crates.io publishing mechanics for v0.2.0 (issue #63)

.github/workflows/concordance.yml

@@ -52,8 +52,13 @@ jobs:
           key: ${{ runner.os }}-cargo-concordance-${{ hashFiles('**/Cargo.lock') }}
           restore-keys: ${{ runner.os }}-cargo-
 
-      - name: Build (release)
-        run: cargo build --release
+      # Built with `--features wfa` because the WFA concordance steps below drive
+      # the experimental backend via `ALIGN_BACKEND=wfa2`. The feature is
+      # off-by-default (issue #63), so without it those steps would hit the
+      # NW-only stub. The resulting binary still defaults to NW for the plain
+      # concordance runs.
+      - name: Build (release, with WFA backend)
+        run: cargo build --release --features wfa
 
       # ---------------- Illumina (in-repo MiSeq tutorial pair) ----------------
       - name: Illumina — run dada2-rs pipeline

CHANGELOG.md

@@ -0,0 +1,56 @@
+# Changelog
+
+All notable changes to this project are documented here. The format is based on
+[Keep a Changelog](https://keepachangelog.com/en/1.1.0/), and the project aims to
+follow [Semantic Versioning](https://semver.org/spec/v2.0.0.html) (pre-1.0, so
+minor versions may carry breaking changes).
+
+## [0.2.0] - Unreleased
+
+### Added
+- `summary` subcommand: per-position quality metrics, cumulative expected-error
+  metrics, and an optional per-read sequence-complexity histogram (#8).
+- `sample` and `errors-from-sample` subcommands for subsampling input FASTQs and
+  learning an error model from the subsample (usable for bootstrapping).
+- `--failed-uniques` diagnostic on `dada` / `dada-pseudo` / `dada-pooled`:
+  emits a TSV of uniques that failed to seed a partition (#60).
+- `chimera-diagnostics` for higher-order (trimera) screening, with
+  nearest-parent and flank gates (#54).
+- Experimental **WFA alignment backend** (`--align-backend wfa2`) with a
+  `--wfa-max-edits` edit-budget cap (#49, #51). ASV-equivalent to Needleman-
+  Wunsch on tested Illumina and PacBio HiFi data, but not byte-identical.
+- `merge-pairs` records input-file provenance and warns on mismatch (#10).
+- `just` / `make` task runners for build, install, test, and docs (#46).
+
+### Changed
+- The experimental WFA backend is now gated behind an **off-by-default `wfa`
+  Cargo feature** (#63). Default builds — and the published crate — are
+  Needleman-Wunsch only; selecting `--align-backend wfa2` without the feature
+  errors rather than silently falling back to NW. Building WFA requires a source
+  checkout (`cargo build --features wfa`) because it depends on a git crate that
+  cannot ship on crates.io.
+- Denoising/error-learning verbose logs now echo the active alignment backend
+  (#51).
+- Trimmed the published crate: development, benchmarking, concordance data
+  (multi-MB PacBio FASTQs), examples, notes, and CI/infra files are excluded.
+
+### Performance
+- Sparse k-mer-8 screen, gated to k ≥ 8, cutting resident memory in the
+  high-k regime (#43).
+- `dada-pooled` streams dereplication into merging instead of holding all
+  dereps in memory, and uses an integer merge-quality accumulator (#39, #41).
+- Various k-mer-vector memory reductions in the alignment screen (#32).
+
+### CI
+- R DADA2 concordance guardrail for Illumina and PacBio, with abundance/recall/
+  precision gates (#35).
+
+## [0.1.0] - 2026-06-03
+
+- Initial crates.io release: Rust ports of the core DADA2 pipeline steps
+  (`filter-and-trim`, `derep`, `learn-errors`, `dada`, `merge-pairs`,
+  `remove-bimera-denovo`, `assign-taxonomy` / `assign-species`, sequence-table
+  helpers).
+
+[0.2.0]: https://github.com/HPCBio/dada2-rs/compare/v0.1.0...HEAD
+[0.1.0]: https://github.com/HPCBio/dada2-rs/releases/tag/v0.1.0

Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "dada2-rs"
-version = "0.1.1"
+version = "0.2.0"
 edition = "2024"
 # Raised from 1.87 to 1.91 by the experimental WFA backend (wfa2lib-rs MSRV).
 # Revisit if the WFA backend is dropped.
@@ -12,7 +12,23 @@ readme = "README.md"
 authors = ["Chris Fields <cjfields@illinois.edu>"]
 keywords = ["bioinformatics", "amplicon", "dada2", "metagenomics", "asv"]
 categories = ["science", "command-line-utilities"]
-exclude = ["**/__pycache__/", "*.pyc"]
+# Keep the published crate lean: development, benchmarking, concordance data
+# (multi-MB PacBio FASTQs), examples, notes, and CI/infra files are not needed by
+# `cargo install` consumers. `data/`, `tmp/` are already gitignored.
+exclude = [
+    "**/__pycache__/",
+    "*.pyc",
+    "/dev",
+    "/examples",
+    "/notes",
+    "/data",
+    "/tmp",
+    "/.github",
+    "/.githooks",
+    "/.readthedocs.yaml",
+    "/AGENTS.md",
+    "/Cross.toml",
+]
 
 [dependencies]
 noodles = { version = "0.91", features = ["fastq", "fasta", "bgzf"] }
@@ -44,6 +60,15 @@ wfa2lib-rs = { git = "https://github.com/HPCBio/wfa2lib-rs", rev = "4cfeda86a3e1
 # runtime and the published crate is Needleman-Wunsch only.
 wfa = ["dep:wfa2lib-rs"]
 
+[lints.rust]
+# The publish script (scripts/publish-crate.sh) strips the `wfa` feature from the
+# manifest for the crates.io release, since it depends on a git crate. Declaring
+# `feature="wfa"` as a known cfg value keeps the `#[cfg(feature = "wfa")]` code in
+# nwalign.rs from emitting `unexpected_cfgs` warnings when built without the
+# feature defined (e.g. `cargo install dada2-rs`). Harmless when the feature is
+# present in the manifest.
+unexpected_cfgs = { level = "warn", check-cfg = ['cfg(feature, values("wfa"))'] }
+
 [dev-dependencies]
 serde_json = "1"
 

Makefile

@@ -22,7 +22,9 @@ SCRIPTS = $(wildcard scripts/*.R) $(wildcard scripts/*.py)
 
 .PHONY: all build build-native build-arm64 install uninstall \
         check fmt fmt-check clippy test clean docs-serve docs-build \
-        check-build-sync help
+        publish-crate check-build-sync help
+
+PUBLISH_ARGS ?=
 
 all: build
 
@@ -85,6 +87,10 @@ docs-build:
 clean:
 	cargo clean
 
+## publish-crate: publish NW-only crate to crates.io (strips WFA git dep; PUBLISH_ARGS=--dry-run to test)
+publish-crate:
+	./scripts/publish-crate.sh $(PUBLISH_ARGS)
+
 ## check-build-sync: fail if justfile recipes and Makefile targets have drifted
 check-build-sync:
 	./scripts/check-build-sync.sh

justfile

@@ -88,6 +88,11 @@ docs-build:
 clean:
     cargo clean
 
+# publish an NW-only crate to crates.io (strips the WFA git dep; see issue #63).
+# Pass --dry-run to verify without uploading: `just publish-crate --dry-run`.
+publish-crate *ARGS:
+    ./scripts/publish-crate.sh {{ARGS}}
+
 # fail if justfile recipes and Makefile targets have drifted apart
 check-build-sync:
     ./scripts/check-build-sync.sh

scripts/publish-crate.sh

@@ -0,0 +1,51 @@
+#!/usr/bin/env bash
+# publish-crate.sh — publish dada2-rs to crates.io as a Needleman-Wunsch-only crate.
+#
+# The experimental WFA backend depends on `wfa2lib-rs` via a *git* dependency,
+# which crates.io rejects outright (issue #63). This script temporarily strips
+# that git dependency and its off-by-default `wfa` feature from Cargo.toml, runs
+# `cargo publish`, then restores the original manifest. The published crate is
+# therefore NW-only; WFA stays a source-checkout developer build
+# (`cargo build --features wfa`).
+#
+# Usage:
+#   scripts/publish-crate.sh --dry-run     # verify packaging without uploading
+#   scripts/publish-crate.sh               # real publish (needs `cargo login`)
+#
+# Any extra arguments are passed straight through to `cargo publish`.
+set -euo pipefail
+cd "$(dirname "$0")/.."
+
+MANIFEST="Cargo.toml"
+BACKUP="$(mktemp)"
+
+restore() {
+    if [ -f "$BACKUP" ]; then
+        cp "$BACKUP" "$MANIFEST"
+        rm -f "$BACKUP"
+        echo "==> Restored original $MANIFEST"
+    fi
+}
+trap restore EXIT
+cp "$MANIFEST" "$BACKUP"
+
+echo "==> Stripping the experimental WFA git dependency + feature for publishing"
+python3 - "$MANIFEST" <<'PY'
+import re, sys
+path = sys.argv[1]
+s = open(path).read()
+before = s
+# Remove the git `wfa2lib-rs` dependency line...
+s = re.sub(r'(?m)^wfa2lib-rs\s*=.*\n', '', s)
+# ...and the off-by-default `wfa` feature that referenced it.
+s = re.sub(r'(?m)^wfa\s*=\s*\[.*\]\s*\n', '', s)
+if s == before:
+    sys.exit("ERROR: expected WFA dependency/feature lines were not found; "
+             "manifest layout may have changed — update publish-crate.sh.")
+open(path, "w").write(s)
+PY
+
+echo "==> cargo publish --allow-dirty $*"
+# --allow-dirty because we have just edited Cargo.toml in place (and callers may
+# publish with other working-tree changes present).
+cargo publish --allow-dirty "$@"