Merge pull request #1 from matthew-brett/update-plus-for-296

MRG: merged current master, refactor dicom import

Author: kastman

.gitignore

@@ -15,9 +15,12 @@
 *.tmp
 .project
 .pydevproject
+*.py.orig
 
-# Not sure what the next two are for
+# Not sure what the next one is for
 *.kpf
+
+# Makefile target file markers
 *-stamp
 
 # Compiled source #
@@ -58,6 +61,8 @@ dist/
 .shelf
 .tox/
 .coverage
+.ropeproject/
+htmlcov/
 
 # Logs and databases #
 ######################

.gitmodules

@@ -4,3 +4,12 @@
 [submodule "nibabel-data/nitest-minc2"]
 	path = nibabel-data/nitest-minc2
 	url = git://github.com/matthew-brett/nitest-minc2.git
+[submodule "nipy-ecattest"]
+	path = nibabel-data/nipy-ecattest
+	url = https://github.com/freec84/nipy-ecattest
+[submodule "nibabel-data/nitest-freesurfer"]
+	path = nibabel-data/nitest-freesurfer
+	url = https://bitbucket.org/nipy/nitest-freesurfer.git
+[submodule "nibabel-data/parrec_oblique"]
+	path = nibabel-data/parrec_oblique
+	url = https://github.com/grlee77/parrec_oblique.git

.mailmap

@@ -27,3 +27,7 @@ Kevin S. Hahn <[email protected]> Kevin S. Hahn <[email protected]>
 Basile Pinsard <[email protected]> bpinsard <[email protected]>
 Basile Pinsard <[email protected]> bpinsard <[email protected]>
 Nguyen, Ly <[email protected]> lxn2 <[email protected]>
+Ben Cipollini <[email protected]> Ben Cipollini <[email protected]>
+Chris Markiewicz <[email protected]> Christopher J. Markiewicz <[email protected]>
+Chris Markiewicz <[email protected]> Christopher J. Markiewicz <[email protected]>
+Chris Markiewicz <[email protected]> Chris Johnson <[email protected]>

.travis.yml

@@ -3,16 +3,31 @@
 # munges each line before executing it to print out the exit status.  It's okay
 # for it to be on multiple physical lines, so long as you remember: - There
 # can't be any leading "-"s - All newlines will be removed, so use ";"s
+
 language: python
+
+# Run jobs on container-based infrastructure, can be overridden per job
+sudo: false
+
+cache:
+  directories:
+    - $HOME/.cache/pip
+addons:
+  apt:
+    packages:
+      - libhdf5-serial-dev
+      # For numpy --pre wheels
+      - libatlas-base-dev
 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
@@ -22,54 +37,105 @@ matrix:
     - python: 2.7
       env:
         - DEPENDS=numpy==1.5.1 PYDICOM=0
+    # Absolute minimum dependencies plus oldest MPL
+    - python: 2.7
+      env:
+        - DEPENDS=numpy==1.5.1 matplotlib==1.3.1 PYDICOM=0
     # Minimum pydicom dependency
     - 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"
+    # test against pre-release builds
+    - python: 2.7
+      env:
+        - EXTRA_PIP_FLAGS="--pre"
     # 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
+    - python: 2.7
+      env:
+        - STYLE=1
+    - python: 3.5
+      env:
+        - STYLE=1
 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 wheel  # upgrade to latest pip find 3.5 wheels; wheel to avoid errors
+    - retry pip install nose flake8  # always
+    - wheelhouse_pip_install $EXTRA_PIP_FLAGS $DEPENDS
     # pydicom <= 0.9.8 doesn't install on python 3
     - if [ "${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
       pip install coverage;
       pip install coveralls;
       fi
-    - if [[ $DEPENDS == *h5py* ]]; then
-      sudo apt-get install libhdf5-serial-dev;
-      fi
 # command to install dependencies
 install:
-    - python setup.py install
+    - |
+      if [ "$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 $EXTRA_PIP_FLAGS dist/*.tar.gz
+      elif [ "$INSTALL_TYPE" == "wheel" ]; then
+          pip install wheel
+          python setup_egg.py bdist_wheel
+          wheelhouse_pip_install $EXTRA_PIP_FLAGS dist/*.whl
+      elif [ "$INSTALL_TYPE" == "requirements" ]; then
+          wheelhouse_pip_install $EXTRA_PIP_FLAGS -r requirements.txt
+          python setup.py install
+      fi
     # Point to nibabel data directory
     - export NIBABEL_DATA_DIR="$PWD/nibabel-data"
 # command to run tests, e.g. python setup.py test
 script:
-    # Change into an innocuous directory and find tests from installation
-    - mkdir for_testing
-    - cd for_testing
-    - if [ "${COVERAGE}" == "1" ]; then
-      cp ../.coveragerc .;
-      COVER_ARGS="--with-coverage --cover-package nibabel";
-      fi
-    - if [ "$DOC_DOC_TEST" == "1" ]; then
-      pip install sphinx;
-      cd ../doc;
-      make html;
-      make doctest;
+    - |
+      if [ "${STYLE}" == "1" ]; then
+          # Run styles only on core nibabel code.
+          flake8 nibabel
       else
-      nosetests --with-doctest $COVER_ARGS nibabel;
+          # Change into an innocuous directory and find tests from installation
+          mkdir for_testing
+          cd for_testing
+          if [ "${COVERAGE}" == "1" ]; then
+              cp ../.coveragerc .;
+              COVER_ARGS="--with-coverage --cover-package nibabel";
+          fi
+          if [ "$DOC_DOC_TEST" == "1" ]; then
+              pip install sphinx numpydoc texext;
+              cd ../doc;
+              make html;
+              make doctest;
+          else
+              nosetests --with-doctest $COVER_ARGS nibabel;
+          fi
       fi
 after_success:
     - if [ "${COVERAGE}" == "1" ]; then coveralls; fi
+
+notifications:
+    webhooks: http://nipy.bic.berkeley.edu:54856/travis

COPYING

@@ -128,27 +128,29 @@ In ``nibabel/externals/ordereddict.py``
 
 Copied from: https://pypi.python.org/packages/source/o/ordereddict/ordereddict-1.1.tar.gz#md5=a0ed854ee442051b249bfad0f638bbec
 
-Copyright (c) 2009 Raymond Hettinger
-
-Permission is hereby granted, free of charge, to any person
-obtaining a copy of this software and associated documentation files
-(the "Software"), to deal in the Software without restriction,
-including without limitation the rights to use, copy, modify, merge,
-publish, distribute, sublicense, and/or sell copies of the Software,
-and to permit persons to whom the Software is furnished to do so,
-subject to the following conditions:
-
-    The above copyright notice and this permission notice shall be
-    included in all copies or substantial portions of the Software.
-
-    THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
-    EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
-    OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
-    NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
-    HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
-    WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
-    FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
-    OTHER DEALINGS IN THE SOFTWARE.
+::
+
+  Copyright (c) 2009 Raymond Hettinger
+
+  Permission is hereby granted, free of charge, to any person
+  obtaining a copy of this software and associated documentation files
+  (the "Software"), to deal in the Software without restriction,
+  including without limitation the rights to use, copy, modify, merge,
+  publish, distribute, sublicense, and/or sell copies of the Software,
+  and to permit persons to whom the Software is furnished to do so,
+  subject to the following conditions:
+
+      The above copyright notice and this permission notice shall be
+      included in all copies or substantial portions of the Software.
+
+      THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+      EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+      OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+      NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+      HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+      WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+      FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+      OTHER DEALINGS IN THE SOFTWARE.
 
 mni_icbm152_t1_tal_nlin_asym_09a
 --------------------------------
@@ -158,6 +160,8 @@ The file ``doc/source/someone.nii.gz`` is a subsampled version of the file
 archive ``mni_icbm152_t1_tal_nlin_asym_09a``.  The original image has the
 following license (where 'softwware' refers to the image):
 
+::
+
     Copyright (C) 1993-2004 Louis Collins, McConnell Brain Imaging Centre,
     Montreal Neurological Institute, McGill University.
 
@@ -204,3 +208,39 @@ The files::
 
 are from https://github.com/yarikoptic/nitest-balls1, also released under the
 the PDDL version 1.0 available at http://opendatacommons.org/licenses/pddl/1.0/
+
+    nibabel/nibabel/tests/data/umass_anonymized.PAR
+
+is courtesy of the University of Massachusetts Medical School, also released
+under the PDDL.
+
+
+Six
+--------------------
+
+In ``nibabel/externals/six.py``
+
+Copied from: https://pypi.python.org/packages/source/s/six/six-1.3.0.tar.gz#md5=ec47fe6070a8a64c802363d2c2b1e2ee
+
+::
+
+    Copyright (c) 2010-2013 Benjamin Peterson
+
+    Permission is hereby granted, free of charge, to any person obtaining a copy of
+    this software and associated documentation files (the "Software"), to deal in
+    the Software without restriction, including without limitation the rights to
+    use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of
+    the Software, and to permit persons to whom the Software is furnished to do so,
+    subject to the following conditions:
+
+    The above copyright notice and this permission notice shall be included in all
+    copies or substantial portions of the Software.
+
+    THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+    IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS
+    FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR
+    COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER
+    IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
+    CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+
+

Changelog

@@ -22,10 +22,58 @@ NiBabel
 Most work on NiBabel so far has been by Matthew Brett (MB), Michael Hanke (MH)
 and Stephan Gerhard (SG).
 
-* 2.0.1
+References like "pr/298" refer to github pull request numbers.
+
+* Upcoming
 
   * Read and write support for DICOM tags in NIfTI Extended Header using
-    pydicom.
+    pydicom (pr/296);
+  * Trackvis reader will now allow final streamline to have fewer points that
+    tne numbe declared in the header, with ``strict=False`` argument to
+    ``read`` function;
+  * Minor API breakage in trackvis reader. We are now raising a DataError if
+    there are too few streamlines in the file, instead of a HeaderError.  We
+    are raising a DataError if the track is truncated when ``strict=True``
+    (the default), rather than a TypeError when trying to create the points
+    array.
+
+* 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,
+  Clemens Bauer, github user freec84.
+
+  * Bugfix release with minor new features;
+  * Added ``axis`` parameter to ``concat_images`` (pr/298) (Ben Cipollini);
+  * Fix for unsigned integer data types in ECAT images (pr/302) (MB, test data
+    and issue report from Github user freec84);
+  * Added new ECAT and Freesurfer data files to automated testing;
+  * Fix for Freesurfer labels error on early numpies (pr/307) (Alexandre
+    Gramfort);
+  * Fixes for PAR / REC header parsing (pr/312) (MB, issue reporting and test
+    data by Clemens C. C. Bauer);
+  * Workaround for reading Freesurfer ico7 surface files (pr/315) (Chris
+    Markiewicz);
+  * Changed to github pages for doc hosting;
+  * Changed docs to point to [email protected] mailing list.
 
 * 2.0.0 (Tuesday 9 December 2014)
 

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 *