Pin hts-sys to bindings compatible with rust-htslib 0.46

[SuhasSrinivasan]

Fixes #665.

Summary

• Constrain hts-sys to 2.2.0, whose bindings compile with the existing rust-htslib 0.46.0 dependency.
• Prevent fresh dependency resolution from selecting hts-sys 2.2.1 and breaking the workspace build.
• Keep the repair to one manifest constraint plus an explanatory comment; no Rust source or generated lockfile changes.

Severity

Severity: High — build reproducibility and development reliability

Rationale: A clean checkout currently fails before modkit can be built or tested. The failure is explicit and cannot corrupt scientific output, but it blocks reproducible development, CI, packaging, and source installation.

Root cause

The workspace does not commit Cargo.lock. rust-htslib 0.46.0 permits the semver-compatible hts-sys 2.x range beginning at 2.1.1, so a fresh solve now selects hts-sys 2.2.1. Its binding field names and integer types do not match rust-htslib 0.46.0's source, producing ten compile errors. Cargo had no repository-level constraint that retained the known-compatible 2.2.0 bindings.

Implementation

Add hts-sys = "=2.2.0" immediately after rust-htslib in modkit-core/Cargo.toml, with a one-line reason. Because all rust-htslib users are in the same workspace graph, Cargo unifies them onto one hts-sys 2.2.0 instance.

Preserved behavior

• rust-htslib remains at 0.46.0 and retains its existing default bzip2, lzma, and curl feature set.
• The dependency graph contains one hts-sys instance rather than parallel binding versions.
• No Rust source, CLI, file format, data path, test fixture, or scientific result changes.
• Cargo.lock remains ignored and absent from the diff.

Non-goals

• No rust-htslib/HTSlib stack upgrade or broad dependency refresh.
• No decision to commit Cargo.lock or require --locked in future CI/install workflows.
• No bindgen/libclang enablement, generated binding changes, or patches to upstream crates.
• No new CI workflow.

Behavior before and after

Case	Before	After	Expected oracle
Fresh dependency solve	hts-sys 2.2.1 selected	hts-sys 2.2.0 selected	One workspace-wide compatible hts-sys instance
cargo check -p mod_kit	Exit 101; ten rust-htslib binding errors	Exit 0	Existing rust-htslib 0.46.0 compiles
Workspace test suite	Cannot start after failed fresh build	179 active tests pass; 14 declared ignored	No test failures

Testing

Test environment

• Revision tested: 18ebf054bed61de2ec7553d41fa81a8cc6938226
• Tree tested and worktree state: 7e1b269f9804ff5e99db0420574462a8f8a6a065; clean
• Parent revision: 5cecc3fb3a9336068d9e3c68d5c08d678153dd2c
• Toolchain: rustc 1.90.0; cargo 1.90.0
• Platform: macOS 26.6, arm64
• Dependency resolution identity: parent generated lock SHA-256 4af98bb22a10b9b65b86e00a4d5831b254fc6aec89fd51931c5aefd2861d0f9a; fixed generated lock SHA-256 d370908c0be24430282110489c8002550edd83a1811cf1bdc1dc68f972c01fc8; neither ignored lockfile is in the diff

Test layer	Exact command, fixture, or matrix	Result and evidence
Core: parent-red regression	Fresh detached parent; cargo generate-lockfile --offline; cargo tree --offline --locked -i hts-sys; env CARGO_TARGET_DIR=/private/tmp/modkit-u01-parent-public-target cargo check --offline --locked -p mod_kit	Resolves hts-sys 2.2.1; exits 101 with exactly ten rust-htslib E0308/E0609 errors
Core: fixed dependency identity	cargo generate-lockfile --offline; cargo tree --offline --locked -i hts-sys	One hts-sys 2.2.0 instance shared by mod_kit, modkit, ochm, safe-record, and rust-htslib
Core: affected package/workspace check	cargo check --offline --locked --workspace --all-targets --quiet	Exit 0; only pre-existing warnings
Core: applicable full workspace gate	Fresh-target cargo test --workspace --all-targets -- --test-threads=1 on the frozen exact head	179 passed, 14 declared ignored, 0 failed
Manifest/feature validation	cargo metadata --offline --locked --format-version 1 --no-deps; cargo tree --offline --locked -e features -i hts-sys	Manifest valid; one hts-sys version; existing bzip2/lzma/curl features retained
Core: diff hygiene	git diff --check upstream/master...HEAD; exact ancestry, diff, and clean-worktree checks	Passed; one commit, one changed manifest, two inserted lines, clean worktree

Tests not performed

• Real sequencing-data regression and output-byte comparisons were not run because the patch changes only dependency resolution and the complete workspace test suite exercises the compiled code.
• Performance, RSS, and I/O benchmarks were not run because the resolved runtime library version is the previously compatible 2.2.0 and no production code changes.
• cargo clippy was not run.
• cargo fmt --all -- --check was run but is not a passing gate: stable rustfmt reports pre-existing formatting differences in unchanged files (modkit/tests/test_bedmethyl_util.rs, modkit-core/src/adjust.rs, and modkit-core/src/entropy/mod.rs) plus the repository's nightly-only setting warnings. This PR changes only TOML; git diff --check passes.

Scientific validation

• Population/eligibility invariant: no read, call, position, or sample-selection logic changes.
• Count/category conservation invariant: no scientific computation or serializer changes.
• Coordinate/strand/interval invariant: not affected.
• Determinism invariant: the fixed source revision now constrains the previously time-dependent hts-sys choice to one exact compatible version.
• Independent oracle: the same parent source fails only with 2.2.1 and succeeds when resolution is constrained to 2.2.0; exact dependency trees and full tests confirm the boundary.

Output and compatibility

• User-visible change: fresh source builds succeed instead of failing in rust-htslib.
• Expected output differences: none.
• Byte-identical controls: not separately run; no Rust code or output path changes, and the full workspace suite passes.
• CLI/API/schema compatibility: unchanged.
• Partial-output or failure semantics: unchanged; this is a compile-time resolution fix.

Reviewer guide

1. Review the two-line modkit-core/Cargo.toml diff and explanatory comment.
2. Reproduce the parent solve with cargo generate-lockfile and cargo tree -i hts-sys.
3. Confirm the fixed solve contains exactly one hts-sys 2.2.0 instance.
4. Rerun cargo check --locked --workspace --all-targets using the fixed generated lockfile.
5. Decide separately, outside this PR, whether modkit should later commit Cargo.lock and enforce --locked workflows.

Checklist

• The issue contains reproducible observed and expected behavior.
• The change is limited to the linked issue’s approved scope.
• The regression is demonstrably red on the exact parent revision.
• All tests actually performed are listed above with their results.
• Unrun or inapplicable tests are disclosed.
• Scientific counts/statistics and output compatibility are explicitly checked.
• Formatting and diff-hygiene results, including unrelated pre-existing findings, are documented.
• No generated data, private sample identifiers, or unrelated changes are included.