timsbuktoolkit/Taskfile.yml at main · TalusBio/timsbuktoolkit · GitHub

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version: "3"

interval: 100ms

# Include child Taskfiles
includes:
  timsseek: ./rust/timsseek

tasks:
  license_check:
    cmds:
      - cargo deny check

  test:
    cmds:
      - cargo test -- --nocapture
      - uv run python -m pytest

  fmt:
    cmds:
      - cargo +nightly fmt --verbose
      - uv run ruff format

  clippy:
    cmds:
      - cargo clippy --fix --allow-dirty --allow-staged {{.CLI_ARGS}} -- -D warnings

  todos:
    cmds:
      - grep -nH -R TODO rust/tims*/src
      - grep -nH -R "todo!" rust/tims*/src

  build_python:
    cmds:
      - uv build --all-packages --verbose

  bumpver:
    cmds:
      # --tag {alpha, beta, dev, rc, post, final}
      - uv run --dev  bumpver update --minor --allow-dirty --no-commit
      - cargo b
      - uv lock

  docker:
    cmds:
      # - cargo install cross --git https://github.com/cross-rs/cross
      - cross build --release --target x86_64-unknown-linux-gnu --bin timsquery_cli
      - cross build --release --target x86_64-unknown-linux-gnu --bin timsseek
      - docker build --platform linux/amd64 -t timsseek:local .

  speclib:build:
    desc: Build spectral library from FASTA
    cmds:
      - cargo run --release -p speclib_build_cli -- {{.CLI_ARGS}}

  speclib:local-koina:
    desc: Start local Koina server (CPU, Docker). First run downloads all models (~10-30 min).
    cmds:
      - |
        if docker ps -a --format '{{.Names}}' | grep -q '^koina-local$'; then
          echo "Restarting existing koina-local container (models already downloaded)"
          docker start koina-local
        else
          echo "Creating new koina-local container (will download models from Zenodo)"
          docker run -d \
            --name koina-local \
            --shm-size 8G \
            -p 8500:8500 -p 8501:8501 -p 8502:8502 \
            ghcr.io/wilhelm-lab/koina:latest
        fi
      - echo "Koina running at http://localhost:8501/v2/models"
      - echo "Use --koina-url http://localhost:8501/v2/models"
      - 'echo "Check readiness: curl -s http://localhost:8501/v2/health/ready"'

  speclib:stop-koina:
    desc: Stop local Koina server
    cmds:
      - docker stop koina-local