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perf: numbafy spatial_autocorr permutations - #1303

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selmanozleyen:perf/numbafy-spatial-autocorr

Draft

perf: numbafy spatial_autocorr permutations#1303
selmanozleyen wants to merge 33 commits into
scverse:mainfrom
selmanozleyen:perf/numbafy-spatial-autocorr

Commits on Oct 1, 2026
Commits on Oct 9, 2026
- Merge main into spatial-autocorr
  selmanozleyen
  committed
  20b651c
- Merge branch 'main' into perf/numbafy-spatial-autocorr
  timtreis
  authored
  5c2a1dc
- Merge branch 'main' into perf/numbafy-spatial-autocorr
  selmanozleyen
  authored
  5c67994
- Read connectivities as CSR
  selmanozleyen
  committed
  b845c6e
- Parallelize the per-row precomputes
  selmanozleyen
  committed
  4980258
Commits on Oct 10, 2026
- Score permutations from feature non-zeros
  selmanozleyen
  committed
  32b9bb9
- Retire comments the rewrite outdated
  selmanozleyen
  committed
  07784fc
- Centre the variance on the observed score
  selmanozleyen
  committed
  04e406b
- Pin the full-gene-list fast path
  selmanozleyen
  committed
  d7cb6f9
- Record how the block cap was chosen
  selmanozleyen
  committed
  35229d9
- Trim absolute figures from the block-cap note
  selmanozleyen
  committed
  937f1af
- Merge branch 'main' into perf/numbafy-spatial-autocorr
  selmanozleyen
  authored
  eb25e39
- Tighten the comments on the block cap
  selmanozleyen
  committed
  ae6b247
- Merge remote-tracking branch 'origin/perf/numbafy-spatial-autocorr' into perf/autocorr-reduce
  selmanozleyen
  committed
  fda6f23
- Dispatch through thread_map
  selmanozleyen
  committed
  ee5da47
- Plainer wording in the new comments
  selmanozleyen
  committed
  f63f117
- Correct the comments that had drifted
  selmanozleyen
  committed
  a83d7b9
- Give degenerate features a NaN z-test
  selmanozleyen
  committed
  7d8e5c6
- Correct the note on the shifted variance
  selmanozleyen
  committed
  34ec4f4
- Correct the block-cap cost at 100M cells
  selmanozleyen
  committed
  2f8d516
- Silence degenerate z-score warning
  selmanozleyen
  committed
  0636ad0
- Centre dense autocorr features
  selmanozleyen
  committed
  7b71495
- Drop GIL note on permutation fill
  selmanozleyen
  committed
  00be7be

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perf: numbafy spatial_autocorr permutations - #1303

perf: numbafy spatial_autocorr permutations#1303
selmanozleyen wants to merge 33 commits into
scverse:mainfrom
selmanozleyen:perf/numbafy-spatial-autocorr

Commits on Oct 1, 2026

Make most arguments keyword-only, enforced by PLR0917 (#1288)

Take only the data positionally in the remaining pl/tl functions, and name v1.9.0 in the warning

Take only the data positionally in private helpers too

Match the positional shims to v1.8.3's order and point warnings at the caller

Name the spawned generators rngs, document random_state on sklearn-style estimators

Keep the positional shim outermost in ligrec, co_occurrence and sepal

Take only the data positionally in the remaining private data helpers

Numbafy spatial_autocorr permutations

Score the observed statistic with the permutation kernel, block the permutations, keep backend in the shim

Name the spawned permutation generators rngs

Commits on Oct 9, 2026

Merge main into spatial-autocorr

Merge branch 'main' into perf/numbafy-spatial-autocorr

Merge branch 'main' into perf/numbafy-spatial-autocorr

Read connectivities as CSR

Parallelize the per-row precomputes

Commits on Oct 10, 2026

Score permutations from feature non-zeros

Retire comments the rewrite outdated

Centre the variance on the observed score

Pin the full-gene-list fast path

Record how the block cap was chosen

Trim absolute figures from the block-cap note

Merge branch 'main' into perf/numbafy-spatial-autocorr

Tighten the comments on the block cap

Merge remote-tracking branch 'origin/perf/numbafy-spatial-autocorr' into perf/autocorr-reduce

Dispatch through thread_map

Plainer wording in the new comments

Correct the comments that had drifted

Give degenerate features a NaN z-test

Correct the note on the shifted variance

Correct the block-cap cost at 100M cells

Silence degenerate z-score warning

Centre dense autocorr features

Drop GIL note on permutation fill