[DOC] Reorganize RTD sidebar and add section to release drafter (#411)

* Move FAQ and Support up a level in the sidebar. * Add "Breaking Changes" section to release drafter. * Switch order of Support and FAQ pages on sidebar. * Update release-drafter.yml Removes breaking changes st we can cut new release and continue discussing this later * Update release-drafter.yml Add in missing space
ME-ICA · Nov 6, 2019 · e57ea58 · e57ea58
1 parent c8e9786
commit e57ea58
Show file tree

Hide file tree

Showing 5 changed files with 58 additions and 56 deletions.
diff --git a/.github/release-drafter.yml b/.github/release-drafter.yml
@@ -1,7 +1,7 @@
 template: |
   ## Release Notes
 
-  
+
   ## Changes
 
   $CHANGES
diff --git a/docs/faq.rst b/docs/faq.rst
@@ -0,0 +1,38 @@
+
+FAQ
+---
+
+ICA has failed to converge.
+```````````````````````````
+The TEDICA step may fail to converge if TEDPCA is either too strict
+(i.e., there are too few components) or too lenient (there are too many).
+
+In our experience, this may happen when preprocessing has not been applied to
+the data, or when improper steps have been applied to the data (e.g., distortion
+correction, rescaling, nuisance regression).
+If you are confident that your data have been preprocessed correctly prior to
+applying tedana, and you encounter this problem, please submit a question to `NeuroStars`_.
+
+
+I think that some BOLD ICA components have been misclassified as noise.
+```````````````````````````````````````````````````````````````````````
+``tedana`` allows users to manually specify accepted components when calling the pipeline.
+You can use the ``--manacc`` argument to specify the indices of components to accept.
+
+
+Why isn't v3.2 of the component selection algorithm supported in ``tedana``?
+````````````````````````````````````````````````````````````````````````````
+There is a lot of solid logic behind the updated version of the TEDICA component
+selection algorithm, first added to the original ME-ICA codebase `here`_ by Dr. Prantik Kundu.
+However, we (the ``tedana`` developers) have encountered certain difficulties
+with this method (e.g., misclassified components) and the method itself has yet
+to be validated in any papers, posters, etc., which is why we have chosen to archive
+the v3.2 code, with the goal of revisiting it when ``tedana`` is more stable.
+
+Anyone interested in using v3.2 may compile and install an earlier release (<=0.0.4) of ``tedana``.
+
+.. _here: https://bitbucket.org/prantikk/me-ica/commits/906bd1f6db7041f88cd0efcac8a74074d673f4f5
+
+.. _NeuroStars: https://neurostars.org
+.. _fMRIPrep: https://fmriprep.readthedocs.io
+.. _afni_proc.py: https://afni.nimh.nih.gov/pub/dist/doc/program_help/afni_proc.py.html
diff --git a/docs/index.rst b/docs/index.rst
@@ -55,10 +55,10 @@ 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`_. 
+For a summary of multi-echo fMRI, which is the imaging technique ``tedana`` builds on,
+visit `Multi-echo fMRI`_.
 
-For a detailed procedure of how ``tedana`` analyzes the data from multi-echo fMRI, 
+For a detailed procedure of how ``tedana`` analyzes the data from multi-echo fMRI,
 visit `Processing pipeline details`_.
 
 .. _ME-ICA: https://github.com/me-ica/me-ica
@@ -148,6 +148,8 @@ tedana is licensed under GNU Lesser General Public License version 2.1.
    usage
    approach
    outputs
+   faq
+   support
    contributing
    roadmap
    api

diff --git a/docs/support.rst b/docs/support.rst
@@ -0,0 +1,14 @@
+.. _support_ref:
+
+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 under the `multi-echo tag`_.
+
+We will also attempt to archive certain common questions and associate answers in the Frequently Asked Questions (FAQ) page.
+
+.. _multi-echo tag: https://neurostars.org/tags/multi-echo
+.. _NeuroStars: https://neurostars.org
diff --git a/docs/usage.rst b/docs/usage.rst
@@ -100,55 +100,3 @@ are likely to differ across echos,
 and the subsequent calculation of voxelwise T2* values will be distorted.
 See the description of ``tedana``'s :doc:`approach <\approach>` for more details
 on how T2* values are calculated.
-
-.. _support_ref:
-
-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 under the `multi-echo tag`_.
-
-We will also attempt to archive certain common questions and associate answers in the Frequently Asked Questions (FAQ) section below.
-
-.. _multi-echo tag: https://neurostars.org/tags/multi-echo
-
-FAQ
----
-
-ICA has failed to converge.
-```````````````````````````
-The TEDICA step may fail to converge if TEDPCA is either too strict
-(i.e., there are too few components) or too lenient (there are too many).
-
-In our experience, this may happen when preprocessing has not been applied to
-the data, or when improper steps have been applied to the data (e.g., distortion
-correction, rescaling, nuisance regression).
-If you are confident that your data have been preprocessed correctly prior to
-applying tedana, and you encounter this problem, please submit a question to `NeuroStars`_.
-
-
-I think that some BOLD ICA components have been misclassified as noise.
-```````````````````````````````````````````````````````````````````````
-``tedana`` allows users to manually specify accepted components when calling the pipeline.
-You can use the ``--manacc`` argument to specify the indices of components to accept.
-
-
-Why isn't v3.2 of the component selection algorithm supported in ``tedana``?
-````````````````````````````````````````````````````````````````````````````
-There is a lot of solid logic behind the updated version of the TEDICA component
-selection algorithm, first added to the original ME-ICA codebase `here`_ by Dr. Prantik Kundu.
-However, we (the ``tedana`` developers) have encountered certain difficulties
-with this method (e.g., misclassified components) and the method itself has yet
-to be validated in any papers, posters, etc., which is why we have chosen to archive
-the v3.2 code, with the goal of revisiting it when ``tedana`` is more stable.
-
-Anyone interested in using v3.2 may compile and install an earlier release (<=0.0.4) of ``tedana``.
-
-.. _here: https://bitbucket.org/prantikk/me-ica/commits/906bd1f6db7041f88cd0efcac8a74074d673f4f5
-
-.. _NeuroStars: https://neurostars.org
-.. _fMRIPrep: https://fmriprep.readthedocs.io
-.. _afni_proc.py: https://afni.nimh.nih.gov/pub/dist/doc/program_help/afni_proc.py.html