Release/0.5

.github/workflows/release.yml

@@ -9,76 +9,50 @@ permissions:
   contents: read
 
 jobs:
-  linux:
-    runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        target: [x86_64, aarch64]
-    steps:
-      - uses: actions/checkout@v4
-      - uses: actions/setup-python@v5
-        with:
-          python-version: "3.10"
-      - name: Build wheels
-        uses: PyO3/maturin-action@v1
-        with:
-          target: ${{ matrix.target }}
-          args: --release --out dist --find-interpreter
-          sccache: "true"
-          manylinux: auto
-      - name: Upload wheels
-        uses: actions/upload-artifact@v4
-        with:
-          name: wheels-linux-${{ matrix.target }}
-          path: dist
-
-  windows:
-    runs-on: windows-latest
-    strategy:
-      matrix:
-        target: [x64, x86]
-    steps:
-      - uses: actions/checkout@v4
-      - uses: actions/setup-python@v5
-        with:
-          python-version: "3.10"
-          architecture: ${{ matrix.target }}
-      - name: Build wheels
-        uses: PyO3/maturin-action@v1
-        with:
-          target: ${{ matrix.target }}
-          args: --release --out dist --find-interpreter
-          sccache: "true"
-      - name: Upload wheels
-        uses: actions/upload-artifact@v4
-        with:
-          name: wheels-windows-${{ matrix.target }}
-          path: dist
-
-  macos:
-    runs-on: ${{ matrix.platform.runner }}
+  build:
+    runs-on: ${{ matrix.runner }}
     strategy:
       matrix:
-        platform:
-          - runner: macos-latest
+        include:
+          - platform: linux
+            runner: ubuntu-latest
             target: x86_64
-          - runner: macos-14
+            manylinux: auto
+          - platform: linux
+            runner: ubuntu-latest
+            target: aarch64
+            manylinux: auto
+          - platform: windows
+            runner: windows-latest
+            target: x64
+          - platform: windows
+            runner: windows-11-arm
+            target: aarch64
+          - platform: macos
+            runner: macos-latest
+            target: x86_64
+          - platform: macos
+            runner: macos-latest
             target: aarch64
     steps:
       - uses: actions/checkout@v4
-      - uses: actions/setup-python@v5
-        with:
-          python-version: "3.10"
+      - name: Set up MSVC environment
+        if: matrix.platform == 'windows'
+        uses: ilammy/msvc-dev-cmd@v1
+      - name: Set cmake generator for Windows
+        if: matrix.platform == 'windows'
+        run: echo "CMAKE_GENERATOR=Ninja" >> $env:GITHUB_ENV
       - name: Build wheels
         uses: PyO3/maturin-action@v1
         with:
-          target: ${{ matrix.platform.target }}
+          target: ${{ matrix.target }}
           args: --release --out dist --find-interpreter
           sccache: "true"
+          manylinux: ${{ matrix.manylinux || '' }}
       - name: Upload wheels
         uses: actions/upload-artifact@v4
         with:
-          name: wheels-macos-${{ matrix.platform.target }}
+          name: wheels-${{ matrix.platform }}-${{ matrix.target }}
           path: dist
 
   sdist:
@@ -99,7 +73,7 @@ jobs:
   release:
     name: Release
     runs-on: ubuntu-latest
-    needs: [linux, windows, macos, sdist]
+    needs: [build, sdist]
     permissions:
       id-token: write
     steps:

.github/workflows/test.yml

@@ -38,6 +38,12 @@ jobs:
         os: [ubuntu-latest, macos-latest, windows-latest]
     steps:
       - uses: actions/checkout@v4
+      - name: Set up MSVC environment
+        if: runner.os == 'Windows'
+        uses: ilammy/msvc-dev-cmd@v1
+      - name: Set cmake generator for Windows
+        if: runner.os == 'Windows'
+        run: echo "CMAKE_GENERATOR=Ninja" >> $env:GITHUB_ENV
       - name: Install Python
         uses: actions/setup-python@v5
         with:

.gitignore

@@ -1,3 +1,7 @@
+.venv*
+.claude/
+.codex-target/
+
 # IDE
 .vscode/
 

CHANGELOG.md

@@ -0,0 +1,100 @@
+# Changelog
+
+All notable changes to this project will be documented in this file.
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
+and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+
+## [Unreleased]
+
+## [0.5.0] - 2026-07-13
+
+First stable 0.5.0 release. No functional changes since 0.5.0-beta.1.
+
+## [0.5.0-beta.1] - 2026-06-18
+
+### Added
+- `annotate_ms2_spectra`: annotate MS2 spectra with theoretical fragment ions
+  (tolerance in Da or ppm, configurable fragmentation model and mass mode)
+- `score_ms2_spectra`: compute per-ion-series MS2 scoring features (matched
+  ions, longest sequence, explained intensity) with optional hyperscore
+- `ms2pip_compute_features`: compute 139 MS2PIP XGBoost feature vectors per
+  cleavage site from ProForma peptide strings
+- `ms2pip_compute_theoretical_mz`: compute theoretical fragment m/z arrays
+  (numpy float32) for arbitrary ion types and charges
+- `ms2pip_extract_targets`: extract per-ion-type observed intensity arrays
+  from annotated spectra for model training
+- `AnnotatedMS2Spectrum` and `FragmentAnnotation` types with pickle support
+- Codebase restructured into `types/`, `io/`, `scoring/`, and `ms2pip/` modules
+- ARM64 wheel builds for Windows and macOS
+
+## [0.4.3] - 2025-09-30
+
+### Fixed
+- Crash on empty spectra (contributed by @di-hardt)
+
+### Changed
+- Updated mzdata to 0.59.2
+
+## [0.4.2] - 2025-04-01
+
+### Changed
+- Updated mzdata to 0.48.3
+
+## [0.4.1] - 2025-01-15
+
+### Fixed
+- Thermo RAW files without pre-centroided peaks now read correctly (vendor
+  centroiding is now requested explicitly)
+
+### Changed
+- Updated timsrust to 0.4
+
+## [0.4.0-1] - 2024-11-20
+
+### Changed
+- Added Python 3.13 wheel builds
+
+## [0.4.0] - 2024-10-24
+
+### Added
+- Thermo RAW file support via mzdata
+- `is_supported_file_type` utility function
+
+### Changed
+- Dropped x86 Linux wheel builds
+- Updated mzdata
+
+## [0.3.0] - 2024-07-17
+
+### Changed
+- Updated timsrust to 0.3.0
+
+## [0.2.1] - 2024-07-01
+
+### Added
+- Tests for `get_ms2_spectra`
+
+### Changed
+- Updated mzdata to 0.20.0
+
+## [0.2.0] - 2024-04-08
+
+### Added
+- `get_ms2_spectra`: read MS2 spectra from spectrum files
+
+## [0.1.0] - 2024-04-05
+
+### Added
+- Initial release: `get_precursor_info` for mzML, MGF, and Bruker TDF files
+
+[Unreleased]: https://github.com/compomics/ms2rescore-rs/compare/v0.5.0-beta.1...HEAD
+[0.5.0-beta.1]: https://github.com/compomics/ms2rescore-rs/compare/v0.4.3...v0.5.0-beta.1
+[0.4.3]: https://github.com/compomics/ms2rescore-rs/compare/v0.4.2...v0.4.3
+[0.4.2]: https://github.com/compomics/ms2rescore-rs/compare/v0.4.1...v0.4.2
+[0.4.1]: https://github.com/compomics/ms2rescore-rs/compare/v0.4.0-1...v0.4.1
+[0.4.0-1]: https://github.com/compomics/ms2rescore-rs/compare/v0.4.0...v0.4.0-1
+[0.4.0]: https://github.com/compomics/ms2rescore-rs/compare/v0.3.0...v0.4.0
+[0.3.0]: https://github.com/compomics/ms2rescore-rs/compare/v0.2.1...v0.3.0
+[0.2.1]: https://github.com/compomics/ms2rescore-rs/compare/v0.2.0...v0.2.1
+[0.2.0]: https://github.com/compomics/ms2rescore-rs/compare/v0.1.0...v0.2.0
+[0.1.0]: https://github.com/compomics/ms2rescore-rs/releases/tag/v0.1.0