Merge remote-tracking branch 'upstream/master' into doc/roadmap

README.md

@@ -1,5 +1,4 @@
-tedana: TE Dependent ANAlysis
-=============================
+# tedana: TE Dependent ANAlysis
 
 The ``tedana`` package is part of the ME-ICA pipeline, performing TE-dependent
 analysis of multi-echo functional magnetic resonance imaging (fMRI) data.
@@ -15,41 +14,57 @@ multi-echo functional magnetic resonance imaging (fMRI) data.
 [![Codecov](https://codecov.io/gh/me-ica/tedana/branch/master/graph/badge.svg)](https://codecov.io/gh/me-ica/tedana)
 [![Join the chat at https://gitter.im/ME-ICA/tedana](https://badges.gitter.im/ME-ICA/tedana.svg)](https://gitter.im/ME-ICA/tedana?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge)
 
-About
------
+## About
 
 ``tedana`` originally came about as a part of the [ME-ICA](https://github.com/me-ica/me-ica) pipeline.
 The ME-ICA pipeline originally performed both pre-processing and TE-dependent
 analysis of multi-echo fMRI data; however, ``tedana`` now assumes that you're
 working with data which has been previously preprocessed.
-If you're in need of a preprocessing pipeline, we recommend
-[fmriprep](https://github.com/poldracklab/fmriprep/), which has been tested
-for compatibility with multi-echo fMRI data and ``tedana``.
 
 ![http://tedana.readthedocs.io/](https://user-images.githubusercontent.com/7406227/40031156-57b7cbb8-57bc-11e8-8c51-5b29f2e86a48.png)
 
-Installation
-------------
+More information and documentation can be found at https://tedana.readthedocs.io/.
 
-You'll need to set up a working development environment to use ``tedana``.
-To set up a local environment, you will need Python >=3.6 and the following
-packages will need to be installed:
+## Installation
 
-- mdp
-- nilearn
-- nibabel>=2.1.0
-- numpy
-- scikit-learn
-- scipy
+You'll need to set up a working development environment to use `tedana`.
+To set up a local environment, you will need Python >=3.6 and the following packages will need to be installed:
 
-You can then install ``tedana`` with:
+[mdp](https://pypi.org/project/MDP/)  
+[numpy](http://www.numpy.org/)   
+[scikit-learn](http://scikit-learn.org/stable/)   
+[scipy](https://www.scipy.org/)    
+[nilearn](https://nilearn.github.io/)     
+[nibabel>=2.1.0](http://nipy.org/nibabel/)      
+
+You can then install `tedana` with
+
+```bash
+pip install tedana
+```
+
+### Creating a miniconda environment for use with `tedana`
+In using `tedana`, you can optionally configure [a conda environment](https://conda.io/docs/user-guide/tasks/manage-environments.html).
+
+We recommend using [miniconda3](https://conda.io/miniconda.html).
+After installation, you can use the following commands to create an environment for `tedana`:
 
 ```bash
+conda create -n ENVIRONMENT_NAME python=3 pip mdp numpy scikit-learn scipy nilearn nibabel
+source activate ENVIRONMENT_NAME
 pip install tedana
 ```
 
-Getting involved
-----------------
+`tedana` will then be available in your path.
+This will also allow any previously existing tedana installations to remain untouched.
+
+To exit this conda environment, use
+
+```bash
+source deactivate
+```
+
+## Getting involved
 
 We :yellow_heart: new contributors!
 To get started, check out [our contributing guidelines](https://github.com/ME-ICA/tedana/blob/master/CONTRIBUTING.md).

docs/contributing.rst

@@ -11,9 +11,14 @@ For a more practical guide to the tedana development, please see our
 Governance
 ----------
 
+<<<<<<< HEAD
 Governance is a hugely important part of any project.
 It is especially important to have clear process and communication channels
 for open source projects that rely on a distributed network of volunteers, such as ``tedana``.
+=======
+Style Guide
+===========
+>>>>>>> upstream/master
 
 ```tedana`` is currently supported by a small group of five core developers.
 Even with only five members involved in decision making processes,
@@ -165,7 +170,11 @@ More information about what is required for a release to proceed is available in
 .. _release checklist:
 
 Release Checklist
+<<<<<<< HEAD
 """""""""""""""""
+=======
+=================
+>>>>>>> upstream/master
 
 This is the checklist of items that must be completed when cutting a new release of tedana.
 These steps can only be completed by a project maintainer, but they are a good resource for

docs/index.rst

@@ -129,11 +129,12 @@ tedana is licensed under GNU Lesser General Public License version 2.1.
    :maxdepth: 2
    :caption: Contents:
 
+   installation
    multi-echo
    usage
-   installation
    approach
    outputs
+   support
    contributing
    roadmap
    api

docs/installation.rst

@@ -17,19 +17,3 @@ You can then install ``tedana`` with:
 .. code-block:: bash
 
   pip install tedana
-
-Getting involved
-----------------
-
-We 💛 new contributors!
-To get started, check out `our contributing guidelines`_.
-
-Want to learn more about our plans for developing ``tedana``?
-Have a question, comment, or suggestion?
-Open or comment on one of `our issues`_!
-
-We ask that all contributions to ``tedana`` respect our `code of conduct`_.
-
-.. _our contributing guidelines: https://github.com/ME-ICA/tedana/blob/master/CONTRIBUTING.md
-.. _our issues: https://github.com/ME-ICA/tedana/issues
-.. _code of conduct: https://github.com/ME-ICA/tedana/blob/master/CODE_OF_CONDUCT.md

docs/support.rst

@@ -0,0 +1,10 @@
+Support and Communication
+-------------------------
+All bugs, concerns and enhancement requests for this software can be submitted here: https://github.com/ME-ICA/tedana/issues.
+
+If you would like to ask a question about usage or tedana's outputs, please submit a question to `NeuroStars`_ with the ``multi-echo`` tag.
+
+All previous tedana-related questions are available `here`_.
+
+.. _NeuroStars: https://neurostars.org
+.. _here: https://neurostars.org/tags/multi-echo