Merge pull request #476 from matthew-brett/to-entry-points

MRG: refactor scripts into entry points

Now we depend on setuptools, use entry points for scripts.

Thanks @effigies for the suggestion.

.appveyor.yml

@@ -15,7 +15,10 @@ environment:
     - PYTHON: C:\Python37
     - PYTHON: C:\Python37-x64
     - PYTHON: C:\Python38
+      # https://stackoverflow.com/a/58582651/1939576
+      EXTRA_FLAGS: "--traverse-namespace"
     - PYTHON: C:\Python38-x64
+      EXTRA_FLAGS: "--traverse-namespace"
 
 install:
   # Prepend newly installed Python to the PATH of this build (this cannot be

.travis.yml

@@ -113,12 +113,12 @@ install:
       elif [ "$INSTALL_TYPE" == "setup" ]; then
         python setup.py install
       elif [ "$INSTALL_TYPE" == "sdist" ]; then
-        python setup_egg.py egg_info  # check egg_info while we're here
-        python setup_egg.py sdist
+        python setup.py egg_info  # check egg_info while we're here
+        python setup.py sdist
         pip install $EXTRA_PIP_FLAGS dist/*.tar.gz
       elif [ "$INSTALL_TYPE" == "wheel" ]; then
         pip install wheel
-        python setup_egg.py bdist_wheel
+        python setup.py bdist_wheel
         pip install $EXTRA_PIP_FLAGS dist/*.whl
       elif [ "$INSTALL_TYPE" == "requirements" ]; then
         pip install $EXTRA_PIP_FLAGS -r requirements.txt

nipy/algorithms/registration/tests/test_scripting.py

@@ -4,6 +4,7 @@
 from __future__ import absolute_import
 
 from os.path import split as psplit
+import gc
 
 import numpy as np
 
@@ -36,6 +37,9 @@ def test_space_time_realign():
             assert_false(np.allclose(xforms[-1].as_affine(), np.eye(4), atol=1e-3))
             img = load_image(out_fname)
             npt.assert_almost_equal(original_affine, img.affine)
+        # To avoid Windows "file ... used by another process" error when
+        # removing temporary directory.
+        gc.collect()
 
 
 def test_aff2euler():

nipy/cli/__init__.py

@@ -0,0 +1,2 @@
+""" Logic for command line scripts.
+"""

scripts/nipy_diagnose → nipy/cli/diagnose.py

@@ -1,4 +1,3 @@
-#!python
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
 DESCRIP = 'Calculate and write results for diagnostic screen'
@@ -29,15 +28,15 @@
 /some/path/max_fname.img`` etc.
 '''
 
-import matplotlib
-matplotlib.use('Agg')
-
 from nipy.externals.argparse import (ArgumentParser,
                                      RawDescriptionHelpFormatter)
 import nipy.algorithms.diagnostics.commands as nadc
 
 
 def main():
+    import matplotlib
+    matplotlib.use('Agg')
+
     parser = ArgumentParser(description=DESCRIP,
                             epilog=EPILOG,
                             formatter_class=RawDescriptionHelpFormatter)
@@ -56,7 +55,3 @@ def main():
     # parse the command line
     args = parser.parse_args()
     nadc.diagnose(args)
-
-
-if __name__ == '__main__':
-    main()

scripts/nipy_3dto4d → nipy/cli/img3dto4d.py

@@ -1,4 +1,3 @@
-#!python
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
 DESCRIP = 'Read 3D image files and write a 4D file'
@@ -60,7 +59,3 @@ def main():
         out_fname = pjoin(pth, froot + '_4d' + ext + gz)
     img4d = do_3d_to_4d(filenames, check_affines=check_affines)
     nib.save(img4d, out_fname)
-
-
-if __name__ == '__main__':
-    main()

scripts/nipy_4dto3d → nipy/cli/img4dto3d.py

@@ -1,4 +1,3 @@
-#!python
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
 DESCRIP = 'Read 4D image file and write 3D nifti file for each volume'
@@ -35,7 +34,3 @@ def main():
     for i, img3d in enumerate(imgs):
         fname3d = '%s_%04d.nii' % (froot, i)
         nib.save(img3d, fname3d)
-
-
-if __name__ == '__main__':
-    main()

scripts/nipy_4d_realign → nipy/cli/realign4d.py

@@ -1,15 +1,14 @@
-#!python
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
-
-"""This is a wrapper of SpaceTimeRealign
+"""Command line wrapper of SpaceTimeRealign
 
 Based on:
 
-Alexis Roche (2011) A Four-Dimensional Registration Algorithm With Application to Joint Correction of Motion and Slice Timing in fMRI. IEEE Trans. Med. Imaging 30(8): 1546-1554
-
+Alexis Roche (2011) A Four-Dimensional Registration Algorithm With Application
+to Joint Correction of Motion and Slice Timing in fMRI. IEEE Trans. Med.
+Imaging 30(8): 1546-1554
 """
-import os
+
 import os.path as op
 import nipy.algorithms.registration as reg
 import nipy.externals.argparse as argparse
@@ -42,26 +41,25 @@
                 help="""Whether to save the motion corrections parameters (3 rotations, 3 translations). {True, False}. Default: False. NOTE: The rotations are not Euler angles, but a rotation vector. Use `nipy.algorithms.registration.to_matrix44` to convert to a 4-by-4 affine matrix""", default=False)
 
 
-# parse the command line
-args = parser.parse_args()
+def main():
+    args = parser.parse_args()
 
-if __name__ == '__main__':
     if args.save_path == 'none':
         save_path = op.split(args.input)[0]
     else:
         save_path = args.save_path
-        
+
     xform = reg.space_time_realign(args.input, float(args.TR),
-                               slice_order=args.slice_order,
-                               slice_dim=int(args.slice_dim),
-                               slice_dir=int(args.slice_dir),
-                               apply=True, # We always apply the xform in the cli
-                               make_figure=args.make_figure,
-                               out_name=save_path)
+                                   slice_order=args.slice_order,
+                                   slice_dim=int(args.slice_dim),
+                                   slice_dir=int(args.slice_dir),
+                                   # We always apply the xform in the cli
+                                   apply=True,
+                                   make_figure=args.make_figure,
+                                   out_name=save_path)
 
     if args.save_params:
-
-        f = file(op.join(save_path, 'mc.par'), 'w')
+        f = open(op.join(save_path, 'mc.par'), 'w')
         for x in xform:
             euler_rot = reg.aff2euler(x.as_affine())
             for r in euler_rot:

nipy/cli/setup.py

@@ -0,0 +1,13 @@
+from __future__ import absolute_import
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
+def configuration(parent_package='',top_path=None):
+    from numpy.distutils.misc_util import Configuration
+
+    config = Configuration('cli', parent_package, top_path)
+
+    return config
+
+if __name__ == '__main__':
+    from numpy.distutils.core import setup
+    setup(**configuration(top_path='').todict())

scripts/nipy_tsdiffana → nipy/cli/tsdiffana.py

@@ -1,10 +1,9 @@
-#!python
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
 DESCRIP = ' Analyze, plot time series difference metrics'
 EPILOG = \
-'''nipy_tsdiffana runs the time series diference algorithm over a 4D
-image volume, often and FMRI volume.
+'''Runs the time series difference algorithm over a 4D image volume, often an
+FMRI volume.
 
 It works in one of three modes:
 
@@ -97,7 +96,3 @@ def main():
     tsdiffana(args)
     if show:
         plt.show()
-
-
-if __name__ == '__main__':
-    main()

nipy/setup.py

@@ -55,6 +55,7 @@ def configuration(parent_package='',top_path=None):
     config.add_subpackage('utils')
     config.add_subpackage('tests')
     config.add_subpackage('externals')
+    config.add_subpackage('cli')
     config.add_subpackage('testing')
 
     # Note: this is a special subpackage containing that will later be

nipy/tests/scriptrunner.py

@@ -128,9 +128,6 @@ def run_command(self, cmd, check_code=True):
             # the script through the Python interpreter
             cmd = [sys.executable,
                    pjoin(self.local_script_dir, cmd[0])] + cmd[1:]
-        elif os.name == 'nt':
-            # Need .bat file extension for windows
-            cmd[0] += '.bat'
         if os.name == 'nt':
             # Quote any arguments with spaces. The quotes delimit the arguments
             # on Windows, and the arguments might be files paths with spaces.

setup.py

@@ -10,6 +10,9 @@
 # update it when the contents of directories change.
 if exists('MANIFEST'): os.remove('MANIFEST')
 
+# Always use setuptools
+import setuptools
+
 from setup_helpers import (generate_a_pyrex_source, get_comrec_build,
                            cmdclass, INFO_VARS)
 
@@ -39,20 +42,19 @@ def configuration(parent_package='',top_path=None):
     return config
 
 ################################################################################
-# Use setuptools
-from setup_egg import extra_setuptools_args
 
 # Hard and soft dependency checking
 DEPS = (
-    ('numpy', INFO_VARS['NUMPY_MIN_VERSION'], 'setup_requires', True),
-    ('scipy', INFO_VARS['SCIPY_MIN_VERSION'], 'install_requires', True),
-    ('nibabel', INFO_VARS['NIBABEL_MIN_VERSION'], 'install_requires', False),
-    ('sympy', INFO_VARS['SYMPY_MIN_VERSION'], 'install_requires', False))
-
-for name, min_ver, req_type, heavy in DEPS:
+    ('numpy', INFO_VARS['NUMPY_MIN_VERSION'], 'setup_requires'),
+    ('scipy', INFO_VARS['SCIPY_MIN_VERSION'], 'install_requires'),
+    ('nibabel', INFO_VARS['NIBABEL_MIN_VERSION'], 'install_requires'),
+    ('sympy', INFO_VARS['SYMPY_MIN_VERSION'], 'install_requires'),
+)
+
+requirement_kwargs = {'setup_requires': [], 'install_requires': []}
+for name, min_ver, req_type in DEPS:
     new_req = '{0}>={1}'.format(name, min_ver)
-    old_reqs = extra_setuptools_args.get(req_type, [])
-    extra_setuptools_args[req_type] = old_reqs + [new_req]
+    requirement_kwargs[req_type].append(new_req)
 
 
 ################################################################################
@@ -100,7 +102,7 @@ def run(self):
 ################################################################################
 
 
-def main(**extra_args):
+def main():
     from numpy.distutils.core import setup
 
     setup(name=INFO_VARS['NAME'],
@@ -116,12 +118,22 @@ def main(**extra_args):
           author_email=INFO_VARS['AUTHOR_EMAIL'],
           platforms=INFO_VARS['PLATFORMS'],
           # version set by config.get_version() above
-          requires=INFO_VARS['REQUIRES'],
           configuration = configuration,
           cmdclass = cmdclass,
-          scripts = glob('scripts/*'),
-          **extra_args)
+          tests_require=['nose>=1.0'],
+          test_suite='nose.collector',
+          zip_safe=False,
+          entry_points={
+              'console_scripts': [
+                  'nipy_3dto4d = nipy.cli.img3dto4d:main',
+                  'nipy_4dto3d = nipy.cli.img4dto3d:main',
+                  'nipy_4d_realign = nipy.cli.realign4d:main',
+                  'nipy_tsdiffana = nipy.cli.tsdiffana:main',
+                  'nipy_diagnose = nipy.cli.diagnose:main',
+              ],
+          },
+          **requirement_kwargs)
 
 
 if __name__ == "__main__":
-    main(**extra_setuptools_args)
+    main()