[config] Modernize cython module compilation

[pieleric]

Remove usage of old numpy API.
Define the cython module in a separate setuptool command.
In practice, this doesn't seem to yield any performance change. Just less warnings when compiling the cython module.

Add comment to indicate the cDataArray2RGB will not raise any exception.
This would improve performance (~30% faster)... but only works on Ubunut 24.04, so for now disabled.

[coderabbitai]

Caution

Review failed

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📝 Walkthrough

Walkthrough

The PR refactors the Cython build in setup.py: imports Extension from setuptools, creates an explicit extensions list containing an Extension for odemis.util.img_fast (with define_macros and include_dirs using numpy.get_include()), and updates setup() to use cythonize(extensions, language_level="3") instead of cythonize(glob(...), language_level=3). In src/odemis/util/img_fast.pyx a TODO comment was added about possible future noexcept use with nogil; the function signature and behavior are unchanged.

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Possibly related PRs

• [config] Modernize cython module compilation #3334 — Modifies the same build setup to use an Extension-based cythonize call and adds the same noexcept TODO in src/odemis/util/img_fast.pyx.

🚥 Pre-merge checks | ✅ 3

✅ Passed checks (3 passed)

Check name	Status	Explanation
Title check	✅ Passed	The title '[config] Modernize cython module compilation' directly summarizes the main change—modernizing the Cython build configuration with the setuptools Extension approach and updated NumPy API usage.
Docstring Coverage	✅ Passed	No functions found in the changed files to evaluate docstring coverage. Skipping docstring coverage check.
Description check	✅ Passed	The PR description accurately describes the changeset, covering the removal of old numpy API usage, the separation of the cython module definition, and the added comment about cDataArray2RGB.

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Actionable comments posted: 1

🤖 Fix all issues with AI agents

In `@setup.py`:
- Around line 120-128: The Extension in setup.py is named "img_fast" but should
use the full package path so the compiled module lands in the package namespace;
update the Extension call that currently sets the name "img_fast" to
"odemis.util.img_fast" (i.e., change the first argument of Extension) so Cython
builds the module into the odemis.util package and imports like
odemis.util.img_fast (used by img.py and img_test.py) will succeed.

[Copilot]

Pull request overview

Modernizes the build configuration for the Cython-based image conversion module to reduce compile-time warnings (NumPy deprecated API) and clarify exception behavior.

Changes:

• Mark cDataArray2RGB as noexcept in the Cython implementation.
• Switch setup.py to define a Cython Extension explicitly and set NPY_NO_DEPRECATED_API to avoid deprecated NumPy C-API usage warnings.
• Adjust cythonize() invocation to use the defined Extension list.

Reviewed changes

Copilot reviewed 2 out of 2 changed files in this pull request and generated 1 comment.

File	Description
src/odemis/util/img_fast.pyx	Declares the core nogil conversion helper as noexcept.
setup.py	Introduces an explicit Extension configuration for Cython build and adds NumPy deprecation macro.