NiftyReg interface raises ValueError: invalid version number

[fepegar]

Summary

Version number is "invalid" when I try to create a RegAladin node.

Actual behavior

C:\Users\fernando\tmp
(vesseg) λ python r.py
180612-15:47:29,796 interface WARNING:
         version_from_command member of CommandLine was Deprecated in nipype-1.0.0 and deleted in 1.1.0
Traceback (most recent call last):
  File "r.py", line 7, in <module>
    aladin = niftyreg.RegAladin()
  File "C:\Users\fernando\Miniconda3\envs\vesseg\lib\site-packages\nipype\interfaces\niftyreg\base.py", line 66, in __init__
    StrictVersion(_version) < StrictVersion(self._min_version):
  File "C:\Users\fernando\Miniconda3\envs\vesseg\lib\distutils\version.py", line 40, in __init__
    self.parse(vstring)
  File "C:\Users\fernando\Miniconda3\envs\vesseg\lib\distutils\version.py", line 137, in parse
    raise ValueError("invalid version number '%s'" % vstring)
ValueError: invalid version number '1.5.58
'

I have temporarily hacked this by replacing this line:

_version = self.version_from_command()

by:

_version = bytes('1.5.58', "utf-8")

How to replicate the behavior

Run

from nipype.interfaces import niftyreg
aladin = niftyreg.RegAladin()

Platform details:

In [1]: import nipype

In [2]: nipype.get_info()
Out[2]:
{'pkg_path': 'C:\\Users\\fernando\\Miniconda3\\envs\\vesseg\\lib\\site-packages\\nipype',
 'commit_source': 'archive substitution',
 'commit_hash': '%h',
 'nipype_version': '1.0.4',
 'sys_version': '3.6.5 |Anaconda, Inc.| (default, Mar 29 2018, 13:32:41) [MSC v.1900 64 bit (AMD64)]',
 'sys_executable': 'C:\\Users\\fernando\\Miniconda3\\envs\\vesseg\\python.exe',
 'sys_platform': 'win32',
 'numpy_version': '1.14.3',
 'scipy_version': '1.1.0',
 'networkx_version': '2.1',
 'nibabel_version': '2.2.1',
 'traits_version': '4.6.0'}

In [3]: nipype.__version__
Out[3]: '1.0.4'

Execution environment

I'm not sure what this means. I'm running Python from a conda environment.

[mgxd]

@mmodat @byvernault mentioning in case you want to take a crack at this

[fepegar]

I don't get this error anymore:

In [9]: nipype.get_info()
Out[9]:
{'pkg_path': '/Users/fernando/miniconda3/lib/python3.6/site-packages/nipype',
 'commit_source': 'installation',
 'commit_hash': '9578f4ddc',
 'nipype_version': '1.1.0',
 'sys_version': '3.6.5 |Anaconda, Inc.| (default, Apr 26 2018, 08:42:37) \n[GCC 4.2.1 Compatible Clang 4.0.1 (tags/RELEASE_401/final)]',
 'sys_executable': '/Users/fernando/miniconda3/bin/python',
 'sys_platform': 'darwin',
 'numpy_version': '1.14.5',
 'scipy_version': '1.1.0',
 'networkx_version': '2.1',
 'nibabel_version': '2.4.0dev',
 'traits_version': '4.6.0'}

But I get a warning:

python
180728-13:10:24,671 nipype.interface WARNING:
	 version_from_command member of CommandLine was Deprecated in nipype-1.0.0 and deleted in 1.1.0

[mmodat]

Hi. I'll update the call to version_from_command.

[effigies]

@mmodat As version_from_command has been deprecated, would it be possible to rework your versioning to use an Info object (sub-classing PackageInfo)?

If you have a command that will produce the package version, you add a version_cmd class attribute; if there's a file in the distribution you can use version_file. In either case, you then write a simple parse_version static method that will produce a version string. I'll append several examples below:

nipype/nipype/interfaces/ants/base.py

Lines 33 to 54 in 715ad0a

	class Info(PackageInfo):
	version_cmd = os.path.join(os.getenv('ANTSPATH', ''),
	'antsRegistration') + ' --version'
	@staticmethod
	def parse_version(raw_info):
	for line in raw_info.splitlines():
	if line.startswith('ANTs Version: '):
	v_string = line.split()[2]
	break
	else:
	return None
	# -githash may or may not be appended
	v_string = v_string.split('-')[0]
	# 2.2.0-equivalent version string
	if 'post' in v_string and \
	LooseVersion(v_string) >= LooseVersion('2.1.0.post789'):
	return '2.2.0'
	else:
	return '.'.join(v_string.split('.')[:3])

nipype/nipype/interfaces/dcm2nii.py

Lines 17 to 25 in 715ad0a

	class Info(PackageInfo):
	"""Handle dcm2niix version information"""
	version_cmd = 'dcm2niix'
	@staticmethod
	def parse_version(raw_info):
	m = re.search(r'version (\S+)', raw_info)
	return m.groups()[0] if m else None

nipype/nipype/interfaces/fsl/base.py

Lines 43 to 72 in 715ad0a

	class Info(PackageInfo):
	"""
	Handle FSL ``output_type`` and version information.
	output type refers to the type of file fsl defaults to writing
	eg, NIFTI, NIFTI_GZ
	Examples
	--------
	>>> from nipype.interfaces.fsl import Info
	>>> Info.version() # doctest: +SKIP
	>>> Info.output_type() # doctest: +SKIP
	"""
	ftypes = {
	'NIFTI': '.nii',
	'NIFTI_PAIR': '.img',
	'NIFTI_GZ': '.nii.gz',
	'NIFTI_PAIR_GZ': '.img.gz'
	}
	if os.getenv('FSLDIR'):
	version_file = os.path.join(os.getenv('FSLDIR'), 'etc', 'fslversion')
	@staticmethod
	def parse_version(raw_info):
	return raw_info.splitlines()[0]

nipype/nipype/interfaces/freesurfer/base.py

Lines 31 to 83 in 715ad0a

	class Info(PackageInfo):
	""" Freesurfer subject directory and version information.
	Examples
	--------
	>>> from nipype.interfaces.freesurfer import Info
	>>> Info.version() # doctest: +SKIP
	>>> Info.subjectsdir() # doctest: +SKIP
	"""
	if os.getenv('FREESURFER_HOME'):
	version_file = os.path.join(
	os.getenv('FREESURFER_HOME'), 'build-stamp.txt')
	@staticmethod
	def parse_version(raw_info):
	return raw_info.splitlines()[0]
	@classmethod
	def looseversion(cls):
	""" Return a comparable version object
	If no version found, use LooseVersion('0.0.0')
	"""
	ver = cls.version()
	if ver is None:
	return LooseVersion('0.0.0')
	vinfo = ver.rstrip().split('-')
	try:
	int(vinfo[-1], 16)
	except ValueError:
	githash = ''
	else:
	githash = '.' + vinfo[-1]
	# As of FreeSurfer v6.0.0, the final component is a githash
	if githash:
	if vinfo[3] == 'dev':
	# This will need updating when v6.0.1 comes out
	vstr = '6.0.0-dev' + githash
	elif vinfo[5][0] == 'v':
	vstr = vinfo[5][1:]
	else:
	raise RuntimeError('Unknown version string: ' + ver)
	# Retain pre-6.0.0 heuristics
	elif 'dev' in ver:
	vstr = vinfo[-1] + '-dev'
	else:
	vstr = ver.rstrip().split('-v')[-1]
	return LooseVersion(vstr)

nipype/nipype/interfaces/spm/base.py

Lines 127 to 149 in 715ad0a

	class Info(PackageInfo):
	"""Handles SPM version information
	If you use `SPMCommand.set_mlab_paths` to set alternate entries for
	matlab_cmd, paths, and use_mcr, then you will need to use the same entries
	to any call in the Info class to maintain memoization. Otherwise, it will
	default to the parameters in the `getinfo` function below.
	"""
	_path = None
	_name = None
	_command = None
	_paths = None
	_version = None
	@classmethod
	def path(klass, matlab_cmd=None, paths=None, use_mcr=None):
	klass.getinfo(matlab_cmd, paths, use_mcr)
	return klass._path
	@classmethod
	def version(klass, matlab_cmd=None, paths=None, use_mcr=None):
	klass.getinfo(matlab_cmd, paths, use_mcr)
	return klass._version

[effigies]

@mmodat Sorry to bother you, but any chance of trying to fix this for the October release?