From ed2da774a02dcb264742a8fdd968fc498cab8eb2 Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauldmccarthy@gmail.com>
Date: Mon, 24 Jul 2023 16:26:24 +0100
Subject: [PATCH] MNT: Replace setup.py with pyproject.toml
---
COPYRIGHT | 2 +-
LICENSE | 2 +-
MANIFEST.in | 13 +---
pyproject.toml | 111 +++++++++++++++++++++++++++++++++
requirements-dev.txt | 5 --
requirements-extra.txt | 5 --
requirements.txt | 5 --
setup.cfg | 23 -------
setup.py | 137 -----------------------------------------
9 files changed, 116 insertions(+), 187 deletions(-)
create mode 100644 pyproject.toml
delete mode 100644 requirements-dev.txt
delete mode 100644 requirements-extra.txt
delete mode 100644 requirements.txt
delete mode 100644 setup.py
diff --git a/COPYRIGHT b/COPYRIGHT
index ca6e31789..ab5e5b029 100644
--- a/COPYRIGHT
+++ b/COPYRIGHT
@@ -1 +1 @@
-Copyright 2016-2021 University of Oxford, Oxford, UK
+Copyright 2016-2023 University of Oxford, Oxford, UK
diff --git a/LICENSE b/LICENSE
index 29dca5745..785c943e8 100644
--- a/LICENSE
+++ b/LICENSE
@@ -1,6 +1,6 @@
The fslpy library
-Copyright 2016-2021 University of Oxford, Oxford, UK.
+Copyright 2016-2023 University of Oxford, Oxford, UK.
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
diff --git a/MANIFEST.in b/MANIFEST.in
index b0332d964..60d1bd0ca 100644
--- a/MANIFEST.in
+++ b/MANIFEST.in
@@ -1,12 +1,5 @@
include AUTHOR
-include LICENSE
-include COPYRIGHT
include CHANGELOG.rst
-include README.rst
-include requirements.txt
-include requirements-dev.txt
-include requirements-extra.txt
-include setup.cfg
-recursive-include doc *
-recursive-exclude doc/html *
-recursive-include tests *
+include COPYRIGHT
+recursive-include doc *
+recursive-include tests *
diff --git a/pyproject.toml b/pyproject.toml
new file mode 100644
index 000000000..bf20ca7f4
--- /dev/null
+++ b/pyproject.toml
@@ -0,0 +1,111 @@
+[build-system]
+requires = ["setuptools"]
+build-backend = "setuptools.build_meta"
+
+
+[project]
+name = "fslpy"
+dynamic = ["version"]
+description = "FSL Python library"
+readme = {file = "README.rst", content-type="text/x-rst"}
+license = {text = "Apache License Version 2.0"}
+requires-python = ">=3.8"
+authors = [{name = "Paul McCarthy", email = "pauldmccarthy@gmail.com"}]
+
+dependencies = [
+ "dill",
+ "h5py >=2.9",
+ "nibabel >=2.4",
+ "numpy >=1",
+ "scipy >=0.18"
+]
+
+classifiers = [
+ "Development Status :: 3 - Alpha",
+ "Intended Audience :: Developers",
+ "License :: OSI Approved :: Apache Software License",
+ "Programming Language :: Python :: 3.8",
+ "Programming Language :: Python :: 3.9",
+ "Programming Language :: Python :: 3.10",
+ "Programming Language :: Python :: 3.11",
+ "Topic :: Software Development :: Libraries :: Python Modules"
+]
+
+
+[project.urls]
+"Repository" = "https://git.fmrib.ox.ac.uk/fsl/fslpy/"
+"Documentation" = "https://open.win.ox.ac.uk/pages/fsl/fslpy/"
+
+
+[project.optional-dependencies]
+extra = [
+ "indexed_gzip >=0.7",
+ "wxpython >=4",
+ "trimesh >=2.37.29",
+ "rtree >=0.8.3",
+ "Pillow >=3.2.0"
+]
+doc = [
+ "sphinx",
+ "sphinx_rtd_theme"
+]
+test = [
+ "pytest",
+ "coverage",
+ "pytest-cov",
+ "tomli; python_version < \"3.11\""
+]
+style = [
+ "pylint",
+ "flake8"
+]
+
+
+[project.scripts]
+imcp = "fsl.scripts.imcp:main"
+imln = "fsl.scripts.imln:main"
+immv = "fsl.scripts.immv:main"
+imrm = "fsl.scripts.imrm:main"
+imglob = "fsl.scripts.imglob:main"
+imtest = "fsl.scripts.imtest:main"
+remove_ext = "fsl.scripts.remove_ext:main"
+fsl_abspath = "fsl.scripts.fsl_abspath:main"
+Text2Vest = "fsl.scripts.Text2Vest:main"
+Vest2Text = "fsl.scripts.Vest2Text:main"
+atlasq = "fsl.scripts.atlasq:main"
+atlasquery = "fsl.scripts.atlasq:atlasquery_emulation"
+fsl_ents = "fsl.scripts.fsl_ents:main"
+resample_image = "fsl.scripts.resample_image:main"
+fsl_convert_x5 = "fsl.scripts.fsl_convert_x5:main"
+fsl_apply_x5 = "fsl.scripts.fsl_apply_x5:main"
+
+
+[tool.setuptools.packages.find]
+include = ["fsl*"]
+
+
+[tool.setuptools.package-data]
+fsl = ["utils/filetree/trees/*"]
+
+
+[tool.setuptools.dynamic]
+version = {attr = "fsl.version.__version__"}
+
+
+[tool.coverage.run]
+include = ["fsl/*"]
+
+
+[tool.pytest.ini_options]
+testpaths = ["tests"]
+addopts = "-v --cov=fsl --showlocals"
+markers = [
+ "fsltest: Requires FSL",
+ "wxtest: Requires wxPython",
+ "dicomtest: Requires dcm2niix",
+ "meshtest: Requires trimesh and rtree",
+ "igziptest: Requires indexed_gzip",
+ "piltest: Requires Pillow",
+ "noroottest: Need to be executed as non-root user (will fail otherwise)",
+ "longtest: Takes a long time",
+ "unixtest: Only works on *nix systems"]
\ No newline at end of file
diff --git a/requirements-dev.txt b/requirements-dev.txt
deleted file mode 100644
index 0077afd5e..000000000
--- a/requirements-dev.txt
+++ /dev/null
@@ -1,5 +0,0 @@
-sphinx
-sphinx_rtd_theme
-coverage
-pytest
-pytest-cov
diff --git a/requirements-extra.txt b/requirements-extra.txt
deleted file mode 100644
index 735bdaff4..000000000
--- a/requirements-extra.txt
+++ /dev/null
@@ -1,5 +0,0 @@
-indexed_gzip>=0.7.0
-wxpython==4.*
-trimesh>=2.37.29
-rtree>=0.8.3
-Pillow>=3.2.0
diff --git a/requirements.txt b/requirements.txt
deleted file mode 100644
index d4f1b242f..000000000
--- a/requirements.txt
+++ /dev/null
@@ -1,5 +0,0 @@
-h5py>=2.9
-nibabel>=2.4
-numpy>=1
-scipy>=0.18
-dill
diff --git a/setup.cfg b/setup.cfg
index 59bf3d21a..2f1e33f90 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -1,25 +1,2 @@
-[aliases]
-test=pytest
-
-[bdist_wheel]
-universal=1
-
-[tool:pytest]
-markers =
- fsltest: Requires FSL
- wxtest: Requires wxPython
- dicomtest: Requires dcm2niix
- meshtest: Requires trimesh and rtree
- igziptest: Requires indexed_gzip
- piltest: Requires Pillow
- noroottest: Need to be executed as non-root user (will fail otherwise)
- longtest: Takes a long time
- unixtest: Only works on *nix systems
-
-
-testpaths = tests
-addopts = -v --cov=fsl -m "not longtest" --showlocals
-
-
[flake8]
ignore = E127,E201,E203,E221,E222,E241,E271,E272,E301,E302,E303,E701,W504
\ No newline at end of file
diff --git a/setup.py b/setup.py
deleted file mode 100644
index c588d8370..000000000
--- a/setup.py
+++ /dev/null
@@ -1,137 +0,0 @@
-#!/usr/bin/env python
-#
-# setup.py - setuptools configuration for installing the fslpy package.
-#
-# Author: Paul McCarthy <pauldmccarthy@gmail.com>
-#
-
-
-from __future__ import print_function
-
-import os.path as op
-import shutil
-import unittest.mock as mock
-
-from setuptools import setup
-from setuptools import find_namespace_packages
-from setuptools import Command
-
-
-# The directory in which this setup.py file is contained.
-basedir = op.dirname(__file__)
-
-# Dependencies are listed in requirements.txt
-with open(op.join(basedir, 'requirements.txt'), 'rt') as f:
- install_requires = [l.strip() for l in f.readlines()]
-
-# Optional dependencies are listed in requirements-extra.txt
-with open(op.join(basedir, 'requirements-extra.txt'), 'rt') as f:
- extra_requires = {'extras' : [l.strip() for l in f.readlines()]}
-
-packages = find_namespace_packages(include=('fsl', 'fsl.*'))
-
-# Figure out the current fslpy version, as defined in fsl/version.py. We
-# don't want to import the fsl package, as this may cause build problems.
-# So we manually parse the contents of fsl/version.py to extract the
-# version number.
-version = {}
-with open(op.join(basedir, "fsl", "version.py")) as f:
- for line in f:
- if line.startswith('__version__'):
- exec(line, version)
- break
-version = version['__version__']
-
-with open(op.join(basedir, 'README.rst'), 'rt') as f:
- readme = f.read()
-
-
-class doc(Command):
- """Build the API documentation. """
-
- user_options = []
-
- def initialize_options(self):
- pass
-
- def finalize_options(self):
- pass
-
- def run(self):
-
- docdir = op.join(basedir, 'doc')
- destdir = op.join(docdir, 'html')
-
- if op.exists(destdir):
- shutil.rmtree(destdir)
-
- print('Building documentation [{}]'.format(destdir))
-
- import sphinx.cmd.build as sphinx_build
-
- mockobj = mock.MagicMock()
- mockobj.__version__ = '2.2.0'
- mockedModules = open(op.join(docdir, 'mock_modules.txt')).readlines()
- mockedModules = [l.strip() for l in mockedModules]
- mockedModules = {m : mockobj for m in mockedModules}
-
- patches = [mock.patch.dict('sys.modules', **mockedModules)]
-
- [p.start() for p in patches]
- sphinx_build.main([docdir, destdir])
- [p.stop() for p in patches]
-
-
-setup(
-
- name='fslpy',
- version=version,
- description='FSL Python library',
- long_description=readme,
- long_description_content_type='text/x-rst',
- url='https://git.fmrib.ox.ac.uk/fsl/fslpy',
- author='Paul McCarthy',
- author_email='pauldmccarthy@gmail.com',
- license='Apache License Version 2.0',
- python_requires='>=3.7',
-
- classifiers=[
- 'Development Status :: 3 - Alpha',
- 'Intended Audience :: Developers',
- 'License :: OSI Approved :: Apache Software License',
- 'Programming Language :: Python :: 3.7',
- 'Programming Language :: Python :: 3.8',
- 'Programming Language :: Python :: 3.9',
- 'Topic :: Software Development :: Libraries :: Python Modules'],
-
- packages=packages,
-
- install_requires=install_requires,
- extras_require=extra_requires,
- package_data={'fsl': ['utils/filetree/trees/*']},
-
- test_suite='tests',
-
- cmdclass={'doc' : doc},
-
- entry_points={
- 'console_scripts' : [
- 'imcp = fsl.scripts.imcp:main',
- 'imln = fsl.scripts.imln:main',
- 'immv = fsl.scripts.immv:main',
- 'imrm = fsl.scripts.imrm:main',
- 'imglob = fsl.scripts.imglob:main',
- 'imtest = fsl.scripts.imtest:main',
- 'remove_ext = fsl.scripts.remove_ext:main',
- 'fsl_abspath = fsl.scripts.fsl_abspath:main',
- 'Text2Vest = fsl.scripts.Text2Vest:main',
- 'Vest2Text = fsl.scripts.Vest2Text:main',
- 'atlasq = fsl.scripts.atlasq:main',
- 'atlasquery = fsl.scripts.atlasq:atlasquery_emulation',
- 'fsl_ents = fsl.scripts.fsl_ents:main',
- 'resample_image = fsl.scripts.resample_image:main',
- 'fsl_convert_x5 = fsl.scripts.fsl_convert_x5:main',
- 'fsl_apply_x5 = fsl.scripts.fsl_apply_x5:main'
- ]
- }
-)
--
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