opentfraw 1.0.0

Rust parser for Thermo Fisher RAW mass spectrometry files.
Documentation 
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# CI for OpenTFRaw.
#
# Jobs:
#   build         - cargo fmt --check, cargo clippy -D warnings, cargo test
#                   (Linux + macOS via WarpBuild)
#   validate-mzml - download a small public Thermo RAW file, convert to mzML,
#                   and run scripts/validate_mzml.py to check structural
#                   conformance.

name: CI

on:
  push:
    branches: ["main"]
  pull_request:
    branches: ["main"]

env:
  CARGO_TERM_COLOR: always
  RUSTFLAGS: -D warnings
  # Small LTQ FT file (~15 MB) from PRIDE PXD054004, used for the mzML
  # validation job.  URL is stable because PRIDE uses year/month archive paths.
  PRIDE_RAW_URL: >-
    https://ftp.pride.ebi.ac.uk/pride/data/archive/2025/05/PXD054004/20171113_Map_NS1_1to139_4deg_50uM_001.raw
  PRIDE_RAW_NAME: test.raw

jobs:
  build:
    name: Build and test (${{ matrix.os }})
    runs-on: ${{ matrix.os }}
    strategy:
      fail-fast: false
      matrix:
        os:
          - ubuntu-latest
          - macos-latest
    steps:
      - uses: actions/checkout@v4

      - name: Install Rust toolchain
        uses: dtolnay/rust-toolchain@stable
        with:
          toolchain: "1.75"
          components: rustfmt, clippy

      - name: Cache cargo
        uses: Swatinem/rust-cache@v2

      - name: cargo fmt
        run: cargo fmt --all -- --check

      - name: cargo clippy
        run: cargo clippy --all-targets -- -D warnings

      - name: cargo test
        run: cargo test --all-targets

  validate-mzml:
    name: mzML structural validation
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v4

      - name: Install Rust toolchain
        uses: dtolnay/rust-toolchain@stable
        with:
          toolchain: "1.75"

      - name: Cache cargo
        uses: Swatinem/rust-cache@v2

      - name: Build to_mzml example (release)
        run: cargo build --release --example to_mzml

      - name: Download test RAW file
        run: |
          wget -q --user-agent="OpenTFRaw-CI/1.0" \
               -O "$PRIDE_RAW_NAME" "$PRIDE_RAW_URL"
          echo "Downloaded $(du -sh $PRIDE_RAW_NAME | cut -f1) RAW file"

      - name: Convert RAW to mzML (centroid)
        run: |
          ./target/release/examples/to_mzml "$PRIDE_RAW_NAME" test_centroid.mzML
          echo "Centroid mzML: $(wc -l < test_centroid.mzML) lines"

      - name: Convert RAW to indexed mzML (centroid)
        run: |
          ./target/release/examples/to_mzml --indexed "$PRIDE_RAW_NAME" test_indexed.mzML
          echo "Indexed mzML: $(wc -l < test_indexed.mzML) lines"

      - name: Convert RAW to mzML (profile)
        run: |
          ./target/release/examples/to_mzml --include-profile "$PRIDE_RAW_NAME" test_profile.mzML
          echo "Profile mzML: $(wc -l < test_profile.mzML) lines"

      - name: Validate mzML structural conformance
        run: |
          python3 scripts/validate_mzml.py \
            test_centroid.mzML \
            test_indexed.mzML \
            test_profile.mzML