This file is indexed.

/usr/lib/python2.7/dist-packages/mdp/configuration.py is in python-mdp 3.5-1.

This file is owned by root:root, with mode 0o644.

The actual contents of the file can be viewed below.

  1
  2
  3
  4
  5
  6
  7
  8
  9
 10
 11
 12
 13
 14
 15
 16
 17
 18
 19
 20
 21
 22
 23
 24
 25
 26
 27
 28
 29
 30
 31
 32
 33
 34
 35
 36
 37
 38
 39
 40
 41
 42
 43
 44
 45
 46
 47
 48
 49
 50
 51
 52
 53
 54
 55
 56
 57
 58
 59
 60
 61
 62
 63
 64
 65
 66
 67
 68
 69
 70
 71
 72
 73
 74
 75
 76
 77
 78
 79
 80
 81
 82
 83
 84
 85
 86
 87
 88
 89
 90
 91
 92
 93
 94
 95
 96
 97
 98
 99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
from future import standard_library
standard_library.install_aliases()
from builtins import zip
from builtins import str
from builtins import object
import sys
import os
import tempfile
import inspect
import mdp
from .repo_revision import get_git_revision
import io as StringIO
from future.utils import with_metaclass


__docformat__ = "restructuredtext en"

class MetaConfig(type):
    """Meta class for config object to allow for pretty printing
    of class config (as we never instantiate it)"""
    def __str__(self):
        return self.info()

    def __repr__(self):
        return self.info()

class config(with_metaclass(MetaConfig, object)):
    """Provide information about optional dependencies.

    This class should not be instantiated, it serves as a namespace
    for dependency information. This information is encoded as a
    series of attributes called ``has_<dependency>``.

    Dependency parameters are object which have a a boolean value
    (``True`` if the dependency is available). If False, they contain an
    error string which will be used in ``mdp.config.info()`` output. If
    ``True``, they contain information about the available version of
    the dependency. Those objects should be created by using the helper
    class methods `ExternalDepFound` and `ExternalDepFailed`.

    >>> bool(config.has_python)
    True

    Dependency parameters are numbered in the order of creation,
    so the output is predictable.

    The selection of the numerical backend (`numpy` or `scipy`) can be
    forced by setting the environment variable MDPNUMX.  The loading
    of an optional dependency can be inhibited by setting the
    environment variables ``MDP_DISABLE_<DEPNAME>`` to a non-empty
    value.

    The following variables are defined:
      ``MDPNUMX``
        either ``numpy`` or ``scipy``. By default the latter is used
        if available.
      ``MDP_DISABLE_PARALLEL_PYTHON``
        inhibit loading of `mdp.parallel` based on parallel python
        (module ``pp``)
      ``MDP_DISABLE_SHOGUN``
        inhibit loading of the shogun classifier
      ``MDP_DISABLE_LIBSVM``
        inhibit loading of the svm classifier
      ``MDP_DISABLE_JOBLIB``
        inhibit loading of the ``joblib`` module and `mdp.caching`
      ``MDP_DISABLE_SKLEARN``
        inhibit loading of the ``sklearn`` module
      ``MDPNSDEBUG``
        print debugging information during the import process
      ``MDP_PP_SECRET``
        set parallel python (pp) secret. If not set, and no secret is known
        to pp, a default secret will be used.
      ``MDP_DISABLE_MONKEYPATCH_PP``
        disable automatic monkeypatching of parallel python worker script,
        otherwise a work around for debian bug #620551 is activated.
    """

    _HAS_NUMBER = 0

    class _ExternalDep(object):
        def __init__(self, name, version=None, failmsg=None):
            assert (version is not None) + (failmsg is not None) == 1

            self.version = str(version) # convert e.g. exception to str
            self.failmsg = str(failmsg) if failmsg is not None else None

            global config
            self.order = config._HAS_NUMBER
            config._HAS_NUMBER += 1
            setattr(config, 'has_' + name, self)

        def __bool__(self):
            return self.failmsg is None

        def __repr__(self):
            if self:
                return self.version
            else:
                return "NOT AVAILABLE: " + self.failmsg

    @classmethod
    def ExternalDepFailed(cls, name, failmsg):
        """Inform that an optional dependency was not found.

        A new `_ExternalDep` object will be created and stored
        in `config`.

        :Parameters:
          name
            identifier of the optional dependency. This should
            be a valid python identifier, because it will be
            accessible as ``mdp.config.has_<name>`` attribute.
          failmsg
            an object convertible to ``str``, which will be displayed in
            ``mdp.config.info()`` output. This will usually be either an
            exception (e.g. ``ImportError``), or a message string.
        """
        return cls._ExternalDep(name, failmsg=failmsg)

    @classmethod
    def ExternalDepFound(cls, name, version):
        """Inform that an optional dependency was found.

        A new `_ExternalDep` object will be created and stored
        in `config`.

        :Parameters:
          name
            identifier of the optional dependency. This should
            be a valid python identifier, because it will be
            accessible as ``mdp.config.has_<name>`` attribute.
          version
            an object convertible to ``str``, which will be displayed in
            ``mdp.config.info()`` output. Something like ``'0.4.3'``.
        """
        return cls._ExternalDep(name, version=version)

    @classmethod
    def info(cls):
        """Return nicely formatted info about MDP.

        >>> print mdp.config.info()                           # doctest: +SKIP
                  python: 2.7.2.final.0
                     mdp: 3.3, MDP-3.2-9-g4bc7356+
         parallel python: 1.6.1-monkey-patched
                  shogun: v1.1.0_02ce3cd_2011-12-12_08:17_
                  libsvm: libsvm.so.3
                  joblib: 0.5.4
                 sklearn: 0.9
                    numx: scipy 0.9.0
                  symeig: scipy.linalg.eigh

        This function is used to provide the py.test report header and
        footer.
        """
        listable_features = [(f[4:].replace('_', ' '), getattr(cls, f))
                             for f in dir(cls) if f.startswith('has_')]
        maxlen = max(len(f[0]) for f in listable_features)
        listable_features = sorted(listable_features, key=lambda f: f[1].order)
        return '\n'.join('%*s: %r' % (maxlen+1, f[0], f[1])
                         for f in listable_features)

def get_numx():
    # find out the numerical extension
    # To force MDP to use one specific extension module
    # set the environment variable MDPNUMX
    # Mainly useful for testing
    USR_LABEL = os.getenv('MDPNUMX')

    # check if the variable is properly set
    if USR_LABEL and USR_LABEL not in ('numpy', 'scipy'):
        err = ("Numerical backend '%s'" % USR_LABEL +
               "not supported. Supported backends: numpy, scipy.")
        raise ImportError(err)

    numx_description = None
    numx_exception = {}

    # if variable is not set or the user wants scipy
    if USR_LABEL is None or USR_LABEL == 'scipy':
        try:
            import scipy as numx
            from scipy import (linalg as numx_linalg,
                               fftpack as numx_fft,
                               random as numx_rand,
                               version as numx_version)
            numx_description = 'scipy'
            config.ExternalDepFound('numx', 'scipy ' + numx_version.version)
        except ImportError as exc:
            if USR_LABEL:
                raise ImportError(exc)
            else:
                numx_exception['scipy'] = exc

    # if the user wants numpy or scipy was not available
    if USR_LABEL == 'numpy' or numx_description is None:
        try:
            import numpy as numx
            from numpy import (linalg as numx_linalg,
                               fft as numx_fft,
                               random as numx_rand,
                               version as numx_version)
            numx_description = 'numpy'
            config.ExternalDepFound('numx', 'numpy ' + numx_version.version)
        except ImportError as exc:
            config.ExternalDepFailed('numx', exc)
            numx_exception['numpy'] = exc

    # fail if neither scipy nor numpy could be imported
    # the test is for numx_description, not numx, because numx could
    # be imported successfully, but e.g. numx_rand could later fail.
    if numx_description is None:
        msg = ([ "Could not import any of the numeric backends.",
                 "Import errors:" ] +
               [ lab+': '+str(exc) for lab, exc in list(numx_exception.items()) ]
               + ["sys.path: " + str(sys.path)])
        raise ImportError('\n'.join(msg))

    return (numx_description, numx, numx_linalg,
            numx_fft, numx_rand, numx_version)

def get_symeig(numx_linalg):
    # if we have scipy, check if the version of
    # scipy.linalg.eigh supports the rich interface
    args = inspect.getargspec(numx_linalg.eigh)[0]
    if len(args) > 4:
        # if yes, just wrap it
        from .utils._symeig import wrap_eigh as symeig
        config.ExternalDepFound('symeig', 'scipy.linalg.eigh')
    else:
        # either we have numpy, or we have an old scipy
        # we need to use our own rich wrapper
        from .utils._symeig import _symeig_fake as symeig
        config.ExternalDepFound('symeig', 'symeig_fake')
    return symeig

def _version_too_old(version, known_good):
    """Return True iff a version is smaller than a tuple of integers.

    This method will return True only if the version string can
    confidently be said to be smaller than ``known_good``. If
    the string cannot be parsed as dot-separated-integers, ``None``
    (which is false) will be returned.

    The comparison is performed part by part, the first non-equal
    one wins.

    >>> _version_too_old('0.4.3', (0,4,3))
    False
    >>> _version_too_old('0.4.2', (0,4,3))
    True
    >>> _version_too_old('0.5.devel', (0,4,3))
    False
    >>> _version_too_old('0.4.devel', (0,4,3))
    """
    for part,expected in zip(version.split('.'), known_good):
        try:
            p = int(part)
        except ValueError:
            return None
        if p < expected:
            return True
        if p > expected:
            break
    return False

class _sys_stdout_replaced(object):
    "Replace systdout temporarily"
    def __enter__(self):
        self.sysstdout = sys.stdout
        sys.stdout = StringIO.StringIO()
        return sys.stdout
    def __exit__(self, *args):
        sys.stdout = self.sysstdout

def _pp_needs_monkeypatching():
    # only run this function the first time mdp is imported
    # otherwise reload(mdp) breaks

    if not hasattr(mdp, '_pp_needs_monkeypatching'):
        # check if we are on one of those broken system were
        # parallel python is affected by
        # http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=620551
        # this is a minimal example to reproduce the problem
        # XXX IMPORTANT XXX
        # This function only works once, i.e. at import
        # if you attempt to call it again afterwards,
        # it does not work [pp does not print the error twice]

        # we need to hijack stdout here, because pp does not raise
        # exceptions: it writes to stdout directly!!!

        # pp stuff
        import pp
        server = pp.Server()
        with _sys_stdout_replaced() as capture:
            try:
                server.submit(lambda: None, (), (), ('numpy',))()
            except TypeError:
                # our py2&3 futurize compatibility breaks this
                # But given that bug 620551 has been fixed,
                # we can safely ignore this error
                pass
            server.destroy()

        # read error from hijacked stdout
        error = capture.getvalue()
        mdp._pp_needs_monkeypatching = 'ImportError' in error

    return mdp._pp_needs_monkeypatching

def set_configuration():
    # set python version
    config.ExternalDepFound('python', '.'.join([str(x)
                                                for x in sys.version_info]))
    version = mdp.__version__
    if mdp.__revision__:
        version += ', ' + mdp.__revision__
    config.ExternalDepFound('mdp', version)

    # parallel python dependency
    try:
        import pp
        # set pp secret if not there already
        # (workaround for debian patch to pp that disables pp's default password)
        pp_secret = os.getenv('MDP_PP_SECRET') or 'mdp-pp-support-password'
        # module 'user' has been deprecated since python 2.6 and deleted
        # completely as of python 3.0.
        # Basically pp can not work on python 3 at the moment.
        import user
        if not hasattr(user, 'pp_secret'):
            user.pp_secret = pp_secret
    except ImportError as exc:
        config.ExternalDepFailed('parallel_python', exc)
    else:
        if os.getenv('MDP_DISABLE_PARALLEL_PYTHON'):
            config.ExternalDepFailed('parallel_python', 'disabled')
        else:
            # even if we can import pp, starting the server may still fail
            # for example with:
            # OSError: [Errno 12] Cannot allocate memory
            try:
                server = pp.Server()
                server.destroy()
            except Exception as exc:
                # no idea what exception the pp server may raise
                # we need to catch all here...
                config.ExternalDepFailed('parallel_python', exc)
            else:
                if _pp_needs_monkeypatching():
                    if os.getenv('MDP_DISABLE_MONKEYPATCH_PP'):
                        config.ExternalDepFailed('parallel_python', pp.version +
                                                 ' broken on Debian')
                    else:
                        config.ExternalDepFound('parallel_python', pp.version +
                                                '-monkey-patched')
                        config.pp_monkeypatch_dirname = tempfile.gettempdir()
                else:
                    config.ExternalDepFound('parallel_python', pp.version)

    # shogun
    try:
        import shogun
        from shogun import (Kernel as sgKernel,
                            Features as sgFeatures,
                            Classifier as sgClassifier)
    except ImportError as exc:
        config.ExternalDepFailed('shogun', exc)
    else:
        if os.getenv('MDP_DISABLE_SHOGUN'):
            config.ExternalDepFailed('shogun', 'disabled')
        else:
            # From now on just support shogun < 2.0
            # Between 0.10 to 1.0 or beyond there are too many API changes...
            try:
                version = sgKernel.Version_get_version_release()
            except AttributeError:
                config.ExternalDepFailed('shogun',
                                         'only shogun v1 is supported')
            else:
                if not version.startswith('v1.'):
                    config.ExternalDepFailed('shogun',
                                             'only shogun v1 is supported')
                else:
                    config.ExternalDepFound('shogun', version)

    # libsvm
    try:
        import svm as libsvm
        libsvm.libsvm
    except ImportError as exc:
        config.ExternalDepFailed('libsvm', exc)
    except AttributeError as exc:
        config.ExternalDepFailed('libsvm', 'libsvm version >= 2.91 required')
    else:
        if os.getenv('MDP_DISABLE_LIBSVM'):
            config.ExternalDepFailed('libsvm', 'disabled')
        else:
            config.ExternalDepFound('libsvm', libsvm.libsvm._name)

    # joblib
    try:
        import joblib
    except ImportError as exc:
        config.ExternalDepFailed('joblib', exc)
    else:
        version = joblib.__version__
        if os.getenv('MDP_DISABLE_JOBLIB'):
            config.ExternalDepFailed('joblib', 'disabled')
        elif _version_too_old(version, (0,4,3)):
            config.ExternalDepFailed('joblib',
                                     'version %s is too old' % version)
        else:
            config.ExternalDepFound('joblib', version)

    # sklearn
    try:
        try:
            import sklearn
        except ImportError:
            import scikits.learn as sklearn
        version = sklearn.__version__
    except ImportError as exc:
        config.ExternalDepFailed('sklearn', exc)
    except AttributeError as exc:
        config.ExternalDepFailed('sklearn', exc)
    else:
        if os.getenv('MDP_DISABLE_SKLEARN'):
            config.ExternalDepFailed('sklearn', 'disabled')
        elif _version_too_old(version, (0,6)):
            config.ExternalDepFailed('sklearn',
                                     'version %s is too old' % version)
        else:
            config.ExternalDepFound('sklearn', version)