python-mvpa 0.4.8-1 / usr / share / pyshared / mvpa / base / dochelpers.py

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#
#   See COPYING file distributed along with the PyMVPA package for the
#   copyright and license terms.
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"""Various helpers to improve docstrings and textual output"""

__docformat__ = 'restructuredtext'

import re, textwrap

# for table2string
import numpy as N
from math import ceil
from StringIO import StringIO
from mvpa import cfg

from mvpa.base import externals
if __debug__:
    from mvpa.base import debug

__add_init2doc = False
__in_ipython = externals.exists('running ipython env')
# if ran within IPython -- might need to add doc to init
if __in_ipython:
    __rst_mode = 0                           # either to do ReST links at all
    _rst_sep = ""
    _rst_sep2 = ""
    from IPython import Release
    # XXX figure out exact version when init doc started to be added to class
    # description
    if Release.version <= '0.8.1':
        __add_init2doc = True
else:
    __rst_mode = 1
    _rst_sep = "`"
    _rst_sep2 = ":"

def _rst(s, snotrst=''):
    """Produce s only in __rst mode"""
    if __rst_mode:
        return s
    else:
        return snotrst

def rstUnderline(text, markup):
    """Add and underline RsT string matching the length of the given string.
    """
    return text + '\n' + markup * len(text)


def singleOrPlural(single, plural, n):
    """Little helper to spit out single or plural version of a word.
    """
    ni = int(n)
    if ni > 1 or ni == 0:
        # 1 forest, 2 forests, 0 forests
        return plural
    else:
        return single


def handleDocString(text, polite=True):
    """Take care of empty and non existing doc strings."""
    if text == None or not len(text):
        if polite:
            return 'No documentation found. Sorry!'
        else:
            return ''
    else:
        # Problem is that first line might often have no offset, so might
        # need to be ignored from dedent call
        if not text.startswith(' '):
            lines = text.split('\n')
            text2 = '\n'.join(lines[1:])
            return lines[0] + "\n" + textwrap.dedent(text2)
        else:
            return textwrap.dedent(text)


def _indent(text, istr='  '):
    """Simple indenter
    """
    return '\n'.join(istr + s for s in text.split('\n'))

__parameters_str_re = re.compile("[\n^]\s*:?Parameters?:?\s*\n")
"""regexp to match :Parameter: and :Parameters: stand alone in a line"""

def _splitOutParametersStr(initdoc):
    """Split documentation into (header, parameters, suffix)

    :Parameters:
      initdoc : string
        The documentation string
    """

    # TODO: bind it to the only word in the line
    p_res = __parameters_str_re.search(initdoc)
    if p_res is None:
        result = initdoc, "", ""
    else:
        # Could have been accomplished also via re.match

        # where new line is after :Parameters:
        # parameters header index
        ph_i = p_res.start()

        # parameters body index
        pb_i = p_res.end()

        # end of parameters
        try:
            pe_i = initdoc.index('\n\n', pb_i)
        except ValueError:
            pe_i = len(initdoc)

        result = initdoc[:ph_i].rstrip('\n '), \
                 initdoc[pb_i:pe_i], initdoc[pe_i:]

    # XXX a bit of duplication of effort since handleDocString might
    # do splitting internally
    return [handleDocString(x, polite=False).strip('\n') for x in result]


__re_params = re.compile('(?:\n\S.*?)+$')
__re_spliter1 = re.compile('(?:\n|\A)(?=\S)')
__re_spliter2 = re.compile('[\n:]')
def _parseParameters(paramdoc):
    """Parse parameters and return list of (name, full_doc_string)

    It is needed to remove multiple entries for the same parameter
    like it could be with adding parameters from the parent class

    It assumes that previousely parameters were unwrapped, so their
    documentation starts at the begining of the string, like what
    should it be after _splitOutParametersStr
    """
    entries = __re_spliter1.split(paramdoc)
    result = [(__re_spliter2.split(e)[0].strip(), e)
              for e in entries if e != '']
    if __debug__:
        debug('DOCH', 'parseParameters: Given "%s", we split into %s' %
              (paramdoc, result))
    return result


def enhancedDocString(item, *args, **kwargs):
    """Generate enhanced doc strings for various items.

    :Parameters:
      item : basestring or class
        What object requires enhancing of documentation
      *args : list
        Includes base classes to look for parameters, as well, first item
        must be a dictionary of locals if item is given by a string
      force_extend : bool
        Either to force looking for the documentation in the parents.
        By default force_extend = False, and lookup happens only if kwargs
        is one of the arguments to the respective function (e.g. item.__init__)
      skip_params : list of basestring
        List of parameters (in addition to [kwargs]) which should not
        be added to the documentation of the class.

    It is to be used from a collector, ie whenever class is already created
    """
    # Handling of arguments
    if len(kwargs):
        if set(kwargs.keys()).issubset(set(['force_extend'])):
            raise ValueError, "Got unknown keyword arguments (smth among %s)" \
                  " in enhancedDocString." % kwargs
    force_extend = kwargs.get('force_extend', False)
    skip_params = kwargs.get('skip_params', [])

    # XXX make it work also not only with classes but with methods as well
    if isinstance(item, basestring):
        if len(args)<1 or not isinstance(args[0], dict):
            raise ValueError, \
                  "Please provide locals for enhancedDocString of %s" % item
        name = item
        lcl = args[0]
        args = args[1:]
    elif hasattr(item, "im_class"):
        # bound method
        raise NotImplementedError, \
              "enhancedDocString is not yet implemented for methods"
    elif hasattr(item, "__name__"):
        name = item.__name__
        lcl = item.__dict__
    else:
        raise ValueError, "Don't know how to extend docstring for %s" % item

    # check whether docstring magic is requested or not
    if not cfg.getboolean('doc', 'pimp docstrings', True):
        return  lcl['__doc__']

    #return lcl['__doc__']
    rst_lvlmarkup = ["=", "-", "_"]

    # would then be called for any child... ok - ad hoc for SVM???
    if hasattr(item, '_customizeDoc') and name=='SVM':
        item._customizeDoc()

    initdoc = ""
    if lcl.has_key('__init__'):
        func = lcl['__init__']
        initdoc = func.__doc__

        # either to extend arguments
        # do only if kwargs is one of the arguments
        # in python 2.5 args are no longer in co_names but in varnames
        extend_args = force_extend or \
                      'kwargs' in (func.func_code.co_names +
                                   func.func_code.co_varnames)

        if __debug__ and not extend_args:
            debug('DOCH', 'Not extending parameters for %s' % name)

        if initdoc is None:
            initdoc = "Initialize instance of %s" % name

        initdoc, params, suffix = _splitOutParametersStr(initdoc)

        if lcl.has_key('_paramsdoc'):
            params += '\n' + handleDocString(lcl['_paramsdoc'])

        params_list = _parseParameters(params)
        known_params = set([i[0] for i in params_list])
        # no need for placeholders
        skip_params = set(skip_params + ['kwargs', '**kwargs'])

        # XXX we do evil check here, refactor code to separate
        #     regressions out of the classifiers, and making
        #     retrainable flag not available for those classes which
        #     can't actually do retraining. Although it is not
        #     actually that obvious for Meta Classifiers
        if hasattr(item, '_clf_internals'):
            clf_internals = item._clf_internals
            skip_params.update([i for i in ('regression', 'retrainable')
                                if not (i in clf_internals)])

        known_params.update(skip_params)
        if extend_args:
            # go through all the parents and obtain their init parameters
            parent_params_list = []
            for i in args:
                if hasattr(i, '__init__'):
                    # XXX just assign within a class to don't redo without need
                    initdoc_ = i.__init__.__doc__
                    if initdoc_ is None:
                        continue
                    splits_ = _splitOutParametersStr(initdoc_)
                    params_ = splits_[1]
                    parent_params_list += _parseParameters(params_.lstrip())

            # extend with ones which are not known to current init
            for i, v in parent_params_list:
                if not (i in known_params):
                    params_list += [(i, v)]
                    known_params.update([i])

        # if there are parameters -- populate the list
        if len(params_list):
            params_ = '\n'.join([i[1].rstrip() for i in params_list
                                 if not i[0] in skip_params])
            initdoc += "\n\n%sParameters%s\n" % ( (_rst_sep2,)*2 ) \
                       + _indent(params_)

        if suffix != "":
            initdoc += "\n\n" + suffix

        initdoc = handleDocString(initdoc)

        # Finally assign generated doc to the constructor
        lcl['__init__'].__doc__ = initdoc

    docs = [ handleDocString(lcl['__doc__']) ]

    # Optionally populate the class documentation with it
    if __add_init2doc and initdoc != "":
        docs += [ rstUnderline('Constructor information for `%s` class' % name,
                               rst_lvlmarkup[2]),
                  initdoc ]

    # Add information about the states if available
    if lcl.has_key('_statesdoc'):
        # no indent is necessary since states list must be already indented
        docs += [_rst('.. note::\n  ') + 'Available state variables:',
                     handleDocString(item._statesdoc)]

    if len(args):
        bc_intro = _rst('  ') + 'Please refer to the documentation of the ' \
                   'base %s for more information:' \
                   % (singleOrPlural('class', 'classes', len(args)))

        docs += [_rst('\n.. seealso::'),
                 bc_intro,
                 '  ' + ',\n  '.join(['%s%s.%s%s' % (_rst(':class:`~'),
                                                      i.__module__,
                                                      i.__name__,
                                                      _rst_sep)
                                      for i in args])
                ]

    itemdoc = '\n\n'.join(docs)
    # remove some bogus new lines -- never 3 empty lines in doc are useful
    result = re.sub("\s*\n\s*\n\s*\n", "\n\n", itemdoc)

    return result


def table2string(table, out=None):
    """Given list of lists figure out their common widths and print to out

    :Parameters:
      table : list of lists of strings
        What is aimed to be printed
      out : None or stream
        Where to print. If None -- will print and return string

    :Returns:
      string if out was None
    """

    print2string = out is None
    if print2string:
        out = StringIO()

    # equalize number of elements in each row
    Nelements_max = max(len(x) for x in table)
    for i, table_ in enumerate(table):
        table[i] += [''] * (Nelements_max - len(table_))

    # figure out lengths within each column
    atable = N.asarray(table)
    markup_strip = re.compile('^@[lrc]')
    col_width = [ max( [len(markup_strip.sub('', x))
                        for x in column] ) for column in atable.T ]
    string = ""
    for i, table_ in enumerate(table):
        string_ = ""
        for j, item in enumerate(table_):
            item = str(item)
            if item.startswith('@'):
                align = item[1]
                item = item[2:]
                if not align in ['l', 'r', 'c']:
                    raise ValueError, 'Unknown alignment %s. Known are l,r,c'
            else:
                align = 'c'

            NspacesL = ceil((col_width[j] - len(item))/2.0)
            NspacesR = col_width[j] - NspacesL - len(item)

            if align == 'c':
                pass
            elif align == 'l':
                NspacesL, NspacesR = 0, NspacesL + NspacesR
            elif align == 'r':
                NspacesL, NspacesR = NspacesL + NspacesR, 0
            else:
                raise RuntimeError, 'Should not get here with align=%s' % align

            string_ += "%%%ds%%s%%%ds " \
                       % (NspacesL, NspacesR) % ('', item, '')
        string += string_.rstrip() + '\n'
    out.write(string)

    if print2string:
        value = out.getvalue()
        out.close()
        return value