setup.cfg

# This file is used to configure your project.
# Read more about the various options under:
# https://setuptools.pypa.io/en/latest/userguide/declarative_config.html
# https://setuptools.pypa.io/en/latest/references/keywords.html

[metadata]
name = susiepca
description = Add a short description here!
author = Dong Yuan
author_email = dongyuan@usc.edu
license = MIT
license_files = LICENSE.txt
long_description = file: README.rst
long_description_content_type = text/x-rst; charset=UTF-8
url = https://github.com/mancusolab/susiepca
# Add here related links, for example:
project_urls =
    Source = https://github.com/mancusolab/susiepca
    Tracker = https://github.com/mancusolab/susiepca/issues

# Change if running only on Windows, Mac or Linux (comma-separated)
platforms = Mac,Linux

# Add here all kinds of additional classifiers as defined under
# https://pypi.org/classifiers/
classifiers =
    Development Status :: 4 - Beta
    Programming Language :: Python

[options]
zip_safe = False
packages = find:
include_package_data = True
python_requires = >=3.8
install_requires =
    numpy
    jax
    jaxlib
    jaxtyping
    pandas
    lineax
    matplotlib
    plum-dispatch
    scikit-learn
    seaborn
    equinox
    optax

[options.packages.find]
exclude =
    tests

[options.extras_require]
# Add here additional requirements for extra features, to install with:
# `pip install func_pca[PDF]` like:
# PDF = ReportLab; RXP

# Add here test requirements (semicolon/line-separated)
testing =
    setuptools
    pytest
    pytest-cov
    pytest-accept
    numpy

[tool:pytest]
# Specify command line options as you would do when invoking pytest directly.
# e.g. --cov-report html (or xml) for html/xml output or --junitxml junit.xml
# in order to write a coverage file that can be read by Jenkins.
# CAUTION: --cov flags may prohibit setting breakpoints while debugging.
#          Comment those flags to avoid this pytest issue.
addopts =
    --cov susiepca --cov-report term-missing
    --verbose
norecursedirs =
    dist
    build
    .tox
testpaths = tests
# Use pytest markers to select/deselect specific tests
# markers =
#     slow: mark tests as slow (deselect with '-m "not slow"')
#     system: mark end-to-end system tests

[devpi:upload]
# Options for the devpi: PyPI server and packaging tool
# VCS export must be deactivated since we are using setuptools-scm
no_vcs = 1
formats = bdist_wheel


[pyscaffold]
# PyScaffold's parameters when the project was created.
# This will be used when updating. Do not change!
version = 4.1.1
package = susiepca