@@ 40,6 40,8 @@
;;; Copyright © 2023, 2025 Artyom V. Poptsov <poptsov.artyom@gmail.com>
;;; Copyright © 2024 chris <chris@bumblehead.com>
;;; Copyright © 2025 Josep Bigorra <jjbigorra@gmail.com>
+;;; Copyright © 2025 Jake Forster <jakecameron.forster@gmail.com>
+;;; Copyright © 2025 Ghislain Vaillant <ghislain.vaillant@inria.fr>
;;;
;;; This file is part of GNU Guix.
;;;
@@ 2024,48 2026,88 @@ and decompress to 32-bit and big-endian pixel buffers (RGBX, XBGR, etc.).")
"1kyhczwa17qp8ik3v876yjqsf4zrjj0z3464j04fak269cii404g"))))))
(define-public niftilib
- (package
- (name "niftilib")
- (version "2.0.0")
- (source (origin
- (method url-fetch)
- (uri (list (string-append "mirror://sourceforge/niftilib/"
- "nifticlib/nifticlib_"
- (string-join (string-split version #\.) "_")
- "/nifticlib-" version ".tar.gz")))
- (sha256
- (base32 "123z9bwzgin5y8gi5ni8j217k7n683whjsvg0lrpii9flgk8isd3"))))
- (build-system gnu-build-system)
- (arguments
- '(#:tests? #f ; there is no test target
- #:parallel-build? #f ; not supported
- #:make-flags
- (list "SHELL=bash"
- (string-append "ZLIB_INC="
- (assoc-ref %build-inputs "zlib") "/include")
- ;; Append "-fPIC" to CFLAGS.
- (string-append "CFLAGS="
- "-Wall -ansi -pedantic -fPIC"))
- #:phases
- (modify-phases %standard-phases
- (replace 'install
- (lambda* (#:key outputs #:allow-other-keys)
- (let ((out (assoc-ref outputs "out")))
- (for-each
- (lambda (dir)
- (copy-recursively dir (string-append out "/" dir)))
- '("bin" "lib" "include")))
- #t))
- (delete 'configure))))
- (inputs
- (list zlib))
- (synopsis "Library for reading and writing files in the nifti-1 format")
- (description "Niftilib is a set of i/o libraries for reading and writing
-files in the nifti-1 data format - a binary file format for storing
-medical image data, e.g. magnetic resonance image (MRI) and functional MRI
-(fMRI) brain images.")
- (home-page "https://niftilib.sourceforge.net")
- (license license:public-domain)))
+ ;; Warning: The version of the test data may not match the package version.
+ (let* ((nifti-test-data-version "3.0.2")
+ (nifti-test-data-file (git-file-name "nifti-test-data"
+ nifti-test-data-version)))
+ (package
+ (name "niftilib")
+ (version "3.0.1")
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/NIFTI-Imaging/nifti_clib")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "0hamm6nvbjdjjd5md4jahzvn5559frigxaiybnjkh59ckxwb1hy4"))))
+ (build-system cmake-build-system)
+ (arguments
+ (list
+ #:configure-flags
+ #~(append
+ (list "-DBUILD_SHARED_LIBS=ON"
+ "-DDOWNLOAD_TEST_DATA=OFF"
+ ;; Test data directory must be writeable.
+ (string-append "-Dfetch_testing_data_SOURCE_DIR="
+ (canonicalize-path ".") "/source/test-data")
+ "-DUSE_CIFTI_CODE=ON")
+ ;; Unable to generate manual pages via help2man when cross-compiling.
+ (if #$(%current-target-system)
+ '()
+ (list "-DNIFTI_INSTALL_NO_DOCS=FALSE")))
+ #:phases
+ #~(modify-phases %standard-phases
+ (add-after 'unpack 'set-version
+ (lambda _
+ (substitute* "CMakeLists.txt"
+ (("0.0.0.0") #$version))))
+ (add-after 'unpack 'prepare-test-data
+ (lambda* (#:key tests? #:allow-other-keys)
+ (when tests?
+ (copy-recursively #$(this-package-native-input
+ nifti-test-data-file)
+ "test-data"))))
+ (add-after 'unpack 'patch-tests
+ (lambda* (#:key tests? #:allow-other-keys)
+ (when tests?
+ (substitute* (string-append "nifti2/nifti_regress_test/"
+ "cmake_testscripts/"
+ "install_linking_test.sh")
+ (("real_easy") "source/real_easy")))))
+ (delete 'check)
+ (add-after 'install 'check
+ (lambda args
+ ;; The 'install_linking' test invokes this package's binaries.
+ (setenv "PATH" (string-append (getenv "PATH") ":"
+ #$output "/bin"))
+ (apply (assoc-ref %standard-phases 'check) args))))))
+ (inputs (list expat zlib))
+ (native-inputs
+ (append
+ (list
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/NIFTI-Imaging/nifti-test-data")
+ (commit (string-append "v" nifti-test-data-version))))
+ (file-name nifti-test-data-file)
+ (sha256
+ (base32 "0jdm8amix7pvfb1zmrb89f7izji2s8fpbfncgamczsngc11yfgcp"))))
+ (if (%current-target-system)
+ '()
+ (list help2man))))
+ (synopsis
+ "C libraries for reading and writing files in @acronym{NIfTI, Neuroimaging
+Informatics Technology Initiative} formats")
+ (description
+ "@code{Nifti_clib} is a set of I/O libraries for reading and writing files
+in the nifti-1, nifti-2, and (to some degree) cifti file formats. These are
+binary file formats for storing medical image data, e.g. @acronym{MRI, magnetic
+resonance imaging} and @acronym{fMRI, functional MRI} brain images.")
+ (home-page "https://github.com/NIFTI-Imaging/nifti_clib")
+ (license license:public-domain))))
(define-public mini
(package