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perf: numbafy spatial_autocorr permutations #1303

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perf: numbafy spatial_autocorr permutations #1303

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def5e23
Make most arguments keyword-only, enforced by PLR0917 (#1288)
selmanozleyen Sep 25, 2026
82eb210
Take only the data positionally in the remaining pl/tl functions, and…
selmanozleyen Sep 29, 2026
ca56c19
Take only the data positionally in private helpers too
selmanozleyen Sep 29, 2026
82beb3e
Match the positional shims to v1.8.3's order and point warnings at th…
selmanozleyen Sep 30, 2026
75b4beb
Name the spawned generators rngs, document random_state on sklearn-st…
selmanozleyen Oct 1, 2026
0337f4f
Keep the positional shim outermost in ligrec, co_occurrence and sepal
selmanozleyen Oct 1, 2026
e5449d0
Take only the data positionally in the remaining private data helpers
selmanozleyen Oct 1, 2026
c6e312e
Numbafy spatial_autocorr permutations
selmanozleyen Sep 11, 2026
973fdc5
Score the observed statistic with the permutation kernel, block the p…
selmanozleyen Sep 30, 2026
b97a1f3
Name the spawned permutation generators rngs
selmanozleyen Oct 1, 2026
20b651c
Merge main into spatial-autocorr
selmanozleyen Oct 9, 2026
5c2a1dc
Merge branch 'main' into perf/numbafy-spatial-autocorr
timtreis Oct 9, 2026
5c67994
Merge branch 'main' into perf/numbafy-spatial-autocorr
selmanozleyen Oct 9, 2026
b845c6e
Read connectivities as CSR
selmanozleyen Oct 9, 2026
4980258
Parallelize the per-row precomputes
selmanozleyen Oct 9, 2026
32b9bb9
Score permutations from feature non-zeros
selmanozleyen Oct 10, 2026
07784fc
Retire comments the rewrite outdated
selmanozleyen Oct 10, 2026
04e406b
Centre the variance on the observed score
selmanozleyen Oct 10, 2026
d7cb6f9
Pin the full-gene-list fast path
selmanozleyen Oct 10, 2026
35229d9
Record how the block cap was chosen
selmanozleyen Oct 10, 2026
937f1af
Trim absolute figures from the block-cap note
selmanozleyen Oct 10, 2026
eb25e39
Merge branch 'main' into perf/numbafy-spatial-autocorr
selmanozleyen Oct 10, 2026
ae6b247
Tighten the comments on the block cap
selmanozleyen Oct 10, 2026
fda6f23
Merge remote-tracking branch 'origin/perf/numbafy-spatial-autocorr' i…
selmanozleyen Oct 10, 2026
ee5da47
Dispatch through thread_map
selmanozleyen Oct 10, 2026
f63f117
Plainer wording in the new comments
selmanozleyen Oct 10, 2026
a83d7b9
Correct the comments that had drifted
selmanozleyen Oct 10, 2026
7d8e5c6
Give degenerate features a NaN z-test
selmanozleyen Oct 10, 2026
34ec4f4
Correct the note on the shifted variance
selmanozleyen Oct 10, 2026
2f8d516
Correct the block-cap cost at 100M cells
selmanozleyen Oct 10, 2026
0636ad0
Silence degenerate z-score warning
selmanozleyen Oct 10, 2026
7b71495
Centre dense autocorr features
selmanozleyen Oct 10, 2026
00be7be
Drop GIL note on permutation fill
selmanozleyen Oct 10, 2026
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