Remove elements that don't appear necessary

.gitmodules

@@ -1,5 +0,0 @@
-[submodule "tests/data/ds000005-fmriprep"]
-	path = tests/data/ds000005-fmriprep
-	url = https://gin.g-node.org/nipreps-data/ds000005-fmriprep
-	datalad-id = 92e566e4-1c80-434e-a4d7-5bf9fb483d76
-	datalad-url = https://gin.g-node.org/nipreps-data/ds000005-fmriprep

.zenodo.json

@@ -10,7 +10,7 @@
   ],
   "creators": [
     {
-      "affiliation": "Department of Psychology, Florida International University",
+      "affiliation": "University of Pennsylvania",
       "name": "Salo, Taylor",
       "orcid": "0000-0001-9813-3167"
     },

README.rst

@@ -31,6 +31,11 @@ Here are a few of the key features:
         In this case, the fMRIPost-AROMA workflow will pull a transform from MNI152NLin2009cAsym
         to MNI152NLin6Asym from TemplateFlow and apply it,
         along with the boldref-to-MNI152NLin2009cAsym transform, to the boldref-space derivatives.
+    -   fMRIPrep with ``--level full`` and raw BOLD data.
+        In this case, the fMRIPost workflow will apply minimal preprocessing steps internally
+        to generate the required derivatives.
+        This will rarely be used, but may be useful for fMRIPost workflows that require raw data,
+        like fMRIPost-phase.
 
     .. warning::
 
@@ -40,3 +45,20 @@ Here are a few of the key features:
 
 4.  General NiPreps infrastructure for running a BIDS App, such as a config file,
     a command-line interface, and tools to generate HTML reports.
+
+
+*****
+Usage
+*****
+
+If you use this template to create a new fMRIPost workflow, you will need to:
+
+1.  Replace all instances of ``fmripost_template`` with the name of your new workflow.
+2.  Replace all instances of ``fMRIPost-template`` with the name of your new workflow.
+3.  Modify the workflows and interfaces to apply your desired processing steps.
+4.  Update the documentation to reflect the new workflow.
+
+Please also include something like the following in your boilerplate:
+
+> Data were postprocessed using *fMRIPost-<name>*,
+> which is based on *fMRIPost-template* ([cite fMRIPost-template version and DOI here]).

docs/api.rst

@@ -1,20 +1,23 @@
 .. include:: links.rst
 
-================
+################
 Developers - API
-================
+################
 
+***************************************************
 The *NiPreps* community and contributing guidelines
----------------------------------------------------
+***************************************************
 
 *fMRIPost-template* is a *NiPreps* application, and abides by the
 `NiPreps Community guidelines <https://www.nipreps.org/community/>`__.
 Please, make sure you have read and understood all the documentation
 provided in the `NiPreps portal <https://www.nipreps.org>`__ before
 you get started.
 
+
+***************************************
 Setting up your development environment
----------------------------------------
+***************************************
 
 We believe that *fMRIPost-template* must be free to use, inspect, and critique.
 Correspondingly, you should be free to modify our software to improve it
@@ -27,13 +30,17 @@ As part of such efforts, we maintain some
 `tips and guidelines for developers <https://www.nipreps.org/devs/devenv/>`__
 to help minimize your burden if you want to modify the software.
 
+
+*****************************
 Internal configuration system
------------------------------
+*****************************
 
 .. automodule:: fmripost_template.config
    :members: from_dict, load, get, dumps, to_filename, init_spaces
 
+
+*********
 Workflows
----------
+*********
 
 .. automodule:: fmripost_template.workflows.base

docs/changes.rst

@@ -1,7 +1,7 @@
 .. include:: links.rst
 
-----------
+##########
 What's new
-----------
+##########
 
 .. include:: ../CHANGES.rst

docs/conf.py

@@ -51,6 +51,7 @@
     'sphinx.ext.linkcode',
     'sphinx.ext.napoleon',
     'sphinxarg.ext',  # argparse extension
+    'sphinxcontrib.bibtex',  # to include references in docs
     'nipype.sphinxext.plot_workflow',
 ]
 
@@ -151,6 +152,13 @@
 # If true, `todo` and `todoList` produce output, else they produce nothing.
 todo_include_todos = False
 
+# -----------------------------------------------------------------------------
+# sphinxcontrib-bibtex
+# -----------------------------------------------------------------------------
+bibtex_bibfiles = ['../src/fmripost_template/data/boilerplate.bib']
+bibtex_style = 'unsrt'
+bibtex_reference_style = 'author_year'
+bibtex_footbibliography_header = ''
 
 # -- Options for HTML output ----------------------------------------------
 

docs/faq.rst

@@ -1,15 +1,17 @@
 .. include:: links.rst
 
-================================
+################################
 FAQ - Frequently Asked Questions
-================================
+################################
 
 .. contents::
     :local:
     :depth: 1
 
+
+*****************
 What is fMRIPost?
------------------
+*****************
 
 fMRIPost workflows are BIDS Apps that ingress fMRI preprocessing derivative datasets.
 They fall under the broader umbrella of NiPost workflows,

docs/index.rst

@@ -6,8 +6,9 @@
 .. include:: links.rst
 .. include:: ../README.rst
 
+********
 Contents
---------
+********
 
 .. toctree::
    :maxdepth: 3

docs/installation.rst

@@ -1,29 +1,34 @@
 .. include:: links.rst
 
-------------
+############
 Installation
-------------
+############
+
 *fMRIPost-template* should be installed using container technologies.
 
 .. code-block:: bash
   docker pull nipreps/fmripost-template:main
 
 
+************************************************
 Containerized execution (Docker and Singularity)
-================================================
+************************************************
+
 *fMRIPost-template* is a *NiPreps* application, and therefore follows some overarching principles
 of containerized execution drawn from the BIDS-Apps protocols.
 For detailed information of containerized execution of *NiPreps*, please visit the corresponding
 `Docker <https://www.nipreps.org/apps/docker/>`__
 or `Singularity <https://www.nipreps.org/apps/singularity/>`__ subsections.
 
+
 External Dependencies
----------------------
-*fMRIPost-template* is written using Python 3.8 (or above), and is based on
+=====================
+
+*fMRIPost-template* is written using Python 3.11 (or above), and is based on
 nipype_.
 
 *fMRIPost-template* requires some other neuroimaging software tools that are
-not handled by the Python's packaging system (Pypi):
+not handled by the Python's packaging system (PyPi):
 
 - FSL_ (version 6.0.7.7)
 - ANTs_ (version 2.5.1)
@@ -33,8 +38,11 @@ not handled by the Python's packaging system (Pypi):
 - `bids-validator <https://github.com/bids-standard/bids-validator>`_ (version 1.14.0)
 - `connectome-workbench <https://www.humanconnectome.org/software/connectome-workbench>`_ (version 1.5.0)
 
+
+***********************************************
 Not running on a local machine? - Data transfer
-===============================================
+***********************************************
+
 If you intend to run *fMRIPost-template* on a remote system, you will need to
 make your data available within that system first.
 

docs/license.rst

@@ -1,11 +1,15 @@
+#######################################
 About the *NiPreps* framework licensing
----------------------------------------
+#######################################
+
 Please check https://www.nipreps.org/community/licensing/ for detailed
 information on the criteria we use to license *fMRIPost-template* and other
 projects of the framework.
 
+
+*******************
 License information
--------------------
+*******************
 Copyright (c) the *NiPreps* Developers.
 
 *fMRIPost-template* is licensed under the Apache License, Version 2.0 (the "License");

docs/links.rst

@@ -1,15 +1,11 @@
 .. _Nipype: https://nipype.readthedocs.io/en/latest/
 .. _BIDS: https://bids.neuroimaging.io/
 .. _`BIDS Derivatives`: https://bids-specification.readthedocs.io/en/stable/05-derivatives/01-introduction.html
-.. _`BEP 011`: https://bids-specification.readthedocs.io/en/bep011/05-derivatives/04-structural-derivatives.html
-.. _`BEP 012`: https://bids-specification.readthedocs.io/en/bep012/05-derivatives/05-functional-derivatives.html
 .. _Installation: installation.html
 .. _workflows: workflows.html
 .. _FSL: https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/
 .. _ANTs: https://stnava.github.io/ANTs/
 .. _FreeSurfer: https://surfer.nmr.mgh.harvard.edu/
-.. _`submillimeter reconstruction`: https://surfer.nmr.mgh.harvard.edu/fswiki/SubmillimeterRecon
-.. _`mri_robust_template`: https://surfer.nmr.mgh.harvard.edu/fswiki/mri_robust_template
 .. _AFNI: https://afni.nimh.nih.gov/
 .. _GIFTI: https://www.nitrc.org/projects/gifti/
 .. _`Connectome Workbench`: https://www.humanconnectome.org/software/connectome-workbench.html
@@ -20,6 +16,4 @@
 .. _Singularity: https://github.com/singularityware/singularity
 ..  _SPM: https://www.fil.ion.ucl.ac.uk/spm/software/spm12/
 .. _TACC: https://www.tacc.utexas.edu/
-.. _tedana: https://github.com/me-ica/tedana
-.. _`T2* workflow`: https://tedana.readthedocs.io/en/latest/generated/tedana.workflows.t2smap_workflow.html#tedana.workflows.t2smap_workflow  # noqa
 .. _`citation boilerplate`: https://www.nipreps.org/intro/transparency/#citation-boilerplates

docs/outputs.rst

@@ -2,9 +2,9 @@
 
 .. _outputs:
 
-------------------------------
+##############################
 Outputs of *fMRIPost-template*
-------------------------------
+##############################
 
 *fMRIPost-template* outputs conform to the :abbr:`BIDS (brain imaging data structure)`
 Derivatives specification (see `BIDS Derivatives`_, along with the
@@ -23,8 +23,9 @@ upcoming `BEP 011`_ and `BEP 012`_).
     Confound time series.
 
 
+******
 Layout
-------
+******
 
 Assuming fMRIPost-template is invoked with::
 
@@ -47,24 +48,26 @@ The log directory contains `citation boilerplate`_ text.
 records metadata recommended by the BIDS standard.
 
 
+**************
 Visual Reports
---------------
+**************
 
 *fMRIPost-template* outputs summary reports,
 written to ``<output dir>/fmripost_template/sub-<label>.html``.
 These reports provide a quick way to make visual inspection of the results easy.
 
 
+**********************************
 Derivatives of *fMRIPost-template*
-----------------------------------
+**********************************
 
 Derivative data are written to
 ``<output dir>/sub-<label>/``.
 The `BIDS Derivatives`_ specification describes the naming and metadata conventions we follow.
 
 
 Functional derivatives
-~~~~~~~~~~~~~~~~~~~~~~
+======================
 
 Functional derivatives are stored in the ``func/`` subfolder.
 All derivatives contain ``task-<task_label>`` (mandatory) and ``run-<run_index>`` (optional), and
@@ -88,8 +91,9 @@ Confounds_ are saved as a :abbr:`TSV (tab-separated value)` file::
       sub-<label>_[specifiers]_desc-confounds_timeseries.tsv
       sub-<label>_[specifiers]_desc-confounds_timeseries.json
 
+
 Confounds
----------
+=========
 
 *fMRIPost-template* outputs a set of confounds that can be used to denoise the data.
 These are stored in a TSV file (``desc-template_timeseries.tsv``) and a JSON file
@@ -102,8 +106,9 @@ Columns starting with ``template_motion_`` are the raw noise ICA component time
 Columns starting with ``template_orth_motion_`` are the noise ICA component time series,
 after z-scoring and orthogonalization with respect to the signal ICA component time series.
 
+
 Confounds and "carpet"-plot on the visual reports
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+=================================================
 
 The visual reports provide several sections per task and run to aid designing
 a denoising strategy for subsequent analysis.