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time windows in statistics#2948

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petrelharp wants to merge 20 commits intotskit-dev:maintskit-dev/tskit:mainfrom petrelharp:time_windowspetrelharp/tskit:time_windowsCopy head branch name to clipboard

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Commits on Oct 21, 2024

• example test for time windows

  

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• a little more flailing at beginning tests

  

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• first simple test for AFS in branch mode with time windows

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• AFS non-naive version with time windows + Some tests

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• Improve AFS branch mode

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• fix AFS tests

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• Fix naive branch general stat

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• intermediate changes to C AFS implementation with time windows

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Commits on Oct 22, 2024

• tw afs C implementation

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• Better dimension drop with time windows

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• AFS branch mode with time windows to review

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Commits on Oct 30, 2024

• Adapting some tests with new time_windows parameter

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• time_windows addition after code rebase

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Commits on Oct 31, 2024

• Fix some tests failing because of time_windows

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• Remove unused parameters in afs function

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• Fixing a memory issue in tsk_treeseq_update_branch_afs

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Commits on Nov 19, 2024

• Fixing some time_windows issues with AFS

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• Adjusting some stats tests using time_windows

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Commits on Dec 11, 2024

• Adjusting some tests trying to pass codecov

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Commits on Jan 18, 2025

• Updating naive_branch_... and branch_allele_freq... in tests

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