• Minimum distance filtering is now substantially faster #249
• combine_feature_dataframes now allows the retention of feature numbers #300
• scikit-learn is now a required dependency; pytables and cf-units are no longer direct dependencies of tobac #204

Bug fixes

• An error is now raised if none of the search range parameters (v_max, d_max, d_min) are set in linking_trackpy #223
• Minimum distance filtering in feature detection (set through min_distance in feature_detection_multithreshold, run through filter_min_distance) has been fixed to properly work when target=minimum. #244
• Interpolated numeric coordinates now preserve their datatypes (i.e., floats stay floats) in feature detection #250
• Fixes to the internal find_axis_from_coord utility to allow for non-dimensional coordinates to be correctly dealt with #255
• Jupyter notebooks changed to use string paths to work around an Iris bug #294
• Minimum distance filtering updated to produce consistent results #249

Documentation

• Enhancements to the documentation of how tobac links features together 210
• Fixes to the API documentation generation when using type hints #305

Internal Enhancements

• New converting decorators (xarray_to_iris, iris_to_xarray, xarray_to_irispandas, irispandas_to_xarray) have been added for internal use that will allow the upcoming transition to xarray throughout tobac to occur more smoothly. #179
• The utils module has been broken up from a single utils.py file to multiple files inside a utils folder, allowing for ease of maintenance and fewer long code files. #191
• scipy.interpolate.interp2d in add_coordinates and add_coordinates_3D has been replaced with scipy.interpolate.interpn as interp2d has been deprecated. #279
• setup.py updated to draw its required packages from requirements.txt #288

Repository Enhancements

• New CI was added to automatically check the example and documentation Jupyter notebooks #258, #290
• The check_formatting CI action has been revised to install dependencies through conda #288
• Repository authors updated #289
• CI added to check author list formatting for Zenodo #292

Deprecations

• All functions in centerofgravity.py (calculate_cog, calculate_cog_untracked, center_of_gravity) have been deprecated and will be removed or significantly changed in v2.0. #200
• plot_mask_cell_track_follow, plot_mask_cell_individual_follow, plot_mask_cell_track_static, plot_mask_cell_individual_static, plot_mask_cell_track_2D3Dstatic, plot_mask_cell_track_3Dstatic, plot_mask_cell_individual_3Dstatic, and plot_mask_cell_track_static_timeseries in plotting.py have been deprecated and will be removed or significantly changed in v2.0. #200
• The wrapper functions in wrapper.py (tracking_wrapper and maketrack) have been deprecated and will be removed in v2.0. #200
• cell_statistics_all, cell_statistics, and cog_cell in the analysis module have been deprecated and will be removed or significantly changed in v2.0. #207
• tobac.utils.combine_tobac_feats has been renamed to tobac.utils.combine_feature_dataframes, and the original name has been deprecated and will be removed in a future release. #300

All changes: v1.4.2...v1.5.0
Full Changelog: https://github.com/tobac-project/tobac/blob/d819159d08896cb4237db6dfb538a6944a879413/CHANGELOG.md

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This discussion was created from the release tobac 1.5.0.