REF: main workflow and utilities

.dockerignore

@@ -8,8 +8,8 @@ build/**/*
 build
 dist/**/*
 dist
-fmriprep.egg-info/**/*
-fmriprep.egg-info
+dmriprep.egg-info/**/*
+dmriprep.egg-info
 .eggs/**/*
 .eggs
 
@@ -39,4 +39,4 @@ out/
 .zenodo.json
 .travis.yml
 .readthedocs.yml
-CONTRIBUTING.md
+CONTRIBUTING.rst

.gitattributes

@@ -0,0 +1 @@
+dmriprep/_version.py export-subst

.github/config.yml

@@ -5,8 +5,8 @@ newPRWelcomeComment: >
   Thanks for opening this pull request!
   We have detected this is the first time for you to contribute
   to *dMRIPrep*.
-  Please check out our [contributing guidelines](https://github.com/nipreps/dmriprep/blob/master/CONTRIBUTING.md).
-  
+  Please check out our [contributing guidelines](https://github.com/nipreps/dmriprep/blob/master/CONTRIBUTING.rst).
+
   We invite you to list yourself as a *dMRIPrep* contributor, so if your name
   is not already mentioned, please modify the
   [``.zenodo.json``](https://github.com/nipreps/dmriprep/blob/master/.zenodo.json)
@@ -25,4 +25,4 @@ newPRWelcomeComment: >
   Of course, if you want to opt-out this time there is no
   problem at all with adding your name later.
   You will be always welcome to add it in the future whenever
-  you feel it should be listed.
+  you feel it should be listed.

.github/release-drafter.yml

@@ -0,0 +1,5 @@
+template: |
+  ## Release Notes
+
+  ## CHANGES
+  $CHANGES

.github/stale.yml

@@ -0,0 +1,20 @@
+# Number of days of inactivity before an issue becomes stale
+daysUntilStale: 900
+# Number of days of inactivity before a stale issue is closed
+daysUntilClose: 200
+# Issues with these labels will never be considered stale
+exemptLabels:
+  - pinned
+  - security
+  - feature
+  - help wanted
+  - low priority
+# Label to use when marking an issue as stale
+staleLabel: stale
+# Comment to post when marking an issue as stale. Set to `false` to disable
+markComment: >
+  This issue has been automatically marked as stale because it has not had
+  recent activity. It will be closed if no further activity occurs. Thank you
+  for your contributions.
+# Comment to post when closing a stale issue. Set to `false` to disable
+closeComment: false

.gitignore

@@ -103,6 +103,3 @@ ENV/
 
 # Mac OS nonsense:
 .DS_Store
-
-#kubernetes stuff
-kubernetes/jobs/

.readthedocs.yml

@@ -0,0 +1,20 @@
+# .readthedocs.yml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+  configuration: docs/conf.py
+
+# Optionally build your docs in additional formats such as PDF and ePub
+formats: all
+
+python:
+  install:
+    - method: pip
+      path: .
+      extra_requirements:
+        - doc

.travis.yml

@@ -0,0 +1,35 @@
+# Config file for automatic testing at travis-ci.org
+
+language: python
+matrix:
+  include:
+    - python: 3.5
+      dist: trusty
+      sudo: false
+    - python: 3.6
+      dist: trusty
+      sudo: false
+    - python: 3.7
+      dist: xenial
+      sudo: true
+
+# Command to install dependencies, e.g. pip install -r requirements.txt --use-mirrors
+install: pip install -U tox-travis
+
+# Command to run tests, e.g. python setup.py test
+script: tox
+
+# Assuming you have installed the travis-ci CLI tool, after you
+# create the Github repo and add it to Travis, run the
+# following command to finish PyPI deployment setup:
+# $ travis encrypt --add deploy.password
+deploy:
+  provider: pypi
+  distributions: sdist bdist_wheel
+  user: nipy
+  password:
+    secure: PLEASE_REPLACE_ME
+  on:
+    tags: true
+    repo: tigrlab/dmriprep
+    python: 3.7

.zenodo.json

@@ -3,6 +3,11 @@
   "title": "dMRIPrep: a robust preprocessing pipeline for diffusion MRI",
   "description": "<p>dMRIPrep is a robust and easy-to-use pipeline for preprocessing of diverse dMRI data. The transparent workflow dispenses of manual intervention, thereby ensuring the reproducibility of the results.</p>",
   "creators": [
+    {
+      "affiliation": "University of Texas at Austin",
+      "name": "Pisner, Derek",
+      "orcid": "0000-0002-1228-0201"
+    },
     {
       "affiliation": "Stanford University",
       "name": "Lerma-Usabiaga, Garikoitz",

CONTRIBUTING.rst

@@ -0,0 +1,181 @@
+.. highlight:: shell
+
+============
+Contributing
+============
+
+We love contributions! dmriprep is open source, built on open source,
+and we'd love to have you hang out in our community.
+
+**Imposter syndrome disclaimer**: We want your help. No, really.
+
+There may be a little voice inside your head that is telling you that
+you're not ready to be an open source contributor; that your skills
+aren't nearly good enough to contribute. What could you possibly offer a
+project like this one?
+
+We assure you - the little voice in your head is wrong. If you can
+write code at all, you can contribute code to open source. Contributing
+to open source projects is a fantastic way to advance one's coding
+skills. Writing perfect code isn't the measure of a good developer (that
+would disqualify all of us!); it's trying to create something, making
+mistakes, and learning from those mistakes. That's how we all improve,
+and we are happy to help others learn.
+
+Being an open source contributor doesn't just mean writing code, either.
+You can help out by writing documentation, tests, or even giving
+feedback about the project (and yes - that includes giving feedback
+about the contribution process). Some of these contributions may be the
+most valuable to the project as a whole, because you're coming to the
+project with fresh eyes, so you can see the errors and assumptions that
+seasoned contributors have glossed over.
+
+Installing a development version of dmriprep
+--------------------------------------------
+
+First, you can install a development version of dmriprep by cloning this repository
+and then typing::
+
+    $ pip install -e .[dev]
+
+Activate the pre-commit formatting hook by typing::
+
+    $ pre-commit install
+
+Before committing your work, you can check for formatting issues or error by typing::
+
+    $ make lint
+    $ make test
+
+Types of Contributions
+----------------------
+
+You can contribute in many ways:
+
+Report Bugs
+~~~~~~~~~~~
+
+Report bugs at https://github.com/nipy/dmriprep/issues.
+
+If you are reporting a bug, please include:
+
+* Your operating system name and version.
+* Any details about your local setup that might be helpful in troubleshooting.
+* Detailed steps to reproduce the bug.
+
+Fix Bugs
+~~~~~~~~
+
+Look through the GitHub issues for bugs. Anything tagged with "bug" and "help
+wanted" is open to whoever wants to implement it.
+
+Implement Features
+~~~~~~~~~~~~~~~~~~
+
+Look through the GitHub issues for features. Anything tagged with "enhancement"
+and "help wanted" is open to whoever wants to implement it.
+
+Write Documentation
+~~~~~~~~~~~~~~~~~~~
+
+dmriprep could always use more documentation, whether as part of the
+official dmriprep docs, in docstrings, or even on the web in blog posts,
+articles, and such.
+
+Submit Feedback
+~~~~~~~~~~~~~~~
+
+The best way to send feedback is to file an issue at https://github.com/nipy/dmriprep/issues.
+
+If you are proposing a feature:
+
+* Explain in detail how it would work.
+* Keep the scope as narrow as possible, to make it easier to implement.
+* Remember that this is a volunteer-driven project, and that contributions
+  are welcome :)
+
+Get Started!
+------------
+
+Ready to contribute? Here's how to set up `dmriprep` for local development.
+
+1. Fork the `dmriprep` repo on GitHub.
+2. Clone your fork locally::
+
+    $ git clone git@github.com:your_name_here/dmriprep.git
+
+3. Install your local copy into a virtualenv. Assuming you have virtualenvwrapper installed, this is how you set up your fork for local development::
+
+    $ mkvirtualenv dmriprep
+    $ cd dmriprep/
+    $ python setup.py develop
+
+4. Create a branch for local development::
+
+    $ git checkout -b name-of-your-bugfix-or-feature
+
+   Now you can make your changes locally.
+
+5. When you're done making changes, check that your changes pass flake8 and the
+   tests, including testing other Python versions with tox::
+
+    $ flake8 dmriprep tests
+    $ python setup.py test or py.test
+    $ tox
+
+   To get flake8 and tox, just pip install them into your virtualenv.
+
+6. Commit your changes and push your branch to GitHub::
+
+    $ git add .
+    $ git commit -m "Your detailed description of your changes."
+    $ git push origin name-of-your-bugfix-or-feature
+
+7. Submit a pull request through the GitHub website.
+
+Pull Request Guidelines
+-----------------------
+
+Before you submit a pull request, check that it meets these guidelines:
+
+1. The pull request should include tests.
+2. If the pull request adds functionality, the docs should be updated. Put
+   your new functionality into a function with a docstring, and add the
+   feature to the list in README.rst.
+3. The pull request should work for Python 3.5, 3.6 and 3.7, and for PyPy. Check
+   https://travis-ci.org/tigrlab/dmriprep/pull_requests
+   and make sure that the tests pass for all supported Python versions.
+
+When opening a pull request, please use one of the following prefixes:
+
+* **[ENH]** for enhancements
+* **[FIX]** for bug fixes
+* **[TST]** for new or updated tests
+* **[DOC]** for new or updated documentation
+* **[STY]** for stylistic changes
+* **[REF]** for refactoring existing code
+
+Tips
+----
+
+To run a subset of tests::
+
+$ py.test tests.test_dmriprep
+
+
+Deploying
+---------
+
+A reminder for the maintainers on how to deploy.
+Make sure all your changes are committed (including an entry in HISTORY.rst).
+Then run::
+
+$ bumpversion patch # possible: major / minor / patch
+$ git push
+$ git push --tags
+
+Travis will then deploy to PyPI if tests pass.
+
+The imposter syndrome disclaimer was originally written by
+`Adrienne Lowe <https://github.com/adriennefriend>`_ for a `PyCon talk <https://www.youtube.com/watch?v=6Uj746j9Heo>`_, and was
+adapted based on its use in the README file for the `MetPy project <https://github.com/Unidata/MetPy>`_.