Taskfile.yml

version: "3"

tasks:
    build:
        silent: true
        vars:
            PROFILE: '{{.PROFILE | default "dev"}}'
        sources:
            - src/**/*.rs
            - build.rs
            - Cargo.toml
            - Cargo.lock
            - pyproject.toml
            - resources/**/*
        generates:
            - .venv/{CACHEDIR.TAG,pyvenv.cfg}
        cmds:
            - uv sync --all-extras --all-groups --no-group benchmark --dev -C "build-args=--profile {{.PROFILE}}" {{.CLI_ARGS}}

    build-local:
        vars:
            PROFILE: '{{.PROFILE | default "dev"}}'
        cmds:
            - task: build
              vars: { PROFILE: "{{.PROFILE}}", CLI_ARGS: "--locked" }
            - pre-commit install

    build-ci:
        vars:
            PROFILE: '{{.PROFILE | default "dev"}}'
        cmd:
            task: build
            vars: { PROFILE: "{{.PROFILE}}", CLI_ARGS: "--locked" }

    test-python:
        vars:
            PROFILE: '{{.PROFILE | default "dev"}}'
        deps:
            - task: build-ci
              vars: { PROFILE: "{{.PROFILE}}" }
        sources:
            - src/**/*.rs
            - build.rs
            - Cargo.toml
            - Cargo.lock
            - pyproject.toml
            - resources/**/*
            - tests/test_*.py
            - docs/**/*.md
        cmds:
            - uv run --no-sync pytest {README.md,docs,tests/test_*.py,immunum} -n  $(( $(nproc) - 2 )) --benchmark-disable {{.CLI_ARGS}}

    test-rust:
        vars:
            PROFILE: '{{.PROFILE | default "dev"}}'
        sources:
            - src/**/*.rs
            - build.rs
            - Cargo.toml
            - Cargo.lock
            - resources/**/*
            - tests/cli.rs
        cmds:
            - cargo test --no-default-features --profile {{.PROFILE}}
            - cargo test --test cli --profile {{.PROFILE}}

    build-wasm:
        sources:
            - src/**/*.rs
            - build.rs
            - Cargo.toml
            - Cargo.lock
            - resources/**/*
        generates:
            - pkg/immunum.js
        cmds:
            - wasm-pack build --target nodejs --features wasm --no-default-features {{.CLI_ARGS}}

    build-wasm-web:
        sources:
            - src/**/*.rs
            - build.rs
            - Cargo.toml
            - Cargo.lock
            - resources/**/*
        generates:
            - docs/assets/wasm/immunum.js
        cmds:
            - wasm-pack build --target web --out-dir docs/assets/wasm --no-default-features --features wasm {{.CLI_ARGS}}

    test-wasm:
        deps:
            - task: build-wasm
        sources:
            - src/**/*.rs
            - build.rs
            - Cargo.toml
            - Cargo.lock
            - resources/**/*
            - tests/test_wasm.mjs
        cmds:
            - node --test tests/test_wasm.mjs

    test:
        aliases: [t]
        vars:
            PROFILE: '{{.PROFILE | default "dev"}}'
        cmds:
            - task: test-rust
              vars: { PROFILE: "{{.PROFILE}}" }
            - task: test-python
              vars: { PROFILE: "{{.PROFILE}}" }
            - task: test-wasm

    lint:
        vars:
            PROFILE: '{{.PROFILE | default "dev"}}'
        deps:
            - task: build
              vars: { PROFILE: "{{.PROFILE}}" }
        cmds:
            - cargo clippy --all-targets --all-features -- -D warnings
            - uv run --no-sync ruff check --config pyproject.toml
            - uv run --no-sync ty check --project .
            - uv run --no-sync pyrefly check -j 0
            - 'git grep "# type: ignore\s*$" src/** && (echo -e "\033[31mBlanket ignores are not allowed\033[0m"; exit 1) || exit 0'

    format:
        vars:
            PROFILE: '{{.PROFILE | default "dev"}}'
        deps:
            - task: build
              vars: { PROFILE: "{{.PROFILE}}" }
        cmds:
            - cargo fmt --all --check
            - uv run --no-sync ruff check --fix --config pyproject.toml
            - uv run --no-sync ruff format --config pyproject.toml

    coverage:
        vars:
            PROFILE: '{{.PROFILE | default "dev"}}'
        deps:
            - task: build
              vars: { PROFILE: "{{.PROFILE}}" }
        cmds:
            - uv run --no-sync coverage run -m pytest {docs,tests/test_*.py} --benchmark-disable {{.CLI_ARGS}}
            - uv run --no-sync coverage report -m

    pysentry:
        cmds:
            - uv run --no-sync pysentry-rs .

    docs-serve:
        deps:
            - task: build-wasm-web
        cmd: uv run --no-sync --group docs mkdocs serve

    docs:
        cmd: task docs-serve

    docs-build:
        deps:
            - task: build-wasm-web
        cmd: uv run --no-sync --group docs mkdocs build {{.CLI_ARGS}}

    benchmark-cli:
        desc: "Speed benchmark using Criterion (benches/speed_benchmark.rs)"
        cmd: cargo bench --no-default-features {{.CLI_ARGS}}

    benchmark-comparison:
        desc: "Speed + correctness benchmark: immunum vs antpack vs anarci (1k IGH sequences)"
        cmd: uv run --group benchmark pytest benches/bench_comparison.py -v --benchmark-columns=min,mean,stddev --benchmark-group-by=func {{.CLI_ARGS}}

    benchmark-speed-polars:
        desc: "Speed benchmark for immunum polars across all chain/scheme fixtures"
        cmd: uv run pytest benches/bench_polars.py -v --benchmark-columns=min,mean,stddev --benchmark-group-by=func {{.CLI_ARGS}}

    bencher-python:
        deps:
            - task: build-ci
              vars: { PROFILE: "{{.PROFILE}}" }
        silent: true
        desc: "Run Python benchmarks with bencher. Alerts are disabled, used only for tracking performance"
        cmd: >-
            bencher run
            --adapter python_pytest
            --token {{.BENCHER_API_TOKEN}}
            --file results.json
            --threshold-measure latency
            --threshold-test t_test
            --threshold-max-sample-size 64
            --threshold-upper-boundary 0.99
            --thresholds-reset
            --err
            "uv run --no-sync pytest --benchmark-json results.json benches/bench_polars.py"

    bencher-rust:
        silent: true
        desc: "Run Criterion benchmarks with bencher"
        cmd: >-
            bencher run
            --adapter rust_criterion
            --token {{.BENCHER_API_TOKEN}}
            --threshold-measure latency
            --threshold-test t_test
            --threshold-max-sample-size 64
            --threshold-upper-boundary 0.99
            --thresholds-reset
            --err
            "cargo bench --no-default-features"

    bencher:
        preconditions:
            - sh: '[ -n "{{.BENCHER_API_TOKEN}}" ]'
              msg: "BENCHER_API_TOKEN is not set"
        cmds:
            - task: bencher-rust
            - task: bencher-python

    benchmark-accuracy:
        desc: "Accuracy benchmark across all fixtures (1k sequences, 7 rounds each)"
        cmds:
            - |
                for f in fixtures/validation/*_imgt.csv; do
                  base=$(basename "$f" .csv)
                  chain=$(echo "$base" | cut -d_ -f2)
                  uv run --group benchmark python benches/bench_comparison.py \
                    --chain "$chain" \
                    --sizes 1000 --rounds 7 \
                    --output "./resources/benchmark_results/results_${base}.csv" \
                    --timeout 1m
                done

    benchmark-speed:
        desc: "Speed benchmark: sizes 100..10M (10x steps), 3 rounds, H/imgt. Pass CLI_ARGS to filter tools, e.g. -- --tools immunum"
        cmd: |
            uv run --group benchmark python benches/bench_comparison.py \
              --sizes 1_000_000 --sizes 500 --sizes 1000 --sizes 5000 --sizes 10_000 --sizes 50_000 --sizes 100_000 --sizes 500_000 --sizes 100 \
              --rounds 3 --output ./resources/benchmark_results/results_speed.csv \
              --timeout 10m --no-correctness-check {{.CLI_ARGS}}

    benchmark:
        desc: "Run all benchmarks and produce plots for them"
        cmds:
            - task: benchmark-accuracy
            - task: benchmark-speed
            - task: plots

    plots:
        desc: "Produce plots from benchmark results"
        cmd: uv run --script scripts/plots.py

    default:
        cmds:
            - task --list-all

    ci:
        env:
            PROFILE: "dev"
        cmds:
            - task: lint
            - task: pysentry
            - task: build-ci
              vars: { PROFILE: "{{.PROFILE}}" }
            - task: test
              vars: { PROFILE: "{{.PROFILE}}" }
            - task: coverage
              vars: { PROFILE: "{{.PROFILE}}" }
            - task: docs-build