clawhdf5

86 Commits 11 Branches 2 Tags

3 Commits

Include renames

Author	SHA1	Message	Date
ClawHDF5 PlannerandClaude Sonnet 4.6	fdc4572ab7	INT-14, INT-15: benchmark CI regression gate and embedding-space anomaly detection INT-14 — Add a dedicated `benchmark` CI job to .gitea/workflows/ci.yml. On pushes to main it saves a Criterion baseline. On pull requests it loads the baseline and fails the job if Criterion reports a regression. INT-15 — Add EmbeddingAnomalyDetector to anomaly.rs. Uses Welford's online algorithm to maintain a running mean and per- dimension variance. Evaluates each new embedding via diagonal Mahalanobis distance (mean squared z-score); embeddings that exceed the threshold are returned as EmbeddingVerdict::Quarantine with a reason string, signalling the caller to store them in a quarantine dataset rather than the primary store. Includes a warmup phase (always Accept) to seed statistics before the detector becomes meaningful. Added 5 unit tests covering warmup, in-distribution, outlier, dimension-mismatch, and count tracking. Co-Authored-By: Claude Sonnet 4.6 <[email protected]>	2026-08-12 11:48:36 +00:00
ClawHDF5 Planner	ec6bc80007	INT-02/03/05: overflow-checks, cargo-audit CI, and knowledge graph cycle tests INT-02: Add [profile.release.package.clawhdf5-format] overflow-checks=true to root Cargo.toml — provides defense-in-depth for untrusted byte offset arithmetic in the HDF5 format parser. INT-03: Install cargo-audit in Gitea CI workflow and call it from ci-test.sh with --deny warnings. The script gracefully skips the step if cargo-audit is not installed locally, so developer machines are unaffected. INT-05: Add three cycle-safety tests for KnowledgeCache: - test_bfs_neighbors_cycle_terminates: A→B→C→A, verifies b and c appear once - test_bfs_neighbors_self_loop_terminates: self-loop A→A, verifies empty result - test_spreading_activation_cycle_converges: cyclic graph with decay_factor 0.5, verifies finite convergence and all nodes receive activation The BFS visited-set guard was already present; these tests lock it in as a regression boundary so future refactors cannot silently remove it.	2026-08-12 11:29:02 +00:00
Omar Sobh	55959b4920	ci: wire up CI, fix no_std build, fix stale package names in scripts CI / test (push) Failing after 15s Details - Add .gitea/workflows/ci.yml running scripts/ci-test.sh (fmt, clippy, test, no_std check) on push/PR to main. - Fix stale rustyhdf5-py/rustyhdf5-format package names in ci-test.sh/check-nostd.sh, which had been silently no-op'ing those checks (cargo warns but doesn't fail on an unknown --exclude/-p target). - With those checks actually running, fix the real issues they surface: - clippy: useless_conversion in chunked_write.rs, byte_char_slices in global_heap.rs/object_header.rs. - cargo fmt: apply formatting across the workspace (whitespace only). - no_std (thumbv7em-none-eabihf) build errors in clawhdf5-format: core::sync::atomic::AtomicU64 doesn't exist on that target (no native 64-bit atomics) — switch profiling.rs's counters to portable-atomic, which falls back to a CAS-based emulation there and is a no-op wrapper elsewhere. Add missing alloc imports for Box (filters.rs), Vec (filters_szip.rs), and format! (dict_encoding.rs) on no_std paths. Replace f64::powi (std/libm-only) with a small local exponentiation-by-squaring helper in the scale-offset filter.	2026-08-05 10:50:13 -07:00

Author

SHA1

Message

Date

ClawHDF5 PlannerandClaude Sonnet 4.6

fdc4572ab7

INT-14, INT-15: benchmark CI regression gate and embedding-space anomaly detection

INT-14 — Add a dedicated `benchmark` CI job to .gitea/workflows/ci.yml.
  On pushes to main it saves a Criterion baseline.  On pull requests it
  loads the baseline and fails the job if Criterion reports a regression.

INT-15 — Add EmbeddingAnomalyDetector to anomaly.rs.
  Uses Welford's online algorithm to maintain a running mean and per-
  dimension variance.  Evaluates each new embedding via diagonal
  Mahalanobis distance (mean squared z-score); embeddings that exceed
  the threshold are returned as EmbeddingVerdict::Quarantine with a
  reason string, signalling the caller to store them in a quarantine
  dataset rather than the primary store.
  Includes a warmup phase (always Accept) to seed statistics before
  the detector becomes meaningful.
  Added 5 unit tests covering warmup, in-distribution, outlier,
  dimension-mismatch, and count tracking.

Co-Authored-By: Claude Sonnet 4.6 <[email protected]>

2026-08-12 11:48:36 +00:00

ClawHDF5 Planner

ec6bc80007

INT-02/03/05: overflow-checks, cargo-audit CI, and knowledge graph cycle tests

INT-02: Add [profile.release.package.clawhdf5-format] overflow-checks=true to
root Cargo.toml — provides defense-in-depth for untrusted byte offset
arithmetic in the HDF5 format parser.

INT-03: Install cargo-audit in Gitea CI workflow and call it from ci-test.sh
with --deny warnings. The script gracefully skips the step if cargo-audit is
not installed locally, so developer machines are unaffected.

INT-05: Add three cycle-safety tests for KnowledgeCache:
- test_bfs_neighbors_cycle_terminates: A→B→C→A, verifies b and c appear once
- test_bfs_neighbors_self_loop_terminates: self-loop A→A, verifies empty result
- test_spreading_activation_cycle_converges: cyclic graph with decay_factor 0.5,
  verifies finite convergence and all nodes receive activation

The BFS visited-set guard was already present; these tests lock it in as a
regression boundary so future refactors cannot silently remove it.

2026-08-12 11:29:02 +00:00

Omar Sobh

55959b4920

ci: wire up CI, fix no_std build, fix stale package names in scripts

CI / test (push) Failing after 15s

Details

- Add .gitea/workflows/ci.yml running scripts/ci-test.sh (fmt, clippy,
  test, no_std check) on push/PR to main.
- Fix stale rustyhdf5-py/rustyhdf5-format package names in
  ci-test.sh/check-nostd.sh, which had been silently no-op'ing those
  checks (cargo warns but doesn't fail on an unknown --exclude/-p
  target).
- With those checks actually running, fix the real issues they surface:
  - clippy: useless_conversion in chunked_write.rs, byte_char_slices in
    global_heap.rs/object_header.rs.
  - cargo fmt: apply formatting across the workspace (whitespace only).
  - no_std (thumbv7em-none-eabihf) build errors in clawhdf5-format:
    core::sync::atomic::AtomicU64 doesn't exist on that target (no
    native 64-bit atomics) — switch profiling.rs's counters to
    portable-atomic, which falls back to a CAS-based emulation there
    and is a no-op wrapper elsewhere. Add missing alloc imports for
    Box (filters.rs), Vec (filters_szip.rs), and format! (dict_encoding.rs)
    on no_std paths. Replace f64::powi (std/libm-only) with a small
    local exponentiation-by-squaring helper in the scale-offset filter.

2026-08-05 10:50:13 -07:00