mzdata 0.65.5

A library to read mass spectrometry data formats and a data model for mass spectra
Documentation 
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on: [push, pull_request]

env:
  RUST_BACKTRACE: full
  RUST_LOG: debug
  CARGO_PROFILE_TEST_BUILD_OVERRIDE_DEBUG: true

name: Test
jobs:

  test:
    strategy:
      matrix:
        os: [ubuntu-latest, windows-latest]
    name: Test Suite
    runs-on: ${{ matrix.os }}
    steps:
      - name: Checkout sources
        uses: actions/checkout@v4

      - name: Install stable toolchain
        uses: actions-rs/toolchain@v1
        with:
          profile: minimal
          toolchain: stable
          override: true
      - name: Rust Cache
        uses: Swatinem/rust-cache@v2
      - name: Run cargo test
        uses: actions-rs/cargo@v1
        with:
          command: test
          args: --features nalgebra,parallelism,async,mzsignal,thermo,numpress,bruker_tdf -- --nocapture --show-output

  test-remote:
    name: PROXI Test Suite
    runs-on: ubuntu-latest
    steps:
      - name: Checkout sources
        uses: actions/checkout@v4

      - name: Install stable toolchain
        uses: actions-rs/toolchain@v1
        with:
          profile: minimal
          toolchain: stable
          override: true
      - name: Rust Cache
        uses: Swatinem/rust-cache@v2
      - name: Run cargo test
        continue-on-error: true
        uses: actions-rs/cargo@v1
        with:
          command: test
          args: --features async,proxi,proxi-async -- --nocapture --show-output

  test-pymzdata:
    name: pymzdata Python Test Suite
    runs-on: ubuntu-latest
    steps:
      - name: Checkout sources
        uses: actions/checkout@v4
      - name: Set up Python
        uses: actions/setup-python@v5
        with:
          python-version: "3.10"
      - name: Build pymzdata wheel
        uses: PyO3/maturin-action@v1
        with:
          args: --release --out dist -m crates/pymzdata/Cargo.toml
          manylinux: off
          rust-toolchain: stable
      - name: Install pymzdata and test dependencies
        run: |

          python -m pip install dist/*.whl
          python -m pip install 'pytest>=7' 'numpy>=1.21' 'pyteomics>=4.6' 'lxml>=4.9' 'psims>=1.3'
      - name: Run Python tests
        working-directory: crates/pymzdata
        run: python -m pytest -v -s

  test-spectra-subset:
    name: mzdata-spectra
    runs-on: ubuntu-latest
    steps:
      - name: Checkout sources
        uses: actions/checkout@v4

      - name: Install stable toolchain
        uses: actions-rs/toolchain@v1
        with:
          profile: minimal
          toolchain: stable
          override: true
      - name: Rust Cache
        uses: Swatinem/rust-cache@v2

      - name: Run cargo test
        continue-on-error: true
        run: |

          cd crates/mzdata-spectra && cargo build --features mzsignal,nalgebra,serde

  test-async-subset:
      name: async_partial
      runs-on: ubuntu-latest
      steps:
        - name: Checkout sources
          uses: actions/checkout@v4

        - name: Install stable toolchain
          uses: actions-rs/toolchain@v1
          with:
            profile: minimal
            toolchain: stable
            override: true
        - name: Rust Cache
          uses: Swatinem/rust-cache@v2
        - name: Run cargo test
          continue-on-error: true
          uses: actions-rs/cargo@v1
          with:
            command: test
            args: --features async_partial -- --nocapture --show-output