Merge pull request #1 from ME-ICA/master

update

.all-contributorsrc

@@ -85,7 +85,10 @@
         "ideas",
         "doc",
         "tutorial",
-        "question"
+        "question",
+        "bug",
+        "test",
+        "review"
       ]
     },
     {
@@ -111,6 +114,15 @@
         "review",
         "talk"
       ]
+    },
+    {
+      "login": "monicayao",
+      "name": "Monica Yao",
+      "avatar_url": "https://avatars1.githubusercontent.com/u/35382166?v=4",
+      "profile": "https://github.com/monicayao",
+      "contributions": [
+        "doc"
+      ]
     }
   ],
   "contributorsPerLine": 5,

.circleci/config.yml

@@ -34,7 +34,7 @@ jobs:
             else
                 mkdir -p /tmp/data
                 curl -L --create-dirs -o \
-                  /tmp/data/three-echo/three_echo_Cornell_zcat.nii.gz https://osf.io/e3hsn/download
+                  /tmp/data/three-echo/three_echo_Cornell_zcat.nii.gz https://osf.io/8fzse/download
             fi
       - run:
           name: Download test five-echo data

CONTRIBUTING.md

@@ -18,6 +18,11 @@ Already know what you're looking for in this guide? Jump to the following sectio
 * [Structuring contributions](#style-guide)
 * [Recognizing contributors](#recognizing-contributions)
 
+Don't know where to get started? 
+Read [Joining the conversation](#joining-the-conversation) and pop into 
+Gitter to introduce yourself! Let us know what your interests are and we 
+will help you find an issue to contribute to. Thanks so much!
+
 ## Joining the conversation
 
 `tedana` is a young project maintained by a growing group of enthusiastic developers— and we're excited to have you join!
@@ -163,6 +168,8 @@ Pull requests should be submitted early and often!
 If your pull request is not yet ready to be merged, please also include the **[WIP]** prefix.
 This tells the development team that your pull request is a "work-in-progress",
 and that you plan to continue working on it.
+We request that you do not use the Draft PR feature at this time, 
+as it interferes with our Continuous Integration tool, Travis.
 
 You can also combine the tags above, for example if you are updating both a test and
 the documentation: **[TST, DOC]**.
@@ -197,8 +204,13 @@ And, if you have any questions, please don't hesitate to ask!
 
 ## Recognizing contributors
 
-We welcome and recognize all contributions from documentation to testing to code development.
-You can see a list of current contributors in the [contributors tab][link_contributors].
+We welcome and recognize [all contributions][link_all-contributors-spec] 
+from documentation to testing to code development.
+You can see a list of current contributors in the 
+README
+(kept up to date by the [all contributors bot][link_all-contributors-bot]). 
+You can see [here][link_all-contributors-bot-usage] for instructions on
+how to use the bot.
 
 ## Thank you!
 
@@ -245,4 +257,7 @@ You're awesome. :wave::smiley:
 [link_rst_guide]: http://docs.sphinxdocs.com/en/latest/step-1.html
 
 [link_contributors]: https://github.com/ME-ICA/tedana/graphs/contributors
+[link_all-contributors-spec]: https://allcontributors.org/docs/en/specification
+[link_all-contributors-bot]: https://allcontributors.org/docs/en/bot/overview
+[link_all-contributors-bot-usage]: https://allcontributors.org/docs/en/bot/usage
 [link_stemmrolemodels]: https://github.com/KirstieJane/STEMMRoleModels

README.md

@@ -13,30 +13,29 @@ multi-echo functional magnetic resonance imaging (fMRI) data.
 [![Documentation Status](https://readthedocs.org/projects/tedana/badge/?version=latest)](http://tedana.readthedocs.io/en/latest/?badge=latest)
 [![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)
-[![All Contributors](https://img.shields.io/badge/all_contributors-9-orange.svg?style=flat-square)](#contributors)
+[![Join our tinyletter mailing list](https://img.shields.io/badge/receive-our%20newsletter%20❤%EF%B8%8F-blueviolet.svg)](https://tinyletter.com/tedana-devs)
+[![All Contributors](https://img.shields.io/badge/all_contributors-10-orange.svg)](#contributors)
 
 
 ## 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.
+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.
 
 ![http://tedana.readthedocs.io/](https://user-images.githubusercontent.com/7406227/40031156-57b7cbb8-57bc-11e8-8c51-5b29f2e86a48.png)
 
-More information and documentation can be found at https://tedana.readthedocs.io/.
+More information and documentation can be found at https://tedana.readthedocs.io.
 
 ## Installation
 
 You'll need to set up a working development environment to use `tedana`.
 To set up a local environment, you will need Python >=3.5 and the following packages will need to be installed:
 
-[numpy](http://www.numpy.org/)  
-[scipy](https://www.scipy.org/)  
-[scikit-learn](http://scikit-learn.org/stable/)  
-[nilearn](https://nilearn.github.io/)  
-[nibabel>=2.1.0](http://nipy.org/nibabel/)  
+* [numpy](http://www.numpy.org/)
+* [scipy](https://www.scipy.org/)
+* [scikit-learn](http://scikit-learn.org/stable/)
+* [nilearn](https://nilearn.github.io/)
+* [nibabel>=2.1.0](http://nipy.org/nibabel/)
 
 You can then install `tedana` with
 
@@ -45,31 +44,30 @@ 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 
+conda create -n ENVIRONMENT_NAME python=3 pip mdp numpy scikit-learn scipy
 conda activate ENVIRONMENT_NAME
 pip install nilearn nibabel
 pip install tedana
 ```
 
 `tedana` will then be available in your path.
-This will also allow any previously existing tedana installations to remain untouched.
+This will also allow any previously existing `tedana` installations to remain untouched.
 
 To exit this conda environment, use
 
 ```bash
 conda deactivate
 ```
 
-NOTE: Conda < 4.6 users will need to use the soon-to-be-deprecated option
-`source` rather than `conda` for the activation and deactivation steps.
-You can read more about managing conda environments and this discrepancy here:
-[here](https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html)
+NOTE: Conda < 4.6 users will need to use the soon-to-be-deprecated option `source` rather than `conda` for the activation and deactivation steps.
+You can read more about managing conda environments and this discrepancy [here](https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html).
 
 ## Getting involved
 
@@ -80,15 +78,22 @@ Want to learn more about our plans for developing ``tedana``?
 Have a question, comment, or suggestion?
 Open or comment on one of [our issues](https://github.com/ME-ICA/tedana/issues)!
 
-We ask that all contributions to ``tedana`` respect our [code of conduct](https://github.com/ME-ICA/tedana/blob/master/CODE_OF_CONDUCT.md).
+If you're not sure where to begin, feel free to pop into [Gitter](https://gitter.im/ME-ICA/tedana) and introduce yourself!
+We will be happy to help you find somewhere to get started.
+
+If you don't want to get lots of notifications, we send out newsletters approximately once per month though our TinyLetter mailing list.
+You can view the [previous newsletters](https://tinyletter.com/tedana-devs/archive) and/or sign up to receive future ones at [https://tinyletter.com/tedana-devs](https://tinyletter.com/tedana-devs).
+
+We ask that all contributors to ``tedana`` across all project-related spaces (including but not limited to: GitHub, Gitter, and project emails), adhere to our [code of conduct](https://github.com/ME-ICA/tedana/blob/master/CODE_OF_CONDUCT.md).
 
 ## Contributors
 
 Thanks goes to these wonderful people ([emoji key](https://allcontributors.org/docs/en/emoji-key)):
 
 <!-- ALL-CONTRIBUTORS-LIST:START - Do not remove or modify this section -->
 <!-- prettier-ignore -->
-<table><tr><td align="center"><a href="https://github.com/dowdlelt"><img src="https://avatars2.githubusercontent.com/u/15126366?v=4" width="100px;" alt="Logan Dowdle"/><br /><sub><b>Logan Dowdle</b></sub></a><br /><a href="https://github.com/ME-ICA/tedana/commits?author=dowdlelt" title="Code">💻</a> <a href="#question-dowdlelt" title="Answering Questions">💬</a> <a href="#design-dowdlelt" title="Design">🎨</a> <a href="https://github.com/ME-ICA/tedana/issues?q=author%3Adowdlelt" title="Bug reports">🐛</a></td><td align="center"><a href="http://emdupre.me"><img src="https://avatars3.githubusercontent.com/u/15017191?v=4" width="100px;" alt="Elizabeth DuPre"/><br /><sub><b>Elizabeth DuPre</b></sub></a><br /><a href="https://github.com/ME-ICA/tedana/commits?author=emdupre" title="Code">💻</a> <a href="https://github.com/ME-ICA/tedana/commits?author=emdupre" title="Documentation">📖</a> <a href="#ideas-emdupre" title="Ideas, Planning, & Feedback">🤔</a> <a href="#infra-emdupre" title="Infrastructure (Hosting, Build-Tools, etc)">🚇</a> <a href="#review-emdupre" title="Reviewed Pull Requests">👀</a> <a href="#example-emdupre" title="Examples">💡</a> <a href="https://github.com/ME-ICA/tedana/commits?author=emdupre" title="Tests">⚠️</a> <a href="#question-emdupre" title="Answering Questions">💬</a></td><td align="center"><a href="https://github.com/javiergcas"><img src="https://avatars1.githubusercontent.com/u/7314358?v=4" width="100px;" alt="javiergcas"/><br /><sub><b>Javier Gonzalez-Castillo</b></sub></a><br /><a href="#ideas-javiergcas" title="Ideas, Planning, & Feedback">🤔</a></td><td align="center"><a href="https://github.com/handwerkerd"><img src="https://avatars3.githubusercontent.com/u/7406227?v=4" width="100px;" alt="Dan Handwerker"/><br /><sub><b>Dan Handwerker</b></sub></a><br /><a href="#design-handwerkerd" title="Design">🎨</a> <a href="https://github.com/ME-ICA/tedana/commits?author=handwerkerd" title="Documentation">📖</a> <a href="#example-handwerkerd" title="Examples">💡</a> <a href="#review-handwerkerd" title="Reviewed Pull Requests">👀</a></td><td align="center"><a href="https://github.com/prantikk"><img src="https://avatars0.githubusercontent.com/u/1636689?v=4" width="100px;" alt="prantikk"/><br /><sub><b>Prantik Kundu</b></sub></a><br /><a href="https://github.com/ME-ICA/tedana/commits?author=prantikk" title="Code">💻</a> <a href="#ideas-prantikk" title="Ideas, Planning, & Feedback">🤔</a></td></tr><tr><td align="center"><a href="http://rossmarkello.me"><img src="https://avatars0.githubusercontent.com/u/14265705?v=4" width="100px;" alt="Ross Markello"/><br /><sub><b>Ross Markello</b></sub></a><br /><a href="https://github.com/ME-ICA/tedana/commits?author=rmarkello" title="Code">💻</a> <a href="#infra-rmarkello" title="Infrastructure (Hosting, Build-Tools, etc)">🚇</a> <a href="#question-rmarkello" title="Answering Questions">💬</a></td><td align="center"><a href="http://tsalo.github.io"><img src="https://avatars3.githubusercontent.com/u/8228902?v=4" width="100px;" alt="Taylor Salo"/><br /><sub><b>Taylor Salo</b></sub></a><br /><a href="https://github.com/ME-ICA/tedana/commits?author=tsalo" title="Code">💻</a> <a href="#ideas-tsalo" title="Ideas, Planning, & Feedback">🤔</a> <a href="https://github.com/ME-ICA/tedana/commits?author=tsalo" title="Documentation">📖</a> <a href="#tutorial-tsalo" title="Tutorials">✅</a> <a href="#question-tsalo" title="Answering Questions">💬</a></td><td align="center"><a href="https://github.com/jbteves"><img src="https://avatars3.githubusercontent.com/u/26722533?v=4" width="100px;" alt="Joshua Teves"/><br /><sub><b>Joshua Teves</b></sub></a><br /><a href="#projectManagement-jbteves" title="Project Management">📆</a> <a href="https://github.com/ME-ICA/tedana/commits?author=jbteves" title="Documentation">📖</a> <a href="#review-jbteves" title="Reviewed Pull Requests">👀</a> <a href="#maintenance-jbteves" title="Maintenance">🚧</a></td><td align="center"><a href="https://whitakerlab.github.io"><img src="https://avatars1.githubusercontent.com/u/3626306?v=4" width="100px;" alt="Kirstie Whitaker"/><br /><sub><b>Kirstie Whitaker</b></sub></a><br /><a href="https://github.com/ME-ICA/tedana/commits?author=KirstieJane" title="Documentation">📖</a> <a href="#projectManagement-KirstieJane" title="Project Management">📆</a> <a href="#review-KirstieJane" title="Reviewed Pull Requests">👀</a> <a href="#talk-KirstieJane" title="Talks">📢</a></td></tr></table>
+<table><tr><td align="center"><a href="https://github.com/dowdlelt"><img src="https://avatars2.githubusercontent.com/u/15126366?v=4" width="100px;" alt="Logan Dowdle"/><br /><sub><b>Logan Dowdle</b></sub></a><br /><a href="https://github.com/ME-ICA/tedana/commits?author=dowdlelt" title="Code">💻</a> <a href="#question-dowdlelt" title="Answering Questions">💬</a> <a href="#design-dowdlelt" title="Design">🎨</a> <a href="https://github.com/ME-ICA/tedana/issues?q=author%3Adowdlelt" title="Bug reports">🐛</a></td><td align="center"><a href="http://emdupre.me"><img src="https://avatars3.githubusercontent.com/u/15017191?v=4" width="100px;" alt="Elizabeth DuPre"/><br /><sub><b>Elizabeth DuPre</b></sub></a><br /><a href="https://github.com/ME-ICA/tedana/commits?author=emdupre" title="Code">💻</a> <a href="https://github.com/ME-ICA/tedana/commits?author=emdupre" title="Documentation">📖</a> <a href="#ideas-emdupre" title="Ideas, Planning, & Feedback">🤔</a> <a href="#infra-emdupre" title="Infrastructure (Hosting, Build-Tools, etc)">🚇</a><br /><a href="#review-emdupre" title="Reviewed Pull Requests">👀</a> <a href="#example-emdupre" title="Examples">💡</a> <a href="https://github.com/ME-ICA/tedana/commits?author=emdupre" title="Tests">⚠️</a> <a href="#question-emdupre" title="Answering Questions">💬</a></td><td align="center"><a href="https://github.com/javiergcas"><img src="https://avatars1.githubusercontent.com/u/7314358?v=4" width="100px;" alt="Javier Gonzalez-Castillo"/><br /><sub><b>Javier Gonzalez-Castillo</b></sub></a><br /><a href="#ideas-javiergcas" title="Ideas, Planning, & Feedback">🤔</a></td><td align="center"><a href="https://github.com/handwerkerd"><img src="https://avatars3.githubusercontent.com/u/7406227?v=4" width="100px;" alt="Dan Handwerker"/><br /><sub><b>Dan Handwerker</b></sub></a><br /><a href="#design-handwerkerd" title="Design">🎨</a> <a href="https://github.com/ME-ICA/tedana/commits?author=handwerkerd" title="Documentation">📖</a> <a href="#example-handwerkerd" title="Examples">💡</a> <a href="#review-handwerkerd" title="Reviewed Pull Requests">👀</a></td><td align="center"><a href="https://github.com/prantikk"><img src="https://avatars0.githubusercontent.com/u/1636689?v=4" width="100px;" alt="Prantik Kundu"/><br /><sub><b>Prantik Kundu</b></sub></a><br /><a href="https://github.com/ME-ICA/tedana/commits?author=prantikk" title="Code">💻</a> <a href="#ideas-prantikk" title="Ideas, Planning, & Feedback">🤔</a></td></tr><tr><td align="center"><a href="http://rossmarkello.me"><img src="https://avatars0.githubusercontent.com/u/14265705?v=4" width="100px;" alt="Ross Markello"/><br /><sub><b>Ross Markello</b></sub></a><br /><a href="https://github.com/ME-ICA/tedana/commits?author=rmarkello" title="Code">💻</a> <a href="#infra-rmarkello" title="Infrastructure (Hosting, Build-Tools, etc)">🚇</a> <a href="#question-rmarkello" title="Answering Questions">💬</a></td><td align="center"><a href="http://tsalo.github.io"><img src="https://avatars3.githubusercontent.com/u/8228902?v=4" width="100px;" alt="Taylor Salo"/><br /><sub><b>Taylor Salo</b></sub></a><br /><a href="https://github.com/ME-ICA/tedana/commits?author=tsalo" title="Code">💻</a> <a href="#ideas-tsalo" title="Ideas, Planning, & Feedback">🤔</a> <a href="https://github.com/ME-ICA/tedana/commits?author=tsalo" title="Documentation">📖</a> <a href="#tutorial-tsalo" title="Tutorials">✅</a><br /><a href="#question-tsalo" title="Answering Questions">💬</a><a href="https://github.com/ME-ICA/tedana/issues?q=author%3Atsalo" title="Bug reports">🐛</a> <a href="https://github.com/ME-ICA/tedana/commits?author=tsalo" title="Tests">⚠️</a> <a href="#review-tsalo" title="Reviewed Pull Requests">👀</a></td><td align="center"><a href="https://github.com/jbteves"><img src="https://avatars3.githubusercontent.com/u/26722533?v=4" width="100px;" alt="Joshua Teves"/><br /><sub><b>Joshua Teves</b></sub></a><br /><a href="#projectManagement-jbteves" title="Project Management">📆</a> <a href="https://github.com/ME-ICA/tedana/commits?author=jbteves" title="Documentation">📖</a> <a href="#review-jbteves" title="Reviewed Pull Requests">👀</a> <a href="#maintenance-jbteves" title="Maintenance">🚧</a></td><td align="center"><a href="https://whitakerlab.github.io"><img src="https://avatars1.githubusercontent.com/u/3626306?v=4" width="100px;" alt="Kirstie Whitaker"/><br /><sub><b>Kirstie Whitaker</b></sub></a><br /><a href="https://github.com/ME-ICA/tedana/commits?author=KirstieJane" title="Documentation">📖</a> <a href="#projectManagement-KirstieJane" title="Project Management">📆</a> <a href="#review-KirstieJane" title="Reviewed Pull Requests">👀</a> <a href="#talk-KirstieJane" title="Talks">📢</a></td><td align="center"><a href="https://github.com/monicayao"><img src="https://avatars1.githubusercontent.com/u/35382166?v=4" width="100px;" alt="Monica Yao"/><br /><sub><b>Monica Yao</b></sub></a><br /><a href="https://github.com/ME-ICA/tedana/commits?author=monicayao" title="Documentation">📖</a></td></tr></table>
+
 
 <!-- ALL-CONTRIBUTORS-LIST:END -->
 

docs/api.rst

@@ -80,23 +80,23 @@ API
 .. _calibration_ref:
 
 
-:mod:`tedana.model`: Computing TE-dependence metrics
+:mod:`tedana.metrics`: Computing TE-dependence metrics
 ----------------------------------------------------
 
-.. automodule:: tedana.model
+.. automodule:: tedana.metrics
    :no-members:
    :no-inherited-members:
 
-.. autosummary:: tedana.model
+.. autosummary:: tedana.metrics
    :toctree: generated/
    :template: function.rst
 
-   tedana.model.dependence_metrics
-   tedana.model.kundu_metrics
+   tedana.metrics.dependence_metrics
+   tedana.metrics.kundu_metrics
 
    :template: module.rst
 
-   tedana.model.fit
+   tedana.metrics.fit
 
 .. currentmodule:: tedana