Merge branch 'main' into dependabot/cargo/noodles-0.109.0

Author: Zethson

.github/workflows/docs.yml

@@ -0,0 +1,62 @@
+name: Deploy website
+
+on:
+  push:
+    branches: [main]
+    paths:
+      - 'docs/**'
+      - '.github/workflows/docs.yml'
+  workflow_dispatch:
+
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+
+concurrency:
+  group: pages
+  cancel-in-progress: true
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        working-directory: docs
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v6
+
+      - name: Install pnpm
+        uses: pnpm/action-setup@v6
+        with:
+          package_json_file: docs/package.json
+
+      - name: Setup Node
+        uses: actions/setup-node@v6
+        with:
+          node-version: 22
+          cache: pnpm
+          cache-dependency-path: docs/pnpm-lock.yaml
+
+      - name: Install dependencies
+        run: pnpm install --frozen-lockfile
+
+      - name: Build site
+        run: pnpm build
+
+      - name: Upload artifact
+        uses: actions/upload-pages-artifact@v5
+        with:
+          path: docs/dist
+
+  deploy:
+    needs: build
+    runs-on: ubuntu-latest
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    steps:
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v5

.github/workflows/release.yml

@@ -72,7 +72,7 @@ jobs:
             exit 1
           fi
 
-          LOCK_VERSION=$(awk '/^name = "ruSTAR"/{found=1} found && /^version =/{print; exit}' Cargo.lock | sed 's/.*"\(.*\)"/\1/')
+          LOCK_VERSION=$(awk '/^name = "rustar-aligner"/{found=1} found && /^version =/{print; exit}' Cargo.lock | sed 's/.*"\(.*\)"/\1/')
           if [ "$LOCK_VERSION" != "$RAW" ]; then
             echo "::error::Cargo.lock version ($LOCK_VERSION) does not match Cargo.toml version ($RAW)"
             exit 1
@@ -160,7 +160,7 @@ jobs:
         id: package
         shell: bash
         run: |
-          BIN="ruSTAR"
+          BIN="rustar-aligner"
           EXT="${{ matrix.ext }}"
           ARCHIVE="${BIN}-${{ matrix.name }}"
 
@@ -402,7 +402,7 @@ jobs:
         run: |
           gh release create "${{ needs.check-release.outputs.version }}" \
             --target "${{ github.sha }}" \
-            --title "ruSTAR ${{ needs.check-release.outputs.version }}" \
+            --title "rustar-aligner ${{ needs.check-release.outputs.version }}" \
             --notes-file /tmp/release-notes.md
 
       - name: Create release (auto-generated notes)
@@ -412,7 +412,7 @@ jobs:
         run: |
           gh release create "${{ needs.check-release.outputs.version }}" \
             --target "${{ github.sha }}" \
-            --title "ruSTAR ${{ needs.check-release.outputs.version }}" \
+            --title "rustar-aligner ${{ needs.check-release.outputs.version }}" \
             --generate-notes
 
   # ------------------------------------------------------------------
@@ -443,16 +443,10 @@ jobs:
 
   # ------------------------------------------------------------------
   # 5. Publish to crates.io (release only, last step)
-  #
-  # TODO: The `rustar` crate name is already taken on crates.io. This job will
-  # fail until a free name is chosen in `Cargo.toml`. Gated off with `if:
-  # false` for now — flip back to `needs.check-release.outputs.is_release ==
-  # 'true'` once the name is resolved (and a crates.io trusted-publisher
-  # config has been set up for this repository).
   # ------------------------------------------------------------------
   publish-crate:
     name: Publish to crates.io
-    if: false
+    if: needs.check-release.outputs.is_release == 'true'
     needs: [check-release, upload-binaries]
     runs-on: ubuntu-latest
     permissions:

CHANGELOG.md

@@ -1,10 +1,10 @@
-# ruSTAR Changelog
+# rustar-aligner Changelog
 
 <!--
 Release notes are extracted from this file by the release workflow.
 Each released version needs a heading of the form:
 
-    ## [Version X.Y.Z](https://github.com/Psy-Fer/ruSTAR/releases/tag/vX.Y.Z) - YYYY-MM-DD
+    ## [Version X.Y.Z](https://github.com/Psy-Fer/rustar-aligner/releases/tag/vX.Y.Z) - YYYY-MM-DD
 
 Sections commonly used: Features, Bug fixes, Other changes.
 -->

CLAUDE.md

@@ -0,0 +1,42 @@
+# Contributing to rustar-aligner
+
+## Building and testing
+
+Rust 2024 edition. Standard Cargo commands:
+
+```bash
+cargo build            # debug build
+cargo build --release  # release build
+cargo test             # run all tests
+cargo clippy           # lint (zero warnings expected)
+cargo fmt --check      # formatting check
+```
+
+CI runs on Linux (x86_64, x86-64-v3, aarch64), macOS (aarch64), and Windows (x86_64). PRs must pass all CI checks before merging.
+
+## Test data
+
+Small synthetic and yeast test data lives in `test/`. Integration tests in `tests/` use the synthetic genome. Differential testing against STAR reference outputs is done via `test/compare_sam.py` and `test/compare_pe.py`.
+
+## Project history
+
+rustar-aligner was written as a faithful port of [STAR](https://github.com/alexdobin/STAR) by Alexander Dobin. Up to the initial release, the goal was behavioral parity with STAR — matching its algorithms, thresholds, and output formats as closely as possible. Notes from that development phase are in `docs-old/` (`docs-old/dev/` and the `phase*.md` files).
+
+Future development is not bound by that constraint. Adding STARsolo, new features, or diverging from STAR behavior is entirely welcome.
+
+## Documentation site
+
+The user-facing docs site is an [Astro Starlight](https://starlight.astro.build/) project under `docs/`:
+
+```bash
+cd docs
+pnpm install
+pnpm dev          # local dev server
+pnpm build        # production build into docs/dist/
+```
+
+Content lives under `docs/src/content/docs/` as Markdown / MDX files with YAML frontmatter (`title`, `description`). Sidebar order is configured in `docs/astro.config.mjs`. Site-wide design tokens (colours, fonts, graph-paper background, wave dividers) live in `docs/src/styles/custom.css` and can be tuned in one place.
+
+## License
+
+MIT, matching the original STAR license.

CONTRIBUTING.md

@@ -1,16 +1,12 @@
 [package]
-name = "ruSTAR"
-# TODO: the `rustar` crate name is already taken on crates.io. A different
-# published name must be chosen before the first `cargo publish` (for example
-# `rustar-aligner` or `rustar-rnaseq`). The `publish-crate` job in
-# `.github/workflows/release.yml` is gated off until this is resolved.
+name = "rustar-aligner"
 version = "0.1.0"
 edition = "2024"
 rust-version = "1.88"
 authors = ["James Ferguson"]
 description = "A Rust reimplementation of STAR (Spliced Transcripts Alignment to a Reference), the RNA-seq aligner"
 license = "MIT"
-repository = "https://github.com/Psy-Fer/ruSTAR"
+repository = "https://github.com/Psy-Fer/rustar-aligner"
 readme = "README.md"
 keywords = ["bioinformatics", "rna-seq", "aligner", "sequencing", "star"]
 categories = ["command-line-utilities", "science"]
@@ -21,18 +17,12 @@ exclude = [
     ".github/",
     "Dockerfile",
     ".dockerignore",
-    "ALIGNMENT_FIXES.md",
-    "BUGFIX_2026-02-09.md",
-    "PERFORMANCE_FIX.md",
-    "PHASE12_COMPLETE.md",
     "ROADMAP.md",
-    "STAR_SA_RESEARCH.md",
-    "TESTING_SUMMARY.md",
     "CLAUDE.md",
 ]
 
 [[bin]]
-name = "ruSTAR"
+name = "rustar-aligner"
 path = "src/main.rs"
 
 [dependencies]
@@ -50,9 +40,9 @@ rayon = "1"
 dashmap = "6"
 chrono = "0.4"
 rand = "0.8"
+tempfile = "3"
 
 [dev-dependencies]
-tempfile = "3"
 assert_cmd = "2"
 predicates = "3"
 

Cargo.lock

@@ -16,8 +16,8 @@ RUN HOST_TRIPLE=$(rustc -vV | awk '/^host:/ {print $2}') && \
     GIT_SHORT_HASH="${GIT_SHORT_HASH}" \
     cargo build --release --target "$HOST_TRIPLE" \
         ${CPU_TARGET:+--config "target.'$HOST_TRIPLE'.rustflags=['-C', 'target-cpu=$CPU_TARGET']"} \
-    && strip "target/$HOST_TRIPLE/release/ruSTAR" \
-    && cp "target/$HOST_TRIPLE/release/ruSTAR" /ruSTAR
+    && strip "target/$HOST_TRIPLE/release/rustar-aligner" \
+    && cp "target/$HOST_TRIPLE/release/rustar-aligner" /rustar-aligner
 
 # ---- Runtime stage ----
 FROM debian:bookworm-slim
@@ -27,7 +27,7 @@ RUN apt-get update && apt-get install -y --no-install-recommends \
     procps \
     && rm -rf /var/lib/apt/lists/*
 
-COPY --from=builder /ruSTAR /usr/local/bin/ruSTAR
-COPY --from=builder /ruSTAR /usr/local/bin/STAR
+COPY --from=builder /rustar-aligner /usr/local/bin/rustar-aligner
+COPY --from=builder /rustar-aligner /usr/local/bin/STAR
 
-CMD ["ruSTAR"]
+CMD ["rustar-aligner"]