Merge remote-tracking branch 'upstream/master' into add/fs-conform

Author: kaczmarj

.azure-pipelines/windows.yml

@@ -11,6 +11,7 @@ jobs:
   variables:
     EXTRA_WHEELS: "https://5cf40426d9f06eb7461d-6fe47d9331aba7cd62fc36c7196769e4.ssl.cf2.rackcdn.com"
     DEPENDS: numpy scipy matplotlib h5py pydicom
+    CHECK_TYPE: test
   strategy:
     matrix:
       ${{ insert }}: ${{ parameters.matrix }}
@@ -29,19 +30,20 @@ jobs:
       displayName: 'Update build tools'
     - script: |
         python -m pip install --find-links %EXTRA_WHEELS% %DEPENDS%
-        python -m pip install nose mock coverage codecov pytest
       displayName: 'Install dependencies'
     - script: |
-        python -m pip install .
+        python -m pip install .[$(CHECK_TYPE)]
         SET NIBABEL_DATA_DIR=%CD%\\nibabel-data
       displayName: 'Install nibabel'
     - script: |
         mkdir for_testing
         cd for_testing
         cp ../.coveragerc .
-        nosetests --with-doctest --with-coverage --cover-package nibabel nibabel
-      displayName: 'Nose tests'
+        pytest --doctest-modules --cov nibabel -v --pyargs nibabel
+      displayName: 'Pytest tests'
+      condition: and(succeeded(), eq(variables['CHECK_TYPE'], 'test'))
     - script: |
+        python -m pip install codecov
         cd for_testing
         codecov
       displayName: 'Upload To Codecov'

.gitignore

@@ -85,3 +85,4 @@ doc/source/reference
 venv/
 .buildbot.patch
 .vscode
+for_testing/

.mailmap

@@ -13,6 +13,7 @@ B. Nolan Nichols <nolan.nichols@gmail.com> Nolan Nichols <nolan.nichols@gmail.co
 Basile Pinsard <basile.pinsard@gmail.com> bpinsard <basile.pinsard@gmail.com>
 Basile Pinsard <basile.pinsard@gmail.com> bpinsard <bpinsard@imed.jussieu.fr>
 Ben Cipollini <ben.cipollini@gmail.com> Ben Cipollini <bcipolli@ucsd.edu>
+Benjamin C Darwin <bcdarwin@gmail.com>
 Bertrand Thirion <bertrand.thirion@inria.fr> bthirion <bertrand.thirion@inria.fr>
 Cameron Riddell <cameronriddell1@gmail.com> <31414128+CRiddler@users.noreply.github.com>
 Christian Haselgrove <christian.haselgrove@umassmed.edu> Christian Haselgrove <Christian.Haselgrove@umassmed.edu>

.travis.yml

@@ -4,91 +4,104 @@
 # 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
 
+os: linux
 dist: xenial
-sudo: true
 language: python
-
 cache: pip
+
 env:
     global:
         - SETUP_REQUIRES="pip setuptools>=30.3.0 wheel"
         - DEPENDS="numpy scipy matplotlib h5py pillow pydicom indexed_gzip"
         - INSTALL_TYPE="setup"
         - CHECK_TYPE="test"
-        - OLD_WHEELS="https://5cf40426d9f06eb7461d-6fe47d9331aba7cd62fc36c7196769e4.ssl.cf2.rackcdn.com"
         - EXTRA_WHEELS="https://3f23b170c54c2533c070-1c8a9b3114517dc5fe17b7c3f8c63a43.ssl.cf2.rackcdn.com"
         - PRE_WHEELS="https://7933911d6844c6c53a7d-47bd50c35cd79bd838daf386af554a83.ssl.cf2.rackcdn.com"
-        - EXTRA_PIP_FLAGS="--find-links=$EXTRA_WHEELS --find-links=$OLD_WHEELS"
+        - EXTRA_PIP_FLAGS="--find-links=$EXTRA_WHEELS"
         - PRE_PIP_FLAGS="--pre $EXTRA_PIP_FLAGS --find-links $PRE_WHEELS"
 
 python:
-    - 3.6
     - 3.7
     - 3.8
 
-matrix:
+jobs:
   include:
     # Basic dependencies only
-    - python: 3.5
+    - python: 3.6
       env:
         - DEPENDS="-r requirements.txt"
     # Clean install
-    - python: 3.5
+    - python: 3.6
       env:
         - DEPENDS=""
         - CHECK_TYPE=skiptests
     # Absolute minimum dependencies
-    - python: 3.5
+    - python: 3.6
       env:
         - SETUP_REQUIRES="setuptools==30.3.0"
         - DEPENDS="-r min-requirements.txt"
     # Absolute minimum dependencies plus oldest MPL
-    - python: 3.5
+    - python: 3.6
       env:
-        - DEPENDS="-r min-requirements.txt matplotlib==1.3.1"
+        - DEPENDS="-r min-requirements.txt matplotlib==1.5.3"
     # Minimum pydicom dependency
-    - python: 3.5
+    - python: 3.6
       env:
         - DEPENDS="-r min-requirements.txt pydicom==0.9.9 pillow==2.6"
     # pydicom master branch
-    - python: 3.5
+    - python: 3.6
       env:
         - DEPENDS="numpy git+https://github.com/pydicom/pydicom.git@master"
-    # test 3.7 against pre-release builds of everything
-    - python: 3.7
+    # test 3.8 against pre-release builds of everything
+    - python: 3.8
+      env:
+        - EXTRA_PIP_FLAGS="$PRE_PIP_FLAGS"
+    # OSX Python support is basically accidental. Take whatever version we can
+    # get and test with full dependencies...
+    - os: osx
+      language: minimal
+    # and pre-releases. No min-requirements.txt because we can't assume a wheel that old.
+    - os: osx
+      language: minimal
       env:
         - EXTRA_PIP_FLAGS="$PRE_PIP_FLAGS"
-    - python: 3.5
+    # Test that PyPI installs from source pass
+    - python: 3.6
       env:
         - INSTALL_TYPE=sdist
-    - python: 3.5
+    # Wheels (binary distributions)
+    - python: 3.6
       env:
         - INSTALL_TYPE=wheel
-    - python: 3.5
+    # Install from git archive (e.g., https://github.com/nipy/nibabel/archive/master.zip)
+    - python: 3.6
       env:
         - INSTALL_TYPE=archive
-    - python: 3.5
+    # Run flake8... Might not be needed now we have pep8speaks
+    - python: 3.6
       env:
         - CHECK_TYPE="style"
     # Documentation doctests
-    - python: 3.5
+    - python: 3.6
       env:
         - CHECK_TYPE="doc"
 
 # Set up virtual environment, build package, build from depends
 before_install:
-    - travis_retry python -m pip install --upgrade pip virtualenv
-    - virtualenv --python=python venv
+    - travis_retry python3 -m pip install --upgrade pip virtualenv
+    - virtualenv --python=python3 venv
     - source venv/bin/activate
-    - python --version # just to check
-    - travis_retry pip install -U $SETUP_REQUIRES
+    - python3 --version # just to check
+    - travis_retry python3 -m pip install -U $SETUP_REQUIRES
+    - which python3
+    - which pip
     - |
       if [ "$INSTALL_TYPE" == "sdist" ]; then
-        python setup.py egg_info  # check egg_info while we're here
-        python setup.py sdist
+        python3 setup.py egg_info  # check egg_info while we're here
+        python3 setup.py sdist
         export ARCHIVE=$( ls dist/*.tar.gz )
       elif [ "$INSTALL_TYPE" == "wheel" ]; then
-        python setup.py bdist_wheel
+        python3 setup.py bdist_wheel
         export ARCHIVE=$( ls dist/*.whl )
       elif [ "$INSTALL_TYPE" == "archive" ]; then
         export ARCHIVE="package.tar.gz"
@@ -100,19 +113,19 @@ before_install:
 install:
     - |
       if [ "$INSTALL_TYPE" == "setup" ]; then
-          python setup.py install
+          python3 setup.py install
       else
           pip install $EXTRA_PIP_FLAGS $ARCHIVE
       fi
     # Basic import check
-    - python -c 'import nibabel; print(nibabel.__version__)'
+    - python3 -c 'import nibabel; print(nibabel.__version__)'
     - if [ "$CHECK_TYPE" == "skiptests" ]; then exit 0; fi
 
 before_script:
     # Point to nibabel data directory
     - export NIBABEL_DATA_DIR="$PWD/nibabel-data"
     # Because nibabel is already installed, will just look up the extra
-    - pip install $EXTRA_PIP_FLAGS "nibabel[$CHECK_TYPE]"
+    - python3 -m pip install $EXTRA_PIP_FLAGS "nibabel[$CHECK_TYPE]"
 
 # command to run tests, e.g. python setup.py test
 script:
@@ -122,20 +135,19 @@ script:
           flake8 nibabel
       elif [ "${CHECK_TYPE}" == "doc" ]; then
           cd doc
-          make html;
-          make doctest;
+          make html && make doctest
       elif [ "${CHECK_TYPE}" == "test" ]; then
           # Change into an innocuous directory and find tests from installation
           mkdir for_testing
           cd for_testing
           cp ../.coveragerc .
-          nosetests --with-doctest --with-coverage --cover-package nibabel nibabel
+          pytest --doctest-modules --cov nibabel -v --pyargs nibabel
       else
           false
       fi
 
 after_script:
-    - travis_retry pip install codecov
+    - travis_retry python3 -m pip install codecov
     - codecov
 
 notifications:

.zenodo.json

@@ -259,6 +259,10 @@
     {
       "name": "Schwartz, Yannick"
     },
+    {
+      "affiliation": "Hospital for Sick Children",
+      "name": "Darwin, Benjamin C"
+    },
     {
       "affiliation": "INRIA",
       "name": "Thirion, Bertrand",
@@ -319,6 +323,9 @@
       "name": "Reddam, Venkateswara Reddy",
       "orcid": "0000-0001-6817-2966"
     },
+    {
+      "name": "Baratz, Zvi"
+    },
     {
       "name": "freec84"
     }

Changelog

@@ -25,8 +25,40 @@ Eric Larson (EL), Demian Wassermann, and Stephan Gerhard.
 
 References like "pr/298" refer to github pull request numbers.
 
-3.0.0 (To Be Determined)
-========================
+3.0.2 (Monday 9 March 2020)
+===========================
+
+Bug fixes
+---------
+* Attempt to find versioneer version when building docs (pr/894) (CM)
+* Delay import of h5py until neded (backport of pr/889) (YOH, reviewed by CM)
+
+Maintenance
+-----------
+* Fix typo in documentation (backport of pr/893) (Zvi Baratz, reviewed by CM)
+* Set minimum matplotlib to 1.5.3 to ensure wheels are available on all
+  supported Python versions. (backport of pr/887) (CM)
+* Remove ``pyproject.toml`` for now. (issue/859) (CM)
+
+
+3.0.1 (Monday 27 January 2020)
+==============================
+
+Bug fixes
+---------
+* Test failed by using array method on tuple. (pr/860) (Ben Darwin, reviewed by
+  CM)
+* Validate ``ExpiredDeprecationError``\s, promoted by 3.0 release from
+  ``DeprecationWarning``\s. (pr/857) (CM)
+
+Maintenance
+-----------
+* Remove logic accommodating numpy without float16 types. (pr/866) (CM)
+* Accommodate new numpy dtype strings. (pr/858) (CM)
+
+
+3.0.0 (Wednesday 18 December 2019)
+==================================
 
 New features
 ------------
@@ -63,9 +95,11 @@ Enhancements
 
 Bug fixes
 ---------
-* Sliced ``Tractogram``s no longer ``apply_affine`` to the original
+* Sliced ``Tractogram``\s no longer ``apply_affine`` to the original
   ``Tractogram``'s streamlines. (pr/811) (MC, reviewed by Serge Koudoro,
   Philippe Poulin, CM, MB)
+* Change strings with invalid escapes to raw strings (pr/827) (EL, reviewed
+  by CM)
 * Re-import externals/netcdf.py from scipy to resolve numpy deprecation
   (pr/821) (CM)
 
@@ -79,6 +113,10 @@ Maintenance
 
 API changes and deprecations
 ----------------------------
+* Fully remove deprecated ``checkwarns`` and ``minc`` modules. (pr/852) (CM)
+* The ``keep_file_open`` argument to file load operations and ``ArrayProxy``\s
+  no longer acccepts the value ``"auto"``, raising a ``ValueError``. (pr/852)
+  (CM)
 * Deprecate ``ArraySequence.data`` in favor of ``ArraySequence.get_data()``,
   which will return a copy. ``ArraySequence.data`` now returns a read-only
   view. (pr/811) (MC, reviewed by Serge Koudoro, Philippe Poulin, CM, MB)
@@ -398,7 +436,7 @@ New features
 * Support for MRtrix TCK streamlines file format (pr/486) (MC, reviewed by
   MB, Arnaud Bore, J-Donald Tournier, Jean-Christophe Houde)
 * Added ``get_fdata()`` as default method to retrieve scaled floating point
-  data from ``DataobjImage``s (pr/551) (MB, reviewed by CM, SG)
+  data from ``DataobjImage``\s (pr/551) (MB, reviewed by CM, SG)
 
 Enhancements
 ------------

azure-pipelines.yml

@@ -6,16 +6,6 @@ jobs:
     vmImage: windows-2019
     matrix:
       py35-x86:
-        PYTHON_VERSION: '3.5'
-        PYTHON_ARCH: 'x86'
-      py35-x64:
-        PYTHON_VERSION: '3.5'
-        PYTHON_ARCH: 'x64'
-      py35-h5py-check:
-        PYTHON_VERSION: '3.5'
-        PYTHON_ARCH: 'x64'
-        PYTHONHASHSEED: 283137131
-        DEPENDS: "h5py==2.9.0"
       py36-x86:
         PYTHON_VERSION: '3.6'
         PYTHON_ARCH: 'x86'

dev-requirements.txt

@@ -1,4 +1,3 @@
 # Requirements for running tests
 -r requirements.txt
-nose
-mock
+pytest

doc-requirements.txt

@@ -3,5 +3,4 @@
 sphinx
 numpydoc
 texext
-matplotlib>=1.3
-mock
+matplotlib >=1.3.1

doc/source/conf.py

@@ -21,10 +21,8 @@
 
 import sys
 import os
-try:
-    from configparser import ConfigParser
-except ImportError:
-    from ConfigParser import ConfigParser  # PY2
+from runpy import run_path
+from configparser import ConfigParser
 
 # Check for external Sphinx extensions we depend on
 try:
@@ -51,9 +49,7 @@
 # -- General configuration ----------------------------------------------------
 
 # We load the nibabel release info into a dict by explicit execution
-rel = {}
-with open(os.path.join('..', '..', 'nibabel', 'info.py'), 'r') as fobj:
-    exec(fobj.read(), rel)
+rel = run_path(os.path.join('..', '..', 'nibabel', 'info.py'))
 
 # Write long description from info
 with open('_long_description.inc', 'wt') as fobj:
@@ -62,10 +58,7 @@
 # Load metadata from setup.cfg
 config = ConfigParser()
 config.read(os.path.join('..', '..', 'setup.cfg'))
-try:
-    metadata = config['metadata']
-except AttributeError:
-    metadata = dict(config.items('metadata'))  # PY2
+metadata = config['metadata']
 
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
@@ -99,7 +92,7 @@
 
 # General information about the project.
 project = u'NiBabel'
-copyright = u'2006-2019, %(maintainer)s <%(author_email)s>' % metadata
+copyright = u'2006-2020, %(maintainer)s <%(author_email)s>' % metadata
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the