Merge branch 'master' of https://github.com/htwangtw/nibabel into gifti_improve_io

* 'master' of https://github.com/htwangtw/nibabel: (94 commits)
  Fixed A-P to P-A in coord systems docs
  DOCTEST: Delete reference to mmap data to avoid warning
  DOCTEST: Avoid fixed ID in doctest
  Re-import externals/netcdf.py from scipy
  DOCTEST: Delete reference to mmap data to avoid warning
  DOCTEST: Avoid fixed ID in doctest
  Re-import externals/netcdf.py from scipy
  MAINT: 2.5.2-dev
  add @hbraunDSP affiliation and ORCID
  MAINT: Update setup.cfg nose version to match installation instructions
  DOC: Add Henry Braun to contributor list
  MAINT: Update zenodo.json
  MAINT: Version 2.5.1
  DOC: Update changelog for upcoming 2.5.1 release
  DOC: Update test_image_api docstring for clarity, consistency
  ENH: Remove img.get_data() from internal use except for appropriate tests
  TEST: Reproduce gh-802
  MAINT: Check nightly builds on 3.7
  MAINT: Check nightly builds on 3.7
  FIX: Coerce data types on writing GIFTI DataArrays
  ...

Author: htwangtw

.azure-pipelines/windows.yml

@@ -10,6 +10,7 @@ jobs:
     vmImage: ${{ parameters.vmImage }}
   variables:
     EXTRA_WHEELS: "https://5cf40426d9f06eb7461d-6fe47d9331aba7cd62fc36c7196769e4.ssl.cf2.rackcdn.com"
+    DEPENDS: numpy scipy matplotlib h5py pydicom
   strategy:
     matrix:
       ${{ insert }}: ${{ parameters.matrix }}
@@ -20,11 +21,14 @@ jobs:
         versionSpec: '$(PYTHON_VERSION)'
         addToPath: true
         architecture: '$(PYTHON_ARCH)'
+    - script: |
+        echo %PYTHONHASHSEED%
+      displayName: 'Display hash seed'
     - script: |
         python -m pip install --upgrade pip setuptools>=30.3.0 wheel
       displayName: 'Update build tools'
     - script: |
-        python -m pip install --find-links %EXTRA_WHEELS% numpy scipy matplotlib h5py pydicom
+        python -m pip install --find-links %EXTRA_WHEELS% %DEPENDS%
         python -m pip install nose mock coverage codecov
       displayName: 'Install dependencies'
     - script: |

.coveragerc

@@ -6,3 +6,4 @@ omit =
     */externals/*
     */benchmarks/*
     */tests/*
+    nibabel/_version.py

.gitattributes

@@ -1 +1 @@
-nibabel/COMMIT_INFO.txt export-subst
+nibabel/_version.py export-subst

.github/CODE_OF_CONDUCT.md

@@ -0,0 +1,107 @@
+# Community Guidelines
+
+Nibabel is a [NIPY](https://nipy.org) project, and we strive to adhere to the
+[NIPY Community Code](https://nipy.org/conduct.html), reproduced below.
+
+The NIPY community is a community of practice devoted to the use of the Python programming language
+in the analysis of neuroimaging data. The following code of conduct is a guideline for our behavior
+as we participate in this community.
+
+It is based on, and heavily inspired by a reading of the Python community code of conduct, the
+Apache foundation code of conduct, the Debian code of conduct, and the Ten Principles of Burning
+Man.
+
+## The code of conduct for the NIPY community
+
+The Neuroimaging in Python (NIPY) community is made up of members with a diverse set of skills,
+personalities, background, and experiences. We welcome these differences because they are the
+source of diverse ideas, solutions and decisions about our work. Decisions we make affect users,
+colleagues, and through scientific results, the general public. We take these consequences
+seriously when making decisions. When you are working with members of the community, we encourage
+you to follow these guidelines, which help steer our interactions and help keep NIPY a positive,
+successful, and growing community.
+
+### A member of the NIPY community is:
+
+#### Open
+
+Members of the community are open to collaboration. Be it on the reuse of data, on the
+implementation of methods, on finding technical solutions, establishing best practices, and
+otherwise. We are accepting of all who wish to take part in our activities, fostering an
+environment where anyone can participate and everyone can make a difference.
+
+#### Be collaborative!
+
+Our work will be used by other people, and in turn we will depend on the work of others. When we
+make something for the benefit of others, we are willing to explain to others how it works, so that
+they can build on the work to make it even better. We are willing to provide constructive criticism
+on the work of others and accept criticism of our own work, as the experiences and skill sets of
+other members contribute to the whole of our efforts.
+
+#### Be inquisitive!
+
+Nobody knows everything! Asking questions early avoids many problems later, so questions are
+encouraged, though they may be directed to the appropriate forum. Those who are asked should be
+responsive and helpful, within the context of our shared goal of improving neuroimaging practice.
+
+#### Considerate
+
+Members of the community are considerate of their peers. We are thoughtful when addressing the
+efforts of others, keeping in mind that often-times the labor was completed simply for the good of
+the community. We are attentive in our communications, whether in person or online, and we are
+tactful when approaching differing views.
+
+#### Be careful in the words that you choose:
+
+We value courtesy, kindness and inclusiveness in all our interactions. Therefore, we take
+responsibility for our own speech. In particular, we avoid:
+
+ * Personal insults.
+ * Violent threats or language directed against another person.
+ * Sexist, racist, or otherwise discriminatory jokes and language.
+ * Any form of sexual or violent material.
+ * Sharing private content, such as emails sent privately or non-publicly, or unlogged forums such
+   as IRC channel history.
+ * Excessive or unnecessary profanity.
+ * Repeated harassment of others. In general, if someone asks you to stop, then stop.
+ * Advocating for, or encouraging, any of the above behaviour.
+
+#### Try to be concise in communication
+
+Keep in mind that what you write once will be read by many others. Writing a short email means
+people can understand the conversation as efficiently as possible. Even short emails should always
+strive to be empathetic, welcoming, friendly and patient. When a long explanation is necessary,
+consider adding a summary.
+
+Try to bring new ideas to a conversation, so that each message adds something unique to the
+conversation. Keep in mind that, when using email, the rest of the thread still contains the other
+messages with arguments that have already been made.
+
+Try to stay on topic, especially in discussions that are already fairly long and complex.
+
+#### Respectful
+
+Members of the community are respectful. We are respectful of others, their positions, their
+skills, their commitments, and their efforts. We are respectful of the volunteer and professional
+efforts that permeate the NIPY community. We are respectful of the processes set forth in the
+community, and we work within them. When we disagree, we are courteous and kind in raising our
+issues.
+
+## Incident Reporting
+
+We put great value on respectful, friendly and helpful communication.
+
+If you feel that any of our Nibabel communications lack respect, or are unfriendly or unhelpful,
+please try the following steps:
+
+* If you feel able, please let the person who has sent the email or comment that you found it
+  disrespectful / unhelpful / unfriendly, and why;
+
+* If you don't feel able to do that, or that didn't work, please contact Chris Markiewicz directly
+  by email (<[email protected]>), and he will do his best to resolve it.
+  If you don't feel comfortable contacting Chris, please email Matthew Brett
+  (<[email protected]>) instead.
+
+## Attribution
+
+The vast majority of the above was taken from the NIPY Code of Conduct.

.github/CONTRIBUTING.md

@@ -0,0 +1,16 @@
+# Contributing to NiBabel
+
+Welcome to the NiBabel repository!
+We're excited you're here and want to contribute.
+
+Please see the [NiBabel Developer Guidelines][link_devguide] on our
+on our [documentation website][link_docs].
+
+These guidelines are designed to make it as easy as possible to get involved.
+If you have any questions that aren't discussed in our documentation, or it's
+difficult to find what you're looking for, please let us know by opening an
+[issue][link_issues]!
+
+[link_docs]: https://nipy.org/nibabel
+[link_devguide]: https://nipy.org/nibabel/devel/devguide.html
+[link_issues]: https://github.com/poldracklab/fmriprep/issues

.gitmodules

@@ -16,3 +16,6 @@
 [submodule "nibabel-data/nitest-cifti2"]
 	path = nibabel-data/nitest-cifti2
 	url = https://github.com/demianw/nibabel-nitest-cifti2.git
+[submodule "nibabel-data/nitest-dicom"]
+	path = nibabel-data/nitest-dicom
+	url = https://github.com/effigies/nitest-dicom

.pep8speaks.yml

@@ -0,0 +1,12 @@
+scanner:
+    diff_only: True  # Only show errors caused by the patch
+    linter: flake8
+
+message:  # Customize the comment made by the bot
+    opened:  # Messages when a new PR is submitted
+        header: "Hello @{name}, thank you for submitting the Pull Request!"
+        footer: "To test for issues locally, `pip install flake8` and then run `flake8 nibabel`."
+    updated:  # Messages when new commits are added to the PR
+        header: "Hello @{name}, Thank you for updating!"
+        footer: "To test for issues locally, `pip install flake8` and then run `flake8 nibabel`."
+    no_errors: "Cheers! There are no style issues detected in this Pull Request. :beers: "

.travis.yml

@@ -8,144 +8,118 @@ dist: xenial
 sudo: true
 language: python
 
-cache:
-  directories:
-    - $HOME/.cache/pip
+cache: pip
 env:
     global:
-        - DEPENDS="six numpy scipy matplotlib h5py pillow pydicom"
-        - OPTIONAL_DEPENDS=""
+        - SETUP_REQUIRES="pip setuptools>=30.3.0 wheel"
+        - DEPENDS="numpy scipy matplotlib h5py pillow pydicom indexed_gzip"
         - INSTALL_TYPE="setup"
         - CHECK_TYPE="test"
         - EXTRA_WHEELS="https://5cf40426d9f06eb7461d-6fe47d9331aba7cd62fc36c7196769e4.ssl.cf2.rackcdn.com"
         - PRE_WHEELS="https://7933911d6844c6c53a7d-47bd50c35cd79bd838daf386af554a83.ssl.cf2.rackcdn.com"
         - EXTRA_PIP_FLAGS="--find-links=$EXTRA_WHEELS"
         - PRE_PIP_FLAGS="--pre $EXTRA_PIP_FLAGS --find-links $PRE_WHEELS"
+
 python:
-    - 3.5
     - 3.6
     - 3.7
+
 matrix:
   include:
-    - python: 3.4
-      dist: trusty
-      sudo: false
-    # Absolute minimum dependencies
-    - python: 2.7
+    # Basic dependencies only
+    - python: 3.5
       env:
-        - DEPENDS="numpy==1.8 setuptools==30.3.0"
+        - DEPENDS="-r requirements.txt"
+    # Clean install
+    - python: 3.5
+      env:
+        - DEPENDS=""
+        - CHECK_TYPE=skiptests
     # Absolute minimum dependencies
-    - python: 2.7
+    - python: 3.5
       env:
-        - DEPENDS="numpy==1.8"
-        - CHECK_TYPE="import"
+        - SETUP_REQUIRES="setuptools==30.3.0"
+        - DEPENDS="-r min-requirements.txt"
     # Absolute minimum dependencies plus oldest MPL
-    # Check these against:
-    # nibabel/info.py
-    # doc/source/installation.rst
-    # requirements.txt
-    - python: 2.7
+    - python: 3.5
       env:
-        - DEPENDS="numpy==1.8 matplotlib==1.3.1"
+        - DEPENDS="-r min-requirements.txt matplotlib==1.3.1"
     # Minimum pydicom dependency
-    - python: 2.7
+    - python: 3.5
       env:
-        - DEPENDS="numpy==1.8 pydicom==0.9.9 pillow==2.6"
+        - DEPENDS="-r min-requirements.txt pydicom==0.9.9 pillow==2.6"
     # pydicom master branch
     - python: 3.5
       env:
         - DEPENDS="numpy git+https://github.com/pydicom/pydicom.git@master"
-    # test 2.7 against pre-release builds of everything
-    - python: 2.7
+    # test 3.7 against pre-release builds of everything
+    - python: 3.7
       env:
         - EXTRA_PIP_FLAGS="$PRE_PIP_FLAGS"
-    # test 3.5 against pre-release builds of everything
     - python: 3.5
-      env:
-        - EXTRA_PIP_FLAGS="$PRE_PIP_FLAGS"
-    - python: 2.7
       env:
         - INSTALL_TYPE=sdist
-    - python: 2.7
+    - python: 3.5
       env:
         - INSTALL_TYPE=wheel
-    - python: 2.7
-      env:
-        - INSTALL_TYPE=requirements
-    - python: 2.7
+    - python: 3.5
       env:
         - INSTALL_TYPE=archive
-    - python: 2.7
-      env:
-        - CHECK_TYPE="style"
     - python: 3.5
       env:
         - CHECK_TYPE="style"
     # Documentation doctests
-    - python: 2.7
-      env:
-        - CHECK_TYPE="doc_doctests"
     - python: 3.5
       env:
-        - CHECK_TYPE="doc_doctests"
-    # Run tests with indexed_gzip present
-    - python: 2.7
-      env:
-        - OPTIONAL_DEPENDS="indexed_gzip"
-    - python: 3.5
-      env:
-        - OPTIONAL_DEPENDS="indexed_gzip"
+        - CHECK_TYPE="doc"
+
+# Set up virtual environment, build package, build from depends
 before_install:
-    - travis_retry python -m pip install --upgrade pip
-    - travis_retry pip install --upgrade virtualenv
+    - travis_retry python -m pip install --upgrade pip virtualenv
     - virtualenv --python=python venv
     - source venv/bin/activate
     - python --version # just to check
-    - travis_retry pip install -U pip setuptools>=27.0 wheel
-    - travis_retry pip install coverage
-    - if [ "${CHECK_TYPE}" == "test" ]; then
-      travis_retry pip install nose mock;
-      fi
-    - if [ "${CHECK_TYPE}" == "style" ]; then
-      travis_retry pip install flake8;
+    - travis_retry pip install -U $SETUP_REQUIRES
+    - |
+      if [ "$INSTALL_TYPE" == "sdist" ]; then
+        python setup.py egg_info  # check egg_info while we're here
+        python setup.py sdist
+        export ARCHIVE=$( ls dist/*.tar.gz )
+      elif [ "$INSTALL_TYPE" == "wheel" ]; then
+        python setup.py bdist_wheel
+        export ARCHIVE=$( ls dist/*.whl )
+      elif [ "$INSTALL_TYPE" == "archive" ]; then
+        export ARCHIVE="package.tar.gz"
+        git archive -o $ARCHIVE HEAD
       fi
-    - travis_retry pip install $EXTRA_PIP_FLAGS $DEPENDS $OPTIONAL_DEPENDS
+    - if [ -n "$DEPENDS" ]; then pip install $EXTRA_PIP_FLAGS $DEPENDS; fi
+
 # command to install dependencies
 install:
     - |
       if [ "$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
-          pip install $EXTRA_PIP_FLAGS dist/*.tar.gz
-      elif [ "$INSTALL_TYPE" == "wheel" ]; then
-          python setup_egg.py bdist_wheel
-          pip install $EXTRA_PIP_FLAGS dist/*.whl
-      elif [ "$INSTALL_TYPE" == "requirements" ]; then
-          pip install $EXTRA_PIP_FLAGS -r requirements.txt
-          python setup.py install
-      elif [ "$INSTALL_TYPE" == "archive" ]; then
-          git archive -o package.tar.gz HEAD
-          pip install $EXTRA_PIP_FLAGS package.tar.gz
+      else
+          pip install $EXTRA_PIP_FLAGS $ARCHIVE
       fi
+    # Basic import check
+    - python -c 'import nibabel; print(nibabel.__version__)'
+    - if [ "$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]"
+
 # command to run tests, e.g. python setup.py test
 script:
     - |
       if [ "${CHECK_TYPE}" == "style" ]; then
           # Run styles only on core nibabel code.
           flake8 nibabel
-      elif [ "${CHECK_TYPE}" == "import" ]; then
-          # Import nibabel without attempting to test
-          # Allows us to check missing dependencies masked by testing libraries
-          printf 'import nibabel\nprint(nibabel.__version__)\n' > import_only.py
-          cat import_only.py
-          coverage run import_only.py
-      elif [ "${CHECK_TYPE}" == "doc_doctests" ]; then
+      elif [ "${CHECK_TYPE}" == "doc" ]; then
           cd doc
-          pip install -r ../doc-requirements.txt
           make html;
           make doctest;
       elif [ "${CHECK_TYPE}" == "test" ]; then
@@ -157,12 +131,10 @@ script:
       else
           false
       fi
-after_success:
-    - |
-      if [ "${CHECK_TYPE}" == "test" ]; then
-        travis_retry pip install codecov
-        codecov
-      fi
+
+after_script:
+    - travis_retry pip install codecov
+    - codecov
 
 notifications:
     webhooks: http://nipy.bic.berkeley.edu:54856/travis