feat(patching): give the read-ahead up before refusing a sweep - #173
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Included review availability: 0 reviews are currently available. Your included PR review attempts over the past 7 days set your current allowance at 4 reviews per hour. 📝 WalkthroughWalkthroughSweep tiling now reduces read-ahead when queued memory exceeds the budget and retries serial execution before refusal. OME-Zarr utilities now load and write remote stores, support lazy stepped-slice fallbacks, and use URI-aware loading across metadata and pyramid paths. ChangesSweep budget handling
Remote OME-Zarr support
Estimated code review effort: 3 (Moderate) | ~25 minutes Merge Risk: ⚪ Minimal · up to The change is merge-ready after normal checks; no actionable merge-blocking risk remains. Sequence Diagram(s)sequenceDiagram
participant OMEZarr as OME-Zarr utilities
participant FSSpec as fsspec filesystem
participant RemoteStore as Remote OME-Zarr store
OMEZarr->>FSSpec: Create mapper or target filesystem
FSSpec->>RemoteStore: Read store or upload staged metadata
RemoteStore-->>OMEZarr: Return store metadata
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🚥 Pre-merge checks | ✅ 4 | ❌ 1❌ Failed checks (1 warning)
✅ Passed checks (4 passed)
Full details: Description checkExplanation The description explains the sweep sizing change and its rationale, but it omits the required template sections for related issues, change type, testing commands and results, checklist confirmation, and breaking changes. Resolution Complete the repository template. Add the change type, testing commands and observed results, checklist status, related issues or state that none apply, and breaking-change or migration information. Keep the existing focused explanation under the Description section. ✨ Finishing Touches📝 Generate docstrings
🧪 Generate unit tests (beta)
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Inline comments:
In `@konfai/utils/ome_zarr.py`:
- Line 1128: Update append_ome_zarr_levels so remote URI strings such as s3://
remain unchanged instead of being converted through Path; use URI-aware mapper
access throughout this writer flow, including the call into _from_ngff_zarr,
while preserving local path handling.
- Line 652: Update the span construction around the index slice normalization to
handle negative-step slices by converting them into an equivalent forward
unit-step range before applying the local reverse stride, preserving indices
such as 10, 8, 6, 4, and 2 for slice(10, 0, -2). Keep existing handling
unchanged for non-negative-step slices and non-slice index items.
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The block a sweep holds is mostly what the chain must hold to run at all: the source window it pulls, the rows it lands, the buffers its widest stage allocates. The read-ahead queue is the one part the sizing CHOSE rather than met, and what it buys is wall clock -- half a second of a 6.7 s run, by _sweep_depth's own measurement. A sweep about to refuse has no clock to buy. So it stops buying it. Three resident source regions become one and the search runs once more; only if that does not fit either does it refuse, now naming both figures so a reader knows which one to clear. On a chain whose stage buffers dominate the band is narrow, 1.31x to 1.34x on the tiling fixture; on a pointwise one it is 2.5x. Inside the band the alternative was not a slower run but no run. _sweep_depth had to learn to go down before it goes up: a tile found without the queue, swept with one, would hold what the sizing was never told about -- the budget's promise lost to a default nobody revisited. And _keeps_the_block now asks the search rather than _sweep_tile, which falls back: a depth that cannot afford the block would otherwise come back holding it, and every depth would look affordable. The refusal test's own budget stopped refusing, which is the feature: half of one row's queued price is bought by the serial retry. It is now set under the serial price, and asserts both figures are named.
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The block a sweep holds is mostly what the chain must hold to run at all: the
source window it pulls, the rows it lands, the buffers its widest stage
allocates. The read-ahead queue is the one part the sizing CHOSE rather than
met, and what it buys is wall clock -- half a second of a 6.7 s run, by
_sweep_depth's own measurement. A sweep about to refuse has no clock to buy.
So it stops buying it. Three resident source regions become one and the search
runs once more; only if that does not fit either does it refuse, now naming both
figures so a reader knows which one to clear. On a chain whose stage buffers
dominate the band is narrow, 1.31x to 1.34x on the tiling fixture; on a
pointwise one it is 2.5x. Inside the band the alternative was not a slower run
but no run.
_sweep_depth had to learn to go down before it goes up: a tile found without the
queue, swept with one, would hold what the sizing was never told about -- the
budget's promise lost to a default nobody revisited. And _keeps_the_block now
asks the search rather than _sweep_tile, which falls back: a depth that cannot
afford the block would otherwise come back holding it, and every depth would
look affordable.
The refusal test's own budget stopped refusing, which is the feature: half of
one row's queued price is bought by the serial retry. It is now set under the
serial price, and asserts both figures are named.
Summary by CodeRabbit
New Features
Bug Fixes
Tests