MRG: Release candidate 2.0.2

.mailmap

@@ -29,3 +29,5 @@ Basile Pinsard <basile.pinsard@gmail.com> bpinsard <bpinsard@imed.jussieu.fr>
 Nguyen, Ly <nguyen60@seattleu.edu> lxn2 <lxn2@uw.edu>
 Ben Cipollini <ben.cipollini@gmail.com> Ben Cipollini <bcipolli@ucsd.edu>
 Chris Markiewicz <effigies@gmail.com> Christopher J. Markiewicz <effigies@bu.edu>
+Chris Markiewicz <effigies@gmail.com> Christopher J. Markiewicz <effigies@gmail.com>
+Chris Markiewicz <effigies@gmail.com> Chris Johnson <effigies@bu.edu>

.travis.yml

@@ -8,11 +8,13 @@ env:
     global:
         - DEPENDS="numpy scipy matplotlib h5py"
         - PYDICOM=1
+        - INSTALL_TYPE="setup"
 python:
     - 2.6
     - 3.2
     - 3.3
     - 3.4
+    - 3.5
 matrix:
   include:
     - python: 2.7
@@ -26,20 +28,37 @@ matrix:
     - python: 2.7
       env:
         - DEPENDS="numpy==1.5.1 pydicom==0.9.7"
+    # pydicom 1.0 (currently unreleased)
+    - python: 2.7
+      env:
+        - PYDICOM="v1.0"
     # Documentation doctests
     - python: 2.7
       env:
         - DOC_DOC_TEST=1
+    - python: 2.7
+      env:
+        - INSTALL_TYPE=sdist
+    - python: 2.7
+      env:
+        - INSTALL_TYPE=wheel
+    - python: 2.7
+      env:
+        - INSTALL_TYPE=requirements
 before_install:
+    - source tools/travis_tools.sh
     - virtualenv --python=python venv
     - source venv/bin/activate
     - python --version # just to check
-    - pip install nose # always
-    - pip install --no-index -f http://travis-wheels.scikit-image.org $DEPENDS
+    - pip install -U pip  # upgrade to latest pip to find 3.5 wheels
+    - retry pip install nose # always
+    - wheelhouse_pip_install $DEPENDS
     # pydicom <= 0.9.8 doesn't install on python 3
     - if [ "${TRAVIS_PYTHON_VERSION:0:1}" == "2" ]; then
         if [ "$PYDICOM" == "1" ]; then
             pip install pydicom;
+        elif [ "$PYDICOM" == "v1.0" ]; then
+            pip install git+https://github.com/darcymason/pydicom.git@43f278444d5cb2e4648135d3edcd430c363c6975;
         fi
       fi
     - if [ "${COVERAGE}" == "1" ]; then
@@ -51,7 +70,21 @@ before_install:
       fi
 # command to install dependencies
 install:
-    - python setup.py install
+    - |
+      if [ "$INSTALL_TYPE" == "setup" ]; then
+          python setup.py install
+      elif [ "$INSTALL_TYPE" == "sdist" ]; then
+          python setup_egg.py egg_info  # check egg_info while we're here
+          python setup_egg.py sdist
+          wheelhouse_pip_install dist/*.tar.gz
+      elif [ "$INSTALL_TYPE" == "wheel" ]; then
+          pip install wheel
+          python setup_egg.py bdist_wheel
+          wheelhouse_pip_install dist/*.whl
+      elif [ "$INSTALL_TYPE" == "requirements" ]; then
+          wheelhouse_pip_install -r requirements.txt
+          python setup.py install
+      fi
     # Point to nibabel data directory
     - export NIBABEL_DATA_DIR="$PWD/nibabel-data"
 # command to run tests, e.g. python setup.py test

Changelog

@@ -24,6 +24,25 @@ and Stephan Gerhard (SG).
 
 References like "pr/298" refer to github pull request numbers.
 
+* 2.0.2 (Monday 23 November 2015)
+
+  * Fix for integer overflow on large images (pr/325) (MB);
+  * Fix for Freesurfer nifti files with unusual dimensions (pr/332) (Chris
+    Markiewicz);
+  * Fix typos on benchmarks and tests (pr/336, pr/340, pr/347) (Chris
+    Markiewicz);
+  * Fix Windows install script (pr/339) (MB);
+  * Support for Python 3.5 (pr/363) (MB) and numpy 1.10 (pr/358) (Chris
+    Markiewicz);
+  * Update pydicom imports to permit version 1.0 (pr/379) (Chris Markiewicz);
+  * Workaround for Python 3.5.0 gzip regression (pr/383) (Ben Cipollini).
+  * tripwire.TripWire object now raises subclass of AttributeError when trying
+    to get an attribute, rather than a direct subclass of Exception.  This
+    prevents Python 3.5 triggering the tripwire when doing inspection prior to
+    running doctests.
+  * Minor API change for tripwire.TripWire object; code that checked for
+    AttributeError will now also catch TripWireError.
+
 * 2.0.1 (Saturday 27 June 2015)
 
   Contributions from Ben Cipollini, Chris Markiewicz, Alexandre Gramfort,

MANIFEST.in

@@ -1,5 +1,5 @@
 include AUTHOR COPYING Makefile* MANIFEST.in setup* README.*
-include Changelog TODO
+include Changelog TODO requirements.txt
 recursive-include doc *
 recursive-include bin *
 recursive-include tools *

doc/source/devel/advanced_testing.rst

@@ -0,0 +1,32 @@
+.. -*- mode: rst -*-
+.. ex: set sts=4 ts=4 sw=4 et tw=79:
+  ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ###
+  #
+  #   See COPYING file distributed along with the NiBabel package for the
+  #   copyright and license terms.
+  #
+  ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ###
+
+.. _advanced_testing:
+
+************
+Advanced Testing
+************
+
+Setup
+-----
+
+Before running advanced tests, please update all submodules of nibabel, by running ``git submodule update --init``
+
+
+Long-running tests
+------------------
+
+Long-running tests are not enabled by default, and can be resource-intensive. To run these tests:
+
+* Set environment variable ``NIPY_EXTRA_TESTS=slow``
+* Run ``nosetests``.
+
+Note that some tests may require a machine with >4GB of RAM.
+
+.. include:: ../links_names.txt

doc/source/devel/index.rst

@@ -14,3 +14,4 @@ Developer documentation page
     add_image_format
     devdiscuss
     make_release
+    advanced_testing

doc/source/devel/make_release.rst

@@ -130,11 +130,9 @@ Release checklist
 * Check on different platforms, particularly windows and PPC. Look at the
   `nipy buildbot`_ automated test runs for this.
 
-* Check the documentation doctests::
+* Check the documentation doctests (forcing Python 2)::
 
-    cd doc
-    make doctest
-    cd ..
+    make -C doc doctest SPHINXBUILD="python $(which sphinx-build)"
 
   This should also be tested by `nibabel on travis`_.
 

doc/source/index.rst

@@ -47,7 +47,7 @@ contributed code and discussion (in rough order of appearance):
 * Bago Amirbekian
 * Brendan Moloney
 * Félix C. Morency
-* Chris Johnson
+* Chris Markiewicz
 * JB Poline
 * Nolan Nichols
 * Nguyen, Ly
@@ -61,8 +61,7 @@ contributed code and discussion (in rough order of appearance):
 * Demian Wassermann
 * Philippe Gervais
 * Justin Lecher
-* Ben Cippolini
-* Chris Markiewicz
+* `Ben Cipollini`_
 * Clemens C. C. Bauer
 
 License reprise

doc/source/installation.rst

@@ -114,7 +114,11 @@ Just install the modules by invoking::
 If sudo is not configured (or even installed) you might have to use
 ``su`` instead.
 
-Now fire up Python and try importing the module to see if everything is fine.
+
+Validating your install
+-----------------------
+
+For a basic test of your installation, fire up Python and try importing the module to see if everything is fine.
 It should look something like this::
 
     Python 2.7.8 (v2.7.8:ee879c0ffa11, Jun 29 2014, 21:07:35)
@@ -123,4 +127,9 @@ It should look something like this::
     >>> import nibabel
     >>>
 
+
+To run the nibabel test suite, from the terminal run ``nosetests nibabel`` or ``python -c "import nibabel; nibabel.test()``.
+
+To run an extended test suite that validates ``nibabel`` for long-running and resource-intensive cases, please see :ref:`advanced_testing`.
+
 .. include:: links_names.txt

doc/source/links_names.txt

@@ -5,7 +5,7 @@
    and name substitutions.  It may be included in many files,
    therefore it should only contain link targets and name
    substitutions.  Try grepping for "^\.\. _" to find plausible
-   candidates for this list.  
+   candidates for this list.
 
 
 .. NOTE: reST targets are
@@ -233,6 +233,7 @@
 .. _Michael Hanke: http://mih.voxindeserto.de
 .. _Gaël Varoquaux: http://gael-varoquaux.info/
 .. _Stephan Gerhard: http://www.unidesign.ch
+.. _Ben Cipollini: http://bcipolli.github.io/
 
 .. Substitutions
 .. |emdash| unicode:: U+02014

nibabel/benchmarks/bench_array_to_file.py

@@ -50,7 +50,7 @@ def bench_array_to_file():
     mtime = measure('array_to_file(arr, BytesIO(), np.int16)', repeat)
     print('%30s %6.2f' % ('Save float64 to int16, infs', mtime))
     # Int16 input, float output
-    arr = np.random.random_integers(low=-1000,high=-1000, size=img_shape)
+    arr = np.random.random_integers(low=-1000, high=1000, size=img_shape)
     arr = arr.astype(np.int16)
     mtime = measure('array_to_file(arr, BytesIO(), np.float32)', repeat)
     print('%30s %6.2f' % ('Save Int16 to float32', mtime))

nibabel/benchmarks/bench_finite_range.py

@@ -42,7 +42,7 @@ def bench_finite_range():
     mtime = measure('finite_range(arr)', repeat)
     print('%30s %6.2f' % ('float64 many infs', mtime))
     # Int16 input, float output
-    arr = np.random.random_integers(low=-1000,high=-1000, size=img_shape)
+    arr = np.random.random_integers(low=-1000, high=1000, size=img_shape)
     arr = arr.astype(np.int16)
     mtime = measure('finite_range(arr)', repeat)
     print('%30s %6.2f' % ('int16', mtime))

nibabel/benchmarks/bench_load_save.py

@@ -56,7 +56,7 @@ def bench_load_save():
     mtime = measure('img.from_file_map(img.file_map)', repeat)
     print('%30s %6.2f' % ('Load from int16, NaNs', mtime))
     # Int16 input, float output
-    arr = np.random.random_integers(low=-1000,high=-1000, size=img_shape)
+    arr = np.random.random_integers(low=-1000, high=1000, size=img_shape)
     arr = arr.astype(np.int16)
     img = Nifti1Image(arr, np.eye(4))
     sio = BytesIO()

nibabel/fileslice.py

@@ -764,9 +764,15 @@ def strided_scalar(shape, scalar=0.):
     strided_arr : array
         Array of shape `shape` for which all values == `scalar`, built by
         setting all strides of `strided_arr` to 0, so the scalar is broadcast
-        out to the full array `shape`.
+        out to the full array `shape`. `strided_arr` is flagged as not
+        `writeable`.
+
+        The array is set read-only to avoid a numpy error when broadcasting -
+        see https://github.com/numpy/numpy/issues/6491
     """
     shape = tuple(shape)
     scalar = np.array(scalar)
     strides = [0] * len(shape)
-    return np.lib.stride_tricks.as_strided(scalar, shape, strides)
+    strided_scalar = np.lib.stride_tricks.as_strided(scalar, shape, strides)
+    strided_scalar.flags.writeable = False
+    return strided_scalar

nibabel/info.py

@@ -9,8 +9,8 @@
 _version_major = 2
 _version_minor = 0
 _version_micro = 2
-_version_extra = 'dev'
-#_version_extra = ''
+#_version_extra = 'dev'
+_version_extra = ''
 
 # Format expected by setup.py and doc/source/conf.py: string of form "X.Y.Z"
 __version__ = "%s.%s.%s%s" % (_version_major,

nibabel/nicom/dicomwrappers.py

@@ -49,10 +49,13 @@ def wrapper_from_file(file_like, *args, **kwargs):
     dcm_w : ``dicomwrappers.Wrapper`` or subclass
        DICOM wrapper corresponding to DICOM data type
     """
-    import dicom
+    try:
+        from dicom import read_file
+    except ImportError:
+        from pydicom.dicomio import read_file
 
     with BinOpener(file_like) as fobj:
-        dcm_data = dicom.read_file(fobj, *args, **kwargs)
+        dcm_data = read_file(fobj, *args, **kwargs)
     return wrapper_from_data(dcm_data)
 
 

nibabel/nicom/tests/test_csareader.py

@@ -31,7 +31,10 @@ def test_csa_header_read():
     assert_true(csa.is_mosaic(hdr))
     # Get a shallow copy of the data, lacking the CSA marker
     # Need to do it this way because del appears broken in pydicom 0.9.7
-    from dicom.dataset import Dataset
+    try:
+        from dicom.dataset import Dataset
+    except ImportError:
+        from pydicom.dataset import Dataset
     data2 = Dataset()
     for element in DATA:
         if (element.tag.group, element.tag.elem) != (0x29, 0x10):

nibabel/nicom/tests/test_dicomreaders.py

@@ -40,7 +40,10 @@ def test_passing_kwds():
     # Check that we correctly pass keywords to dicom
     dwi_glob = 'siemens_dwi_*.dcm.gz'
     csa_glob = 'csa*.bin'
-    import dicom
+    try:
+        from dicom.filereader import InvalidDicomError
+    except ImportError:
+        from pydicom.filereader import InvalidDicomError
     for func in (didr.read_mosaic_dwi_dir, didr.read_mosaic_dir):
         data, aff, bs, gs = func(IO_DATA_PATH, dwi_glob)
         # This should not raise an error
@@ -49,14 +52,14 @@ def test_passing_kwds():
             dwi_glob,
             dicom_kwargs=dict(force=True))
         assert_array_equal(data, data2)
-        # This should raise an error in dicom.read_file
+        # This should raise an error in pydicom.dicomio.read_file
         assert_raises(TypeError,
                       func,
                       IO_DATA_PATH,
                       dwi_glob,
                       dicom_kwargs=dict(not_a_parameter=True))
         # These are invalid dicoms, so will raise an error unless force=True
-        assert_raises(dicom.filereader.InvalidDicomError,
+        assert_raises(InvalidDicomError,
                       func,
                       IO_DATA_PATH,
                       csa_glob)

nibabel/nicom/tests/test_dicomwrappers.py

@@ -9,12 +9,17 @@
 
 import numpy as np
 
+have_dicom = True
 try:
-    import dicom
+    import dicom as pydicom
+    read_file = pydicom.read_file
 except ImportError:
-    have_dicom = False
-else:
-    have_dicom = True
+    try:
+        import pydicom
+    except ImportError:
+        have_dicom = False
+    else:
+        from pydicom.dicomio import read_file
 dicom_test = np.testing.dec.skipif(not have_dicom,
                                    'could not import pydicom')
 
@@ -32,8 +37,8 @@
 DATA_FILE = pjoin(IO_DATA_PATH, 'siemens_dwi_1000.dcm.gz')
 DATA_FILE_PHILIPS = pjoin(IO_DATA_PATH, 'philips_mprage.dcm.gz')
 if have_dicom:
-    DATA = dicom.read_file(gzip.open(DATA_FILE))
-    DATA_PHILIPS = dicom.read_file(gzip.open(DATA_FILE_PHILIPS))
+    DATA = read_file(gzip.open(DATA_FILE))
+    DATA_PHILIPS = read_file(gzip.open(DATA_FILE_PHILIPS))
 else:
     DATA = None
     DATA_PHILIPS = None
@@ -166,7 +171,7 @@ def test_wrapper_from_data():
 
 @dicom_test
 def test_wrapper_args_kwds():
-    # Test we can pass args, kwargs to dicom.read_file
+    # Test we can pass args, kwargs to read_file
     dcm = didw.wrapper_from_file(DATA_FILE)
     data = dcm.get_data()
     # Passing in non-default arg for defer_size
@@ -177,7 +182,7 @@ def test_wrapper_args_kwds():
     assert_array_equal(data, dcm2.get_data())
     # Trying to read non-dicom file raises pydicom error, usually
     csa_fname = pjoin(IO_DATA_PATH, 'csa2_b0.bin')
-    assert_raises(dicom.filereader.InvalidDicomError,
+    assert_raises(pydicom.filereader.InvalidDicomError,
                   didw.wrapper_from_file,
                   csa_fname)
     # We can force the read, in which case rubbish returns