feat(api): define explicit spike timestamp and timebase semantics (#62, RM-368)

[rmems]

User description

Summary

SpikeEvent::timestamp was a bare u64 documented as "or relative step" — ambiguous between an absolute timestamp, a simulation step, and an encoder-local offset. Encoders disagreed in practice: PhaseEncoder emitted an absolute monotonic counter while every other encoder emitted 0.

This defines one time model for every public encoder before the API is frozen:

A SpikeEvent::timestamp is a TickOffset: a count of encoder ticks from the start of the encode / encode_step call that emitted it.

Timestamps are call-relative, so the crate still owns no clock and no scheduler — the caller keeps absolute time in a TimeCursor.

New time module

• TickOffset — the SpikeEvent::timestamp type. Converts to/from u64 and compares against it, so reads like assert_eq!(spike.timestamp, 5) port unchanged. #[serde(transparent)], so the wire format is byte-identical to 0.4.
• Timebase — physical tick duration in whole nanoseconds (integer, so long runs don't drift), with seconds / hertz constructors and offset conversions.
• TimeModel — step_ticks (origin advance per call), span_ticks (bound on offsets a call may emit), optional Timebase. Returned by the new Encoder::time_model(), which has a default impl so out-of-crate Encoder impls keep compiling.
• TimeCursor — caller-side absolute clock; the documented conversion path for downstream simulators and hardware adapters.

Per-encoder model

Encoder	step_ticks	span_ticks	timebase
RateEncoder	1	1	dt_seconds
LatencyEncoder	max_latency + 1	max_latency + 1	none
PhaseEncoder	1	cycle_steps (overlapping)	none
PopulationEncoder, DeltaEncoder, DerivativeEncoder, TemporalEncoder, PredictiveEncoder	1	1	none

Batch and streaming follow the same rule, once per call — documented in rustdoc on every time_model() impl.

Ordering

Specified and enforced: channel-major, non-decreasing offsets within a channel, and coincident repeats (a RateEncoder burst) contiguous and mutually unordered — a run length is a spike count, not a sequence.

Breaking changes

1. SpikeEvent::timestamp is TickOffset, not u64. Construction uses SpikeEvent::new(ch, 5u64, true) / SpikeEvent::at_step_start(ch, true), or TickOffset::new(5) in a struct literal; .ticks() gives a raw u64. Comparisons and serde payloads are unchanged.
2. PhaseEncoder emits call-relative offsets. The previous absolute value is cursor.absolute(spike.timestamp), or encoder.current_phase() + spike.timestamp.ticks() via the new accessor. Cycle position stays absolute % cycle_steps.
3. A latency_scale above 1.0 no longer stretches spikes past max_latency. Latency gains still shorten the window; span_ticks() is now a hard bound on modulated output too.

Migration notes are in the README (Spike time semantics → Migrating from 0.4).

Verification

Full REVIEW.md gate on 38edaf0:

Check	Result
cargo fmt --check	pass (silent)
cargo test --locked	pass (184 lib / 3 / 8 / 23 doc)
cargo test --features serde --locked	pass (9 serde tests)
cargo test --all-features --locked	pass (201 lib / 3 / 9 / 8 / 23 doc)
cargo clippy --all-features --all-targets -- -D warnings	pass, zero warnings
cargo bench --no-run --all-features	pass (benches compile)
Examples (all 9, incl. --features ndarray)	pass, no panics

Test plan

• tests/time_semantics.rs — conformance suite driving every public encoder through the same assertions (span bound, channel-major order, within-channel offset order, contiguous coincident repeats, model stability), across batch, streaming, and modulated paths with identity / silencing / stretching / non-finite gains
• Harness self-test: the shared assertions are proven to reject each violation, so the suite can't pass vacuously
• Repeated-spikes-within-a-step coverage (rate_bursts_are_contiguous_coincident_repeats)
• EmbeddingRateEncoder conformance (keeps its own forward API, same contract)
• Serde wire-compat assertion: {"channel":12,"timestamp":42,"polarity":true}
• New examples/spike_timebase.rs — two encoders, two cursors, one merged nanosecond timeline
• CI green (3 OS + docker verify)

Closes #62
Linear: RM-368

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https://claude.ai/code/session_01BgWKr2iFbuNcjjitaKfbg1

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Note

High Risk
Public API break (TickOffset, PhaseEncoder timestamps) plus timing semantics changes affect every downstream consumer of spike events; broad encoder surface area with strong test coverage mitigates regressions.

Overview
Unifies spike timing so every encoder reports the same rules: SpikeEvent::timestamp is now TickOffset (call-relative ticks), with Timebase, TimeModel, and TimeCursor for absolute timelines and optional physical tick duration.

Adds Encoder::time_model() (default TimeModel::INSTANT) on all built-in encoders plus EmbeddingRateEncoder::time_model(). LatencyEncoder exposes a max_latency + 1 tick window; PhaseEncoder uses an overlapping model (step_ticks 1, span_ticks = cycle). RateEncoder attaches a Timebase from dt_seconds when representable.

Behavior fixes: PhaseEncoder emits cycle offsets instead of current_phase + offset; latency_scale > 1.0 no longer pushes spikes past max_latency. Spike construction moves to SpikeEvent::new / at_step_start.

Docs & integration: README spike-time section and 0.5 migration notes; examples/spike_timebase merges latency + rate streams; tests/time_semantics conformance suite; REVIEW.md guards updated.

^{Reviewed by Cursor Bugbot for commit 38edaf0. Configure here.}

---

Summary by cubic

Unifies spike timing across encoders: SpikeEvent::timestamp is now a call‑relative TickOffset, and encoders report a TimeModel and optional Timebase so absolute timelines are reproducible. Previously PhaseEncoder emitted an absolute counter while others emitted 0; now all emit call‑relative offsets. Side effects: specified ordering (channel‑major, non‑decreasing per channel) and contiguous coincident repeats; latency windows and reported spans are now hard bounds.

• Adds time module: TickOffset (serde‑transparent over u64), Timebase (whole‑ns ticks with seconds/Hz constructors; rejects the nanosecond upper bound and avoids saturation), TimeModel (step_ticks, span_ticks, optional timebase; overlapping clamps step_ticks <= span_ticks to prevent gaps), and TimeCursor for absolute conversion.
• Standardizes time_model(): LatencyEncoder non‑overlapping window (step_ticks = span_ticks = max_latency + 1, offsets clamped to budget; rejects u64::MAX via WindowTooLarge), PhaseEncoder overlapping (step_ticks = 1, span_ticks = cycle_steps), RateEncoder attaches a Timebase when dt_seconds is an in‑range whole‑ns tick, EmbeddingRateEncoder::time_model() is TimeModel::INSTANT.
• Behavior fixes: PhaseEncoder emits call‑relative offsets and documents current_phase() (counter advances after output); Timebase::try_from_hz error messages reference hz. Conformance tests (tests/time_semantics.rs, tests/time_types.rs) and examples/spike_timebase cover the contract. Satisfies Linear RM-368.

Migration

• Replace struct literals with SpikeEvent::new(ch, 5u64, ...) or SpikeEvent::at_step_start(ch, ...); use spike.timestamp.ticks() where a raw u64 is needed.
• PhaseEncoder absolute phase is now cursor.absolute(spike.timestamp) or encoder.current_phase() + spike.timestamp.ticks(); read current_phase() before the emitting call.
• Custom Encoder impls still compile; implement time_model() if the encoder emits non‑zero offsets, or you will advertise TimeModel::INSTANT.
• Do not pass u64::MAX to LatencyEncoder::try_new; choose a representable max_latency (serde construction also rejects this).

^{Written for commit 4e05336. Summary will update on new commits.}

---

CodeAnt-AI Description

Define consistent spike timing semantics and caller-managed timelines

What Changed

• Spike timestamps now represent call-relative tick offsets through the new TickOffset type, while preserving the existing serialized number format and comparisons with u64
• Added TimeModel, Timebase, and TimeCursor so callers can convert encoder output into absolute tick or nanosecond timelines
• All public encoders now report their timing behavior; phase spikes are call-relative, latency windows are explicitly bounded, and rate bursts remain coincident and countable
• Added shared ordering and timing tests, boundary validation for oversized latency windows, and an end-to-end timebase example
• Latency modulation is capped at the configured maximum instead of producing spikes outside the declared window

Impact

✅ Consistent timestamps across all encoders
✅ Reliable merging of encoder streams on an absolute timeline
✅ No spikes outside declared latency windows

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[linear-code]

RM-368

[codeant-ai]

🤖 CodeAnt AI — Review Status

Status	Commit	Started (UTC)	Finished (UTC)
✅ Incremental review completed	7226324	Aug 17, 2026 · 22:21	22:22
✅ Reviewed your PR	38edaf0	Aug 17, 2026 · 06:26	06:30

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• src/encoders/phase.rs

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📝 Walkthrough

Summary by CodeRabbit

New Features

• Added unified spike timing with relative tick offsets, timebases, timing windows, and cursor-based timestamp conversion.
• Added timing metadata for built-in encoders and standardized spike event creation.
• Added the spike_timebase example for timestamp conversion, event merging, and chronological ordering.
• Added phase and cycle accessors for phase-based encoding.
• Added validation for oversized latency windows.

Documentation

• Documented timing semantics, migration guidance, encoder behavior, and batch/streaming equivalence.

Tests

• Added comprehensive timing conformance, regression, ordering, and serialization coverage.

Walkthrough

This PR defines call-relative spike timestamps with typed offsets, timebases, encoder timing models, and caller-owned cursors. It updates encoders, adds conformance tests, and documents migration guidance and absolute-time conversion examples.

Changes

Time semantics

Layer / File(s)	Summary
Timing contract and mapping primitives src/time.rs, src/types.rs, src/lib.rs, src/error.rs, tests/time_types.rs, tests/serde_tests.rs	Adds timing types, changes SpikeEvent.timestamp to TickOffset, and adds the default Encoder::time_model() contract.
Encoder timing implementations src/encoder.rs, src/encoders/*	Encoders use canonical spike constructors and declare instantaneous, windowed, or overlapping timing models.
Cross-encoder validation tests/time_semantics.rs, REVIEW.md	Tests validate bounds, ordering, batch/streaming equivalence, cursor mapping, timebases, rate bursts, and default behavior.
Documentation and integration examples README.md, examples/*	Documents timing and migration semantics. Adds spike_timebase and updates the latency example.

Estimated code review effort: 4 (Complex) | ~60 minutes

Merge Risk: ⚪ Minimal · up to f6e90

The PR standardizes encoder timestamp behavior and adds caller-managed time conversion while preserving serialized timestamp values; no actionable merge-blocking risk remains at the current head.

Sequence Diagram(s)

sequenceDiagram
  participant Encoder
  participant TimeCursor
  participant Timeline
  Encoder->>TimeCursor: Emit call-relative SpikeEvent offsets
  TimeCursor->>Timeline: Convert offsets to absolute nanoseconds
  Timeline->>Timeline: Merge and sort events chronologically

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🚥 Pre-merge checks | ✅ 5

✅ Passed checks (5 passed)

Check name	Status	Explanation
Linked Issues check	✅ Passed	The changes satisfy issue #62 by defining shared timing semantics, documenting integrations, preserving migration guidance, and adding conformance tests.
Out of Scope Changes check	✅ Passed	The documentation, examples, tests, error handling, and encoder updates directly support the linked issue objectives.
Docstring Coverage	✅ Passed	Docstring coverage is 100.00% which is sufficient. The required threshold is 80.00%.
Title check	✅ Passed	The title clearly and concisely describes the PR's main change: explicit spike timestamp and timebase semantics.
Description check	✅ Passed	The description directly explains the timestamp contract, new time APIs, encoder behavior, migration impact, tests, and verification.

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• Commit simplified code in branch claude/github-issue-62-setup-faig40

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[amazon-q-developer]

Summary

This PR successfully implements explicit spike timestamp and timebase semantics, addressing issue #62. The changes define a unified time model across all encoders with call-relative TickOffset timestamps, optional physical Timebase, and comprehensive TimeModel/TimeCursor abstractions for managing absolute time.

Key Improvements:

• Type Safety: TickOffset prevents confusion between relative offsets and absolute timestamps
• Time Abstraction: TimeModel enables generic handling of any encoder's temporal behavior
• Consistency: All encoders now follow the same call-relative timestamp contract
• Testing: Comprehensive conformance suite validates time semantics across all encoders

Breaking Changes (well-documented with migration guidance):

1. SpikeEvent::timestamp now uses TickOffset instead of u64
2. PhaseEncoder emits call-relative offsets (use TimeCursor for absolute values)
3. Latency gains capped at max_latency (hard bound on span_ticks())

Verification:
✅ All tests pass (201 lib + integration + doc tests)
✅ Zero clippy warnings
✅ Examples compile and run
✅ Comprehensive test coverage including edge cases

The implementation is production-ready with proper error handling, extensive documentation, and backward-compatible migration paths.

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Up to standards ✅

🟢 Issues 0 issues

Results:
0 new issues

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🟢 Metrics 67 complexity · 4 duplication

Metric	Results
Complexity	67
Duplication	4

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[rmems]

Review triage — 31e49d6 + 500f173

Seven findings were raised across the automated reviewers. Five were valid and are fixed; two were already addressed by the time they posted.

One real bug, reproduced first

LatencyEncoder::new(u64::MAX, ..) emitted a spike outside its own declared span. span = max_latency + 1 saturated back to u64::MAX, and TimeModel::contains is exclusive, so a NaN input (which maps to max_latency) produced an offset the encoder's own model rejected. Confirmed with a throwaway test before touching anything:

span=18446744073709551615 offset=18446744073709551615 contains=false

Fixed at the source rather than at the boundary: try_new now rejects max_latency == u64::MAX with a new EncoderError::WindowTooLarge, so time_model() needs no saturating add and span_ticks() is a hard bound for every configuration that constructs. Covered by latency_encoder_rejects_an_unrepresentable_window, which asserts the rejection and that max_latency - 1 still contains its own latest spike.

The conformance suite would have caught this if it had been driven with that config — it now is, via the constructor bound.

Also fixed

Finding	Status
Timebase::try_from_hz reported parameter: "tick_seconds"	Fixed — reports "hz", the argument the caller actually passed, on both the guard and the delegated conversion
TimeCursor doc example asserted over an empty vector	Fixed — 200 Hz over 1 ms steps never accumulated a whole spike, so all(..) passed vacuously. Now 2 kHz, asserting the exact nanosecond timeline
current_phase() docs omitted read-before-call ordering	Fixed — the counter advances after output, so the documented cycle-position recipe was off by one tick when read afterwards
"never spill backwards" assertion was vacuous	Fixed — for a non-overlapping model the earliest tick is the origin, so it could never fail. Now asserts the falsifiable direction: a call's latest spike lands before the next call's origin, which is exactly what the saturating span violated

Already addressed

Encoder-table duplication and the large assertion blocks were both fixed in 31e49d6, before those comments landed. The assertion blocks moved further in 500f173: the time-type unit tests now live in tests/time_types.rs, because Codacy scores src/ only (.codacy.yml excludes tests/) and was counting the split-up test module as production complexity. They test entirely public types, so they belong where the repo's config says test code goes.

Local verification on 500f173

Check	Result
cargo fmt --check	pass (silent)
cargo test --all-features --locked	pass (191 lib / 3 / 9 / 8 / 29 / 23 doc)
cargo clippy --all-features --all-targets -- -D warnings	pass, zero warnings
Examples (all 9, incl. --features ndarray)	pass, no panics

---

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All reported issues were addressed across 9 files (changes from recent commits).

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[rmems]

7226324 — the max_latency fix was at the wrong layer

@cubic-dev-ai and @devin-ai-integration independently caught that my previous fix was incomplete, and they were right. Rejecting max_latency == u64::MAX at the constructor did not close the hole: max_latency = u64::MAX - 1 is accepted and still escapes.

max_latency as f64 rounds up to 2^64 (2^64 − 1 has no f64 representation), so (1.0 - normalized) * max_latency as f64 saturates the as u64 cast to u64::MAX — one tick past a span of u64::MAX. Reproduced before fixing:

max_latency as f64 == 2^64: true
span=18446744073709551615 offset=18446744073709551615 contains=false

The real fix is clamping the computed offset to the latency budget, which holds for every accepted configuration regardless of what the float arithmetic does — applied to both the plain and gain-scaled paths. The constructor bound stays, since it's what keeps max_latency + 1 exact.

Why the test missed it: my boundary test drove only the NaN input, which short-circuits to max_latency without touching the f64 product. It now drives range.min and a below-range value as well, and tests/time_semantics.rs runs the extreme window through the shared conformance assertions — so the harness catches this class of bug next time instead of a reviewer.

Also addressed

Finding	Change
README migration note for the old PhaseEncoder timestamp omitted the read-before-the-call requirement the rustdoc carries	Following it literally gave a value one tick high; the README now states it
The u64::MAX rejection also applies on deserialization	Noted in the migration section — the serde impl routes through try_new, so a 0.4 payload with that value now fails to load
Default time_model() silently mislabels out-of-crate encoders emitting non-zero offsets	Trait doc now warns explicitly that nothing catches this at compile time
examples/spike_timebase paired an 8 ms latency window with a 1 ms rate step	Spikes from the same sample drifted 8× apart on a supposedly "merged" timeline; the rate encoder now uses dt = 8 ms so both cover the same span per call, and the streams interleave

Verification on 7226324

Check	Result
cargo fmt --check	pass (silent)
cargo test --all-features --locked	pass (193 lib / 3 / 9 / 9 / 30 / 23 doc)
cargo clippy --all-features --all-targets -- -D warnings	pass, zero warnings
Examples (all 9, incl. --features ndarray)	pass, no panics

CI was fully green on c209c84 (13/13) before this push.

---

Generated by Claude Code

[cubic-dev-ai]

7226324 — the max_latency fix was at the wrong layer

@cubic-dev-ai and @devin-ai-integration independently caught that my previous fix was incomplete, and they were right. Rejecting max_latency == u64::MAX at the constructor did not close the hole: max_latency = u64::MAX - 1 is accepted and still escapes.

max_latency as f64 rounds up to 2^64 (2^64 − 1 has no f64 representation), so (1.0 - normalized) * max_latency as f64 saturates the as u64 cast to u64::MAX — one tick past a span of u64::MAX. Reproduced before fixing:
...

@rmems You're right, and the catch was accurate: rejecting u64::MAX at the constructor only closed the trivial case, because max_latency as f64 rounds up to 2^64 for every value in [2^64 - 1024, 2^64 - 1]. So u64::MAX - 1 was accepted, span_ticks() came out as u64::MAX, and the f64 product in timestamp_for saturated the as u64 cast one tick past the span. The NaN-only boundary test dodged all of it since NaN short-circuits before the product.

The clamping fix is the right layer. offset_within returns ticks.min(latency), and the gain path clamps the scaled budget before delegating, so both routes cap at ≤ max_latency, which is < span_ticks for every accepted configuration. The u64::MAX as f64 saturation on the product is exactly what the .min() neutralizes — good reasoning to apply it to both paths rather than leaning on the constructor.

A couple of small confirmations on the sheet:

• TimeModel::contains is exclusive (offset < span), so clamping to max_latency with span = max_latency + 1 is consistent — nothing lands on the boundary.
• The min(latency) after the saturating cast is the correct total: as u64 saturates to u64::MAX, and min(latency) pulls it back inside.
• Driving the extreme window (and range.min, a below-range value) through the shared assert_call_conforms in tests/time_semantics.rs is the durable part here — that's the regression that was always going to slip past a purpose-built test.

The current_phase read-before-call doc, the deserialization note, and the dt = 8 ms alignment in examples/spike_timebase all match what I'd flagged. Prior comment still stands as written; the new commit closes it.

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Actionable comments posted: 1

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• README.md
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• src/encoders/latency.rs
• src/encoders/phase.rs
• src/encoders/rate.rs
• src/error.rs
• src/lib.rs
• src/time.rs
• tests/time_semantics.rs
• tests/time_types.rs

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