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setup.cfg
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setup.cfg
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# 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 = MultiAssayExperiment
description = Container class for representing and managing multi-omics genomic experiments
author = jkanche
author_email = [email protected]
license = MIT
license_files = LICENSE.txt
long_description = file: README.md
long_description_content_type = text/markdown; charset=UTF-8; variant=GFM
url = https://github.com/BiocPy/MultiAssayExperiment
# Add here related links, for example:
project_urls =
Documentation = https://github.com/BiocPy/MultiAssayExperiment
# Source = https://github.com/pyscaffold/pyscaffold/
# Changelog = https://pyscaffold.org/en/latest/changelog.html
# Tracker = https://github.com/pyscaffold/pyscaffold/issues
# Conda-Forge = https://anaconda.org/conda-forge/pyscaffold
# Download = https://pypi.org/project/PyScaffold/#files
# Twitter = https://twitter.com/PyScaffold
# Change if running only on Windows, Mac or Linux (comma-separated)
platforms = any
# 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_namespace:
include_package_data = True
package_dir =
=src
# Require a min/specific Python version (comma-separated conditions)
python_requires = >=3.9
# Add here dependencies of your project (line-separated), e.g. requests>=2.2,<3.0.
# Version specifiers like >=2.2,<3.0 avoid problems due to API changes in
# new major versions. This works if the required packages follow Semantic Versioning.
# For more information, check out https://semver.org/.
install_requires =
importlib-metadata; python_version<"3.8"
biocframe>=0.5.6
biocutils>=0.1.4
summarizedexperiment>=0.4.5
[options.packages.find]
where = src
exclude =
tests
[options.extras_require]
# Add here additional requirements for extra features, to install with:
# `pip install MultiAssayExperiment[PDF]` like:
# PDF = ReportLab; RXP
optional =
singlecellexperiment[optional]>=0.4.7
genomicranges
delayedarray
# Add here test requirements (semicolon/line-separated)
testing =
setuptools
pytest
pytest-cov
pandas
singlecellexperiment[testing]>=0.4.7
genomicranges
delayedarray
[options.entry_points]
# Add here console scripts like:
# console_scripts =
# script_name = multiassayexperiment.module:function
# For example:
# console_scripts =
# fibonacci = multiassayexperiment.skeleton:run
# And any other entry points, for example:
# pyscaffold.cli =
# awesome = pyscaffoldext.awesome.extension:AwesomeExtension
[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 multiassayexperiment --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
[flake8]
# Some sane defaults for the code style checker flake8
max_line_length = 100
extend_ignore = E203, W503
# ^ Black-compatible
# E203 and W503 have edge cases handled by black
exclude =
.tox
build
dist
.eggs
docs/conf.py
per-file-ignores = __init__.py:F401
[pyscaffold]
# PyScaffold's parameters when the project was created.
# This will be used when updating. Do not change!
version = 4.5
package = multiassayexperiment
extensions =
markdown
pre_commit