Package: guix-patches;
Reported by: Thomas Danckaert <post <at> thomasdanckaert.be>
Date: Wed, 22 Feb 2017 10:31:01 UTC
Severity: normal
Tags: patch
Merged with 25705
Done: Marius Bakke <mbakke <at> fastmail.com>
Bug is archived. No further changes may be made.
View this message in rfc822 format
From: Thomas Danckaert <thomas.danckaert <at> gmail.com> To: 25834 <at> debbugs.gnu.org Cc: Thomas Danckaert <post <at> thomasdanckaert.be> Subject: bug#25834: [PATCH 7/7] gnu: python-scipy: Update to 0.18.1. Date: Wed, 22 Feb 2017 12:22:53 +0100
From: Thomas Danckaert <post <at> thomasdanckaert.be>
* gnu/packages/python.scm (python-scipy): Update to 0.18.1.
[source]: Use github instead of sourceforge.
[native-inputs]: Add python-cython.
---
gnu/packages/python.scm | 113 +++++++++++++++++++++++-------------------------
1 file changed, 53 insertions(+), 60 deletions(-)
diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 9a842cbf7..0b60d4926 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -3900,16 +3900,16 @@ functions.")
(define-public python-scipy
(package
(name "python-scipy")
- (version "0.16.0")
+ (version "0.18.1")
(source
(origin
(method url-fetch)
-; http://downloads.sourceforge.net/project/scipy/scipy/0.16.1/scipy-0.16.1.tar.gz
- (uri (string-append "mirror://sourceforge/scipy/scipy/" version
- "/scipy-" version ".tar.xz"))
+ (uri (string-append "https://github.com/scipy/scipy/archive/v"
+ version ".tar.gz"))
+ (file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
- "0wa0a4skpda3gx7lb12yn19nhbairlyxrvda2lz2bcawk3x5qzz2"))))
+ "17slsrfawjp7if6qrlx03zhgp05350ginxx8ddpw9zqx43x905sn"))))
(build-system python-build-system)
(propagated-inputs
`(("python-numpy" ,python-numpy)
@@ -3919,22 +3919,22 @@ functions.")
`(("lapack" ,lapack)
("openblas" ,openblas)))
(native-inputs
- `(("python-nose" ,python-nose)
+ `(("python-cython" ,python-cython)
+ ("python-nose" ,python-nose)
("python-sphinx" ,python-sphinx)
("python-numpydoc" ,python-numpydoc)
("gfortran" ,gfortran)
- ("texlive" ,texlive)
("perl" ,perl)))
(outputs '("out" "doc"))
(arguments
`(#:phases
- (alist-cons-before
- 'build 'configure-openblas
- (lambda* (#:key inputs #:allow-other-keys)
- (call-with-output-file "site.cfg"
- (lambda (port)
- (format port
- "[blas]
+ (modify-phases %standard-phases
+ (add-before 'build 'configure-openblas
+ (lambda* (#:key inputs #:allow-other-keys)
+ (call-with-output-file "site.cfg"
+ (lambda (port)
+ (format port
+ "[blas]
libraries = openblas
library_dirs = ~a/lib
include_dirs = ~a/include
@@ -3944,53 +3944,46 @@ include_dirs = ~a/include
library_dirs = ~a/lib
atlas_libs = openblas
"
- (assoc-ref inputs "openblas")
- (assoc-ref inputs "openblas")
- (assoc-ref inputs "openblas"))))
- #t)
- (alist-cons-after
- 'install 'install-doc
- (lambda* (#:key inputs outputs #:allow-other-keys)
- (let* ((data (string-append (assoc-ref outputs "doc") "/share"))
- (doc (string-append data "/doc/" ,name "-" ,version))
- (html (string-append doc "/html"))
- (pyver ,(string-append "PYVER=")))
- ;; Make installed package available for building the
- ;; documentation
+ (assoc-ref inputs "openblas")
+ (assoc-ref inputs "openblas")
+ (assoc-ref inputs "openblas"))))
+ #t))
+ (add-after 'install 'install-doc
+ (lambda* (#:key inputs outputs #:allow-other-keys)
+ (let* ((data (string-append (assoc-ref outputs "doc") "/share"))
+ (doc (string-append data "/doc/" ,name "-" ,version))
+ (html (string-append doc "/html"))
+ (pyver ,(string-append "PYVER=")))
+ ;; Make installed package available for building the
+ ;; documentation
+ (add-installed-pythonpath inputs outputs)
+ (with-directory-excursion "doc"
+ ;; Fix generation of images for mathematical expressions.
+ (substitute* (find-files "source" "conf\\.py")
+ (("pngmath_use_preview = True")
+ "pngmath_use_preview = False"))
+ (mkdir-p html)
+ (system* "make" "html" pyver)
+ (with-directory-excursion "build/html"
+ (for-each (lambda (file)
+ (let* ((dir (dirname file))
+ (tgt-dir (string-append html "/" dir)))
+ (install-file file html)))
+ (find-files "." ".*")))))))
+ (add-after 'unpack 'fix-tests
+ (lambda _
+ (substitute* "scipy/integrate/tests/test_quadpack.py"
+ (("libm.so") "libm.so.6"))
+ #t))
+ ;; Tests can only be run after the library has been installed and not
+ ;; within the source directory.
+ (delete 'check)
+ (add-after 'install 'check
+ (lambda* (#:key inputs outputs #:allow-other-keys)
(add-installed-pythonpath inputs outputs)
- (with-directory-excursion "doc"
- ;; Fix generation of images for mathematical expressions.
- (substitute* (find-files "source" "conf\\.py")
- (("pngmath_use_preview = True")
- "pngmath_use_preview = False"))
- (mkdir-p html)
- (system* "make" "html" pyver)
- (system* "make" "latex" "PAPER=a4" pyver)
- (system* "make" "-C" "build/latex" "all-pdf" "PAPER=a4" pyver)
- (copy-file "build/latex/scipy-ref.pdf"
- (string-append doc "/scipy-ref.pdf"))
- (with-directory-excursion "build/html"
- (for-each (lambda (file)
- (let* ((dir (dirname file))
- (tgt-dir (string-append html "/" dir)))
- (install-file file html)))
- (find-files "." ".*"))))))
- ;; Tests can only be run after the library has been installed and not
- ;; within the source directory.
- (alist-cons-after
- 'install 'check
- (lambda _
- (with-directory-excursion "/tmp"
- (zero? (system* "python" "-c" "import scipy; scipy.test()"))))
- (alist-delete
- 'check
- (alist-cons-after
- 'unpack 'fix-tests
- (lambda _
- (substitute* "scipy/integrate/tests/test_quadpack.py"
- (("libm.so") "libm.so.6"))
- #t)
- %standard-phases)))))))
+ (with-directory-excursion "/tmp"
+ (zero? (system* "python" "-c"
+ "import scipy; scipy.test('full', 2)"))))))))
(home-page "http://www.scipy.org/")
(synopsis "The Scipy library provides efficient numerical routines")
(description "The SciPy library is one of the core packages that make up
--
2.11.1
GNU bug tracking system
Copyright (C) 1999 Darren O. Benham,
1997,2003 nCipher Corporation Ltd,
1994-97 Ian Jackson.