Cython "Cython.Compiler.Errors" - Compile Failure in CI

A Cython-backed package compiles .pyx to C and then to a binary. Builds fail when Cython is absent from the build env, when a vendored .c is regenerated against an incompatible Cython, or on a genuine Cython syntax error.

What this error means

A source build fails with a Cython.Compiler.Errors.CompileError, Cython is required to compile, or a C error from generated code. There is no wheel, so pip ran the Cython compile step.

Build output

Error compiling Cython file:
------------------------------------------------------------
  cdef int total = sum(values
                              ^
------------------------------------------------------------
src/fast.pyx:42:30: Expected ')', found newline

Common causes

Cython missing from the build environment

If the project needs Cython to compile .pyx but does not list it in [build-system] requires, the isolated build env has no Cython and fails.

A genuine Cython source error

A syntax or language-level error in a .pyx file (or one surfaced by a newer Cython that is stricter) is a real compile error, not a transient one.

How to fix it

Declare Cython as a build requirement

pyproject.toml

[build-system]
requires = ["setuptools", "wheel", "Cython>=3.0"]
build-backend = "setuptools.build_meta"

Install the C toolchain too

The generated C still needs a compiler and the Python headers.

Terminal

apt-get update && apt-get install -y build-essential python3-dev
pip install --no-build-isolation Cython
pip install .

Fix the source error

For a CompileError in a .pyx, correct the syntax - this never passes on retry. Pin the language level if a newer Cython changed defaults.

How to prevent it

List Cython in [build-system] requires for .pyx projects.
Pin a Cython major version and a # cython: language_level directive.
Prefer publishing wheels so consumers never run the Cython compile.