From 938ab5f4a7a2bce84f6b29c167ecdc74de90b405 Mon Sep 17 00:00:00 2001
From: Vivien Kraus <vivien@planete-kraus.eu>
Date: Thu, 20 Jan 2022 17:38:47 +0100
Subject: [PATCH 04/18] gnu: Add python-nibabel.

* gnu/packages/python-science.scm (python-nibabel): New variable.
---
 gnu/packages/python-science.scm | 63 +++++++++++++++++++++++++++++++++
 1 file changed, 63 insertions(+)

diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm
index 40e31f1526..d8abf2f471 100644
--- a/gnu/packages/python-science.scm
+++ b/gnu/packages/python-science.scm
@@ -54,6 +54,7 @@ (define-module (gnu packages python-science)
   #:use-module (gnu packages sphinx)
   #:use-module (gnu packages statistics)
   #:use-module (gnu packages time)
+  #:use-module (gnu packages version-control)
   #:use-module (gnu packages xdisorg)
   #:use-module (gnu packages xml)
   #:use-module (gnu packages xorg)
@@ -1095,3 +1096,65 @@ (define-public python-eeglabio
     (synopsis "I/O support for EEGLAB files in Python")
     (description "I/O support for EEGLAB files in Python.")
     (license license:bsd-3)))
+
+(define-public python-nibabel
+  (package
+    (name "python-nibabel")
+    (version "3.2.1")
+    (source (origin
+              (method url-fetch)
+              (uri (pypi-uri "nibabel" version))
+              (sha256
+               (base32
+                "17n23w7y0hiz2vma5si7wy184d59bp14zd8nr6hi203ldd1gjbsd"))))
+    (build-system python-build-system)
+    (arguments
+     (list #:phases
+           #~(modify-phases %standard-phases
+               (add-after 'unpack 'fix-tests
+                 (lambda _
+                   ;; Some tests have a setup function, but it is not called
+                   ;; (!)
+                   (for-each (lambda (fix)
+                               (let ((file (open-file (string-append
+                                                       "nibabel/streamlines/tests/test_"
+                                                       (car fix) ".py") "a")))
+                                 (format file "
+~a()"
+                                         (cdr fix))
+                                 (close-port file)))
+                             '(("array_sequence" . "setup_module")
+                               ("streamlines" . "setup")
+                               ("tck" . "setup_module")
+                               ("tractogram" . "setup_module")
+                               ("trk" . "setup_module"))))))))
+    (propagated-inputs (list python-numpy python-packaging))
+    (native-inputs (list python-coverage
+                         python-gitpython
+                         python-pytest
+                         python-pytest-cov
+                         python-pytest-doctestplus
+                         python-twine))
+    (home-page "https://nipy.org/nibabel/")
+    (synopsis "Access a multitude of neuroimaging data formats")
+    (description
+     "This package provides read +/- write access to some common
+medical and neuroimaging file formats, including:
+@url{http://www.grahamwideman.com/gw/brain/analyze/formatdoc.htm,
+ANALYZE} (plain, SPM99, SPM2 and later),
+@url{https://www.nitrc.org/projects/gifti, GIFTI},
+@url{http://nifti.nimh.nih.gov/nifti-1/, NIfTI1},
+@url{http://nifti.nimh.nih.gov/nifti-2/, NIfTI2},
+@url{https://www.nitrc.org/projects/cifti/, CIFTI-2},
+@url{https://en.wikibooks.org/wiki/MINC/Reference/MINC1_File_Format_Reference,
+MINC1},
+@url{https://en.wikibooks.org/wiki/MINC/Reference/MINC2.0_File_Format_Reference,
+MINC2}, @url{https://afni.nimh.nih.gov/pub/dist/src/README.attributes, AFNI
+BRIK/HEAD},
+@url{https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MghFormat, MGH} and
+@url{http://xmedcon.sourceforge.net/Docs/Ecat, ECAT} as well as Philips
+PAR/REC.  We can read and write @url{https://surfer.nmr.mgh.harvard.edu/,
+FreeSurfer} geometry, annotation and morphometry files.  There is some very
+limited support for @url{http://medical.nema.org/, DICOM}.  NiBabel is the
+successor of @url{http://niftilib.sourceforge.net/pynifti/, PyNIfTI}.")
+    (license license:expat)))
-- 
2.34.0