Rename all preafq stuff to dmriprep.

Addresses #7.

Author: arokem

.github/ISSUE_TEMPLATE.md

@@ -1,4 +1,4 @@
-* preAFQ version:
+* dmriprep version:
 * Python version:
 * Operating System:
 

.gitignore

@@ -100,3 +100,6 @@ ENV/
 
 # mypy
 .mypy_cache/
+
+# Mac OS nonsense:
+.DS_Store

.travis.yml

@@ -4,14 +4,14 @@ node_js:
 - '6.0'
 cache:
   directories:
-  - preafqViewer/node_modules
+  - dmriprepViewer/node_modules
 branches:
   only:
   - master
 notifications:
   email: false
 before_script:
-- cd preafqViewer
+- cd dmriprepViewer
 - npm prune
 script:
 - npm install
@@ -21,6 +21,6 @@ after_success:
 - bash ./deploy.sh
 env:
   global:
-  - GH_USER: akeshavan
-  - GH_REPO: preAFQ
+  - GH_USER: nipy
+  - GH_REPO: dmriprep
   - secure: 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

CONTRIBUTING.rst

@@ -15,7 +15,7 @@ Types of Contributions
 Report Bugs
 ~~~~~~~~~~~
 
-Report bugs at https://github.com/akeshavan/preafq/issues.
+Report bugs at https://github.com/nipy/dmriprep/issues.
 
 If you are reporting a bug, please include:
 
@@ -38,14 +38,14 @@ and "help wanted" is open to whoever wants to implement it.
 Write Documentation
 ~~~~~~~~~~~~~~~~~~~
 
-preAFQ could always use more documentation, whether as part of the
-official preAFQ docs, in docstrings, or even on the web in blog posts,
+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/akeshavan/preafq/issues.
+The best way to send feedback is to file an issue at https://github.com/nipy/dmriprep/issues.
 
 If you are proposing a feature:
 
@@ -57,17 +57,17 @@ If you are proposing a feature:
 Get Started!
 ------------
 
-Ready to contribute? Here's how to set up `preafq` for local development.
+Ready to contribute? Here's how to set up `dmriprep` for local development.
 
-1. Fork the `preafq` repo on GitHub.
+1. Fork the `dmriprep` repo on GitHub.
 2. Clone your fork locally::
 
-    $ git clone [email protected]:your_name_here/preafq.git
+    $ git clone [email protected]: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 preafq
-    $ cd preafq/
+    $ mkvirtualenv dmriprep
+    $ cd dmriprep/
     $ python setup.py develop
 
 4. Create a branch for local development::
@@ -79,7 +79,7 @@ Ready to contribute? Here's how to set up `preafq` for local development.
 5. When you're done making changes, check that your changes pass flake8 and the
    tests, including testing other Python versions with tox::
 
-    $ flake8 preafq tests
+    $ flake8 dmriprep tests
     $ python setup.py test or py.test
     $ tox
 
@@ -103,15 +103,15 @@ Before you submit a pull request, check that it meets these guidelines:
    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 2.7, 3.4, 3.5 and 3.6, and for PyPy. Check
-   https://travis-ci.org/akeshavan/preafq/pull_requests
+   https://travis-ci.org/nipy/dmriprep/pull_requests
    and make sure that the tests pass for all supported Python versions.
 
 Tips
 ----
 
 To run a subset of tests::
 
-$ py.test tests.test_preafq
+$ py.test tests.test_dmriprep
 
 
 Deploying

Makefile

@@ -51,7 +51,7 @@ clean-test: ## remove test and coverage artifacts
 	rm -fr .pytest_cache
 
 lint: ## check style with flake8
-	flake8 preafq tests
+	flake8 dmriprep tests
 
 test: ## run tests quickly with the default Python
 	py.test
@@ -60,15 +60,15 @@ test-all: ## run tests on every Python version with tox
 	tox
 
 coverage: ## check code coverage quickly with the default Python
-	coverage run --source preafq -m pytest
+	coverage run --source dmriprep -m pytest
 	coverage report -m
 	coverage html
 	$(BROWSER) htmlcov/index.html
 
 docs: ## generate Sphinx HTML documentation, including API docs
-	rm -f docs/preafq.rst
+	rm -f docs/dmriprep.rst
 	rm -f docs/modules.rst
-	sphinx-apidoc -o docs/ preafq
+	sphinx-apidoc -o docs/ dmriprep
 	$(MAKE) -C docs clean
 	$(MAKE) -C docs html
 	$(BROWSER) docs/_build/html/index.html

README.rst

@@ -1,16 +1,16 @@
 ======
-preAFQ
+dmriprep
 ======
 
 
-.. image:: https://img.shields.io/pypi/v/preafq.svg
-        :target: https://pypi.python.org/pypi/preafq
+.. image:: https://img.shields.io/pypi/v/dmriprep.svg
+        :target: https://pypi.python.org/pypi/dmriprep
 
-.. image:: https://img.shields.io/travis/akeshavan/preafq.svg
-        :target: https://travis-ci.org/akeshavan/preafq
+.. image:: https://img.shields.io/travis/akeshavan/dmriprep.svg
+        :target: https://travis-ci.org/akeshavan/dmriprep
 
-.. image:: https://readthedocs.org/projects/preafq/badge/?version=latest
-        :target: https://preafq.readthedocs.io/en/latest/?badge=latest
+.. image:: https://readthedocs.org/projects/dmriprep/badge/?version=latest
+        :target: https://dmriprep.readthedocs.io/en/latest/?badge=latest
         :alt: Documentation Status
 
 
@@ -20,7 +20,7 @@ Preprocessing of neuroimaging data in preparation for AFQ analysis
 
 
 * Free software: BSD license
-* Documentation: https://preafq.readthedocs.io.
+* Documentation: https://dmriprep.readthedocs.io.
 
 
 Features
@@ -32,10 +32,10 @@ Features
 Contributing
 ------------
 
-We love contributions! preAFQ is open source, built on open source,
+We love contributions! dmriprep is open source, built on open source,
 and we'd love to have you hang out in our community.
 
-We have developed some `guidelines`_ for contributing to preAFQ.
+We have developed some `guidelines`_ for contributing to dmriprep.
 
 **Imposter syndrome disclaimer**: We want your help. No, really.
 

preafq/__init__.py renamed to dmriprep/__init__.py

@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 
-"""Top-level package for preAFQ."""
+"""Top-level package for dmriprep."""
 
 __author__ = """Anisha Keshavan"""
 __email__ = '[email protected]'
@@ -10,7 +10,7 @@
 import logging
 import os
 
-from .preafq import upload_to_s3  # noqa
+from .dmriprep import upload_to_s3  # noqa
 from . import fetch_bids_s3  # noqa
 
 
@@ -48,7 +48,7 @@
 
 # add the handlers to the logger
 module_logger.addHandler(handler)
-module_logger.info('Started new preAFQ session')
+module_logger.info('Started new dmriprep session')
 
 # Reduce verbosity of the boto logs
 logging.getLogger('boto').setLevel(logging.WARNING)

preafq/base.py renamed to dmriprep/base.py

@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 
-"""Base datatypes for preafq"""
+"""Base datatypes for dmriprep"""
 
 from collections import namedtuple
 

preafq/cli.py renamed to dmriprep/cli.py

@@ -1,15 +1,15 @@
 # -*- coding: utf-8 -*-
 
-"""Console script for preafq."""
+"""Console script for dmriprep."""
 import sys
 import click
 
 
 @click.command()
 def main(args=None):
-    """Console script for preafq."""
+    """Console script for dmriprep."""
     click.echo("Replace this message by putting your code into "
-               "preafq.cli.main")
+               "dmriprep.cli.main")
     click.echo("See click documentation at http://click.pocoo.org/")
     return 0
 

preafq/preafq.py renamed to dmriprep/dmriprep.py

@@ -11,7 +11,7 @@
 import nibabel as nib
 
 from . import fetch_bids_s3 as fetch
-from .run_1 import run_preAFQ
+from .run_1 import run_dmriprep
 
 
 mod_logger = logging.getLogger(__name__)
@@ -47,7 +47,7 @@ def upload_to_s3(output_files, outdir, bucket, prefix, site, session, subject):
     ----------
     output_files : list
         Output files to transfer to S3. Assume that the user has passed in
-        relative paths that are appropriate to fill in after the 'preAFQ'
+        relative paths that are appropriate to fill in after the 'dmriprep'
         directory.
 
     outdir : string
@@ -78,7 +78,7 @@ def upload_to_s3(output_files, outdir, bucket, prefix, site, session, subject):
     def filename2s3key(filename):
         return '/'.join([
             prefix, site, subject, session,
-            'derivatives', 'preAFQ',
+            'derivatives', 'dmriprep',
             filename
         ])
 
@@ -106,7 +106,7 @@ def pre_afq_individual(input_s3_keys, s3_prefix, out_bucket,
     scratch_dir = op.join(workdir, 'scratch')
     out_dir = op.join(workdir, 'output')
 
-    run_preAFQ(
+    run_dmriprep(
         dwi_file=input_files.files['dwi'][0],
         dwi_file_AP=input_files.files['epi_ap'][0],
         dwi_file_PA=input_files.files['epi_pa'][0],