feat(cli): leech model train-crf #721

Workflow file for this run

	name: CI

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

	permissions:
	contents: read

	concurrency:
	group: ci-${{ github.workflow }}-${{ github.ref }}
	cancel-in-progress: true

	jobs:
	lint:
	name: Lint
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v7

	- name: Install uv
	uses: astral-sh/setup-uv@v10.0.1
	with:
	enable-cache: true

	- name: Set up Python
	uses: actions/setup-python@v7
	with:
	python-version-file: "pyproject.toml"

	- name: Install linting tools only
	# Pin to the ruff resolved in uv.lock so CI checks the same formatting
	# `uv run ruff` applies locally. Unpinned, any ruff release can fail
	# lint on unrelated PRs -- 0.16.0 started formatting Python code blocks
	# inside Markdown, which reformats 11 docs/ and dev-notes/ files.
	run: \|
	RUFF_VERSION=$(python -c "
	import tomllib
	lock = tomllib.load(open('uv.lock', 'rb'))
	print(next(p['version'] for p in lock['package'] if p['name'] == 'ruff'))
	")
	echo "Pinning ruff==${RUFF_VERSION} (from uv.lock)"
	uv pip install --system "ruff==${RUFF_VERSION}"

	- name: Run ruff format check
	run: ruff format --check --exclude vulture_whitelist.py .

	- name: Run ruff lint
	run: ruff check --exclude vulture_whitelist.py .

	- name: Run type check
	run: uvx ty check src/leech/

	rust-lint:
	name: Rust lint (fmt + clippy)
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v7

	- name: Install Rust toolchain (rustfmt + clippy)
	run: rustup component add rustfmt clippy

	- name: Cache Rust build
	uses: Swatinem/rust-cache@v2
	with:
	workspaces: rust

	- name: rustfmt
	run: cargo fmt --manifest-path rust/Cargo.toml --check

	- name: clippy
	run: cargo clippy --manifest-path rust/Cargo.toml --all-targets -- -D warnings

	test:
	name: Test - Python ${{ matrix.python-version }}
	runs-on: ubuntu-latest
	strategy:
	fail-fast: false
	matrix:
	python-version: ["3.12"]

	steps:
	- uses: actions/checkout@v7

	- name: Install uv
	uses: astral-sh/setup-uv@v10.0.1
	with:
	enable-cache: true

	- name: Set up Python ${{ matrix.python-version }}
	uses: actions/setup-python@v7
	with:
	python-version: ${{ matrix.python-version }}

	# Cache the leech_core build. The bulk of the test job is compiling
	# arrow + escapepod-signal + leech_core via maturin; caching target/ and
	# the cargo registry cuts that from minutes to seconds on unchanged deps.
	- name: Cache Rust build
	uses: Swatinem/rust-cache@v2
	with:
	workspaces: rust

	- name: Install dependencies
	env:
	# GPU-less runner: install the CPU-only torch wheel so uv doesn't pull
	# the multi-GB CUDA stack (nvidia-cu13-*). `uv sync` installs the locked
	# CUDA torch regardless of this, so we install via `uv pip install`,
	# which honors --torch-backend. The lock (and local/cluster GPU installs
	# via `uv sync`) are unchanged.
	UV_TORCH_BACKEND: cpu
	run: \|
	uv venv
	# Only the test runner + runtime deps are needed here — no lint/type
	# tooling (that's the Lint job) and no pipeline/notebook extras (tests
	# don't import snakemake/plotnine). Full install (Rust extension +
	# escapepod); fall back without the Rust extension (leech_core) but keep
	# escapepod (a PyPI wheel), which leech imports unconditionally.
	# `onnx` is here so the export round-trip tests actually RUN rather
	# than skipping: they compare onnxruntime against torch across the
	# serialization boundary, which is the check an in-process assert
	# cannot make.
	uv pip install --torch-backend=cpu -e ".[test,rust,pod5,onnx]" \
	\|\| uv pip install --torch-backend=cpu -e ".[test,pod5,onnx]"

	- name: Run tests
	env:
	UV_TORCH_BACKEND: cpu
	# --no-sync: don't let `uv run` re-sync the env to the CUDA-pinned lock.
	run: uv run --no-sync pytest --cov=leech --cov-report=xml --cov-report=term

	- name: Upload coverage to Codecov
	uses: codecov/codecov-action@v7
	if: matrix.python-version == '3.12'
	with:
	files: ./coverage.xml
	fail_ci_if_error: false

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feat(cli): leech model train-crf #721

Workflow file

feat(cli): leech model train-crf #721

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Workflow file for this run