Merge pull request #16 from TIGRLab/develop

Initial release

.github/ISSUE_TEMPLATE.md

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

.gitignore

@@ -103,3 +103,6 @@ ENV/
 
 # Mac OS nonsense:
 .DS_Store
+
+# data
+notebooks/data/

.travis.yml

@@ -24,5 +24,5 @@ deploy:
     secure: PLEASE_REPLACE_ME
   on:
     tags: true
-    repo: tigrlab/dmripreproc
+    repo: tigrlab/dmripreprocroc
     python: 3.7

CONTRIBUTING.rst

@@ -7,10 +7,10 @@ Contributing
 Contributions are welcome, and they are greatly appreciated! Every little bit
 helps, and credit will always be given.
 
-Installing a development version of dmriprep
+Installing a development version of dmripreproc
 --------------------------------------------
 
-First, you can install a development version of dmriprep by cloning this repository
+First, you can install a development version of dmripreproc by cloning this repository
 and then typing::
 
     $ pip install -e .[dev]
@@ -32,7 +32,7 @@ You can contribute in many ways:
 Report Bugs
 ~~~~~~~~~~~
 
-Report bugs at https://github.com/nipy/dmriprep/issues.
+Report bugs at https://github.com/nipy/dmripreproc/issues.
 
 If you are reporting a bug, please include:
 
@@ -55,14 +55,14 @@ 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,
+dmripreproc could always use more documentation, whether as part of the
+official dmripreproc 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.
+The best way to send feedback is to file an issue at https://github.com/nipy/dmripreproc/issues.
 
 If you are proposing a feature:
 
@@ -74,17 +74,17 @@ If you are proposing a feature:
 Get Started!
 ------------
 
-Ready to contribute? Here's how to set up `dmriprep` for local development.
+Ready to contribute? Here's how to set up `dmripreproc` for local development.
 
-1. Fork the `dmriprep` repo on GitHub.
+1. Fork the `dmripreproc` repo on GitHub.
 2. Clone your fork locally::
 
-    $ git clone [email protected]:your_name_here/dmriprep.git
+    $ git clone [email protected]:your_name_here/dmripreproc.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/
+    $ mkvirtualenv dmripreproc
+    $ cd dmripreproc/
     $ python setup.py develop
 
 4. Create a branch for local development::
@@ -96,7 +96,7 @@ Ready to contribute? Here's how to set up `dmriprep` 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 dmriprep tests
+    $ flake8 dmripreproc tests
     $ python setup.py test or py.test
     $ tox
 
@@ -120,7 +120,7 @@ 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 3.5, 3.6 and 3.7, and for PyPy. Check
-   https://travis-ci.org/nipy/dmriprep/pull_requests
+   https://travis-ci.org/nipy/dmripreproc/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:
@@ -137,7 +137,7 @@ Tips
 
 To run a subset of tests::
 
-$ py.test tests.test_dmriprep
+$ py.test tests.test_dmripreproc
 
 
 Deploying

Makefile

@@ -51,7 +51,7 @@ clean-test: ## remove test and coverage artifacts
 	rm -fr .pytest_cache
 
 lint: ## check style with flake8
-	flake8 dmriprep tests
+	flake8 dmripreproc 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 dmriprep -m pytest
+	coverage run --source dmripreproc -m pytest
 	coverage report -m
 	coverage html
 	$(BROWSER) htmlcov/index.html
 
 docs: ## generate Sphinx HTML documentation, including API docs
-	rm -f docs/dmriprep.rst
+	rm -f docs/dmripreproc.rst
 	rm -f docs/modules.rst
-	sphinx-apidoc -o docs/ dmriprep
+	sphinx-apidoc -o docs/ dmripreproc
 	$(MAKE) -C docs clean
 	$(MAKE) -C docs html
 	$(BROWSER) docs/_build/html/index.html

README.rst

@@ -1,17 +1,17 @@
 .. image:: https://codecov.io/gh/TIGRLab/dmripreproc/branch/master/graph/badge.svg
-  :target: https://codecov.io/gh/TIGRLab/dmripreproc  
+  :target: https://codecov.io/gh/TIGRLab/dmripreproc
 .. image:: https://img.shields.io/badge/code%20style-black-000000.svg
     :target: https://github.com/python/black
 .. image:: https://api.codacy.com/project/badge/Grade/f45ec5c64894427a8860cc87cda1910a
    :alt: Codacy Badge
    :target: https://app.codacy.com/app/josephmje/dmripreproc?utm_source=github.com&utm_medium=referral&utm_content=TIGRLab/dmripreproc&utm_campaign=Badge_Grade_Dashboard
 
-# <img alt="dmriprep" src="docs/img/dmriprep_icon.svg" height="128"> dmriprep
+# <img alt="dmripreproc" src="docs/img/dmripreproc_icon.svg" height="128"> dmripreproc
 
 Preprocessing of neuroimaging data in preparation for AFQ analysis
 
 * Free software: BSD license
-* Documentation: https://dmriprep.readthedocs.io.
+* Documentation: https://dmripreproc.readthedocs.io.
 
 ## Preparing your data
 
@@ -35,28 +35,28 @@ You should have raw data organized in the BIDS format. Also, you should have run
 ## Quickstart
 
 ```bash
-git clone https://github.com/nipy/dmriprep
-cd dmriprep
+git clone https://github.com/nipy/dmripreproc
+cd dmripreproc
 python setup.py install
 
-dmriprep $BIDS_INPUT_DIR $OUTPUT_DIR --participant-label 01
+dmripreproc $BIDS_INPUT_DIR $OUTPUT_DIR --participant-label 01
 ```
 
 ```bash
-git clone https://github.com/nipy/dmriprep
-cd dmriprep
+git clone https://github.com/nipy/dmripreproc
+cd dmripreproc
 make docker
 
 # If you don't want to log into the docker image:
 
-docker run -ti -v $BIDS_INPUT_DIR:/inputs -v $OUTPUT_DIR:/outputs dmriprep:prod dmriprep /inputs /outputs
+docker run -ti -v $BIDS_INPUT_DIR:/inputs -v $OUTPUT_DIR:/outputs dmripreproc:prod dmripreproc /inputs /outputs
 
 # If you want to log into the image:
 
-docker run -ti -v $BIDS_INPUT_DIR:/inputs -v $OUTPUT_DIR:/outputs dmriprep:prod 
+docker run -ti -v $BIDS_INPUT_DIR:/inputs -v $OUTPUT_DIR:/outputs dmripreproc:prod
 
 # Run this inside the docker image:
-dmriprep /inputs /outpus --participant-label 01
+dmripreproc /inputs /outpus --participant-label 01
 ```
 
 ## Features
@@ -65,11 +65,11 @@ dmriprep /inputs /outpus --participant-label 01
 
 ## Contributing
 
-We love contributions! dmriprep is open source, built on open source,
+We love contributions! dmripreproc is open source, built on open source,
 and we'd love to have you hang out in our community.
 
 We have developed some [guidelines](CONTRIBUTING.rst) for contributing to
-dmriprep.
+dmripreproc.
 
 **Imposter syndrome disclaimer**: We want your help. No, really.