Publish dada2-rs to crates.io: gate WFA behind a developer build

[cjfields]

Goal

Publish dada2-rs to crates.io. The crate is currently unpublishable as-is because it has a git dependency (wfa2lib-rs), which crates.io categorically rejects (every dependency must resolve to a registry semver version).

Blocker

Cargo.toml:

wfa2lib-rs = { git = "https://github.com/HPCBio/wfa2lib-rs", rev = "4cfeda86a3e1", default-features = false }

WFA is also not feature-gated — wfa2lib_rs is imported unconditionally in src/nwalign.rs (and the MSRV was bumped 1.87→1.91 solely for it).

Plan: gate WFA behind a developer build

WFA is still experimental; we believe it's a feasible alternative to standard NW if we sort out the upstream filtering steps (k-mer prefilter, band size) to make it tenable. So for now keep it in the repo but out of the published crate.

• Add an off-by-default Cargo feature (e.g. wfa) and make wfa2lib_rs an optional dependency.
• Put all wfa2lib_rs use in src/nwalign.rs (and any other modules) behind #[cfg(feature = "wfa")]; provide a clear runtime/compile error if the WFA backend is selected without the feature.
• Note: a Cargo feature still cannot carry a git source. For the published crate the optional dep line cannot point at git. Approach: keep the dependency commented out / patched in for developer builds, documented as "uncomment the [patch] override + enable --features wfa". The published Cargo.toml ships NW-only.
• Decide whether enabling wfa should also be what bumps MSRV to 1.91; default (NW-only) build should target the lower MSRV if feasible.
• Document the developer WFA build in CONTRIBUTING.md / README.

crates.io release checklist (once unblocked)

• version bump + CHANGELOG entry (currently 0.1.1).
• Verify Cargo.toml metadata: description, repository, readme, license (LGPL-3.0-only), keywords, categories, authors. (Looks complete.)
• Confirm exclude/include keeps the package small — exclude data/, testdata/, notes/, tmp/, dev/, large fixtures from the published tarball.
• cargo publish --dry-run (after cargo package --list review) passes with NW-only default.
• Confirm default build compiles and tests pass with WFA feature off.
• Confirm cargo build --no-default-features and --all-features (locally, with patch) both behave.
• Tag the release in git + create a GitHub release.
• cargo publish.

Future direction (why keep WFA)

WFA may be a viable NW alternative pending upstream filtering work (k-mer screen, band size). Tracked separately; this issue is just about making a clean first crates.io release while preserving the WFA dev path.

[jianshu93]

thanks for the hard work.--Jianshu

[cjfields]

Code-level feature-gating done in a70de7a (branch feat/failed-uniques-issue60).

Done:

• wfa2lib-rs is now optional = true; added [features] wfa = ["dep:wfa2lib-rs"] (off by default).
• All wfa2lib_rs-touching code in nwalign.rs is behind #[cfg(feature = "wfa")]: imports, the USE_WFA_BACKEND/WFA_MAX_STEPS statics, the real align_wfa_endsfree_with_buf + cigar_to_alignment_into, the dispatch branch, and all WFA tests/benches.
• Added an NW-only stub for align_wfa_endsfree_with_buf that aborts with a clear rebuild with --features wfa message, so --align-backend wfa2 errors rather than silently falling back to NW.
• AlignBackend enum, CLI flags, and the wfa_max_edits (plain i32) plumbing are left intact for serde/JSON round-trip stability — minimal churn.

Verified: default build + tests pass (WFA tests excluded); cargo build --features wfa builds and its 18 nwalign tests pass.

Still remaining for a publishable crate (unchanged):

• Strip/comment the git wfa2lib-rs line before cargo publish — crates.io rejects git deps even when optional. The wfa feature stays a source-checkout developer build.
• The rest of the release checklist above (version/CHANGELOG, cargo package --list review, --dry-run, MSRV decision, tag + release).

This work is on a branch off #60; not merging the PR yet.

[cjfields]

Documentation for the experimental WFA backend added in 25a1723:

• docs/installation.md — "Developer build: experimental WFA backend" (cargo build --features wfa, MSRV 1.91, not on crates.io / cargo install).
• docs/parameters.md — "Experimental: WFA alignment backend" section: flag table for --align-backend / --wfa-max-edits + the requires---features wfa / errors-on-default-build caveat.
• README.md — one line in the experimental-features list.
• CONTRIBUTING.md — how to build/test the wfa feature, iterate on a local wfa2lib-rs fork, and the reminder to run tests both with and without the feature.
• Cargo.toml — added the (commented) [patch] override block the manifest already referenced but didn't contain.
• cli.rs — --align-backend help now notes wfa2 needs a --features wfa build.

Remaining for the actual crates.io release (unchanged):

• Strip/comment the git wfa2lib-rs line before cargo publish.
• Version bump + CHANGELOG.
• cargo package --list review (exclude data/, testdata/, notes/, tmp/, dev/).
• cargo publish --dry-run on the NW-only default.
• Confirm --no-default-features and (locally, with patch) --features wfa both behave.
• MSRV decision for the default build.
• Tag + GitHub release, then cargo publish.

[cjfields]

Publishing mechanics implemented in PR #64 (feat/crates-io-publish-issue63).

Done:

• scripts/publish-crate.sh + just/make publish-crate: strips the WFA git dep + wfa feature, runs cargo publish, restores the manifest (EXIT trap). Passing --dry-run verified end-to-end.
• Version bumped to 0.2.0 (0.1.0 already on crates.io).
• Package trimmed 116 → 68 files (~7 MB PacBio concordance FASTQs + dev/examples/notes/CI-infra excluded); 1.1 MiB compressed, well under the 10 MB limit.
• [lints.rust] check-cfg so #[cfg(feature = "wfa")] doesn't warn on the feature-less published build / cargo install.
• CHANGELOG.md added (curated 0.2.0 section).
• Fixed a CI regression the feature-gating introduced: concordance.yml now builds --features wfa (its ALIGN_BACKEND=wfa2 steps otherwise hit the NW-only stub). Note: main's concordance workflow is currently broken until PR crates.io publishing mechanics for v0.2.0 (issue #63) #64 lands.

Remaining (needs crates.io credentials, to be done off this environment):

• Merge PR crates.io publishing mechanics for v0.2.0 (issue #63) #64.
• cargo login with a crates.io token.
• Tag v0.2.0 + push (also triggers release.yml GitHub Release binaries).
• just publish-crate (no --dry-run) to upload.

[cjfields]

Now uploaded to crates.io, v0.2.0.