chore: bump version to 0.3.0 (AI4S-YB fork, Windows-capable)

.github/workflows/release.yml

@@ -421,29 +421,23 @@ jobs:
         env:
           GH_TOKEN: ${{ github.token }}
         run: |
+          # Upload every archive format produced by the Package step:
+          # `.tar.gz` for Linux/macOS and `.zip` for Windows, each with
+          # its matching `.sha256` checksum file.
           gh release upload "${{ needs.create-tag-and-release.outputs.tag }}" \
             /tmp/binaries/*.tar.gz \
+            /tmp/binaries/*.zip \
             /tmp/binaries/*.sha256
 
   # ------------------------------------------------------------------
-  # 5. Publish to crates.io (release only, last step)
+  # 5. Publish to crates.io — intentionally omitted
   # ------------------------------------------------------------------
-  publish-crate:
-    name: Publish to crates.io
-    if: needs.check-release.outputs.is_release == 'true'
-    needs: [check-release, upload-binaries]
-    runs-on: ubuntu-latest
-    permissions:
-      id-token: write
-      contents: read
-    steps:
-      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # ratchet:actions/checkout@v6.0.2
-
-      - name: Authenticate with crates.io
-        id: auth
-        uses: rust-lang/crates-io-auth-action@bbd81622f20ce9e2dd9622e3218b975523e45bbe # ratchet:rust-lang/crates-io-auth-action@v1.0.4
-
-      - name: Publish to crates.io
-        run: cargo publish --no-verify
-        env:
-          CARGO_REGISTRY_TOKEN: ${{ steps.auth.outputs.token }}
+  #
+  # The AI4S-YB fork is not published to crates.io because the `rustqc`
+  # name there belongs to the upstream `seqeralabs` project. Releases
+  # are distributed via GitHub Releases (binaries) and GHCR (Docker
+  # images) only.
+  #
+  # To enable crates.io publishing, rename the crate in Cargo.toml
+  # (e.g. `rustqc-ai4syb`) or coordinate with the upstream owner, then
+  # restore a `publish-crate` job from the repo history.

CHANGELOG.md

@@ -1,5 +1,58 @@
 # RustQC Changelog
 
+## [Version 0.3.0](https://github.com/AI4S-YB/RustQC/releases/tag/v0.3.0) - 2026-04-22
+
+First release of the AI4S-YB fork. Focus: Windows support and a pure-Rust
+alignment-file backend. This is a **hard fork** of `seqeralabs/RustQC` v0.2.1
+and is not published to crates.io.
+
+### Breaking changes
+
+- **CRAM input is no longer supported.** The `rust-htslib` (HTSlib C library)
+  backend was replaced with [`noodles`](https://github.com/zaeleus/noodles).
+  `noodles-cram` 0.88 uses Rust 1.88+ syntax (let-chains), which conflicts
+  with the project's MSRV of 1.87, so CRAM was dropped rather than bumping
+  the toolchain. BAM and SAM remain fully supported. CRAM can return by
+  raising MSRV to ≥ 1.88 and re-adding `noodles-cram`.
+
+### New features
+
+- **Native Windows builds.** `x86_64-pc-windows-msvc` is now a first-class
+  target. Release artifacts include `rustqc-windows-x86_64.zip` alongside
+  the existing `.tar.gz` archives for Linux and macOS.
+
+### Internal changes
+
+- New `src/rna/bam_io.rs` facade module centralizes the semantic differences
+  between `rust-htslib` and `noodles` (MAPQ=255 sentinel handling, 1-based
+  ↔ 0-based position conversion, aux-tag integer extraction, CIGAR op
+  collection, QNAME `*` fallback, 4-bit encoded-base access for sequence
+  hashing). `open()` auto-detects SAM vs BAM and transcodes SAM through
+  noodles at load time so downstream code only sees `bam::Record`.
+- Build pipeline simplified: the htslib-era C dependency chain
+  (`hts-sys`, `openssl-sys`, `curl-sys`, `libz-sys`, `bzip2-sys`,
+  `lzma-sys`, `libclang`) is gone. Linux CI deps shrank from eight
+  system packages to two (`libfontconfig1-dev`, `pkg-config`).
+- `build.rs` no longer shells out to `date`; `qualimap/report.rs`
+  uses `chrono::Local` for local-time formatting. These were the
+  last POSIX-only hold-outs blocking Windows.
+- `plotters`'s `fontconfig-dlopen` feature is now gated behind
+  `cfg(not(windows))`.
+
+### Known regressions
+
+- Multithreaded BGZF decode (the old `bam.set_threads(n)` path) is
+  disabled. Large BAM throughput is lower than upstream v0.2.1 until
+  `noodles_bgzf::io::MultithreadedReader` is wired in; correctness is
+  unaffected. See `TODO(noodles-threading)` markers in
+  `src/rna/dupradar/counting.rs`.
+
+### Tests
+
+- All 234 unit and integration tests pass on Linux, macOS and Windows.
+- `preseq lc_extrap` output is byte-identical to the pre-migration
+  reference (`tests/data/test.preseq_lc_extrap.txt`).
+
 ## [Version 0.2.1](https://github.com/seqeralabs/RustQC/releases/tag/v0.2.1) - 2026-04-09
 
 ### Bug fixes

Cargo.toml

@@ -1,16 +1,16 @@
 [package]
 name = "rustqc"
-version = "0.2.1"
+version = "0.3.0"
 edition = "2021"
 rust-version = "1.87"
 authors = ["Phil Ewels <phil.ewels@seqera.io>", "Jon Manning <jonathan.manning@seqera.io>"]
 description = "Fast RNA-seq QC in a single pass: dupRadar, featureCounts, 8 RSeQC tools, preseq, samtools stats, and Qualimap — reimplemented in Rust"
 license = "GPL-3.0-or-later"
-repository = "https://github.com/seqeralabs/RustQC"
+repository = "https://github.com/AI4S-YB/RustQC"
 readme = "README.md"
 keywords = ["bioinformatics", "rna-seq", "duplication", "qc", "rseqc"]
 categories = ["command-line-utilities", "science"]
-homepage = "https://seqeralabs.github.io/RustQC/"
+homepage = "https://github.com/AI4S-YB/RustQC"
 exclude = ["benchmark/", "docs/", "paper/", "tests/", ".github/", "Dockerfile", ".dockerignore", ".pre-commit-config.yaml", "netlify.toml", "CONTRIBUTING.md", "AGENTS.md"]
 
 [[bin]]