feat(indexing): cache per-document embeddings for incremental FAISS builds - #738
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Included review availability: This review used your included allowance. 3 included reviews remain after this review. Your included PR review attempts over the past 7 days set your current allowance at 5 reviews per hour. 📝 WalkthroughWalkthroughIndex builds apply the current embedding token limit and cache document chunks and vectors by source path, content hash, and configuration. Builds reuse valid caches, encode cache misses, and create FAISS indexes from the resulting vectors. The manifest records source hashes and available cache paths. ChangesIncremental indexing
Priority: ➖ Normal Estimated code review effort: 3 (Moderate) | ~25 minutes Change: Feature · Severity of issue fixed: Medium Sequence Diagram(s)sequenceDiagram
participant build_index_from_sources
participant Manifest
participant DocumentCache
participant SourceLoaders
participant Embedder
participant FAISS
build_index_from_sources->>Manifest: Compare configuration and source hashes
build_index_from_sources->>DocumentCache: Load cached chunks and vectors
alt Cache miss
build_index_from_sources->>SourceLoaders: Load source chunks
build_index_from_sources->>Embedder: Encode chunks
build_index_from_sources->>DocumentCache: Save chunks and vectors
end
build_index_from_sources->>FAISS: Build index from stacked vectors
build_index_from_sources->>Manifest: Write hashes and available cache paths
Merge Risk: ⚪ Minimal · up to The change adds incremental document caching with configuration invalidation and recovery from cache failures. No actionable merge-blocking risk is established; merge after normal checks pass. 🚥 Pre-merge checks | ✅ 4 | ❌ 1❌ Failed checks (1 warning)
✅ Passed checks (4 passed)
✨ Finishing Touches📝 Generate docstrings
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Actionable comments posted: 3
- 🪄 Fix CodeRabbit comments on this PR
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Inline comments:
Review comments at @app/indexing.py:
- Around line 495-498: Add MAX_EMBED_TOKENS to the cache configuration alongside
CHUNK_SIZE, CHUNK_OVERLAP, and EMBED_MODEL so config_ok invalidates document
caches when the embedding truncation limit changes.
- Around line 510-511: Update _embedding_cache_file and the corresponding
document-cache identity so both include the relative source path and a
configuration fingerprint, not just the content hash. Validate these identity
components when loading each document cache, preventing renamed files or caches
built under another configuration from being reused.
- Line 540: Update the exception handler in _load_document_cache to catch
EOFError from np.load() and treat an empty cache file as a cache miss, allowing
the document to be encoded again.
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app/indexing.pyapp/tests/test_incremental_index.py
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Copilot review overview
🟡 Changes recommended
Cache keys omit path-dependent chunk identity and some embedding configuration, allowing stale or incompatible vectors to be reused.
Review effort: Balanced
Findings: 1
Open (2)
What changed in this PR
Adds per-document chunk and embedding caching to accelerate incremental FAISS rebuilds.
Changes:
- Caches chunks and float32 embeddings by content hash.
- Reuses unchanged document caches and rebuilds the normalized FAISS index.
- Adds incremental rebuild, manifest, invalidation, and corruption tests.
| File | Description |
|---|---|
app/indexing.py |
Implements per-document caching and incremental index construction. |
app/tests/test_incremental_index.py |
Tests cache reuse, invalidation, manifests, and rebuild equivalence. |
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Code Review Roast 🔥Verdict: No Issues Found | Recommendation: Merge Oh wait, this PR is actually clean. I need to sit down. I had my flamethrower warmed up and everything. The incremental commits close out all prior feedback: cache-write failures now log through 📊 Overall: Like finding a unicorn in production — I didn't think clean PRs existed anymore, but here we are. Files Reviewed (2 files)
Previous Review Summaries (3 snapshots, latest commit d77fe4e)Current summary above is authoritative. Previous snapshots are kept for context only. Previous review (commit d77fe4e)Verdict: 1 Issue Found | Recommendation: Address before merge Overview
Issue Details (click to expand)
🏆 Best part: All three of the previous review's findings — gone. One token limit now rules the fingerprint, the encoder, and the manifest via a single 💀 Worst part: The one remaining catch-all. Widening 📊 Overall: The cache grew up, got one clock, a janitor, and a test that refuses to be mocked — what is left is a log line, not a liability. File it, ship it. Files Reviewed (2 files)
Note: this branch also carries sync_sources.py / sources.yaml / test_sync_sources.py changes, but they are byte-identical to content already merged to main via #739 and no longer appear in this PR's diff, so they were out of scope for this pass. Fix these issues in Kilo Cloud Previous review (commit 564c006)Verdict: 3 Issues Found | Recommendation: Address before merge Overview
Issue Details (click to expand)
🏆 Best part: The previous review's nine findings? All nine, gone. Cache identity now covers path + bytes + config, writes are atomic and failure-tolerant, 💀 Worst part: 📊 Overall: The cache grew up, got a real identity, atomic writes, and a janitor — what is left is the kind of nit you file, not the kind you lose sleep over. Fix these issues in Kilo Cloud Files Reviewed (2 files)
Previous review (commit 2a50e2f)Verdict: 9 Issues Found | Recommendation: Address before merge Overview
Issue Details (click to expand)
🏆 Best part: The incremental rebuild is genuinely sound where it counts — cache-hit and encode paths keep the FAISS row ↔ 💀 Worst part: Cache invalidation is a vibe. Chunking-code changes, 📊 Overall: A cache with no version fingerprint is just a denial-of-service attack against your future self — well-armed, but pointed the wrong way. Fix these issues in Kilo Cloud Files Reviewed (2 files)
Reviewed by efficient · Input: 0 · Output: 0 · Cached: 0 |
…uilds Reuse cache/embeddings/<content_hash>.npy and cache/chunks/<content_hash>.json so a changed document is the only one passed to embed_texts. The FAISS index is rebuilt from the stacked vectors, and manifest.json records each file hash plus those cache paths. Fixes #697 Co-authored-by: Derek Roberts <DerekRoberts@users.noreply.github.com>
Cache identity now includes the source path and a configuration fingerprint stamped into each cache file, so a rename, a shared byte sequence, or a half-finished build under a new config cannot reuse stale chunks. force=True re-encodes every document, unreadable caches are misses, and unreferenced cache files are removed after the manifest is written. Co-authored-by: Derek Roberts <DerekRoberts@users.noreply.github.com>
564c006 to
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The cache fingerprint and get_embed_model() now share a call-time read of AGNAV_MAX_EMBED_TOKENS. Cache writes log and continue on any Exception, and prune removes .cache-* leftovers older than three hours. Co-authored-by: Derek Roberts <DerekRoberts@users.noreply.github.com>
app/conftest.py replaces get_embed_model with a mock, so the identity assertion compared that mock and failed the unit-test job. Co-authored-by: Derek Roberts <DerekRoberts@users.noreply.github.com>
A document-cache write still catches Exception and continues the build. The log now includes the exception type, message, and traceback so a programming error is not recorded as a one-line write warning. Co-authored-by: Derek Roberts <DerekRoberts@users.noreply.github.com>
Summary
build_index_from_sourcesre-encoded every document whenever the manifest changed. It now keeps float32 embeddings and chunks for each document, and encodes only a cache miss.Cache identity is the relative source path, the file bytes, and a configuration fingerprint. The fingerprint and
get_embed_model()share one call-time token limit (AGNAV_MAX_EMBED_TOKENSwhen set, otherwise the import-timeMAX_EMBED_TOKENS). That same value is written tomax_seq_lengthandtokenizer.model_max_length. The fingerprint also includes the effective embedding model, the embedding dimension, andCACHE_PIPELINE_VERSION. It is part of the cache filename and is stamped into each chunk file, then checked on load. A rename, two paths with the same bytes, or a build that dies under a new config cannot reuse chunks that still carry the old path or vectors.force=Trueskips the document cache and re-encodes every document..npy, bad chunk JSON, or a wrong vector shape is a miss.os.replace. Any writeExceptionis logged with its type, message, and traceback, and the index build continues.embeddings/<sha256>.npyandchunks/<sha256>.jsonfiles are deleted..cache-*temps in those directories older than three hours are deleted too. Younger temps and other files are left alone.CACHE_PIPELINE_VERSIONwhen chunking, citation prefixes, or normalization change.Fixes #697
Tests
Python 3.14 container (
python:3.14-slim),pytest --noconftestonapp/tests/test_incremental_index.pyandapp/tests/test_index.py: 19 passed. The token-limit test restores the realget_embed_modelso the unit-test mock inapp/conftest.pycannot hide a mismatch between the fingerprint and the encoder. The cache-write test checks that aValueErroris logged with its type, message, and traceback.Summary by CodeRabbit