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setup.py
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setup.py
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#!/bin/env python
"""A setuptools based setup module.
See:
https://packaging.python.org/en/latest/distributing.html
https://github.com/pypa/sampleproject
"""
# To use a consistent encoding
from codecs import open
from os import path
# Always prefer setuptools over distutils
from setuptools import find_namespace_packages, find_packages, setup, Extension
import versioneer
here = path.abspath(path.dirname(__file__))
# Get the long description from the README file
with open(path.join(here, "README.rst"), encoding="utf-8") as f:
long_description = f.read()
# Write version number out to VERSION file
version = versioneer.get_version()
try:
with open(path.join(here, "VERSION"), "w", encoding="utf-8") as f:
f.write(version)
except PermissionError:
print("can't write to VERSION file - moving on")
modules_list = [
"rapidtide/OrthoImageItem",
"rapidtide/calccoherence",
"rapidtide/calcnullsimfunc",
"rapidtide/calcsimfunc",
"rapidtide/correlate",
"rapidtide/dlfilter",
"rapidtide/externaltools",
"rapidtide/filter",
"rapidtide/fit",
"rapidtide/glmpass",
"rapidtide/happy_supportfuncs",
"rapidtide/helper_classes",
"rapidtide/io",
"rapidtide/makelaggedtcs",
"rapidtide/maskutil",
"rapidtide/miscmath",
"rapidtide/multiproc",
"rapidtide/peakeval",
"rapidtide/refine",
"rapidtide/refine_factored",
"rapidtide/resample",
"rapidtide/simfuncfit",
"rapidtide/stats",
"rapidtide/util",
"rapidtide/wiener",
"rapidtide/_version",
"rapidtide/workflows/adjustoffset",
"rapidtide/workflows/aligntcs",
"rapidtide/workflows/applydlfilter",
"rapidtide/workflows/atlasaverage",
"rapidtide/workflows/atlastool",
"rapidtide/workflows/calcicc",
"rapidtide/workflows/calctexticc",
"rapidtide/workflows/calcttest",
"rapidtide/workflows/ccorrica",
"rapidtide/workflows/diffrois",
"rapidtide/workflows/endtidalproc",
"rapidtide/workflows/fdica",
"rapidtide/workflows/filtnifti",
"rapidtide/workflows/filttc",
"rapidtide/workflows/fingerprint",
"rapidtide/workflows/fixtr",
"rapidtide/workflows/glmfilt",
"rapidtide/workflows/glmfrommaps",
"rapidtide/workflows/gmscalc",
"rapidtide/workflows/happy",
"rapidtide/workflows/happy2std",
"rapidtide/workflows/happy_parser",
"rapidtide/workflows/histnifti",
"rapidtide/workflows/histtc",
"rapidtide/workflows/localflow",
"rapidtide/workflows/mergequality",
"rapidtide/workflows/niftidecomp",
"rapidtide/workflows/niftistats",
"rapidtide/workflows/pairwisemergenifti",
"rapidtide/workflows/pairproc",
"rapidtide/workflows/parser_funcs",
"rapidtide/workflows/physioproc",
"rapidtide/workflows/pixelcomp",
"rapidtide/workflows/polyfitim",
"rapidtide/workflows/proj2flow",
"rapidtide/workflows/rankimage",
"rapidtide/workflows/rapidtide",
"rapidtide/workflows/rapidtide2std",
"rapidtide/workflows/rapidtide_parser",
"rapidtide/workflows/resampletc",
"rapidtide/workflows/resamplenifti",
"rapidtide/workflows/retroglm",
"rapidtide/workflows/retrolagtcs",
"rapidtide/workflows/roisummarize",
"rapidtide/workflows/showarbcorr",
"rapidtide/workflows/showhist",
"rapidtide/workflows/showstxcorr",
"rapidtide/workflows/showtc",
"rapidtide/workflows/showxcorrx",
"rapidtide/workflows/showxy",
"rapidtide/workflows/simdata",
"rapidtide/workflows/tcfrom2col",
"rapidtide/workflows/tcfrom3col",
"rapidtide/workflows/threeD",
"rapidtide/workflows/tidepool",
"rapidtide/workflows/utils",
"rapidtide/workflows/variabilityizer",
"rapidtide/tidepoolTemplate",
"rapidtide/tidepoolTemplate_alt",
"rapidtide/tidepoolTemplate_qt6",
"rapidtide/tidepoolTemplate_alt_qt6",
]
script_list = [
"rapidtide/scripts/adjustoffset",
"rapidtide/scripts/aligntcs",
"rapidtide/scripts/applydlfilter",
"rapidtide/scripts/atlasaverage",
"rapidtide/scripts/atlastool",
"rapidtide/scripts/calcicc",
"rapidtide/scripts/calctexticc",
"rapidtide/scripts/calcttest",
"rapidtide/scripts/ccorrica",
"rapidtide/scripts/diffrois",
"rapidtide/scripts/endtidalproc",
"rapidtide/scripts/fdica",
"rapidtide/scripts/filtnifti",
"rapidtide/scripts/filttc",
"rapidtide/scripts/fingerprint",
"rapidtide/scripts/fixtr",
"rapidtide/scripts/glmfilt",
"rapidtide/scripts/gmscalc",
"rapidtide/scripts/happy",
"rapidtide/scripts/happy2std",
"rapidtide/scripts/happywarp",
"rapidtide/scripts/histnifti",
"rapidtide/scripts/histtc",
"rapidtide/scripts/localflow",
"rapidtide/scripts/mergequality",
"rapidtide/scripts/pairproc",
"rapidtide/scripts/pairwisemergenifti",
"rapidtide/scripts/physiofreq",
"rapidtide/scripts/pixelcomp",
"rapidtide/scripts/plethquality",
"rapidtide/scripts/polyfitim",
"rapidtide/scripts/proj2flow",
"rapidtide/scripts/rankimage",
"rapidtide/scripts/rapidtide",
"rapidtide/scripts/rapidtide2std",
"rapidtide/scripts/resampletc",
"rapidtide/scripts/resamplenifti",
"rapidtide/scripts/retroglm",
"rapidtide/scripts/retrolagtcs",
"rapidtide/scripts/roisummarize",
"rapidtide/scripts/runqualitycheck",
"rapidtide/scripts/showarbcorr",
"rapidtide/scripts/showhist",
"rapidtide/scripts/showstxcorr",
"rapidtide/scripts/showtc",
"rapidtide/scripts/showxcorr_legacy",
"rapidtide/scripts/showxcorrx",
"rapidtide/scripts/showxy",
"rapidtide/scripts/simdata",
"rapidtide/scripts/spatialdecomp",
"rapidtide/scripts/spatialfit",
"rapidtide/scripts/spatialmi",
"rapidtide/scripts/spectrogram",
"rapidtide/scripts/synthASL",
"rapidtide/scripts/tcfrom2col",
"rapidtide/scripts/tcfrom3col",
"rapidtide/scripts/temporaldecomp",
"rapidtide/scripts/threeD",
"rapidtide/scripts/tidepool",
"rapidtide/scripts/variabilityizer",
]
setup(
name="rapidtide",
# Versions should comply with PEP440. For a discussion on single-sourcing
# the version across setup.py and the project code, see
# https://packaging.python.org/en/latest/single_source_version.html
version=versioneer.get_version(),
cmdclass=versioneer.get_cmdclass(),
description="Tools for performing correlation analysis on fMRI data.",
long_description=long_description,
# The project's main homepage.
url="https://github.com/bbfrederick/rapidtide",
# Author details
author="Blaise Frederick",
author_email="[email protected]",
# Choose your license
license="Apache Software License",
# See https://pypi.python.org/pypi?%3Aaction=list_classifiers
classifiers=[
# How mature is this project? Common values are
# 3 - Alpha
# 4 - Beta
# 5 - Production/Stable
"Development Status :: 5 - Production/Stable",
# Indicate who your project is intended for
"Intended Audience :: Science/Research",
"Topic :: Scientific/Engineering :: Medical Science Apps.",
# Pick your license as you wish (should match "license" above)
"License :: OSI Approved :: Apache Software License",
# Specify the Python versions you support here. In particular, ensure
# that you indicate whether you support Python 2, Python 3 or both.
"Programming Language :: Python :: 3",
"Programming Language :: Python :: 3.9",
"Programming Language :: Python :: 3.10",
"Programming Language :: Python :: 3.11",
"Programming Language :: Python :: 3.12",
],
# What does your project relate to?
keywords=["fMRI", "correlation", "RIPTiDe", "noise"],
# You can just specify the packages manually here if your project is
# simple. Or you can use find_packages().
packages=find_namespace_packages(
exclude=[
"contrib",
"docs",
"rapidtide/data/examples/dst",
"rapidtide/data/examples/extrasrc",
]
),
# Alternatively, if you want to distribute just a my_module.py, uncomment
# this:
# py_modules=["my_module"],
py_modules=modules_list,
# List run-time dependencies here. These will be installed by pip when
# your project is installed. For an analysis of "install_requires" vs pip's
# requirements files see:
# https://packaging.python.org/en/latest/requirements.html
install_requires=[
"numpy",
"scipy",
"pandas",
"pyarrow",
"scikit-image",
"scikit-learn",
"nibabel",
"nilearn",
"matplotlib>=3.3.0",
"pyqtgraph>=0.13.4",
"pyqt",
"pyqt5-sip",
"requests",
"statsmodels",
"pywavelets",
"tomlkit",
"tensorflow>=2.10.0",
"tf-keras",
"tqdm",
],
# List additional groups of dependencies here (e.g. development
# dependencies). You can install these using the following syntax,
# for example:
# $ pip install -e .[dev,test]
extras_require={
"doc": [
"sphinx>=1.8.0",
"sphinx_rtd_theme",
"sphinx-argparse",
"sphinx-gallery",
"myst-parser",
"numpydoc",
"sphinxcontrib-bibtex",
],
"tests": [
"codecov",
"coverage",
"coveralls",
"flake8-black",
"pytest",
"pytest-cov",
],
},
# If there are data files included in your packages that need to be
# installed, specify them here. If using Python 2.6 or less, then these
# have to be included in MANIFEST.in as well.
include_package_data=True,
zip_safe=False,
package_data={
"examples": [
"data/examples/src/test*",
"data/examples/src/installtestdata",
],
"reference": [
"data/reference/JHU-ArterialTerritoriesNoVent-LVL*.xml",
"data/reference/JHU-ArterialTerritoriesNoVent-LVL*regions.txt",
"data/reference/JHU-ArterialTerritoriesNoVent-LVL*2mm.nii.gz",
"data/reference/ASPECTS*",
"data/reference/ATT*",
"data/reference/HCP1200*",
"data/reference/MNI152*",
"data/reference/slicetimes/*",
],
"models": [
"data/models/*",
],
"testdata": [
"tests/testdata/*.txt",
],
"tmpdata": [
"tests/tmp/.placeholder.txt",
],
},
# additional_packagedata={
# "testtargets": [
# "tests/testtargets/*.txt",
# "tests/testtargets/*.nii.gz",
# ],
# },
# To provide executable scripts, use entry points in preference to the
# "scripts" keyword. Entry points provide cross-platform support and allow
# pip to create the appropriate form of executable for the target platform.
scripts=script_list,
)