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feat(simplex): route the simplex command onto the declarative chain builder - #894
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ChangesSimplex chain execution
Estimated code review effort: 4 (Complex) | ~45 minutes Merge Risk: ⚪ Minimal · up to The PR routes threaded simplex execution through the declarative builder and adds validation for incorrectly sorted input; no actionable merge-blocking risk remains at the current head. Sequence Diagram(s)sequenceDiagram
participant Simplex_execute
participant execute_chain
participant ChainBuilder
participant SimplexChain
Simplex_execute->>Simplex_execute: run pre-flight validation
Simplex_execute->>execute_chain: dispatch consensus threaded execution
execute_chain->>ChainBuilder: build single-stage chain
ChainBuilder->>SimplexChain: provide shared execution context
SimplexChain->>SimplexChain: run simplex pipeline
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## main #894 +/- ##
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+ Coverage 92.95% 93.05% +0.10%
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Inline comments:
In `@src/lib/commands/simplex.rs`:
- Around line 711-712: Preserve the raw input header before ChainBuilder::new or
its equivalent injects the command `@PG` record, and pass that untouched header to
the rejects sink used by add_simplex. Keep the processed header for normal
output, and extend the threaded rejects parity test to assert that the rejects
header matches the original input header.
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src/lib/commands/simplex.rssrc/lib/pipeline/chains/builder.rstests/integration/test_simplex_command.rs
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Inline comments:
In `@src/lib/pipeline/chains/builder.rs`:
- Line 3248: Make rejects-header selection stage-aware in the builder: use
raw_source_header only when Simplex is the first stage, otherwise use the
current self.header updated by preceding stages such as add_sort. Apply this
policy consistently in the relevant Simplex logic and in add_duplex and
add_codec, preserving the current-stage input metadata for chained pipelines.
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src/lib/pipeline/chains/builder.rstests/integration/test_simplex_command.rs
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…uilder Add the consensus-gated execute_chain to Simplex and dispatch to it from execute() when --threads N is set on a consensus-feature build, before the timer/reader are constructed. The no-threads single-threaded fast path is unchanged and serves as the in-process parity oracle. On a non-consensus build the dispatch is compiled out and --threads falls through to the legacy execute_threads_mode, so simplex-only builds keep --threads support. Folded in a blocking parity fix found during implementation: add_simplex was missing the check_consensus_sort_order guard that both legacy paths already call after opening the reader. Without it, a mis-sorted input on the chain path was silently mis-grouped by GroupByMi instead of rejected. Added the same guard call add_simplex now makes, mirroring the legacy behavior exactly. Extends the simplex integration test suite with chain-vs-single-threaded parity coverage across plain consensus, rejects, stats (byte-compare), methylation mode, disabled overlapping-consensus calling, allow-unmapped, a multi-batch fixture, and the coordinate-sorted rejection that proves the new guard.
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What
Route
fgumi simplexonto the declarative chain builder — R3.3, the first of the consensus trio.simplex --threads N(on aconsensus-feature build) now runs throughexecute_chain→ChainSpec::single_stage(Stage::Simplex, …)→build_for(spec)?.run(). The no---threadssingle-threaded fast path is kept unchanged as an in-process parity oracle (legacyexecute_threads_moderetained, removed in a follow-up).Feature-gating (the consensus-trio concern)
commands::simplexis gatedsimplex, but the chain machinery (StageOptionsBag.simplex,add_simplex) is gatedconsensus, andsimplexdoes not implyconsensus. Soexecute_chainand its dispatch are#[cfg(feature = "consensus")]-gated, and on a non-consensusbuild the dispatch is absent and execution falls through to the legacy threaded path (no regression, no bail). Verified:cargo check -p fgumi --no-default-features --features simplexcompiles, alongside the default and--all-featuresbuilds.Correctness fix the cutover exposed (folded in)
check_consensus_sort_orderguard inadd_simplex. Both legacy simplex paths call it right after opening the reader (it accepts template-coordinate/query-grouped input and rejects coordinate-sorted / plain-queryname / unsorted).add_simplexnever did, andGroupByMihas no out-of-order detection — so--threads Nwould have silently mis-grouped a badly-sorted input into wrong consensus calls instead of rejecting it. Added the same guard (the onebuilder.rsedit). (add_duplex/add_codecalmost certainly share this gap — noted for their cutovers.)Dispatch placement
The dispatch moves ahead of the timer/reader: the reader-free pre-flight (
io.validate, output-collision check,validate_read_bounds, the--ref/--methylation-modebail) runs first on both paths, then the consensus-gated--threadsdispatch, then the unchanged legacy tail. An invalid run no longer prints the timer/banner before erroring — intentional, matching dedup's ordering.Tests
Chain-vs-oracle parity across plain,
--rejects,--stats(byte-compare), methylation mode, overlapping-consensus (--consensus-call-overlapping-bases false, the disabled path),--allow-unmapped, a multi-batch case, and a coordinate-sorted rejection proving the new sort-order guard.Review
Spec Fable-reviewed against the code (the sort-order guard came from that review). A deep gauntlet review is running and any findings will be addressed before this is presented for merge.
Verification
cargo ci-fmt && cargo ci-lint && RUSTDOCFLAGS="-D warnings" cargo ci-doc && cargo ci-test— all green (9768 tests); simplex suite 111 passing; the three feature-check legs (--no-default-features --features simplex, default,--all-features) all compile. No newunsafe.Risk: threaded consensus simplex output changes, pinned by single-threaded parity and sort-order rejection tests;
unsafe: none, with noCLAUDE.mdallowlist update; memory bounds, queue capacity, and thread/backpressure policy: none.Fix: Route consensus-feature threaded simplex execution through the declarative chain builder. Preserve the legacy fallback and add consensus sort-order validation to
add_simplex.