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

Author: Jakub Kaczmarzyk

.azure-pipelines/windows.yml

@@ -0,0 +1,49 @@
+
+parameters:
+  name: ''
+  vmImage: ''
+  matrix: []
+
+jobs:
+- job: ${{ parameters.name }}
+  pool:
+    vmImage: ${{ parameters.vmImage }}
+  variables:
+    EXTRA_WHEELS: "https://5cf40426d9f06eb7461d-6fe47d9331aba7cd62fc36c7196769e4.ssl.cf2.rackcdn.com"
+    DEPENDS: numpy scipy matplotlib h5py pydicom
+  strategy:
+    matrix:
+      ${{ insert }}: ${{ parameters.matrix }}
+
+  steps:
+    - task: UsePythonVersion@0
+      inputs:
+        versionSpec: '$(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% %DEPENDS%
+        python -m pip install nose mock coverage codecov pytest
+      displayName: 'Install dependencies'
+    - script: |
+        python -m pip install .
+        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'
+    - script: |
+        cd for_testing
+        codecov
+      displayName: 'Upload To Codecov'
+      env:
+        CODECOV_TOKEN: $(CODECOV_TOKEN)

.coveragerc

@@ -5,5 +5,5 @@ include = */nibabel/*, */nisext/*
 omit =
     */externals/*
     */benchmarks/*
-    */ast.py
-    */codegen.py
+    */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

.gitignore

@@ -16,6 +16,7 @@
 .project
 .pydevproject
 *.py.orig
+.DS_Store
 
 # Not sure what the next one is for
 *.kpf
@@ -83,3 +84,4 @@ Thumbs.db
 doc/source/reference
 venv/
 .buildbot.patch
+.vscode

.gitmodules

@@ -6,7 +6,7 @@
 	url = git://github.com/matthew-brett/nitest-minc2.git
 [submodule "nipy-ecattest"]
 	path = nibabel-data/nipy-ecattest
-	url = https://github.com/freec84/nipy-ecattest
+	url = https://github.com/effigies/nipy-ecattest
 [submodule "nibabel-data/nitest-freesurfer"]
 	path = nibabel-data/nitest-freesurfer
 	url = https://bitbucket.org/nipy/nitest-freesurfer.git
@@ -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

.mailmap

@@ -7,37 +7,56 @@
 #
 # This file is up-to-date if the command git log --format="%aN <%aE>" | sort -u
 # gives no duplicates.
-Michael Hanke <[email protected]> <mhanke-guest@82381867-18eb-0310-98a2-9474e637aba2>
-Michael Hanke <[email protected]> <[email protected]>
-Yaroslav Halchenko <[email protected]> <yoh-guest@82381867-18eb-0310-98a2-9474e637aba2>
+Alexandre Gramfort <[email protected]> Alexandre Gramfort <[email protected]>
+Ariel Rokem <[email protected]> arokem <[email protected]>
+B. Nolan Nichols <[email protected]> Nolan Nichols <[email protected]>
+Basile Pinsard <[email protected]> bpinsard <[email protected]>
+Basile Pinsard <[email protected]> bpinsard <[email protected]>
+Ben Cipollini <[email protected]> Ben Cipollini <[email protected]>
 Bertrand Thirion <[email protected]> bthirion <[email protected]>
-Stephan Gerhard <[email protected]> Stephan Gerhard <git@github.com>
+Cameron Riddell <[email protected]> <[email protected].github.com>
 Christian Haselgrove <[email protected]> Christian Haselgrove <[email protected]>
+Christopher J. Markiewicz <[email protected]> Chris Johnson <[email protected]>
+Christopher J. Markiewicz <[email protected]> Chris Markiewicz <[email protected]>
+Christopher J. Markiewicz <[email protected]> Chris Markiewicz <[email protected]>
+Christopher J. Markiewicz <[email protected]> Christopher J. Markiewicz <[email protected]>
+Christopher J. Markiewicz <[email protected]> Christopher J. Markiewicz <[email protected]>
 Cindee Madison <[email protected]> CindeeM <[email protected]>
 Cindee Madison <[email protected]> cindeem <[email protected]>
-Ian Nimmo-Smith <[email protected]> Ian Nimmo-Smith <[email protected]>
-Jean-Baptiste Poline <[email protected]> jbpoline <[email protected]>
+Demian Wassermann <[email protected]> Demian Wassermann <[email protected]>
+Dimitri Papadopoulos Orfanos <[email protected]> Dimitri Papadopoulos <[email protected]>
+Eric Larson <[email protected]> Eric89GXL <[email protected]>
+Eric Larson <[email protected]> larsoner <[email protected]>
+Fernando Pérez-García <[email protected]> Fernando <[email protected]>
 Félix C. Morency <[email protected]> Felix C. Morency <[email protected]>
 Félix C. Morency <[email protected]> Félix C. Morency <[email protected]>
-Krish Subramaniam <[email protected]> Krish Subramaniam <[email protected]>
-Eric Larson <[email protected]> Eric89GXL <[email protected]>
-Alexandre Gramfort <[email protected]> Alexandre Gramfort <[email protected]>
 Gael Varoquaux <[email protected]> GaelVaroquaux <[email protected]>
-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]> Christopher J. Markiewicz <[email protected]>
-Chris Markiewicz <[email protected]> Chris Johnson <[email protected]>
+Gregory R. Lee <[email protected]> Gregory R. Lee <[email protected]>
+Ian Nimmo-Smith <[email protected]> Ian Nimmo-Smith <[email protected]>
 Jaakko Leppäkangas <[email protected]> jaeilepp <[email protected]>
-Ariel Rokem <[email protected]> arokem <[email protected]>
-Oliver P. Hinds <[email protected]> ohinds <[email protected]>
-Marc-Alexandre Côté <[email protected]> Marc-Alexandre Cote <[email protected]>
-Satrajit Ghosh <[email protected]> Satrajit Ghosh <[email protected]>
 Jasper J.F. van den Bosch <[email protected]> Jasper <[email protected]>
-Gregory R. Lee <[email protected]> Gregory R. Lee <[email protected]>
-Demian Wassermann <[email protected]> Demian Wassermann <[email protected]>
+Jean-Baptiste Poline <[email protected]> jbpoline <[email protected]>
+Jon Haitz Legarreta <[email protected]> Jon Haitz Legarreta Gorroño <[email protected]>
+Kesshi Jordan <[email protected]> kesshijordan <[email protected]>
+Kevin S. Hahn <[email protected]> Kevin S. Hahn <[email protected]>
+Konstantinos Raktivan <[email protected]> constracti <[email protected]>
+Krish Subramaniam <[email protected]> Krish Subramaniam <[email protected]>
+Krzysztof J. Gorgolewski <[email protected]>
+Krzysztof J. Gorgolewski <[email protected]> <[email protected]>
+Marc-Alexandre Côté <[email protected]> Marc-Alexandre Cote <[email protected]>
+Mathias Goncalves <[email protected]> mathiasg <[email protected]>
+Matthew Cieslak <[email protected]> Matt Cieslak <[email protected]>
+Michael Hanke <[email protected]> <mhanke-guest@82381867-18eb-0310-98a2-9474e637aba2>
+Michael Hanke <[email protected]> <[email protected]>
+Michiel Cottaar <[email protected]> Michiel Cottaar <[email protected]>
+Ly Nguyen <[email protected]> lxn2 <[email protected]>
+Oliver P. Hinds <[email protected]> ohinds <[email protected]>
+Oscar Esteban <[email protected]>
 Paul McCarthy <[email protected]> Paul McCarthy <[email protected]>
+Satrajit Ghosh <[email protected]> Satrajit Ghosh <[email protected]>
+Serge Koudoro <[email protected]> skoudoro <[email protected]>
+Stephan Gerhard <[email protected]> Stephan Gerhard <[email protected]>
+Thomas Roos <[email protected]> Roosted7 <[email protected]>
+Venkateswara Reddy Reddam <[email protected]> R3DDY97 <[email protected]>
+Yaroslav O. Halchenko <[email protected]> <yoh-guest@82381867-18eb-0310-98a2-9474e637aba2>
+Yaroslav O. Halchenko <[email protected]> Yaroslav Halchenko <[email protected]>

.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: "