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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 = aspring
description = Alternatively Spliced Pseudo Repeat IN-Gene
author = Antoine Szatkownik, Diego Javier Zea, Hugues Richard & Elodie Laine
author_email = [email protected]
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/PhyloSofS-Team/aspring
# Add here related links, for example:
project_urls =
Documentation = https://aspring.readthedocs.io/en/latest/
Source = https://github.com/PhyloSofS-Team/aspring
Changelog = https://github.com/PhyloSofS-Team/aspring/changelog.html
Tracker = https://github.com/PhyloSofS-Team/aspring/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 = Linux, Mac
# Add here all kinds of additional classifiers as defined under
# https://pypi.org/classifiers/
classifiers =
Development Status :: 4 - Beta
Intended Audience :: Science/Research
License :: OSI Approved :: MIT License
Natural Language :: English
Programming Language :: Python :: 3
[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 = >=3.7,<3.12
# 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"
numpy>=1.12.0,<1.30
pandas>=0.21.0,<1.6
networkx>=2.3.0,<2.9
requests>=2.25,<2.27
biomart>=0.9.2,<0.10
[options.packages.find]
where = src
exclude =
tests
[options.extras_require]
# Add here additional requirements for extra features, to install with:
# `pip install aspring[PDF]` like:
# PDF = ReportLab; RXP
# Add here test requirements (semicolon/line-separated)
testing =
setuptools
pytest
pytest-cov
# Add here documentation requirements (semicolon/line-separated)
docs =
sphinx-argparse
[options.entry_points]
console_scripts =
aspring = aspring.main:run
step_01_preprocess = aspring.step_01_preprocess:run
step_02_hmm_maker = aspring.step_02_hmm_maker:run
step_03_hmm_aligner = aspring.step_03_hmm_aligner:run
step_04_gettable = aspring.step_04_gettable:run
step_05_filter = aspring.step_05_filter:run
step_06_stats = aspring.step_06_stats:run
step_07_reformat = aspring.step_07_reformat:run
step_08_ASRUs = aspring.step_08_ASRUs:run
step_09_clean = aspring.step_09_clean:run
step_10_struct = aspring.step_10_struct:run
# Add here console scripts like:
# console_scripts =
# script_name = aspring.module:function
# For example:
# console_scripts =
# fibonacci = aspring.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 aspring --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 = 88
extend_ignore = E203, W503
# ^ Black-compatible
# E203 and W503 have edge cases handled by black
exclude =
.tox
build
dist
.eggs
docs/conf.py
[pyscaffold]
# PyScaffold's parameters when the project was created.
# This will be used when updating. Do not change!
version = 4.4
package = aspring
extensions =
github_actions