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pyproject.toml
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# SPDX-License-Identifier: GPL-3.0-or-later
[build-system]
requires = ['setuptools >= 62.2.0', 'wheel', 'argparse-manpage[setuptools]', 'tomli >= 1.1.0 ; python_version < "3.11"']
build-backend = 'setuptools.build_meta'
[project]
name = 'bidscoin'
description = 'Converts and organises raw MRI data-sets according to the Brain Imaging Data Structure (BIDS)'
version = '4.3.0'
readme = 'README.rst'
requires-python = '>= 3.8'
license = {file = 'LICENSE.txt'}
keywords = ['bids','mri','imaging','neuroimaging','dicom','par','rec','nifti','bidsapp','defacing','echo-combination','skull-stripping','HPC']
authors = [{email = 'm.zwiers@donders.ru.nl'}, {name = 'Marcel Zwiers'}]
classifiers = ['Programming Language :: Python :: 3.8',
'License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)',
'Operating System :: OS Independent',
'Intended Audience :: Science/Research']
dependencies = ['pandas',
'matplotlib',
'numpy',
'pydicom >= 2',
'PyQt6',
'ruamel-yaml > 0.17.2',
'tomli >= 1.1.0 ; python_version < "3.11"',
'coloredlogs',
'tqdm >= 4.60.0',
'multiecho >= 0.25',
'python-dateutil',
'nibabel',
'bids-validator',
'jsonschema',
'drmaa',
'duecredit']
[project.optional-dependencies]
dcm2niix2bids = ['dcm2niix']
spec2nii2bids = ['spec2nii >= 0.6.1']
deface = ['pydeface']
siemens = ['dicom-parser']
# pet2bids = ['pypet2bids >= 1.0.12']
# phys2bidscoin = ['bioread >= 1.0.5', 'pymatreader >= 0.0.24', 'phys2bids >= 2.0.0, < 3.0.0']
all = ['bidscoin[dcm2niix2bids,spec2nii2bids,deface]'] # + siemens + pet2bids + phys2bidscoin
dev = ['bidscoin[spec2nii2bids,deface,siemens]', 'tox', 'pytest', 'jsonschema', 'sphinx-rtd-theme', 'myst-parser'] # + pet2bids + phys2bidscoin
[project.urls]
documentation = 'https://bidscoin.readthedocs.io'
homepage = 'https://github.com/Donders-Institute/bidscoin'
repository = 'https://github.com/Donders-Institute/bidscoin'
[project.scripts]
bidscoin = 'bidscoin.bcoin:main'
bidseditor = 'bidscoin.bidseditor:main'
bidsmapper = 'bidscoin.bidsmapper:main'
bidscoiner = 'bidscoin.bidscoiner:main'
echocombine = 'bidscoin.bidsapps.echocombine:main'
deface = 'bidscoin.bidsapps.deface:main'
medeface = 'bidscoin.bidsapps.medeface:main'
skullstrip = 'bidscoin.bidsapps.skullstrip:main'
slicereport = 'bidscoin.bidsapps.slicereport:main'
dicomsort = 'bidscoin.utilities.dicomsort:main'
bidsparticipants = 'bidscoin.utilities.bidsparticipants:main'
rawmapper = 'bidscoin.utilities.rawmapper:main'
physio2tsv = 'bidscoin.utilities.physio2tsv:main'
plotphysio = 'bidscoin.utilities.plotphysio:main'
[tool.build_manpages]
manpages = ['man/bidscoin.1:function=get_parser:pyfile=bidscoin/cli/_bcoin.py',
'man/bidseditor.1:function=get_parser:pyfile=bidscoin/cli/_bidseditor.py',
'man/bidsmapper.1:function=get_parser:pyfile=bidscoin/cli/_bidsmapper.py',
'man/bidscoiner.1:function=get_parser:pyfile=bidscoin/cli/_bidscoiner.py',
'man/echocombine.1:function=get_parser:pyfile=bidscoin/cli/_echocombine.py',
'man/deface.1:function=get_parser:pyfile=bidscoin/cli/_deface.py',
'man/medeface.1:function=get_parser:pyfile=bidscoin/cli/_medeface.py',
'man/skullstrip.1:function=get_parser:pyfile=bidscoin/cli/_skullstrip.py',
'man/slicereport.1:function=get_parser:pyfile=bidscoin/cli/_slicereport.py',
'man/dicomsort.1:function=get_parser:pyfile=bidscoin/cli/_dicomsort.py',
'man/bidsparticipants.1:function=get_parser:pyfile=bidscoin/cli/_bidsparticipants.py',
'man/rawmapper.1:function=get_parser:pyfile=bidscoin/cli/_rawmapper.py',
'man/physio2tsv.1:function=get_parser:pyfile=bidscoin/cli/_physio2tsv.py',
'man/plotphysio.1:function=get_parser:pyfile=bidscoin/cli/_plotphysio.py']
[tool.setuptools.cmdclass]
build_py = "build_manpages.build_py"
install = "build_manpages.install"
build_manpages = "build_manpages.build_manpages"
[tool.setuptools.package-data]
'*' = ['*.yaml', 'schema.json', 'BIDS_VERSION', 'bidscoin.ico', 'bidscoin_logo.png', 'rightarrow.png'] # package names should match these glob patterns (["*"] by default)
[tool.pytest.ini_options]
testpaths = ['tests']
[tool.tox]
legacy_tox_ini = """
[tox]
min_version = 4.0
envlist = py38, py39, py310, py311, py312, docs
[testenv]
extras = all
deps = pytest
jsonschema
argparse-manpage[setuptools]
allowlist_externals = rm
setenv = DUECREDIT_ENABLE=yes
commands = rm -f .duecredit.p
pytest
rm .duecredit.p
[testenv:docs]
deps = sphinx-rtd-theme
myst-parser
linkchecker
tomli >= 1.1.0 ; python_version < "3.11"
pyspelling
allowlist_externals = make
commands = make -C docs html
linkchecker docs/_build/html/index.html
pyspelling -c docs/.pyspelling.yml
"""
# Ref: https://github.com/codespell-project/codespell#using-a-config-file
[tool.codespell]
skip = '.git,*.pdf,*.svg,go.sum'
check-hidden = true
ignore-regex = '\b(PULS|TE|ALS)\b'
ignore-words-list = 'compliancy,uptodate,mis'