Inital commit of tedana package

CONTRIBUTING.md

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+# Contributing to tedana
+
+Welcome to the tedana repository! We're excited you're here and want to contribute.  
+
+These guidelines are designed to make it as easy as possible to get involved. If you have any questions that aren't discussed below, please let us know by opening an [issue][link_issues]!
+
+Before you start you'll need to set up a free [GitHub][link_github] account and sign in. Here are some [instructions][link_signupinstructions].
+
+### Labels
+
+The current list of labels are [here][link_labels] and include:
+
+* [![Help Wanted](https://img.shields.io/badge/-help%20wanted-159818.svg)][link_helpwanted] *These issues contain a task that a member of the team has determined we need additional help with.*
+
+    If you feel that you can contribute to one of these issues, we especially encourage you to do so!
+
+* [![Bugs](https://img.shields.io/badge/-bugs-fc2929.svg)][link_bugs] *These issues point to problems in the project.*
+
+    If you find new a bug, please give as much detail as possible in your issue, including steps to recreate the error.
+    If you experience the same bug as one already listed, please add any additional information that you have as a comment.
+
+* [![Requests](https://img.shields.io/badge/-requests-fbca04.svg)][link_requests] *These issues are asking for new features to be added to the project.*
+
+    Please try to make sure that your requested feature is distinct from any others that have already been requested or implemented. If you find one that's similar but there are subtle differences please reference the other request in your issue.
+
+## Making a change
+
+We appreciate all contributions to tedana, but those accepted fastest will follow a workflow similar to the following:
+
+**1. Comment on an existing issue or open a new issue referencing your addition.**
+
+This allows other members of the tedana development team to confirm that you aren't overlapping with work that's currently underway and that everyone is on the same page with the goal of the work you're going to carry out.
+
+[This blog][link_pushpullblog] is a nice explanation of why putting this work in up front is so useful to everyone involved.
+
+**2. [Fork][link_fork] the [tedana repository][link_tedana] to your profile.**
+
+This is now your own unique copy of tedana. Changes here won't effect anyone else's work, so it's a safe space to explore edits to the code!
+
+Make sure to [keep your fork up to date][link_updateupstreamwiki] with the master repository.
+
+**3. Make the changes you've discussed.**
+
+Try to keep the changes focused. We've found that working on a [new branch][link_branches] makes it easier to keep your changes targeted.
+
+**4. Submit a [pull request][link_pullrequest].**
+
+A member of the development team will review your changes to confirm that they can be merged into the main codebase.
+
+## Recognizing contributions
+
+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].
+
+## Thank you!
+
+You're awesome. :wave::smiley:
+
+<br>
+
+*&mdash; Based on contributing guidelines from the [STEMMRoleModels][link_stemmrolemodels] project.*
+
+[link_github]: https://github.com/
+[link_tedana]: https://github.com/ME-ICA/tedana
+[link_signupinstructions]: https://help.github.com/articles/signing-up-for-a-new-github-account
+[link_react]: https://github.com/blog/2119-add-reactions-to-pull-requests-issues-and-comments
+[link_issues]: https://github.com/ME-ICA/tedana/issues
+[link_labels]: https://github.com/ME-ICA/tedana/labels
+[link_discussingissues]: https://help.github.com/articles/discussing-projects-in-issues-and-pull-requests
+
+[link_bugs]: https://github.com/ME-ICA/tedana/labels/bug
+[link_helpwanted]: https://github.com/ME-ICA/tedana/labels/help%20wanted
+[link_requests]: https://github.com/ME-ICA/tedana/labels/requests
+
+[link_pullrequest]: https://help.github.com/articles/creating-a-pull-request/
+[link_fork]: https://help.github.com/articles/fork-a-repo/
+[link_pushpullblog]: https://www.igvita.com/2011/12/19/dont-push-your-pull-requests/
+[link_branches]: https://help.github.com/articles/creating-and-deleting-branches-within-your-repository/
+[link_updateupstreamwiki]: https://help.github.com/articles/syncing-a-fork/
+[link_stemmrolemodels]: https://github.com/KirstieJane/STEMMRoleModels
+[link_contributors]: https://github.com/ME-ICA/tedana/graphs/contributors

Code_of_Conduct.md

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+# Code of Conduct
+
+In the interest of fostering an open and welcoming environment we want
+participation in our project and our community to be a harassment-free
+experience for everyone.
+
+Although no list can hope to be all-encompassing, we explicitly honor diversity in age,
+body size, disability, ethnicity, gender identity and expression, level of experience, native language, education, socio-economic status, nationality, personal appearance, race, religion,
+or sexual identity and orientation.
+
+## Our Standards
+
+We aim to promote behavior that contributes to a positive and welcoming environment.
+Examples of such behavior include:
+
+* Using inclusive language
+* Being respectful of differing viewpoints and experiences
+* Showing empathy towards other community members
+
+We do not tolerate harassment or other, inappropriate behavior in our community.
+Examples of unacceptable behavior by participants include:
+
+* The use of sexualized language or imagery and unwelcome sexual attention or
+  advances
+* Personal or political attacks on contributors, and insulting or derogatory
+  comments on contributed code with the intent to undermine contributions
+* Public or private harassment
+
+## Our Responsibilities
+
+The maintainers are responsible for clarifying the standards
+of acceptable behavior and are expected to take appropriate and fair corrective
+action in response to any instances of unacceptable behavior.
+
+The maintainers have the right and responsibility to remove,
+edit, or reject comments, commits, code, issues, and other contributions
+that are not aligned to this Code of Conduct, or to ban temporarily or
+permanently any contributor for other behaviors that they deem inappropriate,
+threatening, offensive, or harmful.
+
+## Scope
+
+This Code of Conduct applies both within our online GitHub repository
+and in public spaces when an individual is representing the project or its community.
+Examples of representing a project or community include using an official project e-mail
+address, posting via an official social media account, or acting as an appointed
+representative at an online or offline event.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported by contacting Elizabeth DuPre at elizabeth.dupre@mail.mcgill.ca.
+Confidentiality will be respected in reporting.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 1.4,
+available at https://www.contributor-covenant.org/version/1/4/code-of-conduct.html
+
+[homepage]: https://www.contributor-covenant.org

README.md

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 # tedana
-TE-Dependent Analysis
+
+TE-Dependent Analysis (_tedana_) is a Python module for denoising multi-echo fMRI data.
+
+tedana is part of the ME-ICA pipeline, and therefore assumes that you're working with already preprocessed data. 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.
+
+## About
+
+Multi-echo fMRI data collection entails acquires multiple TEs (commonly called [echo times](http://mriquestions.com/tr-and-te.html)) for each collected fMRI volume. Our signal of interest, Blood Oxygen-Level Dependent or [BOLD signal](http://www.fil.ion.ucl.ac.uk/spm/course/slides10-zurich/Kerstin_BOLD.pdf), is known to decay at a set rate within each fMRI volume. Collecting multiple echos therefore allows us to infer if components of fMRI signal are BOLD-related or driven by acquisition artifacts, like partipant motion. For a review, see [Kundu et al. (2017), _NeuroImage_](https://paperpile.com/shared/eH3PPu).
+
+In tedana, we combine all collected echos, then decompose the resulting timeseries into components that can be classified as BOLD or non-BOLD based. This is performed in a series of steps including:
+
+* Principle components analysis
+* Independent components analysis
+* Component classification
+
+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. We provide a Dockerfile for this purpose (check out [tips on using Docker](https://neurohackweek.github.io/docker-for-scientists/)), or you can set up your environment locally. If you choose the latter, make sure the following packages are installed:
+
+mdp  
+nilearn  
+nibabel>=2.1.0  
+numpy  
+pybids>=0.4.0  
+scikit-learn  
+
+tedana will eventually be hosted on PyPi. In the mean time, you can still install it with `pip` using:
+
+```
+pip install https://github.com/ME-ICA/tedana/archive/master.tar.gz
+```
+
+## Development
+
+We :yellow_heart: new contributors ! To get started, check out [our contributing guidelines](https://github.com/emdupre/tedana/blob/master/CONTRIBUTING.md).
+
+Want to learn more about our plans for developing tedana ? Check out [our roadmap](https://github.com/emdupre/tedana/projects). Have a question, comment, or suggestion ? Open or comment on one of [our issues](https://github.com/emdupre/tedana/issues) !
+
+We ask that all contributions to tedana respect our [code of conduct](https://github.com/emdupre/tedana/blob/master/Code_of_Conduct.md).

config.yml

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+# Python CircleCI 2.0 configuration file
+#
+# Check https://circleci.com/docs/2.0/language-python/ for more details
+#
+version: 2
+jobs:
+  build:
+    docker:
+      - image: emdupre/meica-docker:0.0.3
+
+    working_directory: /home/neuro/code/
+
+    steps:
+      - checkout
+
+      - run:
+          name: download data
+          command: curl -L -o /home/neuro/data/zcat_ffd.nii.gz https://www.dropbox.com/s/ljeqskdmnc6si9d/zcat_ffd.nii.gz?dl=0
+
+      - run:
+          name: download and unzip processed data
+          command: |
+            curl -L -o /home/neuro/data/test_res.tar.gz https://www.dropbox.com/s/yzswu6ljnfxlhyo/test_res.tar.gz?dl=0
+            tar -xvzf /home/neuro/data/test_res.tar.gz -C /home/neuro/data
+
+
+      - run:
+          name: install dependencies
+          command: |
+            conda create --name venv python=3.6
+            source activate venv
+            pip install pytest
+            pip install -r requirements.txt
+            python setup.py install
+
+      # run tests!
+      - run:
+          name: run tests
+          command: |
+            source activate venv
+            py.test ./tedana/tests/test_tedana.py
+          no_output_timeout: "40m"
+          post: bash <(curl -s https://codecov.io/bash)

docs/Makefile

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+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = python -msphinx
+SPHINXPROJ    = meica
+SOURCEDIR     = .
+BUILDDIR      = _build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/_static/theme_overrides.css

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+/* override table width restrictions */
+@media screen and (min-width: 767px) {
+
+   .wy-table-responsive table td {
+      /* !important prevents the common CSS stylesheets from overriding
+         this as on RTD they are loaded after this stylesheet */
+      white-space: normal !important;
+   }
+
+   .wy-table-responsive {
+      overflow: visible !important;
+   }
+}