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Merge main into v1.6.0 branch #463

Merged
merged 145 commits into from
Jan 6, 2025
Merged

Merge main into v1.6.0 branch #463

merged 145 commits into from
Jan 6, 2025

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freemansw1
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I couldn't figure out how to easily do this as part of #462 , so doing it in a separate PR, if that's ok @w-k-jones .

This PR merges the changes that are now in main (and from RC_V1.5.x) into RC_v1.6.0.

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w-k-jones and others added 30 commits November 29, 2023 11:37
@w-k-jones
Change distance search in merge_split_MEST to use BallTree query, and…
41a6ed0 
… add PBC support
@w-k-jones
Fix dimension order for coordinates in merge_split
098e4d8
@w-k-jones
Add tests for merge_split with PBCs
6b5cb68
@w-k-jones
Speed up adding edges to graph using add_weighted_edges_from
3deffa9
@w-k-jones
Remove unused imports
2d5d366
@w-k-jones
Apply frame_len filter before assigning edges to the graph, and add n…
1c7ed6f 
…ew test for frame_len parameter
@w-k-jones
Use connected_components from scipy.sparse.csgraph to link cells into…
a51f027 
… tracks
@w-k-jones
Fix handling of unassigned features in merge_split_MEST and add test …
5b4aa05 
…for unassigned features
@w-k-jones
Remove unused import
ce36b3b
@w-k-jones
Fix distance calculation for 2D case
eff22f6
@w-k-jones
Add flag for cells starting with split/ending with merge
de01424
@w-k-jones
Rename cell_starts_with_merge flag
0b75bae
@w-k-jones
Add test for 3D merge/split and fix coordinate stack axis
c888bf9
@w-k-jones
Fix application of dxy and dz to 3D feature locations in filter_min_d…
81bdcce 
…istance
@w-k-jones
Switch to using scipy.sparse.csgraph implementation of minimum spanni…
71c4b39 
…ng tree
@w-k-jones
Cast start_node_cells and end_node_cells to np.int32 to avoid type mi…
c63632a 
…smatch
@w-k-jones
Use groupby instead of bincount to count number of child cells/features
fa4659c
@w-k-jones
Recalculate start and end node cells after applying minimum spanning …
e9ec119 
…tree
@freemansw1
Added notebook for big datasets
68f2978
@freemansw1
Merge remote-tracking branch 'upstream/RC_v1.5.x' into tobathon_big_d…
7584bd4 
…ataset_update
@freemansw1
Merge branch 'RC_v1.5.x' into tobathon_big_dataset_update
08a5420
updated docstrings for n_min_threshold
adabf96
black formatting
3a18cfb
@w-k-jones
Add optional typing for default None keywords
900f72b
@w-k-jones
Clip values to range of hdim size in feature_position, or hdim size +…
cdfc8dd 
… 1 if periodic
@w-k-jones
Reformatting
8d0fcb8
@w-k-jones
Remove erroneus docstring entry
294ced5
@freemansw1
removed index.rst and black-formatted the notebook and documentation …
39ae935 
…page
@freemansw1
Update to improve visibility of example notebooks
61371a6
@freemansw1
black format all notebooks
a9c74c7
@freemansw1
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We should hold off merging this until #465 is merged.

w-k-jones
w-k-jones approved these changes Nov 4, 2024
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Great, thanks for sorting this! All the merge conflicts are resolved as well as the issues in some places where the merge was overwriting changes. Happy for this to be merged after #465

freemansw1 and others added 10 commits November 8, 2024 14:15
@freemansw1
Merge pull request tobac-project#465 from freemansw1/fix_CI_issues
706b3ee 
Fix CI issues due to old conda version
@freemansw1
fix linting syntax error
dd83955
@freemansw1
update checkout version
ddf7f96
@freemansw1
fix python versions not tested
de4b9c7
@freemansw1
add future annotations
0d06863
@freemansw1
add future annotations to tracking
dfb21a6
@freemansw1
add future annotations to tracking tests
e527b5e
@w-k-jones
Change .data to .values call in get_statistics_from_mask to prevent p…
0b75b46 
…assing dask array to get_statistics, and added test for dask array input
@freemansw1
Merge pull request tobac-project#468 from freemansw1/fix_typing_error
cafc779 
Fix Matrix Testing & Typing Error
@w-k-jones
Merge pull request tobac-project#474 from w-k-jones/fix_calculate_are…
feeff81 
…a_dask

Fix bug in bulk_statistics when providing a DataArray or iris cube with dask array data
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Just as a reminder that we should merge the additional changes from main once v1.5.5 is released

JuliaKukulies
JuliaKukulies approved these changes Jan 5, 2025
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@freemansw1, will you merge in the latest changes from main now that the release of v.1.5.5 was pushed to conda-forge?

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Thanks all. Merging now. Note that the failing test is linting, which as previously discussed, always uses the old version of the CI script, so it should be resolved regardless.

@freemansw1 freemansw1 merged commit 76fdd71 into tobac-project:RC_v1.6.0 Jan 6, 2025
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@w-k-jones w-k-jones w-k-jones approved these changes

@JuliaKukulies JuliaKukulies JuliaKukulies approved these changes

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