REFACTOR: Use pyproject.toml project definition

MANIFEST.in

@@ -6,7 +6,7 @@ include requirements-dev.txt
 include requirements-setup.txt
 include versioneer.py
 
-recursive-include radiomics *
+recursive-include src/radiomics *
 
 recursive-include data/baseline *
 recursive-include data *_image.nrrd
@@ -24,4 +24,3 @@ recursive-include bin *.py
 
 recursive-exclude * __pycache__
 recursive-exclude * *.py[cod]
-recursive-exclude * nosetests.xml

pyproject.toml

@@ -0,0 +1,47 @@
+[build-system]
+requires = ["setuptools>=61.0", "numpy", "versioneer"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "pyradiomics"
+version = "3.0.1a1"
+authors = [
+    { name = "PyRadimiomics Community", email = "pyradiomics@googlegroups.com"}
+]
+description = "Radiomics features library for python"
+readme = "README.md"
+requires-python =">=3.5"
+license = { file = "LICENSE.txt"}
+keywords = [ "radiomics", "cancerimaging", "medicalresearch", "computationalimaging" ]
+classifiers = [
+    'Development Status :: 5 - Production/Stable',
+    'Environment :: Console',
+    'Intended Audience :: Developers',
+    'Intended Audience :: Science/Research',
+    'License :: OSI Approved :: BSD License',
+    'Operating System :: OS Independent',
+    'Programming Language :: C',
+    'Programming Language :: Python :: 3.5',
+    'Programming Language :: Python :: 3.6',
+    'Programming Language :: Python :: 3.7',
+    'Programming Language :: Python :: 3.8',
+    'Programming Language :: Python :: 3.9',
+    'Topic :: Scientific/Engineering :: Bio-Informatics'
+]
+dependencies = [
+    "numpy",
+    "SimpleITK",
+    "PyWavelets",
+    "pykwalify",
+    "six"
+]
+
+[project.scripts]
+pyradiomics = "radiomics.scripts.__init__:parse_args"
+
+[project.urls]
+"Homepaget" = "http://github.com/AIM-Harvard/pyradiomics#readme"
+"Radiomics.io" = "https://www.radiomics.io/"
+"Documentation" = "https://pyradiomics.readthedocs.io/en/latest/index.html"
+"Docker" = "https://hub.docker.com/r/radiomics/pyradiomics/"
+"Github" = "https://github.com/AIM-Harvard/pyradiomics"

scikit-ci.yml

@@ -46,11 +46,7 @@ build:
 
 test:
   commands:
-    - $<RUN_ENV> python setup.py test  --args="--with-xunit --logging-level=DEBUG"
-
-  circleci:
-    commands:
-      - cp nosetests.xml $CIRCLE_TEST_REPORTS
+    - $<RUN_ENV> pytest
 
 after_test:
   commands:

setup.cfg

@@ -1,9 +1,23 @@
 [metadata]
-description-file = README.md
+description_file = README.md
 
-[nosetests]
-verbosity=3
-where=tests
+[options]
+install_requires =
+    numpy
+    SimpleITK
+    PyWavelets
+    pykwalify
+    six
+include_package_data=False
+
+[options.packages.find]
+include=radiomics*
+exclude=radiomics.schemas
+
+[options.package_data]
+radiomics =
+      schemas/paramSchema.yaml
+      schemas/schemaFuncs.py
 
 [versioneer]
 VCS = git

setup.py

@@ -2,59 +2,15 @@
 
 from distutils import sysconfig
 import platform
-import sys
 
 import numpy
 from setuptools import Extension, setup
-from setuptools.command.test import test as TestCommand
 import versioneer
 
-# Check if current PyRadiomics is compatible with current python installation (> 2.6, 64 bits)
-if sys.version_info < (2, 6, 0):
-  raise Exception("pyradiomics > 0.9.7 requires python 2.6 or later")
-
 if platform.architecture()[0].startswith('32'):
   raise Exception('PyRadiomics requires 64 bits python')
 
-with open('requirements.txt', 'r') as fp:
-  requirements = list(filter(bool, (line.strip() for line in fp)))
-
-with open('requirements-dev.txt', 'r') as fp:
-  dev_requirements = list(filter(bool, (line.strip() for line in fp)))
-
-with open('requirements-setup.txt', 'r') as fp:
-  setup_requirements = list(filter(bool, (line.strip() for line in fp)))
-
-with open('README.md', 'rb') as fp:
-  long_description = fp.read().decode('utf-8')
-
-
-class NoseTestCommand(TestCommand):
-  """Command to run unit tests using nose driver after in-place build"""
-
-  user_options = TestCommand.user_options + [
-    ("args=", None, "Arguments to pass to nose"),
-  ]
-
-  def initialize_options(self):
-    self.args = []
-    TestCommand.initialize_options(self)
-
-  def finalize_options(self):
-    TestCommand.finalize_options(self)
-    if self.args:
-      self.args = __import__('shlex').split(self.args)
-
-  def run_tests(self):
-    # Run nose ensuring that argv simulates running nosetests directly
-    nose_args = ['nosetests']
-    nose_args.extend(self.args)
-    __import__('nose').run_exit(argv=nose_args)
-
-
 commands = versioneer.get_cmdclass()
-commands['test'] = NoseTestCommand
-
 incDirs = [sysconfig.get_python_inc(), numpy.get_include()]
 
 ext = [Extension("radiomics._cmatrices", ["radiomics/src/_cmatrices.c", "radiomics/src/cmatrices.c"],
@@ -65,56 +21,10 @@ def run_tests(self):
 setup(
   name='pyradiomics',
 
-  url='http://github.com/Radiomics/pyradiomics#readme',
-  project_urls={
-    'Radiomics.io': 'https://www.radiomics.io/',
-    'Documentation': 'https://pyradiomics.readthedocs.io/en/latest/index.html',
-    'Docker': 'https://hub.docker.com/r/radiomics/pyradiomics/',
-    'Github': 'https://github.com/Radiomics/pyradiomics'
-  },
-
-  author='pyradiomics community',
-  author_email='pyradiomics@googlegroups.com',
-
   version=versioneer.get_version(),
   cmdclass=commands,
 
   packages=['radiomics', 'radiomics.scripts'],
   ext_modules=ext,
   zip_safe=False,
-  package_data={'radiomics': ['schemas/paramSchema.yaml', 'schemas/schemaFuncs.py']},
-
-  entry_points={
-    'console_scripts': [
-      'pyradiomics=radiomics.scripts.__init__:parse_args'
-    ]},
-
-  description='Radiomics features library for python',
-  long_description=long_description,
-  long_description_content_type='text/markdown',
-
-  license='BSD License',
-
-  classifiers=[
-    'Development Status :: 5 - Production/Stable',
-    'Environment :: Console',
-    'Intended Audience :: Developers',
-    'Intended Audience :: Science/Research',
-    'License :: OSI Approved :: BSD License',
-    'Operating System :: OS Independent',
-    'Programming Language :: C',
-    'Programming Language :: Python :: 2',
-    'Programming Language :: Python :: 2.7',
-    'Programming Language :: Python :: 3.4',
-    'Programming Language :: Python :: 3.5',
-    'Programming Language :: Python :: 3.6',
-    'Topic :: Scientific/Engineering :: Bio-Informatics',
-  ],
-
-  keywords='radiomics cancerimaging medicalresearch computationalimaging',
-
-  install_requires=requirements,
-  test_suite='nose.collector',
-  tests_require=dev_requirements,
-  setup_requires=setup_requirements
 )

tests/test_wavelet.py

@@ -8,7 +8,7 @@
 
 logger = logging.getLogger('radiomics.testing')
 testCases = ('test_wavelet_64x64x64', 'test_wavelet_37x37x37')
-baselineFile = '../data/baseline/wavelet.npy'
+baselineFile = os.path.join(os.path.dirname(__file__), '../data/baseline/wavelet.npy')
 
 
 def pytest_generate_tests(metafunc):