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Merge pull request #2797 from oesteban/maint/strip-help-from-interfaces
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[MAINT] Offload interfaces with help formatting
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@effigies
effigies authored Dec 14, 2018
2 parents 8173dcf + 7861a4a commit fbed1f3
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Showing 6 changed files with 199 additions and 198 deletions.
3 changes: 1 addition & 2 deletions nipype/interfaces/base/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -22,5 +22,4 @@
OutputMultiObject, InputMultiObject,
OutputMultiPath, InputMultiPath)

from .support import (Bunch, InterfaceResult, load_template,
NipypeInterfaceError)
from .support import (Bunch, InterfaceResult, NipypeInterfaceError)
204 changes: 29 additions & 175 deletions nipype/interfaces/base/core.py
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Original file line number Diff line number Diff line change
Expand Up @@ -20,18 +20,17 @@
from copy import deepcopy
from datetime import datetime as dt
import os
import re
import platform
import subprocess as sp
import shlex
import sys
from textwrap import wrap
import simplejson as json
from dateutil.parser import parse as parseutc
from future import standard_library

from ... import config, logging, LooseVersion
from ...utils.provenance import write_provenance
from ...utils.misc import trim, str2bool, rgetcwd
from ...utils.misc import str2bool, rgetcwd
from ...utils.filemanip import (FileNotFoundError, split_filename,
which, get_dependencies)
from ...utils.subprocess import run_command
Expand All @@ -42,9 +41,9 @@
from .specs import (BaseInterfaceInputSpec, CommandLineInputSpec,
StdOutCommandLineInputSpec, MpiCommandLineInputSpec,
get_filecopy_info)
from .support import (Bunch, InterfaceResult, NipypeInterfaceError)
from .support import (Bunch, InterfaceResult, NipypeInterfaceError,
format_help)

from future import standard_library
standard_library.install_aliases()

iflogger = logging.getLogger('nipype.interface')
Expand All @@ -68,47 +67,42 @@ class Interface(object):

input_spec = None # A traited input specification
output_spec = None # A traited output specification

# defines if the interface can reuse partial results after interruption
_can_resume = False
_can_resume = False # See property below
_always_run = False # See property below

@property
def can_resume(self):
"""Defines if the interface can reuse partial results after interruption.
Only applies to interfaces being run within a workflow context."""
return self._can_resume

# should the interface be always run even if the inputs were not changed?
_always_run = False

@property
def always_run(self):
"""Should the interface be always run even if the inputs were not changed?
Only applies to interfaces being run within a workflow context."""
return self._always_run

def __init__(self, **inputs):
"""Initialize command with given args and inputs."""
raise NotImplementedError

@classmethod
def help(cls):
""" Prints class help"""
raise NotImplementedError

@classmethod
def _inputs_help(cls):
""" Prints inputs help"""
raise NotImplementedError

@classmethod
def _outputs_help(cls):
""" Prints outputs help"""
@property
def version(self):
"""interfaces should implement a version property"""
raise NotImplementedError

@classmethod
def _outputs(cls):
""" Initializes outputs"""
raise NotImplementedError

@property
def version(self):
@classmethod
def help(cls, returnhelp=False):
""" Prints class help """
allhelp = format_help(cls)
if returnhelp:
return allhelp
print(allhelp)
return None # R1710

def __init__(self):
"""Subclasses must implement __init__"""
raise NotImplementedError

def run(self):
Expand Down Expand Up @@ -190,142 +184,6 @@ def __init__(self, from_file=None, resource_monitor=None,
for name, value in list(inputs.items()):
setattr(self.inputs, name, value)

@classmethod
def help(cls, returnhelp=False):
""" Prints class help
"""

if cls.__doc__:
# docstring = cls.__doc__.split('\n')
# docstring = [trim(line, '') for line in docstring]
docstring = trim(cls.__doc__).split('\n') + ['']
else:
docstring = ['']

allhelp = '\n'.join(docstring + cls._inputs_help(
) + [''] + cls._outputs_help() + [''] + cls._refs_help() + [''])
if returnhelp:
return allhelp
else:
print(allhelp)

@classmethod
def _refs_help(cls):
""" Prints interface references.
"""
if not cls.references_:
return []

helpstr = ['References::']

for r in cls.references_:
helpstr += ['{}'.format(r['entry'])]

return helpstr

@classmethod
def _get_trait_desc(self, inputs, name, spec):
desc = spec.desc
xor = spec.xor
requires = spec.requires
argstr = spec.argstr

manhelpstr = ['\t%s' % name]

type_info = spec.full_info(inputs, name, None)

default = ''
if spec.usedefault:
default = ', nipype default value: %s' % str(
spec.default_value()[1])
line = "(%s%s)" % (type_info, default)

manhelpstr = wrap(
line,
70,
initial_indent=manhelpstr[0] + ': ',
subsequent_indent='\t\t ')

if desc:
for line in desc.split('\n'):
line = re.sub("\s+", " ", line)
manhelpstr += wrap(
line, 70, initial_indent='\t\t', subsequent_indent='\t\t')

if argstr:
pos = spec.position
if pos is not None:
manhelpstr += wrap(
'flag: %s, position: %s' % (argstr, pos),
70,
initial_indent='\t\t',
subsequent_indent='\t\t')
else:
manhelpstr += wrap(
'flag: %s' % argstr,
70,
initial_indent='\t\t',
subsequent_indent='\t\t')

if xor:
line = '%s' % ', '.join(xor)
manhelpstr += wrap(
line,
70,
initial_indent='\t\tmutually_exclusive: ',
subsequent_indent='\t\t ')

if requires:
others = [field for field in requires if field != name]
line = '%s' % ', '.join(others)
manhelpstr += wrap(
line,
70,
initial_indent='\t\trequires: ',
subsequent_indent='\t\t ')
return manhelpstr

@classmethod
def _inputs_help(cls):
""" Prints description for input parameters
"""
helpstr = ['Inputs::']

inputs = cls.input_spec()
if len(list(inputs.traits(transient=None).items())) == 0:
helpstr += ['', '\tNone']
return helpstr

manhelpstr = ['', '\t[Mandatory]']
mandatory_items = inputs.traits(mandatory=True)
for name, spec in sorted(mandatory_items.items()):
manhelpstr += cls._get_trait_desc(inputs, name, spec)

opthelpstr = ['', '\t[Optional]']
for name, spec in sorted(inputs.traits(transient=None).items()):
if name in mandatory_items:
continue
opthelpstr += cls._get_trait_desc(inputs, name, spec)

if manhelpstr:
helpstr += manhelpstr
if opthelpstr:
helpstr += opthelpstr
return helpstr

@classmethod
def _outputs_help(cls):
""" Prints description for output parameters
"""
helpstr = ['Outputs::', '']
if cls.output_spec:
outputs = cls.output_spec()
for name, spec in sorted(outputs.traits(transient=None).items()):
helpstr += cls._get_trait_desc(outputs, name, spec)
if len(helpstr) == 2:
helpstr += ['\tNone']
return helpstr

def _outputs(self):
""" Returns a bunch containing output fields for the class
"""
Expand Down Expand Up @@ -645,7 +503,7 @@ def save_inputs_to_json(self, json_file):
A convenient way to save current inputs to a JSON file.
"""
inputs = self.inputs.get_traitsfree()
iflogger.debug('saving inputs {}', inputs)
iflogger.debug('saving inputs %s', inputs)
with open(json_file, 'w' if PY3 else 'wb') as fhandle:
json.dump(inputs, fhandle, indent=4, ensure_ascii=False)

Expand Down Expand Up @@ -777,14 +635,6 @@ def set_default_terminal_output(cls, output_type):
raise AttributeError(
'Invalid terminal output_type: %s' % output_type)

@classmethod
def help(cls, returnhelp=False):
allhelp = 'Wraps command **{cmd}**\n\n{help}'.format(
cmd=cls._cmd, help=super(CommandLine, cls).help(returnhelp=True))
if returnhelp:
return allhelp
print(allhelp)

def __init__(self, command=None, terminal_output=None, **inputs):
super(CommandLine, self).__init__(**inputs)
self._environ = None
Expand All @@ -804,6 +654,10 @@ def __init__(self, command=None, terminal_output=None, **inputs):
@property
def cmd(self):
"""sets base command, immutable"""
if not self._cmd:
raise NotImplementedError(
'CommandLineInterface should wrap an executable, but '
'none has been set.')
return self._cmd

@property
Expand Down
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