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fix(lineage_fate_correlation): use cached clone trajectory data #659

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Merged
merged 32 commits into from
Mar 31, 2025
Merged

fix(lineage_fate_correlation): use cached clone trajectory data #659

merged 32 commits into from
Mar 31, 2025

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cameronraysmith
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@cameronraysmith
chore(scripts): add script to generate clone trajectory data
e49ee6d 
Signed-off-by: Cameron Smith <cameron.ray.smith@gmail.com>
@cameronraysmith cameronraysmith self-assigned this Mar 25, 2025
@cameronraysmith cameronraysmith added this to the 0.4.x milestone Mar 25, 2025
@cameronraysmith cameronraysmith added bug Something isn't working data build-images Control image build on PRs dev-mode Do not rebuild images and use branch name instead of git short SHA for image tags labels Mar 25, 2025
@cameronraysmith
fix(datasets): add clone trajectory data sets
e2b4e5c 
Signed-off-by: Cameron Smith <cameron.ray.smith@gmail.com>
@cameronraysmith
fix(time_fate_correlation): refactor create_time_lineage_fate_correla…
695a98c 
…tion_plot for workflow usage

Signed-off-by: Cameron Smith <cameron.ray.smith@gmail.com>
@cameronraysmith
fix(workflows): use create_time_lineage_fate_correlation_plot task fu…
07b0ee3 
…nction

Signed-off-by: Cameron Smith <cameron.ray.smith@gmail.com>
@cameronraysmith
chore(workflows): revert cache to 2024.8.15
18e70f9 
Signed-off-by: Cameron Smith <cameron.ray.smith@gmail.com>
@cameronraysmith
chore(workflows): bump lineage fate correlation cache to 2024.8.15.6
e7f2196 
Signed-off-by: Cameron Smith <cameron.ray.smith@gmail.com>
@cameronraysmith
fix(constants): disable demo flag
ef3518b 
Signed-off-by: Cameron Smith <cameron.ray.smith@gmail.com>
@cameronraysmith cameronraysmith added skip-ci Skip CI workflow execute-workflow Control workflow execution on PRs and removed skip-ci Skip CI workflow labels Mar 26, 2025
@cameronraysmith
fix(main_workflow): reenable all data sets
776ed2c 
Signed-off-by: Cameron Smith <cameron.ray.smith@gmail.com>
@cameronraysmith cameronraysmith added execute-workflow Control workflow execution on PRs and removed execute-workflow Control workflow execution on PRs labels Mar 27, 2025
@cameronraysmith
fix(lineage_fate_correlation): absorb nan cleanup from plotting funct…
d194fea 
…ion to get_clone_trajectory

Signed-off-by: Cameron Smith <cameron.ray.smith@gmail.com>
@cameronraysmith
fix(tasks): compute clone trajectories in time lineage fate correlati…
4f557a9 
…on task

- removed from plotting function

Signed-off-by: Cameron Smith <cameron.ray.smith@gmail.com>
@cameronraysmith
refactor(_trajectory): migrate analysis code from plots to analysis
54178c3 
Signed-off-by: Cameron Smith <cameron.ray.smith@gmail.com>
@cameronraysmith
fix(trajectory): use input times and error on empty centroids
71174d2 
Signed-off-by: Cameron Smith <cameron.ray.smith@gmail.com>
@cameronraysmith
fix(analysis): include trajectory functions
16d382e 
Signed-off-by: Cameron Smith <cameron.ray.smith@gmail.com>
@cameronraysmith
fix(plots): use trajectory functions from analysis package
38809fc 
Signed-off-by: Cameron Smith <cameron.ray.smith@gmail.com>
@cameronraysmith
fix(tasks): use trajectory functions from analysis package
6f50788 
Signed-off-by: Cameron Smith <cameron.ray.smith@gmail.com>
@cameronraysmith
fix(scripts): use trajectory functions from analysis package
5c38692 
Signed-off-by: Cameron Smith <cameron.ray.smith@gmail.com>
@cameronraysmith
chore(workflows): lineage fate correlation cache 2024.8.15.7
d14d288 
Signed-off-by: Cameron Smith <cameron.ray.smith@gmail.com>
@cameronraysmith
fix(make): support cleaning up workflow artifacts for multiple data sets
9fcd1af 
Signed-off-by: Cameron Smith <cameron.ray.smith@gmail.com>
@cameronraysmith
chore(archive): add larry data assembly archive
5693fe1 
Signed-off-by: Cameron Smith <cameron.ray.smith@gmail.com>
@cameronraysmith
chore(archive): add larry data subpopulation extraction archive
deb5fca 
Signed-off-by: Cameron Smith <cameron.ray.smith@gmail.com>
@cameronraysmith
chore(analysis): add subpopulation extraction from archive
3bb108b 
Signed-off-by: Cameron Smith <cameron.ray.smith@gmail.com>
@cameronraysmith
test(analysis): add subpopulation extraction smoke test
634278e 
Signed-off-by: Cameron Smith <cameron.ray.smith@gmail.com>
@cameronraysmith
fix(fixture): add function to generate larry data fixture
9b9491c 
Signed-off-by: Cameron Smith <cameron.ray.smith@gmail.com>
@cameronraysmith
test(data): add larry multilineage 50x6 fixture
cb4064c 
Signed-off-by: Cameron Smith <cameron.ray.smith@gmail.com>
@cameronraysmith
test(conftest): add adata_larry_multilineage_50_6 fixture
0b0388a 
Signed-off-by: Cameron Smith <cameron.ray.smith@gmail.com>
@cameronraysmith
test(trajectory): add smoke tests for trajectory module
43a9aef 
Signed-off-by: Cameron Smith <cameron.ray.smith@gmail.com>
@cameronraysmith
fix(tasks): use vendored data for multilineage clone trajectory
ce26b54 
Signed-off-by: Cameron Smith <cameron.ray.smith@gmail.com>
@cameronraysmith
fix(subpopulation): update types
cc3b3d8 
Signed-off-by: Cameron Smith <cameron.ray.smith@gmail.com>
@cameronraysmith
fix(plots): prefer hexbin in lineage fate correlation plot
77e2487 
Signed-off-by: Cameron Smith <cameron.ray.smith@gmail.com>
@cameronraysmith
fix(plots): downsample cluster data for larger than 5000 obs
e02e02f 
Signed-off-by: Cameron Smith <cameron.ray.smith@gmail.com>
@cameronraysmith
chore(workflows): lineage fate correlation cache 2024.8.15.8
1a49838 
Signed-off-by: Cameron Smith <cameron.ray.smith@gmail.com>
@cameronraysmith
chore(version): 0.4.1
bab3401 
Signed-off-by: Cameron Smith <cameron.ray.smith@gmail.com>
@cameronraysmith cameronraysmith added skip-ci Skip CI workflow and removed build-images Control image build on PRs execute-workflow Control workflow execution on PRs dev-mode Do not rebuild images and use branch name instead of git short SHA for image tags labels Mar 31, 2025
@cameronraysmith cameronraysmith marked this pull request as ready for review March 31, 2025 04:13
@cameronraysmith cameronraysmith requested a review from a team as a code owner March 31, 2025 04:13
@cameronraysmith cameronraysmith merged commit bab3401 into main Mar 31, 2025
19 of 21 checks passed
@cameronraysmith cameronraysmith deleted the 656-merge branch March 31, 2025 04:14
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estimation of lineage-traced clonal fate progression on multilineage data requires merge rather than recomputation
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