[JOSS] Add accepted JOSS manuscript to main (#813)

* Add manuscript. Still need to check references. * [skip-ci] Add newline at end. * Update Asyraff reference. * Remove unused citations. * Fix citations. * [skip ci] Minor change from @emdupre. * Fix in-text citations. * Add co-first authorship, corresponding, and multi-affiliations. * Remove DuPre's middle initial. Co-authored-by: Elizabeth DuPre <[email protected]> * Apply suggestions from code review Co-authored-by: Dan Handwerker <[email protected]> * Apply suggestions from code review Co-authored-by: Elizabeth DuPre <[email protected]> Co-authored-by: Joshua Teves <[email protected]> * (skip ci) Add comma Co-authored-by: Elizabeth DuPre <[email protected]> * Try out alternate formatting. * Change S0 too. * Add DOIs and fix author list Thanks @emdupre! Co-authored-by: Elizabeth DuPre <[email protected]> * Apply suggestions from code review Thanks @KirstieJane! Co-authored-by: Kirstie Whitaker <[email protected]> * Update submission date. * Update @smoia's article. Co-authored-by: Stefano Moia <[email protected]> * Remove extra URL parts from DOI. * Add newline between sections. * Address martinagvilas JOSS review comments * Edit gitignore to allow for notebooks * Correct workflow walkthrough notebooks Xlink * Sync update index, installation in docs Co-authored-by: Elizabeth DuPre <[email protected]> Co-authored-by: Dan Handwerker <[email protected]> Co-authored-by: Joshua Teves <[email protected]> Co-authored-by: Kirstie Whitaker <[email protected]> Co-authored-by: Stefano Moia <[email protected]>
ME-ICA · Sep 28, 2021 · 4d5c645 · 4d5c645
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diff --git a/.gitignore b/.gitignore
@@ -108,7 +108,6 @@ ENV/
 
 # jupyter notebooks
 .ipynb_checkpoints/
-*.ipynb
 
 # vim swap files
 *.swp
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
@@ -132,7 +132,7 @@ Make sure to always [keep your fork up to date][link_updateupstreamwiki] with th
 To test a change, you may need to set up your local repository to run a `tedana` workflow.
 To do so, run
 ```
-pip install -e .[all]
+pip install -e .'[all]'
 ```
 from within your local `tedana` repository. This should ensure all packages are correctly organized and linked on your user profile.
 

diff --git a/README.md b/README.md
@@ -1,10 +1,5 @@
 # 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.
-``TE``-``de``pendent ``ana``lysis (``tedana``) is a Python module for denoising
-multi-echo functional magnetic resonance imaging (fMRI) data.
-
 [![Latest Version](https://img.shields.io/pypi/v/tedana.svg)](https://pypi.python.org/pypi/tedana/)
 [![PyPI - Python Version](https://img.shields.io/pypi/pyversions/tedana.svg)](https://pypi.python.org/pypi/tedana/)
 [![DOI](https://zenodo.org/badge/110845855.svg)](https://zenodo.org/badge/latestdoi/110845855)
@@ -19,11 +14,10 @@ multi-echo functional magnetic resonance imaging (fMRI) data.
 [![All Contributors](https://img.shields.io/badge/all_contributors-20-orange.svg?style=flat-square)](#contributors)
 [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
 
-
-## 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.
+``TE``-``de``pendent ``ana``lysis (``tedana``) is a Python library for denoising multi-echo functional magnetic resonance imaging (fMRI) data.
+``tedana`` originally came about as a part of the [ME-ICA](https://github.com/me-ica/me-ica) pipeline, although it has since diverged.
+An important distinction is that while the ME-ICA pipeline originally performed both pre-processing and TE-dependent analysis of multi-echo fMRI data,
+``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)
 
@@ -75,6 +69,20 @@ 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](https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html).
 
+You can confirm that ``tedana`` has successfully installed by launching a Python instance and running:
+
+```python
+import tedana
+```
+
+You can check that it is available through the command line interface (CLI) with:
+
+```bash
+tedana --help
+```
+
+If no error occurs, ``tedana`` has correctly installed in your environment!
+
 ### Use and contribute to `tedana` as a developer
 
 If you aim to contribute to the `tedana` code base and/or documentation, please first read the developer installation instructions in [our contributing section](https://github.com/ME-ICA/tedana/blob/main/CONTRIBUTING.md). You can then continue to set up your preferred development environment.

diff --git a/docs/approach.rst b/docs/approach.rst
@@ -19,6 +19,8 @@ This is performed in a series of steps, including:
 .. image:: /_static/tedana-workflow.png
   :align: center
 
+We provide more detail on each step below.
+The figures shown in this walkthrough are generated in the `provided notebooks <https://github.com/ME-ICA/tedana/tree/joss/docs/notebooks>`_.
 
 ***************
 Multi-echo data

diff --git a/docs/index.rst b/docs/index.rst
@@ -4,11 +4,6 @@
 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.
-``TE``-``de``\pendent ``ana``\lysis (``tedana``) is a Python module for denoising
-multi-echo functional magnetic resonance imaging (fMRI) data.
-
 .. image:: https://img.shields.io/pypi/v/tedana.svg
    :target: https://pypi.python.org/pypi/tedana/
    :alt: Latest Version
@@ -62,14 +57,15 @@ multi-echo functional magnetic resonance imaging (fMRI) data.
 About
 *****
 
+``TE``-``de``pendent ``ana``lysis (``tedana``) is a Python library for denoising multi-echo functional magnetic resonance imaging (fMRI) data.
+``tedana`` originally came about as a part of the [ME-ICA](https://github.com/me-ica/me-ica) pipeline, although it has since diverged.
+An important distinction is that while the ME-ICA pipeline originally performed both pre-processing and TE-dependent analysis of multi-echo fMRI data,
+``tedana`` now assumes that you're working with data which has been previously preprocessed.
+
+
 .. image:: https://user-images.githubusercontent.com/7406227/40031156-57b7cbb8-57bc-11e8-8c51-5b29f2e86a48.png
   :target: http://tedana.readthedocs.io/
 
-``tedana`` originally came about as a part of the `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.
-
 For a summary of multi-echo fMRI, which is the imaging technique ``tedana`` builds on,
 visit `Multi-echo fMRI`_.
 
@@ -116,12 +112,12 @@ When using tedana, please include the following citations:
       <img src onerror='fillCitation()' alt=""/>
 
       <p>
-      2. Kundu, P., Inati, S. J., Evans, J. W., Luh, W. M. & Bandettini, P. A. (2011).
+      1. Kundu, P., Inati, S. J., Evans, J. W., Luh, W. M. & Bandettini, P. A. (2011).
       <a href=https://doi.org/10.1016/j.neuroimage.2011.12.028>Differentiating BOLD and non-BOLD signals in fMRI time series using multi-echo EPI.</a>
       <i>NeuroImage</i>, <i>60</i>, 1759-1770.
       </p>
       <p>
-      3. Kundu, P., Brenowitz, N. D., Voon, V., Worbe, Y., Vértes, P. E., Inati, S. J.,
+      1. Kundu, P., Brenowitz, N. D., Voon, V., Worbe, Y., Vértes, P. E., Inati, S. J.,
       Saad, Z. S., Bandettini, P. A., & Bullmore, E. T. (2013).
       <a href=https://doi.org/10.1073/pnas.1301725110>Integrated strategy for improving functional connectivity mapping using multiecho fMRI.</a>
       <i>Proceedings of the National Academy of Sciences</i>, <i>110</i>, 16187-16192.

diff --git a/docs/installation.rst b/docs/installation.rst
@@ -13,11 +13,27 @@ packages will need to be installed:
 - scipy
 - mapca
 
-You can then install ``tedana`` with:
+You can also install several optional dependencies, notably ``duecredit``.
+Please see the :doc:`FAQ <faq>` for more information on how tedana uses ``duecredit``.
+
+After installing relevant dependencies, you can then install ``tedana`` with:
 
 .. code-block:: bash
 
   pip install tedana
 
 In addition to the Python package, installing ``tedana`` will add the ``tedana``
 and ``t2smap`` workflow CLIs to your path.
+You can confirm that ``tedana`` has successfully installed by launching a Python instance and running:
+
+.. code-block:: python
+
+  import tedana
+
+You can check that it is available through the command line interface (CLI) with:
+
+.. code-block:: bash
+
+  tedana --help
+
+If no error occurs, ``tedana`` has correctly installed in your environment!
diff --git a/examples/plot_approach_figures.ipynb → docs/notebooks/plot_approach_figures.ipynb b/examples/plot_approach_figures.ipynb → docs/notebooks/plot_approach_figures.ipynb
diff --git a/examples/plot_metric_simulations.ipynb → docs/notebooks/plot_metric_simulations.ipynb b/examples/plot_metric_simulations.ipynb → docs/notebooks/plot_metric_simulations.ipynb
diff --git a/paper/figure_01.png b/paper/figure_01.png