fix(ci): resolve clippy 1.97 lints and RUSTSEC advisories - #107
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CI's clippy advanced to 1.97 (new lints fail the `-D warnings` gate) and rustsec flagged several advisories in the dependency tree. Both block all PRs. Clippy: - src/index/suffix_array.rs: assert!(x == 0) -> assert_eq! (manual_assert_eq) - src/io/sam.rs, tests/alignment_features.rs: byte-slice literals -> byte strings, e.g. [b'S', b'M'] -> *b"SM" (byte_char_slices) - src/quant/transcriptome.rs: if-let/else-return-None -> `?` (question_mark) Security audit (Cargo.lock only, no manifest change): - memmap2 0.9.10 -> 0.9.11 (RUSTSEC-2026-0186, out-of-bounds pointer offset) - crossbeam-epoch 0.9.18 -> 0.9.20 (RUSTSEC-2026-0204, invalid pointer deref) - anyhow 1.0.102 -> 1.0.104 (RUSTSEC-2026-0190, unsound downcast_mut) No behavioural change. Unblocks CI for open and future PRs. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
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CI is currently red on
mainfor reasons unrelated to any single change, which blocks all PRs. This fixes both the lint and audit gates.Clippy (
-D warnings)CI's clippy advanced to 1.97, adding lints that now fail on existing code:
src/index/suffix_array.rs—assert!(x == 0)→assert_eq!(manual_assert_eq)src/io/sam.rs,tests/alignment_features.rs— byte-slice literals → byte strings, e.g.[b'S', b'M']→*b"SM"(byte_char_slices)src/quant/transcriptome.rs—if let … else { return None }→?(question_mark)Security audit (Cargo.lock only, no manifest change)
memmap20.9.10 → 0.9.11 — RUSTSEC-2026-0186 (out-of-bounds pointer offset tomadvise/msync)crossbeam-epoch0.9.18 → 0.9.20 — RUSTSEC-2026-0204 (invalid pointer deref infmt::Pointer)anyhow1.0.102 → 1.0.104 — RUSTSEC-2026-0190 (unsounddowncast_mut)The memmap2/anyhow bumps overlap with dependabot #100/#101; this PR additionally fixes the clippy 1.97 breakage and the crossbeam-epoch advisory, so the whole gate goes green in one shot. Happy to close in favour of the dependabot PRs + a clippy-only PR if the team prefers.
No behavioural change. Verified locally with
cargo clippy --all-targets -- -D warnings,cargo fmt --check, andcargo test.🤖 Generated with Claude Code