marimo-cython

Cython compilation support for marimo notebooks. Write Cython-accelerated functions directly in notebook cells and run them at native speed — no build system boilerplate required.

This is the marimo equivalent of Jupyter's %%cython magic, redesigned for marimo's reactive DAG model.

Installation

Requires Python 3.10+.

uv add marimo-cython

Or with pip:

pip install marimo-cython

Runtime dependencies: cython>=3.0 and setuptools (for C extension building).

Quick start

import cython
from marimo_cython import cy

@cy.compile
def fib(n: cython.int) -> cython.int:
    a: cython.int = 0
    b: cython.int = 1
    i: cython.int
    for i in range(n):
        a, b = b, a + b
    return a

fib(50)  # runs compiled native code

API

Three entry points, all available via cy.* or as direct imports from marimo_cython:

@cy.compile — decorator

Compiles a pure-Python Cython function. The function must use Cython's pure Python syntax (cython.int, cython.double, typed memoryviews, etc.).

@cy.compile
def fib(n: cython.int) -> cython.int:
    a: cython.int = 0
    b: cython.int = 1
    i: cython.int
    for i in range(n):
        a, b = b, a + b
    return a

With options:

@cy.compile(boundscheck=False, wraparound=False, cdivision=True)
def mandelbrot(
    out: cython.int[:, :],
    xmin: cython.double,
    xmax: cython.double,
    ymin: cython.double,
    ymax: cython.double,
    max_iter: cython.int,
) -> None:
    rows: cython.Py_ssize_t = out.shape[0]
    cols: cython.Py_ssize_t = out.shape[1]
    # ...

Using C library functions

To call C library functions (like sqrt, fabs, etc.) from a decorated function, use from cython.cimports.* at cell/module level above the function. Cython provides runtime Python stubs for these, so they are valid Python imports:

from cython.cimports.libc.math import sqrt, fabs

@cy.compile(boundscheck=False)
def fast_sqrt(x: cython.double) -> cython.double:
    return sqrt(fabs(x))

The decorator automatically picks up from cython.cimports.* imports written above the function in the same cell or file, and includes them in the compiled module.

As a fallback, the cimports parameter accepts raw cimport strings (which use Cython syntax, not valid Python):

@cy.compile(cimports=["from libc.math cimport sqrt, fabs"])
def fast_sqrt(x: cython.double) -> cython.double:
    return sqrt(fabs(x))

cy.compile_module(source) — compile a string

Compiles a Cython source string into a module. Supports full .pyx syntax including cdef, cimport, and typed function signatures.

mod = cy.compile_module("""
from libc.math cimport sqrt

def norm(double[:] v):
    cdef Py_ssize_t i
    cdef double s = 0.0
    for i in range(v.shape[0]):
        s += v[i] * v[i]
    return sqrt(s)
""", boundscheck=False, wraparound=False)

mod.norm(np.array([3.0, 4.0]))  # => 5.0

cy.compile_file(path) — compile a .pyx file

mod = cy.compile_file("solver.pyx", cplus=True, libraries=["lapack"])
mod.solve(matrix)

cy.clear_cache() — remove compiled artifacts

cy.clear_cache()  # removes .marimo_cython_cache/ and all contents
cy.clear_cache(cache_dir="custom_cache/")  # custom cache directory

Returns the number of files removed.

Compile options

All three entry points accept the same keyword arguments. These map to the CompileOptions dataclass:

C/C++ compilation

Cython compiler directives

None means "use Cython's default". Set to True/False to override.

Other options

How it works

Pipeline

All three APIs converge into the same path: normalize source, compute cache key, build or load.

Source → Normalize → Cache check → Cythonize (.pyx → .c) → Build (.c → .so) → Load

Source extraction (@cy.compile)

The decorator uses inspect.getsource(fn) to get the function source. This works in marimo because marimo populates linecache for exec'd cell code (the same mechanism Python uses for tracebacks — not a private API). Decorator lines are stripped before compilation.

Cimport context recovery

inspect.getsource only returns the function body. from cython.cimports.* imports written above the function in the same cell are not included. To recover them, _collect_context_cimports AST-parses all lines above the function definition, finds ImportFrom nodes matching cython.cimports.*, and prepends them to the source.

Auto import cython

import cython is auto-prepended if missing (needed for cython.int, cython.double annotations). Detection uses ast.parse, not regex. Critically, from cython.cimports.* does NOT count as a cython import — it imports C symbols, not the cython module. Getting this wrong causes cython.double to fail with "Unknown type declaration".

Content-addressed caching

The cache key is a SHA-256 of: source (post-normalization), all C/C++ flags, all compiler directives, EXT_SUFFIX (Python ABI), and Cython.__version__. Module name becomes {prefix}_{hash[:16]}. On hit, the .so loads directly via importlib.

Build

On cache miss: write .pyx → cythonize() to .c → setuptools build_ext to .so → load with importlib. Build temp uses a short-lived tempfile.mkdtemp to avoid path-length issues. Intermediate .c/.cpp files are cleaned after success; .pyx is kept for debugging.

Other details

• Numpy: auto-detected from source; numpy.get_include() added to include_dirs automatically
• Linker warnings: -Wl,-w suppresses CPython 3.14's stale Modules/_hacl path warnings
• CythonModule: wrapper that delegates attribute access to the compiled module and supports marimo rich display (_mime_()) for annotation HTML
• Cache dir: .marimo_cython_cache/ by default (add to .gitignore)

Annotations

Compile with annotate=True to get Cython's annotation HTML rendered in marimo cell output:

mod = cy.compile_module(source, annotate=True)
mod  # displays annotation HTML in marimo

Cross-cell interaction

Compiled modules and functions work across marimo cells like any other Python object. Define a module in one cell and call its functions from another:

# Cell 1
linalg = cy.compile_module("""
from libc.math cimport sqrt
def norm(double[:] v):
    ...
""")

# Cell 2 — uses linalg from Cell 1
result = linalg.norm(my_array)

Running the demos

uv sync --extra dev
uv run marimo edit demo.py

The demo covers the core API: fibonacci benchmark, cimport patterns, compile_module, and cross-cell interaction.

Examples

The examples/ directory contains standalone notebooks:

• examples/mandelbrot.py — Interactive Mandelbrot set with a resolution slider. Runs Cython and Python side-by-side with progressive rendering (Cython result appears instantly, Python fills in when done). PEP 723 compatible — run with uv run --sandbox examples/mandelbrot.py.

uv sync --extra dev
uv run marimo run examples/mandelbrot.py

Development

uv sync --extra dev
uv run ruff check src/
uv run pytest

License

MIT