Merge pull request #857 from effigies/fix/expired_deprecations

FIX: Validate ExpiredDeprecationErrors

Author: effigies

nibabel/pkg_info.py

@@ -22,14 +22,19 @@ def _cmp(a, b):
 
 
 def cmp_pkg_version(version_str, pkg_version_str=__version__):
-    """ Compare `version_str` to current package version
+    """ Compare ``version_str`` to current package version
 
     To be valid, a version must have a numerical major version followed by a
     dot, followed by a numerical minor version.  It may optionally be followed
     by a dot and a numerical micro version, and / or by an "extra" string.
-    *Any* extra string labels the version as pre-release, so `1.2.0somestring`
-    compares as prior to (pre-release for) `1.2.0`, where `somestring` can be
-    any string.
+    The extra string may further contain a "+". Any value to the left of a "+"
+    labels the version as pre-release, while values to the right indicate a
+    post-release relative to the values to the left. That is,
+    ``1.2.0+1`` is post-release for ``1.2.0``, while ``1.2.0rc1+1`` is
+    post-release for ``1.2.0rc1`` and pre-release for ``1.2.0``.
+
+    This is an approximation of `PEP-440`_, and future versions will fully
+    implement PEP-440.
 
     Parameters
     ----------
@@ -50,15 +55,38 @@ def cmp_pkg_version(version_str, pkg_version_str=__version__):
     1
     >>> cmp_pkg_version('1.2.0dev', '1.2.0')
     -1
+    >>> cmp_pkg_version('1.2.0dev', '1.2.0rc1')
+    -1
+    >>> cmp_pkg_version('1.2.0rc1', '1.2.0')
+    -1
+    >>> cmp_pkg_version('1.2.0rc1+1', '1.2.0rc1')
+    1
+    >>> cmp_pkg_version('1.2.0rc1+1', '1.2.0')
+    -1
+
+    .. _`PEP-440`: https://www.python.org/dev/peps/pep-0440/
     """
     version, extra = _parse_version(version_str)
     pkg_version, pkg_extra = _parse_version(pkg_version_str)
-    if version != pkg_version:
-        return _cmp(StrictVersion(version), StrictVersion(pkg_version))
-    return (0 if extra == pkg_extra
-            else 1 if extra == ''
-            else -1 if pkg_extra == ''
-            else _cmp(extra, pkg_extra))
+
+    # Normalize versions
+    quick_check = _cmp(StrictVersion(version), StrictVersion(pkg_version))
+    # Nothing further to check
+    if quick_check != 0 or extra == pkg_extra == '':
+        return quick_check
+
+    # Before + is pre-release, after + is additional increment
+    pre, _, post = extra.partition('+')
+    pkg_pre, _, pkg_post = pkg_extra.partition('+')
+    quick_check = _cmp(pre, pkg_pre)
+    if quick_check != 0:  # Excludes case where pre and pkg_pre == ''
+        # Pre-releases are ordered but strictly less than non-pre
+        return (1 if pre == ''
+                else -1 if pkg_pre == ''
+                else quick_check)
+
+    # All else being equal, compare additional information lexically
+    return _cmp(post, pkg_post)
 
 
 def pkg_commit_hash(pkg_path=None):

nibabel/tests/test_arrayproxy.py

@@ -112,9 +112,6 @@ def test_tuplespec():
                          ):
         assert_array_equal(getattr(ap_header, method)(*args),
                            getattr(ap_tuple, method)(*args))
-    # Tuple-defined ArrayProxies have no header to store
-    with warnings.catch_warnings():
-        assert_true(ap_tuple.header is None)
     # Partial tuples of length 2-4 are also valid
     for n in range(2, 5):
         ArrayProxy(bio, tuple_spec[:n])
@@ -141,10 +138,6 @@ def test_nifti1_init():
     ap = ArrayProxy(bio, hdr)
     assert_true(ap.file_like == bio)
     assert_equal(ap.shape, shape)
-    # Check there has been a copy of the header
-    with warnings.catch_warnings():
-        warnings.simplefilter("ignore")
-        assert_false(ap.header is hdr)
     # Get the data
     assert_array_equal(np.asarray(ap), arr * 2.0 + 10)
     with InTemporaryDirectory():

nibabel/tests/test_image_api.py

@@ -47,6 +47,7 @@
 from numpy.testing import assert_almost_equal, assert_array_equal, assert_warns, assert_allclose
 from ..testing import clear_and_catch_warnings
 from ..tmpdirs import InTemporaryDirectory
+from ..deprecator import ExpiredDeprecationError
 
 from .test_api_validators import ValidateAPI
 from .test_helpers import (bytesio_round_trip, bytesio_filemap,
@@ -422,10 +423,8 @@ def validate_ndim(self, imaker, params):
     def validate_shape_deprecated(self, imaker, params):
         # Check deprecated get_shape API
         img = imaker()
-        with clear_and_catch_warnings() as w:
-            warnings.simplefilter('always', DeprecationWarning)
-            assert_equal(img.get_shape(), params['shape'])
-            assert_equal(len(w), 1)
+        with assert_raises(ExpiredDeprecationError):
+            img.get_shape()
 
     def validate_mmap_parameter(self, imaker, params):
         img = imaker()

nibabel/tests/test_minc1.py

@@ -26,6 +26,7 @@
 from ..tmpdirs import InTemporaryDirectory
 from ..testing import (assert_true, assert_equal, assert_false, assert_raises, assert_warns,
                        assert_array_equal, data_path, clear_and_catch_warnings)
+from ..deprecator import ExpiredDeprecationError
 
 from . import test_spatialimages as tsi
 from .test_fileslice import slicer_samples
@@ -105,25 +106,16 @@ def test_old_namespace():
     arr = np.arange(24).reshape((2, 3, 4))
     aff = np.diag([2, 3, 4, 1])
 
-    with clear_and_catch_warnings() as warns:
-        from .. import Minc1Image, MincImage
-        assert_equal(warns, [])
-        # But the old named import, imported from new, is not the same
-        assert_false(Minc1Image is MincImage)
-        assert_equal(warns, [])
-        # Create object using old name
-        mimg = MincImage(arr, aff)
-        # Call to create object created warning
-        assert_equal(warns.pop(0).category, FutureWarning)
-        assert_array_equal(mimg.get_fdata(), arr)
-        # Another old name
-        from ..minc1 import MincFile, Minc1File
-        assert_false(MincFile is Minc1File)
+    from .. import Minc1Image, MincImage
+    assert_false(Minc1Image is MincImage)
+    with assert_raises(ExpiredDeprecationError):
+        MincImage(arr, aff)
         assert_equal(warns, [])
+    # Another old name
+    from ..minc1 import MincFile, Minc1File
+    assert_false(MincFile is Minc1File)
+    with assert_raises(ExpiredDeprecationError):
         mf = MincFile(netcdf_file(EG_FNAME))
-        # Call to create object created warning
-        assert_equal(warns.pop(0).category, FutureWarning)
-        assert_equal(mf.get_data_shape(), (10, 20, 20))
 
 
 class _TestMincFile(object):

nibabel/tests/test_pkg_info.py

@@ -63,6 +63,14 @@ def test_cmp_pkg_version():
                                        ('1.2.1rc', '1.2.1rc1', -1),
                                        ('1.2.1b', '1.2.1a', 1),
                                        ('1.2.1a', '1.2.1b', -1),
+                                       ('1.2.0+1', '1.2', 1),
+                                       ('1.2', '1.2.0+1', -1),
+                                       ('1.2.1+1', '1.2.1', 1),
+                                       ('1.2.1', '1.2.1+1', -1),
+                                       ('1.2.1rc1+1', '1.2.1', -1),
+                                       ('1.2.1', '1.2.1rc1+1', 1),
+                                       ('1.2.1rc1+1', '1.2.1+1', -1),
+                                       ('1.2.1+1', '1.2.1rc1+1', 1),
                                       ):
         assert_equal(cmp_pkg_version(test_ver, pkg_ver), exp_out)
     assert_raises(ValueError, cmp_pkg_version, 'foo.2')

nibabel/tests/test_proxy_api.py

@@ -58,6 +58,7 @@
 from numpy.testing import assert_almost_equal, assert_array_equal, assert_allclose
 
 from ..testing import data_path as DATA_PATH, assert_dt_equal, clear_and_catch_warnings
+from ..deprecator import ExpiredDeprecationError
 
 from ..tmpdirs import InTemporaryDirectory
 
@@ -324,12 +325,8 @@ def validate_slope_inter_offset(self, pmaker, params):
 
     def validate_deprecated_header(self, pmaker, params):
         prox, fio, hdr = pmaker()
-        with warnings.catch_warnings(record=True) as warns:
-            warnings.simplefilter("always")
-            # Header is a copy of original
-            assert_false(prox.header is hdr)
-            assert_equal(prox.header, hdr)
-            assert_equal(warns.pop(0).category, DeprecationWarning)
+        with assert_raises(ExpiredDeprecationError):
+            prox.header
 
 
 class TestSpm99AnalyzeProxyAPI(TestAnalyzeProxyAPI):

nibabel/tests/test_scaling.py

@@ -11,11 +11,12 @@
 import numpy as np
 
 from io import BytesIO
-from ..volumeutils import (calculate_scale, scale_min_max, finite_range,
-                           apply_read_scaling, array_to_file, array_from_file)
+from ..volumeutils import finite_range, apply_read_scaling, array_to_file, array_from_file
 from ..casting import type_info
 from ..testing import suppress_warnings
 
+from .test_volumeutils import _calculate_scale
+
 from numpy.testing import (assert_array_almost_equal, assert_array_equal)
 
 from nose.tools import (assert_true, assert_equal, assert_raises,
@@ -26,56 +27,6 @@
 DEBUG = True
 
 
-def test_scale_min_max():
-    mx_dt = np.maximum_sctype(np.float)
-    for tp in np.sctypes['uint'] + np.sctypes['int']:
-        info = np.iinfo(tp)
-        # Need to pump up to max fp type to contain python longs
-        imin = np.array(info.min, dtype=mx_dt)
-        imax = np.array(info.max, dtype=mx_dt)
-        value_pairs = (
-            (0, imax),
-            (imin, 0),
-            (imin, imax),
-            (1, 10),
-            (-1, -1),
-            (1, 1),
-            (-10, -1),
-            (-100, 10))
-        for mn, mx in value_pairs:
-            # with intercept
-            scale, inter = scale_min_max(mn, mx, tp, True)
-            if mx - mn:
-                assert_array_almost_equal, (mx - inter) / scale, imax
-                assert_array_almost_equal, (mn - inter) / scale, imin
-            else:
-                assert_equal, (scale, inter), (1.0, mn)
-            # without intercept
-            if imin == 0 and mn < 0 and mx > 0:
-                (assert_raises, ValueError,
-                 scale_min_max, mn, mx, tp, False)
-                continue
-            scale, inter = scale_min_max(mn, mx, tp, False)
-            assert_equal, inter, 0.0
-            if mn == 0 and mx == 0:
-                assert_equal, scale, 1.0
-                continue
-            sc_mn = mn / scale
-            sc_mx = mx / scale
-            assert_true, sc_mn >= imin
-            assert_true, sc_mx <= imax
-            if imin == 0:
-                if mx > 0:  # numbers all +ve
-                    assert_array_almost_equal, mx / scale, imax
-                else:  # numbers all -ve
-                    assert_array_almost_equal, mn / scale, imax
-                continue
-            if abs(mx) >= abs(mn):
-                assert_array_almost_equal, mx / scale, imax
-            else:
-                assert_array_almost_equal, mn / scale, imin
-
-
 def test_finite_range():
     # Finite range utility function
     for in_arr, res in (
@@ -122,26 +73,6 @@ def test_finite_range():
     assert_raises(TypeError, finite_range, a)
 
 
-def test_calculate_scale():
-    # Test for special cases in scale calculation
-    npa = np.array
-    # Here the offset handles it
-    res = calculate_scale(npa([-2, -1], dtype=np.int8), np.uint8, True)
-    assert_equal(res, (1.0, -2.0, None, None))
-    # Not having offset not a problem obviously
-    res = calculate_scale(npa([-2, -1], dtype=np.int8), np.uint8, 0)
-    assert_equal(res, (-1.0, 0.0, None, None))
-    # Case where offset handles scaling
-    res = calculate_scale(npa([-1, 1], dtype=np.int8), np.uint8, 1)
-    assert_equal(res, (1.0, -1.0, None, None))
-    # Can't work for no offset case
-    assert_raises(ValueError,
-                  calculate_scale, npa([-1, 1], dtype=np.int8), np.uint8, 0)
-    # Offset trick can't work when max is out of range
-    res = calculate_scale(npa([-1, 255], dtype=np.int16), np.uint8, 1)
-    assert_not_equal(res, (1.0, -1.0, None, None))
-
-
 def test_a2f_mn_mx():
     # Test array to file mn, mx handling
     str_io = BytesIO()
@@ -213,9 +144,9 @@ def test_array_file_scales():
         info = type_info(in_type)
         arr[0], arr[1] = info['min'], info['max']
         if not err is None:
-            assert_raises(err, calculate_scale, arr, out_dtype, True)
+            assert_raises(err, _calculate_scale, arr, out_dtype, True)
             continue
-        slope, inter, mn, mx = calculate_scale(arr, out_dtype, True)
+        slope, inter, mn, mx = _calculate_scale(arr, out_dtype, True)
         array_to_file(arr, bio, out_type, 0, inter, slope, mn, mx)
         bio.seek(0)
         arr2 = array_from_file(arr.shape, out_dtype, bio)
@@ -266,7 +197,7 @@ def check_int_a2f(in_type, out_type):
         data[1] = this_max + 0j
     str_io = BytesIO()
     try:
-        scale, inter, mn, mx = calculate_scale(data, out_type, True)
+        scale, inter, mn, mx = _calculate_scale(data, out_type, True)
     except ValueError as e:
         if DEBUG:
             print(in_type, out_type, e)

nibabel/tests/test_spatialimages.py

@@ -28,6 +28,7 @@
 from ..testing import (clear_and_catch_warnings, suppress_warnings,
                        memmap_after_ufunc)
 from ..tmpdirs import InTemporaryDirectory
+from ..deprecator import ExpiredDeprecationError
 from .. import load as top_load
 
 
@@ -284,8 +285,8 @@ def test_data_shape(self):
         img = img_klass(arr, np.eye(4))
         # Shape may be promoted to higher dimension, but may not reorder or
         # change size
-        assert_equal(img.get_shape()[:1], (4,))
-        assert_equal(np.prod(img.get_shape()), 4)
+        assert_equal(img.shape[:1], (4,))
+        assert_equal(np.prod(img.shape), 4)
         img = img_klass(np.zeros((2, 3, 4), dtype=np.float32), np.eye(4))
         assert_equal(img.shape, (2, 3, 4))
 
@@ -305,19 +306,13 @@ def test_str(self):
         assert_true(len(str(img)) > 0)
 
     def test_get_shape(self):
-        # Check there is a get_shape method
-        # (it is deprecated)
+        # Check that get_shape raises an ExpiredDeprecationError
         img_klass = self.image_class
         # Assumes all possible images support int16
         # See https://github.com/nipy/nibabel/issues/58
         img = img_klass(np.arange(1, dtype=np.int16), np.eye(4))
-        with suppress_warnings():
-            # Shape may be promoted to higher dimension, but may not reorder or
-            # change size
-            assert_equal(img.get_shape()[:1], (1,))
-            assert_equal(np.prod(img.get_shape()), 1)
-            img = img_klass(np.zeros((2, 3, 4), np.int16), np.eye(4))
-            assert_equal(img.get_shape(), (2, 3, 4))
+        with assert_raises(ExpiredDeprecationError):
+            img.get_shape()
 
     def test_get_fdata(self):
         # Test array image and proxy image interface for floating point data
@@ -568,18 +563,14 @@ def from_file_map(self, file_map=None):
         bio = BytesIO()
         file_map = FakeImage.make_file_map({'image': bio})
 
-        with clear_and_catch_warnings() as w:
-            warnings.simplefilter('always', DeprecationWarning)
+        with assert_raises(ExpiredDeprecationError):
             img.to_files(file_map)
-            assert_equal(len(w), 1)
+        with assert_raises(ExpiredDeprecationError):
             img.to_filespec('an_image')
-            assert_equal(len(w), 2)
-            img = FakeImage.from_files(file_map)
-            assert_equal(len(w), 3)
-            file_map = FakeImage.filespec_to_files('an_image')
-            assert_equal(list(file_map), ['image'])
-            assert_equal(file_map['image'].filename, 'an_image.foo')
-            assert_equal(len(w), 4)
+        with assert_raises(ExpiredDeprecationError):
+            FakeImage.from_files(file_map)
+        with assert_raises(ExpiredDeprecationError):
+            FakeImage.filespec_to_files('an_image')
 
 
 class MmapImageMixin(object):