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setup.cfg
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setup.cfg
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[metadata]
name = ont-remora
version = attr: src.remora.__init__.__version__
description = Nanopore methylation/modified base calling detached from basecalling
license = ont_public_licence
long_description = file: README.rst
long_description_content_type = text/x-rst; charset=UTF-8; variant=GFM
url = https://github.com/nanoporetech/remora
# Change if running only on Windows, Mac or Linux (comma-separated)
platforms = any
classifiers =
Development Status :: 4 - Beta
Programming Language :: Python
[options]
zip_safe = False
packages = remora, remora.trained_models
package_dir =
=src
include_package_data = True
# project dependencies (tests deps listed in next section)
install_requires =
tqdm
toml
torch
numpy
scikit-learn
thop
pod5 >= 0.2.8
pysam >= 0.20.0
parasail
requests
polars
# compatability issue with patchworklib in notebooks
# see https://github.com/ponnhide/patchworklib/issues/56
plotnine == 0.12.4
# remove with python 3.8 support
importlib_resources
[options.extras_require]
tests =
pytest
pytest-cov
black==22.8.0
flake8
sphinx
build
jupyter
patchworklib == 0.6.3
scipy
[options.packages.find]
where =
src/
src/remora
exclude =
docs
tests
.eggs
[options.entry_points]
console_scripts =
remora = remora.main:run
[test]
extras = True
[tool:pytest]
addopts =
--cov src/remora
--verbose
--ignore *.egg*
--durations=10
--doctest-ignore-import-errors
norecursedirs =
dist
build
.tox
.eggs
testpaths = tests
markers =
format
unit
main
etl
duplex
smoke
notebook
[aliases]
dists = bdist_wheel
[bdist_wheel]
# Use this option if your package is pure-python
universal = 1
[build_sphinx]
source_dir = docs
build_dir = build/sphinx
[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]
# ignore:
# E203 whitespace before ':'
# W503 line break before binary operator
ignore = E203,W503
max-line-length = 80
exclude =
.eggs
.git
.venv
venv
_build
build
dist
docs
models
# TODO flake up the scripts dir
scripts