Commit graph

101 commits

Author SHA1 Message Date
Trevon
604e68e17b
feat(memory-sync): apply paged winners through bounded adapters (#330)
Use pinned, governed pages for metadata, content, vectors and topology.
Preflight identity/content/model prerequisites before writes and continue
independent records without softening authentication, capacity or I/O errors.

Apply topology deletions, nodes and edges in one real KG batch with bounded
transaction-local reads. Preserve ordinary-read isolation, report exact edge
deferrals independently of bounded diagnostic samples and avoid empty commits.

Retract absent local topology only from exact committed own observations and
conditionally erase the same envelope, including off-resident/stale-winner
regressions. Probe local KG presence with fallible scalar SQL rather than
materializing properties; retain SQL errors as errors, not absent records.

The public C++ KG/batch interfaces gain virtual capabilities. Defaults provide
source-level hard errors only: installed/old-binary ABI compatibility is NOT
established and providers must be rebuilt/reviewed before promotion.

Signed-off-by: trvon <git@trevon.dev>
2026-10-22 07:12:24 -06:00
Trevon
f7ca95427d
fix(daemon): run memory_sync catch-up sweeps only when a store changed (#295)
Some checks failed
Fuzz Smoke / libFuzzer smoke (push) Has been cancelled
* test(daemon): memory_sync catch-up sweeps must go idle on unchanged stores

The vector and topology catch-up sweeps restart a full pass as soon as
one ends, so an idle node reads and re-checks every node, edge, vector,
and committed topology record forever. On a 3-node mesh limited to 2
CPUs each this held every node at ~24% of a core with nothing changing.

New cases drive the production backfill through ServiceManager:
- after a completed pass with no writes, further cycles serve no sweep
  item and take no graph-store connection;
- a node, edge, and vector written after a pass are published by the
  next pass while unchanged records keep their committed operation;
- a node deleted after the sweeps went idle is retracted with its edge.

Store seams: KnowledgeGraphStore::changeGeneration() and
VectorDatabase::changeGeneration() move on writes and batch commits,
not on reads.

Red: catch2_memory_sync_apply "[idle]" 3 failed (items 52 == 32,
acquisitions 157 == 97); kg_store and vector_smoke do not compile.

Signed-off-by: trvon <me@trevon.dev>

* fix(daemon): run memory_sync catch-up sweeps only when a store changed

The vector and topology catch-up sweeps in publishMemorySyncBackfill
restarted a full pass as soon as one ended. An idle node therefore read
and re-checked every node, edge, vector, and committed topology record
forever, and every published record cost each peer a delta exchange and
an apply. On a 3-node mesh limited to 2 CPUs each this held every node
at ~24% of a core with nothing changing; on a real corpus the first
pass never ends.

Each store now exposes a change generation: KnowledgeGraphStore counts
write transactions (single writes through the write pool and write
batch commits), VectorDatabase counts inserts, updates, and deletes. A
sweep records the generation a pass began at and, once the pass
completes, does not start another until the generation differs. Writes
behind a running pass's cursor move the generation past the pass's own
reading, so the following pass still covers them; deletes move it too,
so the retraction phase still runs after a rebuild drops records. With
nothing changed, a cycle costs each sweep one atomic read.

No config knob: the gate is a property of the stores, not a tunable.

Tests: catch2_memory_sync_apply (14 cases, incl. 3 new [idle] cases),
catch2_kg_store, catch2_vector_submodule.

Signed-off-by: trvon <me@trevon.dev>

---------

Signed-off-by: trvon <me@trevon.dev>
2026-10-14 08:32:56 -06:00
Trevon
c26294a938
feat(topology): opt-in medoid representative and BQ rotation (#277)
* test(topology): characterize degree representatives and raw BQ sign bits

Pin the current behaviour before adding opt-in representative and BQ
rotation options:

- connected, louvain and kmeans engines on a skewed cluster (dense
  clique plus a weak-edge hub): medoid hash, score, extra routing
  representatives and roles;
- equal-degree ties go to the smaller document hash;
- the unrotated BinaryQuantizedIndex matches a raw-coordinate sign-bit
  reference, with and without a prefix dimension.

Signed-off-by: trvon <me@trevon.dev>

* feat(topology): add an opt-in medoid representative rule

topology.representative_rule = degree (default) | medoid selects how a
cluster's representative document is chosen. Degree keeps the max
within-cluster weighted degree. Medoid picks the member minimising
sum_j sqrt(max(0, 2(1 - cos))) over the other members.

- one shared helper, applyRepresentativeRule(), is called by the
  connected, louvain and kmeans engines after their unchanged degree
  choice; medoid falls back to it without usable geometry;
- clusters above 256 usable members are searched on a deterministic
  hash-ordered stride sample (kMedoidRepresentativeMaxMembers);
- ties within 1e-9 go to the smaller document hash;
- with medoid, farthest-first extra routing representatives are seeded
  from the medoid instead of the centroid;
- the rule is stored in the formerly reserved first header byte of the
  binary snapshot (0 = degree, so old snapshots keep their meaning) and
  extends the construction fingerprint only when it is not degree;
- search debug stats report topology_representative_rule.

Signed-off-by: trvon <me@trevon.dev>

* feat(topology): add an opt-in randomized Hadamard rotation for BQ routing

search.topology.bq_rotation = none (default) | fwht selects the rotation
applied before the centroid BQ shortlist takes sign bits. Raw-coordinate
sign bits make cos(pi * h / d) a poor estimate on anisotropic embeddings;
after x -> (1/sqrt(n)) H D [x; 0] every bit is a random hyperplane.

- RandomizedHadamardRotation in yams/vector: fixed splitmix64 sign
  diagonal plus an in-place FWHT, zero-padded to a power of two; Simeon's
  FWHT projection works on int32 sketches with row subsampling, so a
  small local transform is used instead;
- BinaryQuantizedIndex::build() takes the rotation and seed, rotates
  stored vectors before the prefix is taken, and rotates every float
  query itself, so centroids and queries always share one seed
  (kDefaultBinaryRotationSeed);
- the routing snapshot cache records bqRotation and bqRotationSeed and
  rebuilds the route index when either differs;
- the routing policy fingerprint changes only for a non-default rotation;
- search debug stats report topology_route_bq_rotation.

Signed-off-by: trvon <me@trevon.dev>

* test(bench): map representative rule and BQ rotation arm knobs

Harness-only env knobs written into the isolated benchmark config.toml,
so arms go through ConfigResolver like the other topology settings:

- YAMS_BENCH_TOPOLOGY_REPRESENTATIVE_RULE=degree|medoid
  -> [topology] representative_rule
- YAMS_BENCH_TOPOLOGY_BQ_ROTATION=none|fwht
  -> [search.topology] bq_rotation, next to bq_candidate_limit and
     bq_prefix_dim

The debug-file setup entry records the requested values; per-query
search_stats carry the effective topology_representative_rule and
topology_route_bq_rotation. Portability allowlist lines are shifted for
the inserted code.

Signed-off-by: trvon <me@trevon.dev>

---------

Signed-off-by: trvon <me@trevon.dev>
2026-10-08 14:30:27 -06:00
Trevon
4ec044afd6
fix(vector): rank vec0 by cosine on unit-normalized copies (#275)
* test(vector): pin vec0 ranking to cosine order on non-unit rows

vec0 ranks by L2 distance, which matches cosine order only for unit
vectors. Insert rows whose L2 order disagrees with cosine order and
assert vec0 returns cosine order, agrees with the exact cosine scan,
skips zero rows and rejects a zero query. Pins a vector-enabled env
so the cases run under the CI test env.

Signed-off-by: trvon <me@trevon.dev>

* fix(vector): rank vec0 by cosine on unit-normalized copies

vec0 ranks by L2 distance, which matches cosine order only when both
sides are unit length. Stored rows reach the vectors table at whatever
magnitude the provider, config, import or sync produced, and the vec0
aux table copied them as-is, so vec0 selected and ordered rows
differently from the Simeon PQ and exact cosine paths.

The vec0 table is a derived index rebuilt from vectors.embedding, so
write the unit direction into it and leave the source blob, which
export/sync and exact scoring read, untouched. Normalize the query the
same way. Zero rows are left out of vec0 and never match; a zero or
non-finite query is rejected as the exact scan rejects it. Returned
rows are ordered by their cosine score with the PQ tie-break.

No schema change. The aux table is rebuilt on first use in each
process (ready dims are in-memory), so existing non-unit rows are
normalized on the next rebuild without a repair step.

Signed-off-by: trvon <me@trevon.dev>

* test(topology): pin the k-means stored centroid to the unit direction

Spherical k-means assigns against unit centroids but stored the shorter
arithmetic mean. Assert the stored centroid is unit length along the
member mean direction, with and without boundary spill. Add a SOAR case
showing that with unit centroids the spill follows angular distance,
and that a short mean centroid reorders the candidates.

Reformat the touched k-means test file to the lint formatter.

Signed-off-by: trvon <me@trevon.dev>

* fix(topology): store the unit k-means centroid

The k-means engine clusters by cosine against normalized centroids,
then stored the unnormalized member mean as centroidEmbedding. Routing
reads the centroid by cosine and does not care, but SOAR boundary spill
measures Euclidean residuals against it. A loose cluster's short mean
adds a radial term to those residuals, so spill candidates were ranked
in a different space from the one the clusters were built and routed
in.

Store the unit mean direction for k-means, which is the converged
Lloyd centroid. Connected-component and Louvain keep the arithmetic
mean, as their tests and contract require. Correct the stale field
comment.

Signed-off-by: trvon <me@trevon.dev>

---------

Signed-off-by: trvon <me@trevon.dev>
2026-10-08 14:30:26 -06:00
Trevon
44daa47b94
fix(memory-sync): skip bad vector records instead of stalling the stage (#265)
* fix(ci): size the onnx resource budget for aarch64 page alignment

libyams_onnx_resource.so is 67,624 bytes on aarch64 against a 64,000-byte budget, which failed the v0.20.4 linux-arm64 release job. It holds 23 KB of sections; aarch64 links with 64 KiB segment alignment (LOAD align 0x10000), which pads the file. The budget was measured on x86_64. 81,000 is the aarch64 size plus 20% headroom. Every other aarch64 payload is within 86% of its budget.

Signed-off-by: trvon <me@trevon.dev>

* fix(plugins): declare the S3 legacy factory with the plugin export macro

93f24394 marked the S3 plugin's yams_plugin_create/destroy_object_storage definitions YAMS_PLUGIN_API so they stay exported under hidden visibility, but include/yams/plugins/object_storage.h still declared them without it. MSVC rejects a definition whose linkage differs from the first declaration (C2375), so the v0.20.4 Windows release job failed to compile s3_plugin.cpp. GCC and Clang accept the mismatch, which is why the Linux and macOS lanes passed.

The header now includes yams/plugins/abi.h and declares both functions YAMS_PLUGIN_API, matching how abi.h declares the rest of the plugin C ABI. Checked with MSVC 14.51 (x64 target): a translation unit with the s3_plugin.cpp definitions fails with C2375 against the old header and compiles against the new one.

Signed-off-by: trvon <me@trevon.dev>

* fix(build): drop install_tag from the mobile install_headers call

324be33a passed install_tag: 'devel' to install_headers(), which accepts no such keyword. Meson 1.12 fails the configure with "install_headers got unknown keyword arguments install_tag" whenever -Denable-mobile-bindings=true, which broke the Tests linux-x86_64-mobile lane on experimental. Meson tags installed headers 'devel' by itself, so the header still ships only with the devel set (checked with meson introspect --install-plan and meson install --tags devel|runtime --dry-run on grim).

Signed-off-by: trvon <me@trevon.dev>

* fix(packaging): install the Windows onnx resource DLL next to the executables

yams-cli.exe, yams-daemon.exe and yams-mcp-server.exe import
yams_onnx_resource-0.dll at load time, but Meson installed it to lib\ and
yams.wxs never packaged it. The shipped v0.20.3 MSI therefore installs a
yams.exe that cannot start: extracting it (msiexec /a) and running
`yams.exe --version` exits 0xC00004BC with no output, and dumpbin
/dependents lists yams_onnx_resource-0.dll. The release job never runs the
staged CLI on Windows, so CI stayed green.

Drop the explicit Windows install_dir so Meson installs the DLL to bindir
(the import library stays in libdir) and add it to the MSI. With the change
`meson install` stages bin\yams_onnx_resource-0.dll and the staged
`yams.exe --version` prints the version.

Signed-off-by: trvon <me@trevon.dev>

* ci(release): smoke-test the staged Windows CLI before building the MSI

The v0.20.3 MSI shipped a yams.exe that exits 0xC00004BC because a load-time DLL was not packaged, and nothing in the release job ran the staged binary. Run the staged yams.exe --version with a 60 s timeout after meson install and fail the job on a non-zero exit. Checked on a Windows host against the old stage layout (exits 0xC00004BC, step fails) and the fixed one (prints 0.20.5, step passes).

Signed-off-by: trvon <me@trevon.dev>

* fix(cli): keep init vector tests hermetic and the sentinel tied to disk

cli_init_command and cli_commands failed on every platform since #247.
The Tests workflow runs unit lanes with YAMS_VDB_IN_MEMORY=1 and vectors
disabled, so the vector store init creates is in memory: no vectors.db
was written (init_command_catch2_test.cpp:350) and a forced re-init,
seeing no file, overwrote the 384 sentinel with 1024 (:455).

The two cases assert on the on-disk store, so they now pin that
environment with ScopedEnvVar instead of inheriting the CI one.

Init also stamped a dimension sentinel for the in-memory store even
though nothing was written to disk. Stamp it only when this init created
vectors.db, and cover the in-memory case.

Signed-off-by: trvon <me@trevon.dev>

* fix(test): ignore worker-thread stages in memory sync serialization test

daemon_memory_sync_apply_serialization failed on Windows with
contentStages 3 == 2 and "memory_sync stage observer threw at
apply.after_content". The memory_sync worker reconciles once as soon as
it starts and runs the apply callback on its thread. On a slow host that
first cycle lands after the harness reports ready, inside the test's
observer window, so a third apply hit the observer and set an already
satisfied promise.

Reproduced on Linux under CPU load (1 of 192 runs, same signature).
The observers now count only stages reported from the test's own caller
threads, and the attempts check allows an extra worker attempt. 0 of 384
runs fail under the same load.

Signed-off-by: trvon <me@trevon.dev>

* fix(vector): do not mmap vectors.db on Windows

repair_maintenance failed on Windows only: the live vectors.db VACUUM
reported "4 MB -> 4 MB" and the file never shrank
(repair_maintenance_catch2_test.cpp:301). The standalone VACUUM case,
with no other connection open, passes there.

The vector backend connection sets mmap_size=256MB. On Windows,
SetEndOfFile from another handle fails with ERROR_USER_MAPPED_FILE while
a view of the file is mapped, and SQLite's winTruncate ignores that
error, so the truncate at the end of the VACUUM connection's checkpoint
is silently skipped. Linux and macOS can truncate a mapped file.

Skip the mmap pragma on Windows so the idle VACUUM in RepairService can
reclaim disk.

Signed-off-by: trvon <me@trevon.dev>

* ci: name the red Tests streak when a nightly is refused

The nightly gate refused with only "no successful Tests run for SHA",
so a run of red Tests on experimental stayed silent. On refusal, also
report the Tests conclusion for that SHA, the newest failing Tests run on
experimental with its SHA and failing jobs, and the last green run, as
annotations and in the job summary. The gate itself is unchanged.

Signed-off-by: trvon <me@trevon.dev>

* fix(daemon): claim the clean-shutdown stamp exclusively on Windows

db_recovery failed on Windows with "clean shutdown stamp has only one
consumer" (db_recovery_test.cpp:108): both concurrent consumers
rejected a valid stamp.

The claim renamed the stamp with MoveFileExW. That opens the source
sharing read, write and delete and renames through the handle, so two
callers can both open the stamp and both succeed, the second moving the
first's claim file away; their opens also fail each other's reads with
ERROR_SHARING_VIOLATION. Driving the real stamp code from two threads on
Windows x64, 205 of 2000 rounds ended with both consumers rejecting it
("stamp missing or malformed"); never with both trusting it.

On Windows, open the stamp with no sharing, retrying briefly while
another opener holds it, and rename through that handle. A concurrent
consumer then finds no stamp. Same driver: 2000 of 2000 rounds with
exactly one trusted consumer and no leftover claim files. The dropped
MOVEFILE_WRITE_THROUGH only affects cross-volume copy moves; the claim is
a same-directory rename. POSIX keeps rename(2).

The test now captures both consumers' reasons on failure.

Signed-off-by: trvon <me@trevon.dev>

* test(memory-sync): cover vector records that cannot apply or publish

One bad vector record should cost only itself. Add red tests for the
vector sync adapter (corrupt payload, dimension mismatches, non-hash
document identity, key/identity mismatch sorted between two good
records), for the daemon apply cycle reporting such a record in apply
health while the good embedding lands, and for the outbound backfill
publishing good vectors past a row with no model identity.

Add a YAMS_TESTING hook to inject a vector database into the
ServiceManager so the daemon vector stage and backfill can be driven
in-process.

Signed-off-by: trvon <me@trevon.dev>

* fix(memory-sync): skip bad vector records instead of stalling the stage

Inbound: VectorSyncAdapter::apply() returned an error on the first
winner it could not apply (corrupt payload, dimension or identity
mismatch, non-hash document id, a model the store cannot hold for its
chunk, a failed store write or content probe). It validated the whole
batch before any write, so one such winner kept every vector winner
from applying on every cycle until a newer winner replaced it.

Each winner is now applied, deferred, or skipped on its own, as the
content stage does. A skipped winner is reported through failure()
(first failure, prefixed with its logical key), which the daemon maps
to ApplyStagePass::failure, so apply health counts it as a vector stage
failure while good records land. Skipped winners are never marked
applied and are retried on the next pass. Winners that disagree on a
chunk's model are all skipped, so the outcome does not depend on
arrival order. Reconciliation and index rebuild failures still end the
pass.

Outbound: the backfill threw on any vector publish error without
advancing its (document_hash, chunk_id) cursor, so a row that can
never publish (for example one with no model id) stopped the vector
sweep on that row for good. Such rows are now skipped with a warning,
as unrecoverable documents are; transient failures still propagate
and are retried next cycle.

Signed-off-by: trvon <me@trevon.dev>

* test(memory-sync): pin the vector-store environment in the vector cases

CI runs the unit lanes with YAMS_DISABLE_VECTORS=1, YAMS_SQLITE_VEC_SKIP_INIT=1 and YAMS_VDB_IN_MEMORY=1. VectorDatabase then skips creating its tables, so every vector insert in these cases failed under the CI environment while passing in a clean shell. Clear those variables for each case that attaches a vector store, as the init command tests do.

Signed-off-by: trvon <me@trevon.dev>

---------

Signed-off-by: trvon <me@trevon.dev>
2026-10-02 18:47:39 -06:00
Trevon
7be908e5b7
fix(p2p): stop the memory-sync apply/publish deadlock and report apply health (#243)
* fix(daemon): never gate memory-sync publish on inbound apply

applyMemorySyncWinners() ran the inbound stages content -> metadata ->
vector -> topology and returned on the first stage failure, before the
node's own outbound backfill. In a mesh where every node holds an inbound
record whose prerequisite only a peer can publish (an embedding whose
content blob has not replicated, an edge whose target node has not), every
node refused to publish, so the prerequisites never arrived: a stable
mutual deadlock with healthy transport and nothing converging.

The outbound publish now runs after the inbound stages whatever their
outcome; only a stop request ends a cycle early. Each inbound stage also
runs even when an earlier one failed. Cross-stage dependencies (metadata
and vectors need local content bytes, edges need their endpoint nodes) are
checked per record against the local stores, so a failed stage shows up
downstream as unapplied records rather than as skipped stages. Stages keep
their prerequisite order so a prerequisite landing in a cycle is visible to
its dependents in that same cycle.

A two-node test drives real ServiceManager apply cycles over a shared
store, each node holding an edge whose target only the other can publish;
it converges in a bounded number of rounds only with this change.

Signed-off-by: trvon <me@trevon.dev>

* fix(memory-sync): defer records whose prerequisite has not replicated

Vector, metadata, and topology apply treated a missing replicated
prerequisite as a hard error and rejected the whole batch: one embedding
whose content blob had not arrived, or one edge whose target node had not,
blocked every other winner in that stage on every cycle. These are
ordering races between independently published records, not failures.

Each adapter now defers such a record instead: it is skipped, the rest of
the batch applies, and its logical key is reported through deferredKeys().
Nothing marks it applied, so it remains a winner in the replicated index
and the next cycle retries it once the prerequisite lands; apply needs no
pending queue of its own and loses nothing across restarts. An edge whose
endpoint is being deleted in the same batch is deferred too rather than
inserted against a stale node id. Malformed records, probe failures, and
store errors still fail the stage.

Content blobs are independent, so the content stage now attempts every
blob and fails afterwards with the first genuine error; a corrupt blob no
longer starves the blobs after it. A blob whose bytes are not hydrated in
the sync cache yet is deferred like the other stages.

Signed-off-by: trvon <me@trevon.dev>

* feat(p2p): report memory-sync apply health in status

The mesh deadlock was invisible: every node reported failed_cycles=0 and a
climbing successful_cycles while nothing converged, because a cycle counts
as successful once reconciliation completes, whatever the apply stages did
afterwards. Deferred records would be just as invisible without a signal.

ServiceManager now keeps an ApplyHealth record of the apply path:

- deferred records per stage, and the age of the oldest one still pending,
  with a warning once a deferral passes ten minutes (its prerequisite
  likely never arrived). Ages are tracked for at most 4096 keys per stage,
  keeping the oldest; counts stay exact.
- hard failures per stage, plus the last failure's stage, message, and age.
- apply_cycles and apply_failed_cycles. failed_cycles keeps meaning
  reconciliation failures; a cycle whose apply stage hard-failed is counted
  in apply_failed_cycles instead of passing as a plain success.
- publish_skipped_cycles (delete outbox preempted the cycle) and
  publish_failed_cycles (an outbound backfill domain failed).

The fields travel through MemorySyncStatus, MemorySyncResponse, and
protobuf fields 22-37 to `yams p2p status` (new key=value tokens on the
first line, an `apply` line with per-stage counts, a last-apply-failure
line, and an `apply` object in --json) and to the memory-sync section of
`yams daemon status`. The p2p status formatter moves behind a header so it
can be tested without a daemon.

Signed-off-by: trvon <me@trevon.dev>

* fix(memory-sync): keep content deferrals when the same scan hits a failure

The content stage scans every blob and fails afterwards with the first
genuine error, but the apply cycle discarded the deferred keys that the
same scan collected whenever it failed. A corrupt blob therefore hid every
blob still waiting for its bytes: the deferred count stayed at its previous
value (0 on the first pass) and the stale-deferral warning never fired for
a prerequisite that was actually missing.

A stage pass now carries both outcomes. The content-blob scan moves into
ContentBlobSyncAdapter::applyWinners, which reports the applied count, the
deferred keys, and the first failure of one complete scan, and
ApplyHealth::recordPass records the failure and replaces the deferred set
together. A stage that returns an error still leaves the deferred set as
last observed, since an aborted scan says nothing about prerequisites.

The tracked-deferral cap already carried every still-deferred tracked key
before admitting new ones, but its carry loop had a cap check that read as
if it could stop early. Drop it (the tracked set never exceeds the cap) and
pin the behaviour with tests that place the oldest key after more than the
cap's worth of new keys and that refill a full tracked set.

Signed-off-by: trvon <me@trevon.dev>

---------

Signed-off-by: trvon <me@trevon.dev>
2026-10-01 12:18:47 -06:00
trvon
c3b667ee40
feat(retrieval): SGC topology smoothing, Matryoshka BQ prefix, and fragment outer-MaxSim
Implement three research-backed retrieval optimizations connecting
paperbridge literature findings with YAMS subsystems:

1. SGC Feature Smoothing (Proposal A):
   - Add sgcHops and sgcNormalize to TopologyBuildConfig.
   - Diffuse document embeddings across reciprocal nearest-neighbor graph
     edges prior to clustering, formalizing Lean SGC.lean.
   - Re-normalize diffused embeddings to preserve unit hypersphere metric geometry.
   - Wire into ConnectedComponent, Louvain, and KMeans topology engines.

2. Matryoshka Prefix Binary Quantization (Proposal C):
   - Add maxDimensions parameter to BinaryQuantizer::quantize and
     maxPrefixDimension to BinaryQuantizedIndex::build.
   - Support fast 64-bit word-aligned prefix Hamming shortlisting in
     SparseGuidedClusterRouter via bqPrefixDimension.

3. Fragment Outer-MaxSim Reranker (Proposal B):
   - Implement SimeonScoringMode { SingleVectorCosine, FragmentOuterMaxSim }
     in SimeonModelProvider.
   - Add extractDocumentFragments and late-interaction outer-MaxSim scoring
     inspired by ColBERTv2/PLAID/SPLATE to prevent relevance dilution in long docs.
   - Expose simeonRerankOuterMaxSim on SearchEngineConfig and ConfigResolver.
   - Add Catch2 test coverage and verify BEIR scifact benchmark metrics.

Signed-off-by: trvon <me@trevon.dev>
2026-09-22 07:37:35 -06:00
trvon
052031a484
feat(vector): binary quantization (BQ) pre-filter for cluster routing
- Add BinaryQuantizer and BinaryQuantizedIndex in include/yams/vector/binary_quantization.h
  and src/vector/binary_quantization.cpp implementing 1-bit sign quantization,
  packed 64-bit word storage, hardware popcount Hamming distance, and cosine
  similarity estimation.
- Integrate centroidBqIndex into SparseRouteIndex, constructing compact BQ
  centroids alongside dense ANN indices during SparseGuidedClusterRouter::buildRouteIndex.
- Add bqCandidateLimit to TopologyRouteRequest and tracking metrics (bqUsed,
  bqCandidates, bqDistanceEvaluations) to SparseRouteWork.
- Enable fast candidate pre-filtering in SparseGuidedClusterRouter::route with
  1-bit Hamming distance scans, providing sub-millisecond coarse candidate
  shortlisting and automatic fallback when the dense ANN index is omitted.
- Add Catch2 unit test suites in tests/unit/vector/binary_quantization_catch2_test.cpp
  and tests/unit/topology/topology_baseline_catch2_test.cpp.

Signed-off-by: trvon <me@trevon.dev>
2026-09-22 07:37:35 -06:00
Trevon
9883a4382b
refactor(vector): decouple embedding generator policy (#83)
* refactor(vector): add injectable executor for the embedding daemon bridge

await_with_timeout spawned coroutines unconditionally on the daemon
global IO context, coupling the vector-layer embedding generator to
daemon globals. EmbeddingConfig gains an optional
boost::asio::any_io_executor executorOverride; the bridge uses it when
present and keeps the global executor as the default — identical
behavior for all existing callers (embedding_service, model providers,
CLI all construct without an override).

Lead 1 plan step (b) of the embedding_generator vector->daemon
decomposition (Brick audit follow-up).

Validation: full ninja build green; meson test yams:service_manager,
vector_submodule, yams:embedding_lifecycle, yams:embedding_recovery —
all green.

Signed-off-by: trvon <me@trevon.dev>

* refactor(vector): split DaemonBackend into own TU

Keep daemon client/IPC headers out of the vector-layer generator TU;
EmbeddingGenerator builds the backend via createDaemonBackend factory
on the existing IEmbeddingBackend seam. Behavior-preserving.

Brick audit lead 1: 5 file-level cycles hubbed on
embedding_generator.cpp.

Signed-off-by: trvon <me@trevon.dev>

* revert(vector): keep bridge executor out of public EmbeddingConfig

Pre-push gate caught it: the config layer includes the vector header
transitively (ConfigResolver.h -> document_chunker.h ->
embedding_generator.h) and has no boost asio include path, so
<boost/asio/any_io_executor.hpp> in the public header breaks the
config build.

Executor selection stays in embedding_daemon_backend.cpp (daemon-facing
TU by design); per-instance injection needs the config->vector include
direction fixed first — recorded as follow-up.

Signed-off-by: trvon <me@trevon.dev>

* refactor(vector): trust resolved backend policy

Remove EmbeddingGenerator's ambient ConfigResolver read. Callers now own
backend-policy resolution; EmbeddingService marks its already-resolved
runtime policy unconditionally. Keep TuneAdvisor only for the process-wide
concurrency gate, where instance-local policy would not coordinate admission.

Tests pin typed backend authority against conflicting environment state.

Signed-off-by: trvon <me@trevon.dev>

* chore(vector): remove stale config include

The generator no longer reads config helpers after backend policy moved to
callers, so drop the misleading DaemonBackend comment and unused include.

Signed-off-by: trvon <me@trevon.dev>

---------

Signed-off-by: trvon <me@trevon.dev>
2026-09-02 10:12:46 -04:00
trvon
a34f49f39e
test(ci): stabilize platform matrix 2026-08-18 21:07:59 -06:00
trvon
9fdf75eb60
feat(memory-sync): add vector adapter 2026-08-17 21:43:11 -06:00
trvon
8b501a344e
refactor(config): consolidate embedding policy 2026-08-05 20:53:18 -04:00
trvon
5066fc0893
test: isolate process environment 2026-08-04 21:31:39 -04:00
trvon
fbb8fcb915
perf(vector): persist reusable warm starts 2026-08-03 17:52:58 -04:00
Trevon
0dd3985db4
refactor: simplify runtime paths and harden retrieval (#61)
* refactor(tuning): prune dormant runtime knobs

Remove unused tuning controls and adaptive search budget state. Extract testable ONNX slot reconciliation and search telemetry hydration seams, and correct the Apple Silicon sysctl value width.

* refactor(vector): retire dormant backends

Remove unused FAISS, model-infrastructure, VectorIndexManager, and TurboQuant paths while keeping Simeon PQ and float-vector storage.

Migrate unused V2.2 quantized schemas transactionally to V2.3. Databases containing non-default quantized formats or packed-code blobs fail closed with recovery guidance and no mutation.

* refactor(plugins): remove legacy SDK tooling

Remove the Ghidra and SDK submodules, their bespoke tests, and stale scan exclusions. Retain generic PluginProcess coverage against the repository mock fixture.

* build(vector): remove stale FAISS overrides

* refactor(ipc): remove dormant FSM snapshots

* refactor(ingest): unify bounded KG enqueue

* fix(plugins): harden allocation contracts

Keep ABI outputs null or fully initialized when allocations fail, and represent empty object payloads without relying on malloc(0).

* fix(storage): define empty object reads

Return a null buffer with zero length for successful empty-object reads instead of treating malloc(0) as an allocation contract.

* refactor(storage): trim through string views

* test: prune dormant harness helpers

Remove unused readiness and fixture helpers, and keep benchmark client-count doubling in a wide integer domain.

* chore(cpp): initialize analyzer-facing locals

* build(simeon): advance analyzer cleanup

* refactor(config): drop dead daemon client keys

* refactor(ipc): inject daemon client transport

Socket and in-process execution now share DaemonClient request dispatch, so CLI fallbacks do not need alternate service paths.

* refactor(retrieval): route CLI through daemon

Search and grep now use the same daemon handlers over socket or in-process transport. Live grep remains an explicit freshness inspection.

* refactor(graph): move CLI scope into daemon

Graph CLI requests now share daemon handlers across socket and in-process transports. CWD filtering occurs before pagination so scoped totals and pages stay correct.

* build: isolate test-only runtime controls

* refactor(metadata): decouple lock telemetry

* fix(services): return on request timeout

* fix(retrieval): enforce workspace scope

* fix(graph): scope nodes before pagination

* fix(grep): drop binary result lines

* fix(daemon): bound checkpoint wait

* fix(repair): use KG health checks

* fix(storage): always verify compressed CRC

* perf(vector): skip unchanged PQ snapshots

* build(zyp): exclude bench from default build

* build: protect Meson files from formatter

* refactor: remove unreachable production APIs

* refactor(daemon): remove dormant runtime state

* fix(vector): harden daemon provider calls

Timed-out coroutines must own their client and requests. Provider discovery must also fail instead of returning synthetic embeddings in production.

* refactor(storage): remove unusable adapters

* fix(cli): unify in-process add requests

* fix(tsan): preserve async worker progress

* test(cli): isolate daemon-dependent suites

* fix(repair): expose queue backoff progress
2026-07-31 14:16:45 -04:00
trvon
a23038f589
refactor: remove dead code and duplicate helpers
Make FAISS index ownership explicit and remove unused Rabin tables.
2026-07-29 16:17:10 -04:00
Trevon
3f37e8f564
Sync experimental into main: Search retrieval improvements (#60)
* fix(graph): handle qualified C++ symbols

Signed-off-by: trvon <me@trevon.dev>

* refactor(vector)!: remove dead transition APIs

Split Simeon vector and retrieval linkage so consumers inherit only the runtime surface they use.

BREAKING CHANGE: remove unused async/model/config helpers and the undefined vector-backend factory from public headers.

Signed-off-by: trvon <me@trevon.dev>

* fix(vector): harden PQ snapshot lifecycle

Validate and atomically install persisted generations, revalidate after races, and fall back to exact search when a snapshot is stale. Add the exact-scan reference lane and distinguish observed work counters from unavailable backend metrics.

Signed-off-by: trvon <me@trevon.dev>

* feat(topology): expose route coordinates

Persist chart distortion and local-dimension evidence, retain pre-scalarization route axes, and emit detailed trace rows without treating unavailable vector work as zero.

Signed-off-by: trvon <me@trevon.dev>

* feat(xplan): add vector decision gates

Track binary and corpus identity, preserve missing-work semantics, and add repeated PQ routing, crossover, and rerank plans with quality and cost summaries.

Signed-off-by: trvon <me@trevon.dev>

* feat(topology): formalize coordinate routing

Separate chart geometry from route-risk admission and prove candidate-stage recall and strict-focus boundaries. Record the measured atlas limitations and literature basis for the next construction experiment.

Signed-off-by: trvon <me@trevon.dev>

* fix(search): serialize SymSpell readers

SQLite-backed lookups reuse mutable prepared statements, so shared-reader locking is unsafe. Advance the owned SymSpell revision for batched delete insertion and cover concurrent root lookups under TSAN.

Signed-off-by: trvon <me@trevon.dev>

* fix(vector): make mutations atomic

Preserve stored vectors on replacement and commit failures, reject cross-thread writes during explicit transactions, and restore exact reranking for quantized-primary PQ rows.

* fix(search)!: surface SymSpell write errors

Propagate persistent dictionary failures through metadata ingestion, roll back failed batches, and make clear remove stored terms.

BREAKING CHANGE: SymSpellSearch mutations now return Result values.

* feat(topology): formalize candidate expansion

* feat(vector): add coordinate-aware embeddings

* feat(topology): preserve protected relation cover

* feat(search): add graph candidate rescue

* feat(daemon): expose retrieval hydration telemetry

* feat(xplan): add rescue and hydration gates

* refactor(content): dedupe media handlers

Reuse shared graph presenter helpers and centralize repeated audio/video/archive buffer processing, validation, lifecycle, and stats helper logic.

* feat(lifecycle): prune stale corpus data

Keep cleanup preview-first while retention stays opt-in and long prune work no longer holds IPC responses open.

* feat(search): add topology candidate rescue

Preserve high-value routed candidates across vector backends while keeping exact rerank diagnostics explicit.

* feat(search): expose evidence paths

* docs: define mobile host contract

* formal: model bounded candidate rescue

* fix(prune): inspect extensionless signatures

* fix(prune): tolerate stale extensions

---------

Signed-off-by: trvon <me@trevon.dev>
2026-07-24 19:00:22 -04:00
Trevon
7df64b1161
perf(search): bound topology routing and harden runtime paths (#59)
* fix: address review build issues

* perf(search): bound topology routing

Cache route membership, shortlist centroids with static ANN, and route SPQ through explicit allowed-document budgets.

* test(xplan): measure routed vector work

Pin benchmark binary identity and export route, cache, and phase costs for repeated equal-budget comparisons.

* test(search): use portable jthread wrapper

* fix(daemon): serialize detached cancellation

* fix(cli): honor pinned daemon sockets

* fix(xplan): support Windows contract imports

* fix(list): apply metadata filters before paging

* docs(prompts): require memory hydration

Treat search results as candidates and hydrate selected artifacts before use. Quote argument hints for strict YAML loaders.

* test(cli): keep add on pinned daemon

* test(metadata): isolate performance timing

* fix(graph): tolerate stale snippet ranges

Source files may change before persisted symbol metadata is refreshed. Omit stale snippets instead of aborting graph exploration.

* test(daemon): await request readiness

Reuse the retrying list probe before asserting post-shutdown error quality under sanitizer load.

* ci(release): use hosted cmake

Resolve Conan CMake tool requirements from PATH so cold ARM64 caches do not depend on cmake.org. Default BUILD_DIR for failure cleanup.
2026-07-19 14:53:10 -04:00
Trevon
a3d065dd8d
feat(search): make topology-assisted retrieval the default (#57)
* fix(release): repair package repo publish

Arch repo metadata and R2 uploads need to be reproducible from CI, with retry hardening for transient Cloudflare failures.

* fix(daemon): stop shutdown log storm

Init waiter must treat ShuttingDown as terminal so daemon shutdown tests do not flood Meson logs while the daemon is stopping.

* refactor(cli): delegate serve to MCP binary

Keep yams serve UX while removing MCP server linkage from yams-cli. The standalone MCP binary owns stdio serving and exits on stdin EOF.

* refactor(cli): move daemon path helpers

Keep CLI path resolution out of YamsDaemon so later link cuts can separate CLI and daemon internals. Full yams_daemon removal still needs a socket-only daemon-client split.

* refactor(daemon): split embedded client

* perf(search): add lean-guided benchmark gates

Add Lean topology/search models, ingestion ablation docs, and focused regression tests for topology and compression threshold behavior.

Extract search observability, keep benchmark-only ablation controls, and make retrieval quality benchmarks default to Simeon while preserving explicit ONNX opt-in.

* refactor(config): move daemon policies

* refactor(daemon): extract plugin runtime

* refactor(daemon): untangle service coordinators

Untangle CLI/MCP from daemon service coordinators and the daemon static lib.

- MetadataRepository uses a daemon-neutral tree-diff callback. The
  GraphComponent wrapper moves to src/daemon/components/metadata_graph_bridge.cpp,
  owned by the daemon library.
- WriteCoordinator moves to a dedicated build-only yams_write_coordinator
  static lib. Drop ResourceGovernor coupling inside the writer loop; batch
  sizing still respects config.maxBatchSize.
- AppContext gains enqueuePostIngest callback. ServiceManager wires it to
  its own enqueuePostIngest; app services no longer call ServiceManager
  directly.
- Embedding repair uses BulkIngestLease/BeginBulkIngestCallback instead of
  concrete VectorIndexCoordinator::BulkScope. Daemon dispatchers provide a
  lease factory backed by the real coordinator.
- CLI daemon_command uses config helpers instead of YamsDaemon::getXDGRuntimeDir.
- Remove explicit dependency('yams_daemon') from src/cli and tools/yams-mcp.
- Declare missing yams_extraction/yams_ingest deps on yams_app_services so
  app services link cleanly without daemon.

Validated:
  meson compile -C build/release -j4 yams-daemon yams-cli yams-mcp-server
  ninja -C build/release -t commands tools/yams-cli/yams-cli tools/yams-mcp/yams-mcp-server | grep -c libyams_daemon.a -> 0
  yams-cli --version, yams-mcp-server init, yams serve --help smoke tests

Size drop on macOS release: yams-cli 41M -> 32M, yams-mcp-server 37M -> 22M.

* fix(cli): keep stdin add local fallback

No embedded daemon now. When yams add - buffers stdin and daemon IPC is missing, store via local app services instead of failing socket_missing.

Validated:
  meson compile -C build/debug -j4 yams-cli catch2_cli_commands
  MESON_BUILD_ROOT=/Users/trevon/work/tools/yams/build/debug build/debug/tests/catch2_cli_commands 'AddCommand - reads from piped stdin and stores content'
  MESON_BUILD_ROOT=/Users/trevon/work/tools/yams/build/debug build/debug/tests/catch2_cli_commands
  meson compile -C build/release -j4 yams-cli yams-mcp-server
  meson compile -C build/asan-api -j2 yams-cli catch2_cli_commands
  MESON_BUILD_ROOT=/Users/trevon/work/tools/yams/build/asan-api ASAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1 build/asan-api/tests/catch2_cli_commands 'AddCommand - reads from piped stdin and stores content'
  ninja -C build/release -t commands tools/yams-cli/yams-cli tools/yams-mcp/yams-mcp-server | grep libyams_daemon.a -> no output

* feat(bench): add xplan multi-arm experiment harness

Unified plan runner, ablation axes, REPORT/ablation docs, and
KPI snapshot so optimization loops stop living in shell matrices.

* feat(formal): expand topology/search Lean contracts

Boundary models for search provenance, construction gates,
and cluster/route objectives so Lean guides correctness while
xplan ranks performance levers.

* feat(search,topology): construction purity + graph expansion path

Raise topology build defaults (min edge 0.25, max component 64) and
split oversized CC pieces so hybrid assist is quality-positive on
scifact. Add GraphNeighbors expansion with medoid-anchor fallback,
structured helpers instead of nested session logic, and BEIR-default
xplan plans. Search engine extraction (fanout/classic pipeline) rides
along as the integration surface for routing.

* feat(topology): add KMeans engine and SGC identity contracts

Register kmeans in the factory with deterministic spherical k-means
over embeddings, and enforce SGC document-identity invariants in
debug builds with matching unit coverage.

* feat(daemon): topology readiness gates and selectable reranker

Drive topologyReady from published epoch/freshness/rebuild/dirty
ingest state (not just KG drain), surface those fields in search
stats, and wire onnx|simeon|auto|none cross-reranker selection.

* chore(search): drop meta_path tuner knobs

Meta-path routing is gone; remove dead TunedParams fields and the
ConfigResolver test for [search.meta_path].

* feat(bench): add topology_purity_validate plan

Repeats=3 validation matrix for construction-purity winners vs
topo_off so MRR deltas can clear run-to-run noise.

* chore: format add_command and config include order

Mechanical clang-format / include reorder only; no behavior change.

* feat(bench): decision-grade xplan loop for search engine

Document search-engine measurement in AGENTS; harden xplan with
repeats=3 plans, quality×latency primaries, mechanism metrics from
debug.jsonl, multi-rep log promotion, and archive superseded topology
plans.

* feat(graph): denser product semantic_neighbor topK

Raise default YAMS_GRAPH_SEMANTIC_TOPK fallback from 4 to 8 so product
graphs leave fewer degree-0 docs for GraphNeighbors expansion.

* feat(search): extract topology assist and cross-rerank seams

Pull topology assist into search_topology_stage (seed merge, skip
reasons, optional vector seed probe default 0). Extract cross_rerank
compute from search_engine. Wire probe via typed config/ConfigResolver.

* feat(bench): product-path search engine ablation plans

Add topology-off component, vector-weight, and tiered-execution xplan
plans (repeats=3) and wire them into the AGENTS measurement loop table.

* fix(ci): repair pre-push fallbacks

* feat(bench): lock-free mid-run builds + multi-corpus gates

xplan skips meson rebuild when the quality binary exists (flock +
YAMS_BENCH_FORCE_BUILD override) to stop multi-arm link races. Add
graph_vector weight and nfcorpus transfer-gate plans; document in AGENTS.

* fix(daemon): keep SearchEngine alive via shared_ptr cache

getCachedEngine previously published a raw pointer that metrics polling
used through rebuild, racing destructor of SearchEngine::Impl (TSAN).
Store and return a shared_ptr snapshot so diagnostic readers pin the
engine for the duration of getConfig/health checks.

Also adds the cautious vectorWeight 0.30→0.20 multi-corpus xplan plan.

* feat(search): route vectors through cached topology

Build and reuse validated topology snapshots, rank routed members by query similarity, and narrow the vector leg to the accepted document set with explicit work diagnostics.

Remove the retired HDBSCAN engine and vendor dependency, preserve typed topology policy through search tuning, and cover the runtime/configuration contracts.

* feat(bench): consolidate search decision plans

Enforce deterministic experiment identity and declared baselines, expose routed/global vector work metrics, and register the focused benchmark contracts.

Promote the compact repeats=3 routing-budget gate, archive superseded topology mechanism screens, and add multi-corpus product calibration plans.

* feat(search): refine topology vector routing

* fix(search): propagate daemon readiness

* feat(bench): measure generalized memory health

* fix(cli): honor in-process fallbacks

* ci: harden smolvm debug builds

* perf(search): route topology through filtered ANN

* feat(bench): measure read-write pressure

* perf(metadata): index symbol lookups on read pool

* fix(daemon): isolate startup reads and maintenance

* feat(bench): replay isolated generalized corpora

* feat(search): add evidence routing pipeline

Replace the blocking smolvm pre-push path with host ASan/TSan validation, harden sanitizer-sensitive smoke tests, and add recovery cleanup for malformed SQLite WAL sidecars.

* refactor(search): unify topology evidence path

Remove classic and sidecar fusion lanes so topology augments the recall-preserving ANN and lexical candidate pool through one product path.

* refactor(bench): prune superseded search lanes

Measure the topology-plus-ANN product path with stable experiment identity and remove obsolete sidecar and tiered controls.

* docs(search): retire stale experiment notes

Keep the benchmark handoff focused on the topology-plus-ANN product lane and its active decision plans.

* refactor(search): prune dead search surfaces

Remove unused fusion, reranker, policy, and router abstractions.
Bound topology materialization and keep document trace payloads opt-in.

* fix(cli): clear build warnings

* fix(xplan): reject stale run identity

* refactor(search)!: remove legacy query stack

Replace the unused AST/ranker/post-processor surface with focused facet aggregation used by product search.

BREAKING CHANGE: removes query parser, result ranker, search filter, and SearchResults container APIs from yams_search.

* refactor(search): type value stage traces

Remove synthetic ComponentResult markers for embedding and concept stages. Preserve failure and timeout states instead of overwriting them with fake successful results.

* refactor(search): isolate benchmark env overlays

Move test-only search environment parsing behind an injectable internal adapter. Keep all existing overlay keys and tuner pin semantics while restoring SearchEngineBuilder to composition.

* refactor(search): unify topology routing options

Snapshot topology policy once at the assist boundary and pass it through routing sessions and diagnostics. Remove repeated scalar copying without changing routing behavior or metric keys.

* fix(search): unify tuner config ownership

Use one complete config-to-params overlay for runtime seeding and no-tuner policy resolution. Reseed attached tuners on setConfig so reported and executed configuration cannot diverge.

* fix(search): snapshot tuner state per query

Read tuned config, params, and state under one lock before routing. Add a TSAN correlation test so adaptive observation cannot produce a torn logical query snapshot.

* fix(search): enforce topology routing contract

Generated configs must preserve hybrid-assist shadow routing, while daemon-backed search must abstain when published topology artifacts are stale. Keep standalone validation and global ANN recall intact.

* fix(daemon): let SQLite reclaim its file

Directly resizing a live database from sampled page counts can truncate pages allocated by concurrent writers. VACUUM must remain the only file-reclamation mechanism.

* fix(metadata): tolerate missing symbol FTS

Readiness lookups can race an unavailable optional FTS migration. Retain the indexed fast path, but retry against the base table when prepare or cached-statement execution proves the capability absent.

* build(fuzz): drop removed query parser target

The optional AFL build still referenced the deleted legacy query parser API and could no longer compile.

* fix(bench): include writes in drain oracle

A zero post-ingest queue is not durable drain while coordinated writes remain queued or in flight.

* fix(daemon): vacuum padded WAL databases safely
2026-07-13 20:26:43 -04:00
trvon
568902817a
fix(windows): unblock build and flaky tests
- use real Python and Scoop executables under SSH and CI
   - prefer python over python3 on Windows Meson probes
   - keep forced socket mode pinned for both socket env names
   - make forced-socket smoke test deterministic on Windows
   - clean sqlite WAL/SHM sidecars and randomize temp DB names
   - make video header parsing MSVC-safe and reject false MP4 hits
   - give integrity_catch2 more time on Windows runners
2026-07-01 18:21:19 -04:00
trvon
c1e5ec0da6
fix(docs): Replace
missing paths where feasible, fail fast where support is
   not real, and sync docs with live behavior.

   - add vector/metadata and buffer extraction coverage
   - narrow storage and s3/plugin loader contracts
   - refresh pipeline, build, and test docs
2026-06-27 16:28:08 -04:00
trvon
a217a41ee7
test: lift coverage for core paths
Add focused API, CLI, doctor, downloader, search, and vector
   infrastructure coverage.

   Cover retry seams, path-scoped search fallback, renderer fail-soft
   paths, router helpers, and model infrastructure without changing
   production behavior.

   Keep coverage gates stable by skipping Zyp on Darwin coverage builds
   and ignoring SIGPIPE in daemon protocol tests.
2026-06-22 10:25:28 -04:00
Trevon
d5e9b65639
fix: windows test fixes for servicemanager
Signed-off-by: trvon <me@trevon.dev>
2026-06-21 19:57:02 -04:00
trvon
a21dc6ae02
fix: test fixes for ci
Signed-off-by: trvon <me@trevon.dev>
2026-06-21 19:57:02 -04:00
Trevon
771deebc84
fix: harden CI and metadata stability (#48)
* feat: dead code removal, profling foudnation improvements, addressing code smells in reference db implementation

* fix: test fixes and optimmizations for benchmarks

* fix: harden audit findings

   Reject invalid tokenizer ids, fix move-order hazards, bound manifest
   and audio IO, and guard numeric/process edge cases found by Fold.

* fix: route SymSpell writes through coordinator

* test: fix batch content initializers

* fix(ci): restore cross-platform builds

* fix: address Copilot review findings
2026-06-11 16:42:54 -04:00
Trevon
9cb6421593
feat: daemon stability fixes, vector search optimizations, and docs refresh (#46)
* fix(daemon): resolve sign-conversion warnings

* fix(daemon): add IO thread startup barrier

* refactor: consolidate toLowerCopy clones

* fix(daemon): add atexit handler for static host map cleanup

* fix(build): add missing include, fix daemon_helpers syntax, use atomic barrier

* feat(docs): docs cleanup, and metadata refactor updates

* fix(daemon): resolve Windows-only PostIngestQueue shutdown SIGSEGV (#45)

Co-authored-by: Claude Opus 4.8 <noreply@anthropic.com>

* feat: submodule bump, multiclient optimizations and benchmark optimizations

* feat(perf): reduced contention with update to placement of flushPathCacheBuffer()

* fix(metadata): invalidate path cache on document mutation

* fix(metadata): hydrate cached counters before first write

---------

Co-authored-by: Claude Opus 4.8 <noreply@anthropic.com>
2026-06-10 10:30:38 -04:00
Trevon
2d01ba314c
Assertion hardening, metadata correctness, & daemon lifecycle fixes (#41)
* fix(core): add assertions and harden daemon lifecycle

* fix(daemon): tighten shutdown lifecycle invariants

* fix(test): add PressureLimitedPoller capability-sleep shutdown test

* refactor(vector): harden backend contracts

Split the vector backend surface into narrower contracts and
move entity read paths to Result<> so callers can distinguish
backend errors from empty results.

Also fixes the TurboQuant lazy-init race, makes VectorDatabase
error state thread-safe, wires eager index preparation, and
adds regression plus memory-scaling benchmark coverage.

* fix(vector): address audit findings plus hardening

Fix the five confirmed bugs: coroutine lifetime hazard in
embedding_generator (await_with_timeout outliving captured state),
VectorSystemManager init retry latch poisoning, incremental HNSW
persistence race, vec0 registry key collisions, and simeon PMI
output_dim/config() drift.

Add invariant hardening: PostIngestQueue stage validation +
numChunks assertion, VectorSystemManager success postcondition,
VectorDatabase TurboQuant non-null assertions on all quantize/
dequantize paths, and sqlite_vec_backend Simeon PQ range and
divisibility preconditions.

Also adds regression coverage for init-retry and lock-busy paths
and a locked node snapshot helper for safe incremental HNSW
persistence.

* fix(test): add PressureLimitedPoller wake-timer shutdown tests

* chore(vector): resolve clang-tidy hygiene across queue, vdb, and sqlite-vec

Replace unprotected std::getenv calls with locked getenvCopy helpers,
add debug-level logging to previously-silent catch blocks in
PostIngestQueue, VectorDatabase, and SqliteVecBackend, wrap
PostIngestQueue timer-detach allocations in try-catch, and fix
unsigned-widening / optional-deref / unused-include hygiene.

Verified with LSP diagnostics and rebuilds of catch2_vector_submodule
and catch2_daemon_component_submodule.

* fix(daemon): harden PressureLimitedPoller inFlightCounter null check

* fix(daemon): harden PostIngestQueue wait_until deadline checks

* fix(daemon): clean up recovery sentinels regardless of salvage count

Previously the .recovered-* sentinel and .corrupt-* file cleanup
was gated on documentsSalvaged > 0, leaving quarantine
artifacts to accumulate on repeated crash/recovery cycles where
the corrupt DB had 0 salvageable docs.

Move cleanup outside the salvage-count guard so stale
quarantine artifacts are always removed after examination.

* feat(vec0): restore persisted ANN index on daemon restart

After vec0 rebuild, probe for vectors_<dim>_hnsw_meta shadow tables
and load a previously-persisted HNSW index.  When found, the ANN
index is set directly on the vec0 table, skipping the O(n log n)
rebuild that was previously paid on every daemon restart.

Removes the stub restoreVec0AnnIndexIfPresentUnlocked() in favor
of inline restoration in rebuildVec0DimUnlocked(), which has
the vec0 table already created and ready for ann_index assignment.

* fix: enable DCHECK by default and assert metadata counter consistency

* fix(services): assert document deletion ordering content-before-metadata

* fix(test): add fork-based assertion validation tests

* fix(test): expand assertion tests for POSTCONDITION, DCHECK, UNREACHABLE

* fix(ci): enable -Denable-dcheck=true in all test CI lanes

* fix(test): address assertion review findings

* refactor(daemon): isolate poller config assertion checks

* refactor(services): reduce deletion and poller complexity

* style(ci): normalize test workflow spacing

* refactor(services): extract list query helpers

* refactor(services): extract list hydration helpers

* refactor(daemon): extract metrics snapshot helpers

* refactor(daemon): extract metrics counter snapshot

* refactor(daemon): extract metrics resource snapshot

* feat(graph): add daemon-backed explore

Wire graph explore through daemon IPC, keep CLI rendering stable,
and fall back locally when daemon transport or protocol skew fails.

Also add graph context service/tests, improve graph follow-up hints,
and keep release builds working with the current JSON library.

* fix(services): prevent prune delete metadata orphans

* fix(cli): honor data-dir in graph explore

- bypass daemon explore when the CLI pins a data dir so\n  temp fixtures do not resolve against a long-lived global DB\n- guard snippet truncation and ratio math to remove Fold-\n  reported underflow and div-by-zero paths\n- clamp zero-based symbol lines before rendering graph\n  context

* fix(daemon): make lifecycle stop completion safe

* fix(daemon): gate db-open startup against shutdown

* fix(metadata): serialize FTS indexed counter updates

* test(daemon): simulate vector lock contention cross-process

* test(daemon): isolate post-ingest identity batch

* style(daemon): normalize test include order

* refactor(graph): split cli graph helpers

Keep graph command paths smaller and easier to evolve.

Lock graph explore/topology contracts into focused presenter,
dispatcher, and support tests so follow-up refactors keep the
current IPC and hot-path behavior intact.

* fix(config): harden expand_tilde and fix Windows XDG state path doubling

- expand_tilde: handle bare ~ and ~/ explicitly to avoid std::out_of_range
  on substr(2) for single-char input
- getXDGStateHome: on Windows, go up two levels from %LOCALAPPDATA%\yams\state
  to %LOCALAPPDATA% so callers' xdg/yams append doesn't double the yams segment

* fix(static-analysis): add logging to empty catch blocks and fix nosemgrep syntax

* fix(static-analysis): strip trailing text from nosemgrep comments

* fix(doctor): add logging to daemon_check empty catch blocks

* fix(db_repair): add logging to empty catch blocks

* fix(chunking): add precondition checks for rabin polynomial and windowSize

* fix(safety): add null precondition checks for Fold proved null-deref sites

* fix(daemon): widen init-failure dispatch, add null/dbz preconditions

InitializationFailedEvent races with shutdown — async init
fails after teardown begins. Widen canDispatch to accept
Ready/ShuttingDown. Add static_assert on SnapshotRing N>0.
Add YAMS_PRECONDITION null guards on hex/stages/data/bytes.

* ci(ubsan): use restricted build targets to avoid runner timeout

* fix(daemon): detach wake timers on Windows stop path to prevent SIGSEGV

* fix(config): cast parseTomlU32 to size_t for batch fields

* fix(ci): use static helper for Windows timer leak, restrict ubsan tests
2026-06-04 12:53:42 -04:00
Trevon
bfe7cd94ca
test: expand storage-readiness coverage — 48.1%→59.8% broad, 74.3% narrow (#38)
* fix(daemon): avoid socket cancel on stop

Signal active sockets with shutdown only so pending I/O wakes without entering Boost.Asio's reactor cancel path during teardown.

* fix(metadata): open read pools read-only

* ci: fix coverage report generation

* fix(metadata): tag unscoped pool holders

* test(daemon): avoid ipc teardown takeover

* ci: skip plugin coverage objects

* fix(daemon): repair completed FTS5 ghosts

* build(vector): guard unusable FAISS headers

* ci: use clang gcov for coverage

* test(daemon): stabilize arm CI flakes

* Harden search and compression numeric config

* fix(daemon): reconcile orphan vector embeddings

* fix: address vector cleanup review comments

* chore(main): release 0.16.1

* Harden search ranking divisors

* Harden snippet distance and command registration

* test(storage): add readiness coverage gate

Document the distributed sync readiness surface and add direct adapter, refcount, and GC failure-path coverage.

* test(storage): cover strict resolver fallback

* fix(search): tighten retrieval ranking

Honor component weights in default RRF, over-fetch vector chunks before document aggregation, and persist topology centroids for sparse-guided routing.

* fix(search): route weak queries through topology

* fix(search): improve rerank and weak queries

Wire provider-backed cross reranking, add direct Simeon candidates for weak lexical pools, and report stage-level retrieval metrics.

* fix(storage): honor explicit plugin names

Add readiness coverage for factory, URL backend, and compressed storage failure paths.

* fix(storage): avoid remote size listing

* fix(api): rollback failed content adds

* test(storage): cover engine readiness

* test(storage): cover compressed readiness

* fix(core): harden delete and recovery paths

Route prune and local delete fallback through DocumentService so content, metadata, vectors, and KG cleanup stay consistent.

Treat transient SQLite quick_check lock failures as ResourceBusy, refresh IPC activity on streaming writes, and preserve reranker config in tuner seeding.

* test(storage): cover URL backend readiness

* fix(api): harden content rollback

* feat(storage): add list seam, URL listing, and write-edge coverage

* feat(api): reconcile ambiguous remote manifest writes

* feat(storage): add deep compressed scan validation

* test(storage): add plugin loader error path coverage

* fix(gc): prune reference rows after collection

* test(api,storage): add health, compact, gc, and verify edge coverage

* docs: update storage-readiness coverage to 71.8%

* test(metadata): add connection pool shutdown-while-leased coverage

* test(metadata): add tree builder snapshot root stability coverage

* test(vector): add before-init and after-close operation rejection coverage

* test(metadata): add database post-close, open-failure, and cache-clear coverage

* test(integrity): add P2P wrong-hash rejection + batch matrix resolution

* docs: audit and resolve all matrix rows — 18 fully covered

* test(metadata): add failed-migration and rollback coverage

* test(storage): add getBlockSize-invalid-key, empty-verify, PUT/DELETE retry coverage

* feat(storage): add file-open and rename failure hooks + ContentStore retrieve edge coverage

* docs: add broad-surface coverage with per-subsystem breakdown

* test(integrity): add chunk validator manifest validation coverage

* test(vector): add batch insert, delete, and update operation coverage

* docs: update integrity subsystem coverage to 46.4%

* docs: consolidate coverage report — clean matrix, remove boilerplate

* docs: update coverage with complete-suite numbers — 59.8% broad, 74.3% narrow

* test(storage): add URLBackend HEAD exists with 2xx coverage

* bump submodules

* fix: address PR review — curl_slist leak, ec ordering, CAS rollback, production hooks

---------

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
2026-05-25 22:58:15 -04:00
trvon
ff7696a0ff
ci: addressing warm issues with ci. staging bug fixes and search research work 2026-04-29 17:22:20 -04:00
trvon
f825bc3cf5
feat: ci/test regressions updates, reinstated onnxruntime (simeon will still be default), expanding topology instrumentation in search, newsletter update with throughput comparison 2026-04-26 17:03:37 -04:00
trvon
42ee44cef4
fix(ci): ci test and bug fixes. Improvements for testing topology construction 2026-04-26 13:08:55 -04:00
trvon
8de19b84f0
feat: adding instrumentation and config options for build and repair system. Bumping simeon and improving topology system with experimental findings 2026-04-24 17:38:24 -04:00
trvon
7de4d95a43
feat: repair logic improvements, expanding config options to disable rebuilding/repair for memory constrained systems 2026-04-24 10:53:15 -04:00
trvon
e88578a9fc
feat: adding support for phss vector search, test fixes, daemon status regression fix, ci fixes for docker builds with new third-party library 2026-04-23 11:02:18 -04:00
trvon
d8cb0764d8
feat: address test drift, removing hnsw remants for simeon backend implementation, continued refactor of vector backend 2026-04-22 15:03:36 -04:00
trvon
be0feac605
feat: refactor vector engine to reduce monoliths in codebase 2026-04-22 08:36:55 -04:00
trvon
a3f1d529c9
fix: addressing unoptimal copies of vectors in repair path 2026-04-22 02:09:58 -04:00
trvon
4617bf4d8f
feat: further removing hnsw references and centralizing on simeon pq implementation 2026-04-22 01:10:57 -04:00
trvon
d669c009d0
feat: removing experiments and unifying compression in embeddings storage. 2026-04-21 18:13:37 -04:00
trvon
1b6f137132
fix: prune fixes for build artifacts, readiness improvements and hnsw api unification 2026-04-21 17:03:58 -04:00
trvon
bdcff5b636
fix: HNSW and topology rebuilds are now batched in repair. Cleaning up from previous migration work 2026-04-21 13:58:10 -04:00
trvon
6c2c31f2bc
fix: cli clean up of old comments and duplicate code. search improvements as we migrate yams to simeon. 2026-04-21 10:20:01 -04:00
trvon
8c313fc023
feat: expanding topology system and search for better testing and simeon integration 2026-04-19 09:25:28 -04:00
trvon
bb0d33a436
feat: vector optimizations. Most performance gains in search felt on macos 2026-04-12 18:16:10 -04:00
trvon
ef3d925797
feat: continued corectness improvements, ANN / vectordb improvements 2026-04-12 12:53:29 -04:00
trvon
57b7e20657
fix: concurrency and race condition fixes 2026-04-12 11:37:06 -04:00
trvon
61d92c9f5a
fix: address daemon starvation/deadlock paths and aligning ownership of run loop lifecycle 2026-04-12 10:04:50 -04:00
trvon
814672f4dd
feat: removing unnecessary abstraction and adding some optimizations for embeddings generation 2026-04-07 18:04:34 -04:00
trvon
825d9aa666
feat: improving repair logic and search engine metrics for tuning logic 2026-04-06 11:23:02 -04:00
trvon
c32db6e34d
fix: windows build fixes and test instrumentation to resolve ANN precision issues 2026-03-29 08:18:58 -04:00