Merge pull request #838 from djarecka/ci/pytest_nibabeltests

adding testing_pytest that removed nose (it will be used temp. for te…

Author: chrisgorgo

nibabel/testing_pytest/__init__.py

@@ -0,0 +1,223 @@
+# emacs: -*- mode: python-mode; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
+### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
+#
+#   See COPYING file distributed along with the NiBabel package for the
+#   copyright and license terms.
+#
+### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
+''' Utilities for testing '''
+
+import re
+import os
+import sys
+import warnings
+from pkg_resources import resource_filename
+from os.path import dirname, abspath, join as pjoin
+
+import numpy as np
+from numpy.testing import assert_array_equal, assert_warns
+from numpy.testing import dec
+skipif = dec.skipif
+slow = dec.slow
+
+from ..deprecated import deprecate_with_version as _deprecate_with_version
+
+
+from itertools import zip_longest
+
+
+def test_data(subdir=None, fname=None):
+    if subdir is None:
+        resource = os.path.join('tests', 'data')
+    elif subdir in ('gifti', 'nicom', 'externals'):
+        resource = os.path.join(subdir, 'tests', 'data')
+    else:
+        raise ValueError("Unknown test data directory: %s" % subdir)
+
+    if fname is not None:
+        resource = os.path.join(resource, fname)
+
+    return resource_filename('nibabel', resource)
+
+
+# set path to example data
+data_path = test_data()
+
+
+from .np_features import memmap_after_ufunc
+
+def assert_dt_equal(a, b):
+    """ Assert two numpy dtype specifiers are equal
+
+    Avoids failed comparison between int32 / int64 and intp
+    """
+    assert np.dtype(a).str == np.dtype(b).str
+
+
+def assert_allclose_safely(a, b, match_nans=True, rtol=1e-5, atol=1e-8):
+    """ Allclose in integers go all wrong for large integers
+    """
+    a = np.atleast_1d(a)  # 0d arrays cannot be indexed
+    a, b = np.broadcast_arrays(a, b)
+    if match_nans:
+        nans = np.isnan(a)
+        np.testing.assert_array_equal(nans, np.isnan(b))
+        to_test = ~nans
+    else:
+        to_test = np.ones(a.shape, dtype=bool)
+    # Deal with float128 inf comparisons (bug in numpy 1.9.2)
+    # np.allclose(np.float128(np.inf), np.float128(np.inf)) == False
+    to_test = to_test & (a != b)
+    a = a[to_test]
+    b = b[to_test]
+    if a.dtype.kind in 'ui':
+        a = a.astype(float)
+    if b.dtype.kind in 'ui':
+        b = b.astype(float)
+    assert np.allclose(a, b, rtol=rtol, atol=atol)
+
+
+def assert_arrays_equal(arrays1, arrays2):
+    """ Check two iterables yield the same sequence of arrays. """
+    for arr1, arr2 in zip_longest(arrays1, arrays2, fillvalue=None):
+        assert (arr1 is not None and arr2 is not None)
+        assert_array_equal(arr1, arr2)
+
+
+def assert_re_in(regex, c, flags=0):
+    """Assert that container (list, str, etc) contains entry matching the regex
+    """
+    if not isinstance(c, (list, tuple)):
+        c = [c]
+    for e in c:
+        if re.match(regex, e, flags=flags):
+            return
+    raise AssertionError("Not a single entry matched %r in %r" % (regex, c))
+
+
+def get_fresh_mod(mod_name=__name__):
+    # Get this module, with warning registry empty
+    my_mod = sys.modules[mod_name]
+    try:
+        my_mod.__warningregistry__.clear()
+    except AttributeError:
+        pass
+    return my_mod
+
+
+class clear_and_catch_warnings(warnings.catch_warnings):
+    """ Context manager that resets warning registry for catching warnings
+
+    Warnings can be slippery, because, whenever a warning is triggered, Python
+    adds a ``__warningregistry__`` member to the *calling* module.  This makes
+    it impossible to retrigger the warning in this module, whatever you put in
+    the warnings filters.  This context manager accepts a sequence of `modules`
+    as a keyword argument to its constructor and:
+
+    * stores and removes any ``__warningregistry__`` entries in given `modules`
+      on entry;
+    * resets ``__warningregistry__`` to its previous state on exit.
+
+    This makes it possible to trigger any warning afresh inside the context
+    manager without disturbing the state of warnings outside.
+
+    For compatibility with Python 3.0, please consider all arguments to be
+    keyword-only.
+
+    Parameters
+    ----------
+    record : bool, optional
+        Specifies whether warnings should be captured by a custom
+        implementation of ``warnings.showwarning()`` and be appended to a list
+        returned by the context manager. Otherwise None is returned by the
+        context manager. The objects appended to the list are arguments whose
+        attributes mirror the arguments to ``showwarning()``.
+
+        NOTE: nibabel difference from numpy: default is True
+
+    modules : sequence, optional
+        Sequence of modules for which to reset warnings registry on entry and
+        restore on exit
+
+    Examples
+    --------
+    >>> import warnings
+    >>> with clear_and_catch_warnings(modules=[np.core.fromnumeric]):
+    ...     warnings.simplefilter('always')
+    ...     # do something that raises a warning in np.core.fromnumeric
+    """
+    class_modules = ()
+
+    def __init__(self, record=True, modules=()):
+        self.modules = set(modules).union(self.class_modules)
+        self._warnreg_copies = {}
+        super(clear_and_catch_warnings, self).__init__(record=record)
+
+    def __enter__(self):
+        for mod in self.modules:
+            if hasattr(mod, '__warningregistry__'):
+                mod_reg = mod.__warningregistry__
+                self._warnreg_copies[mod] = mod_reg.copy()
+                mod_reg.clear()
+        return super(clear_and_catch_warnings, self).__enter__()
+
+    def __exit__(self, *exc_info):
+        super(clear_and_catch_warnings, self).__exit__(*exc_info)
+        for mod in self.modules:
+            if hasattr(mod, '__warningregistry__'):
+                mod.__warningregistry__.clear()
+            if mod in self._warnreg_copies:
+                mod.__warningregistry__.update(self._warnreg_copies[mod])
+
+
+class error_warnings(clear_and_catch_warnings):
+    """ Context manager to check for warnings as errors.  Usually used with
+    ``assert_raises`` in the with block
+
+    Examples
+    --------
+    >>> with error_warnings():
+    ...     try:
+    ...         warnings.warn('Message', UserWarning)
+    ...     except UserWarning:
+    ...         print('I consider myself warned')
+    I consider myself warned
+    """
+    filter = 'error'
+
+    def __enter__(self):
+        mgr = super(error_warnings, self).__enter__()
+        warnings.simplefilter(self.filter)
+        return mgr
+
+
+class suppress_warnings(error_warnings):
+    """ Version of ``catch_warnings`` class that suppresses warnings
+    """
+    filter = 'ignore'
+
+
+@_deprecate_with_version('catch_warn_reset is deprecated; use '
+                         'nibabel.testing.clear_and_catch_warnings.',
+                         since='2.1.0', until='3.0.0')
+class catch_warn_reset(clear_and_catch_warnings):
+    pass
+
+
+EXTRA_SET = os.environ.get('NIPY_EXTRA_TESTS', '').split(',')
+
+
+def runif_extra_has(test_str):
+    """Decorator checks to see if NIPY_EXTRA_TESTS env var contains test_str"""
+    return skipif(test_str not in EXTRA_SET,
+                  "Skip {0} tests.".format(test_str))
+
+
+def assert_arr_dict_equal(dict1, dict2):
+    """ Assert that two dicts are equal, where dicts contain arrays
+    """
+    assert set(dict1) == set(dict2)
+    for key, value1 in dict1.items():
+        value2 = dict2[key]
+        assert_array_equal(value1, value2)

nibabel/testing_pytest/np_features.py

@@ -0,0 +1,23 @@
+""" Look for changes in numpy behavior over versions
+"""
+
+import numpy as np
+
+
+def memmap_after_ufunc():
+    """ Return True if ufuncs on memmap arrays always return memmap arrays
+
+    This should be True for numpy < 1.12, False otherwise.
+
+    Memoize after first call.  We do this to avoid having to call this when
+    importing nibabel.testing, because we cannot depend on the source file
+    being present - see gh-571.
+    """
+    if memmap_after_ufunc.result is not None:
+        return memmap_after_ufunc.result
+    with open(__file__, 'rb') as fobj:
+        mm_arr = np.memmap(fobj, mode='r', shape=(10,), dtype=np.uint8)
+        memmap_after_ufunc.result = isinstance(mm_arr + 1, np.memmap)
+    return memmap_after_ufunc.result
+
+memmap_after_ufunc.result = None