chore: swap build backend from setuptools to maturin

.github/workflows/test.yml

@@ -17,6 +17,7 @@ jobs:
       - uses: astral-sh/setup-uv@v7
         with:
           python-version: "3.11"
+      - uses: dtolnay/rust-toolchain@1.95.0 # pinned; keep in sync with rust-toolchain.toml
       - run: uv sync --frozen
       - run: PYTHONPATH=. uv run pytest --collect-only -q
       - run: PYTHONPATH=. uv run pytest -m unit --no-cov -q
@@ -34,5 +35,6 @@ jobs:
       - uses: astral-sh/setup-uv@v7
         with:
           python-version: "3.11"
+      - uses: dtolnay/rust-toolchain@1.95.0 # pinned; keep in sync with rust-toolchain.toml
       - run: uv sync --frozen
       - run: PYTHONPATH=. uv run pytest --network -m "unit or network or slow" --no-cov -q

.gitignore

@@ -36,3 +36,10 @@ docs/sources/*/impact-report/modified-cliques.json
 .coverage
 .coverage.*
 htmlcov/
+
+# maturin / Rust build artifacts
+rust/target/
+# native extension dropped into src/ by `maturin develop` (don't commit compiled binaries)
+src/rs.*.so
+src/rs.*.pyd
+src/rs.*.dylib

Dockerfile

@@ -36,13 +36,18 @@ RUN adduser --home ${ROOT} --uid 1000 nru
 # Set up a $ROOT directory with the source code to work in.
 RUN mkdir -p ${ROOT}
 WORKDIR ${ROOT}
+
+# Rust toolchain — required because the build backend is maturin (compiles a native extension).
+RUN apt-get update && apt-get install -y cargo
+
 USER nru
 COPY --chown=nru . ${ROOT}
 
-# Install and run `uv sync` to install packages.
+# Install uv and sync packages. `--frozen` installs exactly the committed uv.lock
+# (no re-resolution), keeping the image reproducible and matching CI's `uv sync --frozen`.
 RUN pipx install uv
 ENV PATH="${ROOT}/.local/bin:${PATH}"
-RUN uv sync
+RUN uv sync --frozen
 
 # Our default entrypoint is to start the Babel run.
 ENTRYPOINT ["bash", "-c", "uv run snakemake --cores ${CORES}"]

pyproject.toml

@@ -39,6 +39,7 @@ Issues = "https://github.com/NCATSTranslator/Babel/issues"
 [dependency-groups]
 dev = [
     "ipykernel>=7.1.0",
+    "maturin>=1.0,<2.0",
     "py-spy>=0.4.2",
     "ruff>=0.14.14",
     "rumdl>=0.2.4",
@@ -55,12 +56,16 @@ source-impact-report = "src.tools.source_impact_report.cli:main"
 package = true
 
 [build-system]
-requires = ["setuptools>=83.0.0"]
-build-backend = "setuptools.build_meta"
+requires = ["maturin>=1.0,<2.0"]
+build-backend = "maturin"
 
-[tool.setuptools.packages.find]
-where = ["."]
-include = ["src", "src.*"]
+[tool.maturin]
+# The importable Python package is literally named `src` (flat layout). A dotted module-name
+# places the compiled extension at `src/rs.*` and tells maturin the package to bundle is `src`
+# (auto-resolved to the repo root since src-layout detection won't fire).
+module-name = "src.rs"
+# Rust source lives under rust/ so Cargo never collides with the Python `src/` dir.
+manifest-path = "rust/Cargo.toml"
 
 
 # Linting/formatting configuration
@@ -84,6 +89,13 @@ ignore = [
 fixable = ["ALL"]
 unfixable = []
 
+[tool.ruff.format]
+# Ruff 0.16.0 began formatting Python code fences inside Markdown, which overlaps with the
+# dedicated rumdl Markdown check and broke CI when astral-sh/ruff-action@v3 floated to 0.16.0
+# (pyproject pins only a floor, >=0.14.14). Keep ruff's formatter scoped to Python source and
+# leave Markdown to rumdl so formatting CI stays deterministic across ruff releases.
+exclude = ["*.md"]
+
 [tool.snakefmt]
 line_length = 120
 include = '\.snakefile$|^Snakefile'

rust-toolchain.toml

@@ -0,0 +1,6 @@
+# Pin the Rust toolchain so local builds, CI, and any rustup-based environment all
+# compile the maturin/PyO3 extension with the same compiler version. The CI action ref
+# (dtolnay/rust-toolchain in .github/workflows/test.yml) is pinned to match this; bump
+# both together when upgrading Rust.
+[toolchain]
+channel = "1.95.0"

rust/Cargo.toml

@@ -0,0 +1,11 @@
+[package]
+name = "babel-pipeline"
+version = "1.17.0"   # valid SemVer (3 parts); published version is "1.17" from root pyproject
+edition = "2021"
+
+[lib]
+name = "rs"                   # matches the #[pymodule] fn + module-name's last component
+crate-type = ["cdylib"]
+
+[dependencies]
+pyo3 = { version = "0.23", features = ["abi3-py311", "extension-module"] }

rust/src/lib.rs

@@ -0,0 +1,13 @@
+//! Placeholder native extension for babel-pipeline.
+//!
+//! The build backend is maturin; this empty module exists only so the project builds as a
+//! mixed Rust/Python package. Real functionality will land in a follow-up PR.
+
+use pyo3::prelude::*;
+
+/// Empty pyo3 module, importable as `from src import rs`. Name must match the last component
+/// of `[tool.maturin] module-name` ("src.rs" → `rs`).
+#[pymodule]
+fn rs(_m: &Bound<'_, PyModule>) -> PyResult<()> {
+    Ok(())
+}