pyconcord 0.4.2

A minimal example package (with pybind11)

pyconcord

CI	status
conda.recipe
pip builds

Installation

• Clone this repository
• brew install eigen
• cd [this_repo]
• uv venv .venv --python 3.9 && source .venv/bin/activate
• uv pip install .[test]

To run tests:

pytest -s

To install from pypi:

uv pip install pyconcord --no-sources

Test call

import numpy as np
from scipy.sparse import identity
import pyconcord as pc
x = np.random.randn(13, 9)

n, p = x.shape
x0 = identity(p).tocoo()
omega = pc.concord(x, x0=x0, lambda1=0.3)
cov = np.round(omega.todense(), 2)
assert ~np.isinf(cov[0,0])
assert cov[0, 1] == cov[1, 0]

Files

This example has several files that are a good idea, but aren't strictly necessary. The necessary files are:

• pyproject.toml: The Python project file
• CMakeLists.txt: The CMake configuration file
• src/main.cpp: The source file for the C++ build
• src/pyconcord/__init__.py: The Python portion of the module. The root of the module needs to be <package_name>, src/<package_name>, or python/<package_name> to be auto-discovered.

These files are also expected and highly recommended:

• .gitignore: Git's ignore list, also used by scikit-build-core to select files for the SDist
• README.md: The source for the PyPI description
• LICENSE: The license file

There are also several completely optional directories:

• .github: configuration for Dependabot and GitHub Actions
• conda.recipe: Example recipe. Normally you should submit projects to conda-forge instead of building them yourself, but this is useful for testing the example.
• docs/: Documentation
• tests/: Tests go here

And some optional files:

• .pre-commit-config.yaml: Configuration for the fantastic static-check runner pre-commit.

This is a simplified version of the recommendations in the Scientific-Python Development Guide, which is a highly recommended read for anyone interested in Python package development (Scientific or not). The guide also has a cookiecutter that includes scikit-build-core and pybind11 as a backend choice.

CI Examples

There are examples for CI in .github/workflows. A simple way to produces binary "wheels" for all platforms is illustrated in the "wheels.yml" file, using cibuildwheel.

License

pybind11 is provided under a BSD-style license that can be found in the LICENSE file. By using, distributing, or contributing to this project, you agree to the terms and conditions of this license.