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Merge v1.5.4 into RC_v1.6.0#462

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w-k-jones wants to merge 116 commits intoRC_v1.6.0tobac-project/tobac:RC_v1.6.0from maintobac-project/tobac:mainCopy head branch name to clipboard

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Commits on Nov 29, 2023

• Change distance search in merge_split_MEST to use BallTree query, and add PBC support

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• Fix dimension order for coordinates in merge_split

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• Add tests for merge_split with PBCs

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• Speed up adding edges to graph using add_weighted_edges_from

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• Remove unused imports

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• Apply frame_len filter before assigning edges to the graph, and add new test for frame_len parameter

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• Use connected_components from scipy.sparse.csgraph to link cells into tracks

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• Fix handling of unassigned features in merge_split_MEST and add test for unassigned features

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• Remove unused import

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• Fix distance calculation for 2D case

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• Add flag for cells starting with split/ending with merge

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• Rename cell_starts_with_merge flag

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• Add test for 3D merge/split and fix coordinate stack axis

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• Fix application of dxy and dz to 3D feature locations in filter_min_distance

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• Switch to using scipy.sparse.csgraph implementation of minimum spanning tree

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• Cast start_node_cells and end_node_cells to np.int32 to avoid type mismatch

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Commits on Nov 30, 2023

• Use groupby instead of bincount to count number of child cells/features

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• Recalculate start and end node cells after applying minimum spanning tree

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Commits on Feb 16, 2024

• Added notebook for big datasets

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Commits on Mar 13, 2024

• Merge remote-tracking branch 'upstream/RC_v1.5.x' into tobathon_big_dataset_update

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Commits on May 9, 2024

• Merge branch 'RC_v1.5.x' into tobathon_big_dataset_update

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Commits on Jun 21, 2024

• updated docstrings for n_min_threshold

  

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• black formatting

  

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Commits on Jun 24, 2024

• Add optional typing for default None keywords

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• Clip values to range of hdim size in feature_position, or hdim size + 1 if periodic

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• Reformatting

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• Remove erroneus docstring entry

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Commits on Jul 18, 2024

• removed index.rst and black-formatted the notebook and documentation page

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• Update to improve visibility of example notebooks

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• black format all notebooks

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• fix code block

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Commits on Jul 23, 2024

• fix warning statement when feature IDs are not unique

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• Merge remote-tracking branch 'upstream/RC_v1.5.x' into tobathon_big_dataset_update

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• fix for sphinx_toolbox

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• allow for different ID column name at locations where it was not fixed yet

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• added parameters for bulk statistic tests and an extra warning when feature labels are non-unique within the same timestep

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• black formatting

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• black formatting with right versiobn

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• add sphinx_toolbox to requirements

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• fix to just import sphinx toolbox code module

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• fixed message

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• fix code block

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• and one more formatting

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Commits on Jul 24, 2024

• Merge remote-tracking branch 'upstream/RC_v1.5.x' into tobathon_big_dataset_update

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• Merge remote-tracking branch 'upstream/RC_v1.5.x' into bulk_stats_bug_fix

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• made warning message more readable

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Commits on Aug 14, 2024

• fixed docstrings and type hint according to Fabians comments

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• Merge pull request #432 from JuliaKukulies/n_min_thresholds_docs

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Commits on Aug 15, 2024

• Merge pull request #408 from freemansw1/tobathon_big_dataset_update

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• Merge pull request #437 from JuliaKukulies/bulk_stats_bug_fix

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Commits on Sep 11, 2024

• Merge pull request #434 from w-k-jones/fix_interp_fp_bug

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Commits on Sep 19, 2024

• fixed error message in bulk statistics when none of the feature labels matches with segmentation mask

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• tested with notebook

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Commits on Sep 20, 2024

• corrected warning for feature labels in every time step

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• formatting

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• allows calculation of statistics on raw data

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• black formatting

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• black formatting

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• black formatting

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• more formatting

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Commits on Sep 23, 2024

• removed tests from notebook

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• updated reference

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Commits on Sep 24, 2024

• Fix bug in transform_feature_points when warning of dropped features but no features have been removed

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• Formatting

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• Fix depreciation warnings in tests

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• Add python 3.12 to matrix testing

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• Add optional use of dz or vertical_coord for specifying vertical locations of features in merge split, and improve documentation

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• Remove erroneus import

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• Merge branch 'RC_v1.5.x' of https://github.com/climate-processes/tobac into merge_split_pbc

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• Fix changed import location of build_distance_function

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• added the main tobac publications to top of publication list

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• Merge branch 'matrix_testing_fix' into reference_update

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Commits on Sep 25, 2024

• Fix bug that caused statistics to be recalculated for each threshold during feature detection

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• Move filter_min_distance to after coordinate interpolation in feature detection

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• Enable use of vertical coordinate rather than fixed dz in filter_min_distance

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• Add tests for minimum distance filtering using vertical coord

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• Formatting

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• Manually reformat

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Commits on Sep 26, 2024

• Merge pull request #451 from w-k-jones/matrix_testing_fix

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• merge in matrix test fix

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• Merge remote-tracking branch 'origin/RC_v1.5.x' into RC_v1.5.4

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• Merge branch 'RC_v1.5.x' of https://github.com/climate-processes/tobac into min_distance_3D_fix

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• Merge branch 'RC_v1.5.x' of https://github.com/climate-processes/tobac into merge_split_pbc

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• directly pass data_i to statistics function instead of making a copy

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• added accidently removed pre-commit yaml file

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Commits on Sep 28, 2024

• Merge pull request #372 from w-k-jones/merge_split_pbc

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Commits on Oct 11, 2024

• corrected type hints and docstrings because we require *fields to be an xarray dataarray

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• allow some tolerance in the time selection for xarray in the statistics calculation

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Commits on Oct 12, 2024

• added test for bulk stats to ensure all timesteps are added to feature output dataframe

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• corrected notebook issue

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Commits on Oct 14, 2024

• Merge pull request #450 from JuliaKukulies/reference_update

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• Merge pull request #449 from JuliaKukulies/bulk_stats_on_raw_input

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• Merge branch 'RC_v1.5.x' into min_distance_3D_fix

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• Merge remote-tracking branch 'upstream/RC_v1.5.x' into RC_v1.5.4

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Commits on Oct 15, 2024

• Merge pull request #448 from JuliaKukulies/RC_v1.5.4

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• switch json schema to basic github actions python install

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• update check_formatting job

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Commits on Oct 17, 2024

• Re-add statistics on unsmoothed data

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• Merge pull request #452 from tobac-project/min_distance_3D_fix

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• update black formatting check

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• update black formatting check

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• remove python version requirement

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• switch to micromamba

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• updates to micromamba-shell

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• switch to using an environment file rather than mamba install

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• reformatted files with black 24.x

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• Merge branch 'RC_v1.5.x' into fix_json_check

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• merged latest changes and reformatted

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Commits on Oct 18, 2024

• Merge pull request #457 from freemansw1/fix_json_check

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• updated version in __init__.py

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• Merge remote-tracking branch 'upstream/RC_v1.5.x' into RC_v1.5.x

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• rerun notebooks

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• updated changelog

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• fix bug with some iris/xarray combinations for the example notebook

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Commits on Oct 19, 2024

• fix ffmpeg error in notebook

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Commits on Oct 21, 2024

• Merge pull request #459 from tobac-project/RC_v1.5.x

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