Drop and modify infrastructure files (#40)

Drop and modify a lot of infrastructure files.

.zenodo.json

@@ -55,6 +55,11 @@
       "affiliation": "Johns Hopkins Bloomberg School of Public Health",
       "orcid": "0000-0003-4141-1343"
     },
+    {
+      "name": "Salo, Taylor",
+      "affiliation": "Perelman School of Medicine, University of Pennsylvania",
+      "orcid": "0000-0001-9813-3167"
+    },
     {
       "name": "Sydnor, Valerie Jill",
       "affiliation": "Perelman School of Medicine, University of Pennsylvania",

CONTRIBUTING.md

@@ -1,7 +1,9 @@
-# Contributing to qsirecon
+# Contributing to QSIRecon
 
-Contributions are welcome. Please see the guidelines for contributing to fmriprep and follow those here.
+Contributions are welcome.
+Please see the guidelines for contributing to fMRIPrep and follow those here.
 
 ## Licensing
 
-qsirecon is licensed under the BSD 3-clause license. Any contributions will be licensed under the same terms.
+QSIRecon is licensed under the BSD 3-clause license.
+Any contributions will be licensed under the same terms.

LICENSE

@@ -1,4 +1,4 @@
-Copyright (c) 2015-2018, the BBL developers team.
+Copyright (c) 2024-, Lifespan Informatics and Neuroimaging Center
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without

MANIFEST.in

@@ -6,6 +6,5 @@ include requirements.txt
 include CHANGES.rst
 include LICENSE
 
-# versioneer
-include versioneer.py
+# hatchling
 include qsirecon/_version.py

README.rst

@@ -54,8 +54,8 @@ connectivity.
 
 
 Note
-------
+----
 
-The ``qsirecon`` pipeline uses much of the code from ``FMRIPREP``. It is critical
-to note that the similarities in the code **do not imply that the authors of
-FMRIPREP in any way endorse or support this code or its pipelines**.
+The ``QSIRecon`` pipeline uses much of the code from ``fMRIPrep``.
+It is critical to note that the similarities in the code
+**do not imply that the authors of fMRIPrep in any way endorse or support this code or its pipelines**.

long_description.rst

@@ -1,15 +1,11 @@
-QSIRecon borrows heavily from fMRIPrep to build workflows for preprocessing q-space images
+QSIRecon borrows heavily from fMRIPrep to build workflows for reconstructing q-space images
 such as Diffusion Spectrum Images (DSI), multi-shell HARDI and compressed sensing DSI (CS-DSI).
-It utilizes Dipy and ANTs to implement a novel high-b-value head motion correction approach
-using q-space methods such as 3dSHORE to iteratively generate head motion target images for each
-gradient direction and strength.
-
-Since qsirecon uses the fMRIPrep workflow-building strategy, it can also generate methods
-boilerplate and quality-check figures.
-
-Users can also reconstruct orientation distribution functions (ODFs), fiber orientation
+QSIRecon can reconstruct orientation distribution functions (ODFs), fiber orientation
 distributions (FODs) and perform tractography, estimate anisotropy scalars and connectivity
 estimation using a combination of Dipy, MRTrix and DSI Studio using a JSON-based pipeline
 specification.
 
+Since QSIRecon uses the fMRIPrep workflow-building strategy,
+it can also generate methods boilerplate and quality-check figures.
+
 [Documentation `qsirecon.org <https://qsirecon.readthedocs.io>`_]

pyproject.toml

@@ -134,7 +134,6 @@ exclude = '''
     | _build
     | build
     | dist
-    | qsirecon/niworkflows
   )/
   | qsirecon/_version.py
 )
@@ -156,7 +155,6 @@ exclude = [
     "qsirecon/config.py",
     "qsirecon/data/",
     "qsirecon/tests/",
-    "qsirecon/niworkflows/",
     "qsirecon/utils/sentry.py",
 ]
 ignore = ["D107", "E203", "E402", "E722", "W503", "N803", "N806", "N815", "W605"]