refactor

Author: josephmje

.gitattributes

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

.github/ISSUE_TEMPLATE.md

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

.gitignore

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

.travis.yml

@@ -31,5 +31,5 @@ deploy:
     secure: PLEASE_REPLACE_ME
   on:
     tags: true
-    repo: tigrlab/dmripreproc
+    repo: tigrlab/dmriprep
     python: 3.7

AUTHORS.rst

@@ -1,14 +1,19 @@
-============
+=======
 Credits
-============
+=======
 
 Development Leads
 -----------------
 
+- Anisha Keshavan <[email protected]> [Corresponding developer]
+- Adam Richie-Halford <[email protected]>
+
 - Michael Joseph <[email protected]> [Corresponding developer]
 - Salim Mansour <[email protected]>
 
 Contributors
 ------------
 
-None yet. Why not be the first?
+- Ariel Rokem <[email protected]>
+- Michael Joseph <[email protected]>
+- Salim Mansour <[email protected]>

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 dmripreproc
+Installing a development version of dmriprep
 --------------------------------------------
 
-First, you can install a development version of dmripreproc by cloning this repository
+First, you can install a development version of dmriprep 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/tigrlab/dmripreproc/issues.
+Report bugs at https://github.com/nipy/dmriprep/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
 ~~~~~~~~~~~~~~~~~~~
 
-dmripreproc could always use more documentation, whether as part of the
-official dmripreproc 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/tigrlab/dmripreproc/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:
 
@@ -74,17 +74,17 @@ If you are proposing a feature:
 Get Started!
 ------------
 
-Ready to contribute? Here's how to set up `dmripreproc` for local development.
+Ready to contribute? Here's how to set up `dmriprep` for local development.
 
-1. Fork the `dmripreproc` repo on GitHub.
+1. Fork the `dmriprep` repo on GitHub.
 2. Clone your fork locally::
 
-    $ git clone [email protected]:your_name_here/dmripreproc.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 dmripreproc
-    $ cd dmripreproc/
+    $ mkvirtualenv dmriprep
+    $ cd dmriprep/
     $ python setup.py develop
 
 4. Create a branch for local development::
@@ -96,7 +96,7 @@ Ready to contribute? Here's how to set up `dmripreproc` 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 dmripreproc tests
+    $ flake8 dmriprep 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/tigrlab/dmripreproc/pull_requests
+   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:
@@ -137,7 +137,7 @@ Tips
 
 To run a subset of tests::
 
-$ py.test tests.test_dmripreproc
+$ py.test tests.test_dmriprep
 
 
 Deploying

Dockerfile

@@ -1,4 +1,5 @@
-FROM poldracklab/fmriprep:1.3.2
+# Use Ubuntu 16.04 LTS
+FROM ubuntu:xenial-20190610
 
 # Used command:
 # neurodocker generate docker --base=debian:stretch --pkg-manager=apt
@@ -8,16 +9,19 @@ FROM poldracklab/fmriprep:1.3.2
 # Getting required installation tools
 RUN apt-get update && \
     apt-get install -y --no-install-recommends \
+        apt-utils \
+        bzip2 \
+        ca-certificates \
+        curl \
+        locales \
+        unzip \
         bc \
         libtool \
         tar \
         dpkg \
-        curl \
         wget \
-        unzip \
         gcc \
         git \
-        bzip2 \
         libstdc++6
 
 # Neurodocker Setup
@@ -52,10 +56,12 @@ RUN export ND_ENTRYPOINT="/neurodocker/startup.sh" \
 
 ENTRYPOINT ["/neurodocker/startup.sh"]
 
+# install ANTS v2.3.1
+curl -sSL https://github.com/ANTsX/ANTs/archive/v2.3.1.tar.gz
+
+
 # ANTS (used from BIDS-Apps https://github.com/BIDS-Apps/dockerfile-templates/blob/master/ANTs/Dockerfile)
-RUN apt-get update && \
-    apt-get install -y curl && \
-		mkdir -p /opt/ants && \
+RUN mkdir -p /opt/ants && \
     curl -sSL "https://github.com/stnava/ANTs/releases/download/v2.1.0/Linux_Ubuntu14.04.tar.bz2" \
     | tar -xjC /opt/ants --strip-components 1 && \
     rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
@@ -193,12 +199,12 @@ RUN apt-get update && \
     apt-get install -y --no-install-recommends \
         libopenblas-base
 
-# setting up an install of dmripreproc (manual version) inside the container
-ADD https://api.github.com/repos/TIGRLab/dmripreproc/git/refs/heads/master version.json
-RUN git clone -b master https://github.com/TIGRLab/dmripreproc.git
-#RUN mkdir dmripreproc
-#COPY ./ dmripreproc/
-RUN cd dmripreproc && ls && python setup.py install && pip list
+# setting up an install of dmriprep (manual version) inside the container
+ADD https://api.github.com/repos/TIGRLab/dmriprep/git/refs/heads/master version.json
+RUN git clone -b master https://github.com/TIGRLab/dmriprep.git
+#RUN mkdir dmriprep
+#COPY ./ dmriprep/
+RUN cd dmriprep && ls && python setup.py install && pip list
 RUN pip install pybids==0.9.1 && pip list
 
 ENTRYPOINT ["dmriprep"]

MANIFEST.in

@@ -9,3 +9,5 @@ recursive-exclude * __pycache__
 recursive-exclude * *.py[co]
 
 recursive-include docs *.rst conf.py Makefile make.bat *.jpg *.png *.gif
+include versioneer.py
+include dmriprep/_version.py

Makefile

@@ -51,7 +51,7 @@ clean-test: ## remove test and coverage artifacts
 	rm -fr .pytest_cache
 
 lint: ## check style with flake8
-	flake8 dmripreproc 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 dmripreproc -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/dmripreproc.rst
+	rm -f docs/dmriprep.rst
 	rm -f docs/modules.rst
-	sphinx-apidoc -o docs/ dmripreproc
+	sphinx-apidoc -o docs/ dmriprep
 	$(MAKE) -C docs clean
 	$(MAKE) -C docs html
 	$(BROWSER) docs/_build/html/index.html

README.rst

@@ -1,77 +1,88 @@
-.. image:: https://codecov.io/gh/TIGRLab/dmripreproc/branch/master/graph/badge.svg
+.. highlight:: shell
+
+===========
+dmriprep
+===========
+
+.. image:: https://codecov.io/gh/TIGRLab/dmriprep/branch/master/graph/badge.svg
   :alt: Codecov Badge
-  :target: https://codecov.io/gh/TIGRLab/dmripreproc
+  :target: https://codecov.io/gh/TIGRLab/dmriprep
 .. image:: https://img.shields.io/badge/code%20style-black-000000.svg
   :alt: Black Badge
   :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="dmripreproc" src="docs/img/dmripreproc_icon.svg" height="128"> dmripreproc
+   :target: https://app.codacy.com/app/josephmje/dmriprep?utm_source=github.com&utm_medium=referral&utm_content=TIGRLab/dmriprep&utm_campaign=Badge_Grade_Dashboard
 
 Preprocessing of neuroimaging data in preparation for AFQ analysis
+------------------------------------------------------------------
 
 * Free software: BSD license
-* Documentation: https://dmripreproc.readthedocs.io.
+* Documentation: https://dmriprep.readthedocs.io.
 
-## Preparing your data
+Preparing your data
+-------------------
 
 You should have raw data organized in the BIDS format. Also, you should have run Freesurfer and the results should be in a derivatives/ folder:
 
-    BIDS_input_dir
-    ├── sub-01
-    │   ├── dwi
-    │   │   ├── sub-01_ses-01_dwi.nii.gz
-    │   │   ├── sub-01_ses-01_dwi.bval
-    │   │   ├── sub-01_ses-01_dwi.bvec
-    │   ├── fmap
-    │   │   ├── sub-01_ses-01_acq-dwi_dir-AP_epi.nii.gz
-    │   │   ├── sub-01_ses-01_acq-dwi_dir-PA_epi.nii.gz
-    │   │   ├── sub-01_ses-01_acq-dwi_dir-AP_epi.json
-    │   │   ├── sub-01_ses-01_acq-dwi_dir-PA_epi.json
-    ├── derivatives
-    │   ├── sub-01
-    │   │   ├── freesurfer
-
-## Quickstart
-
-```bash
-git clone https://github.com/tigrlab/dmripreproc
-cd dmripreproc
-python setup.py install
-
-dmripreproc $BIDS_INPUT_DIR $OUTPUT_DIR --participant-label 01
+```
+bids
+├── derivatives
+│   └── sub-01
+│       └── freesurfer
+└── sub-01
+  ├── dwi
+  │   ├── sub-01_ses-01_dwi.bval
+  │   ├── sub-01_ses-01_dwi.bvec
+  │   ├── sub-01_ses-01_dwi.json
+  │   └── sub-01_ses-01_dwi.nii.gz
+  └── fmap
+      ├── sub-01_ses-01_acq-dwi_dir-AP_epi.json
+      ├── sub-01_ses-01_acq-dwi_dir-AP_epi.nii.gz
+      ├── sub-01_ses-01_acq-dwi_dir-PA_epi.json
+      └── sub-01_ses-01_acq-dwi_dir-PA_epi.nii.gz
 ```
 
-```bash
-git clone https://github.com/tigrlab/dmripreproc
-cd dmripreproc
-make docker
+Quickstart
+----------
+
+.. code-block:: bash
+  git clone https://github.com/tigrlab/dmriprep
+  cd dmriprep
+  python setup.py install
 
-# If you don't want to log into the docker image:
+  dmriprep $BIDS_INPUT_DIR $OUTPUT_DIR --participant-label 01
 
-docker run -ti -v $BIDS_INPUT_DIR:/inputs -v $OUTPUT_DIR:/outputs dmripreproc:prod dmripreproc /inputs /outputs
+.. code-block:: bash
+git clone https://github.com/tigrlab/dmriprep
+cd dmriprep
+make docker
 
-# If you want to log into the image:
+If you don't want to log into the docker image:
+.. code-block:: bash
+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
+If you want to log into the image:
+.. code-block:: bash
+docker run -ti -v $BIDS_INPUT_DIR:/inputs -v $OUTPUT_DIR:/outputs dmriprep:prod
 
-# Run this inside the docker image:
-dmripreproc /inputs /outpus --participant-label 01
-```
+Run this inside the docker image:
+.. code-block:: bash
+dmriprep /inputs /output --participant-label 01
 
-## Features
+Features
+--------
 
 * TODO
 
-## Contributing
+Contributing
+------------
 
-We love contributions! dmripreproc 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](CONTRIBUTING.rst) for contributing to
-dmripreproc.
+dmriprep.
 
 **Imposter syndrome disclaimer**: We want your help. No, really.
 
@@ -96,7 +107,8 @@ 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.
 
-## Credits
+Credits
+-------
 
 This package was created with [Cookiecutter](https://github.com/audreyr/cookiecutter) and the [`audreyr/cookiecutter-pypackage`](https://github.com/audreyr/cookiecutter-pypackage) project template.