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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 = gReLU
description = gReLU is a python library to train, interpret, and apply deep learning models to DNA sequences
author = lal.avantika,eraslan.gokcen
author_email = [email protected]
license = MIT
license_files = LICENSE.txt
long_description = file: README.md
long_description_content_type = text/markdown; charset=UTF-8
url = https://code.roche.com/gred-rb-ai-ml-regulatory-genomics/grelu
# Add here related links, for example:
project_urls =
Documentation = https://code.roche.com/gred-rb-ai-ml-regulatory-genomics/grelu
Source = https://code.roche.com/gred-rb-ai-ml-regulatory-genomics/grelu
# 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
# Change if running only on Windows, Mac or Linux (comma-separated)
platforms = 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_namespace:
include_package_data = True
package_dir =
=src
# Require a min/specific Python version (comma-separated conditions)
python_requires = >=3.8
# 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
importlib-resources
wandb >= 0.14
numpy
pandas
seaborn
matplotlib
plotnine >= 0.8
anndata >= 0.8
scikit-learn
torch >= 2.0
pytorch-lightning >= 2.0
torchmetrics >= 1.1
modisco-lite >= 2.2.1
biopython
enformer-pytorch
genomepy
bioframe >= 0.4
captum == 0.5.0
logomaker >= 0.8
pyBigWig
ledidi
tangermeme >= 0.4.0
pygenomeviz <= 0.4.4
statsmodels >=0.11.1
pyjaspar >=3.0
[options.packages.find]
where = src
exclude =
tests
[options.extras_require]
# Add here additional requirements for extra features, to install with:
# `pip install grelu[PDF]` like:
# PDF = ReportLab; RXP
# Add here test requirements (semicolon/line-separated)
testing =
setuptools
pytest
pytest-cov
[options.entry_points]
# Add here console scripts like:
# console_scripts =
# script_name = grelu.module:function
# For example:
# console_scripts =
# fibonacci = grelu.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 grelu --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 = 120
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 = 4.4.1
package = grelu
extensions =
gitlab
no_skeleton
pre_commit