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.
Message #20 received at 25834 <at> debbugs.gnu.org (full text, mbox):
From: Thomas Danckaert <thomas.danckaert <at> gmail.com> To: 25834 <at> debbugs.gnu.org Cc: Thomas Danckaert <post <at> thomasdanckaert.be> Subject: [PATCH 4/7] gnu: python-numpy: Update to 1.12.0. Date: Wed, 22 Feb 2017 12:22:50 +0100
From: Thomas Danckaert <post <at> thomasdanckaert.be>
* gnu/packages/python.scm (python-numpy): Update to 1.12.0.
[source]: Use github instead of sourceforge.
[native-inputs]: Add python-cython.
To simplify the handling of dependency cycles (numpy documentation depends
on matplotlib, which depends on numpy), we split out the documentation into
a separate package:
(python-numpy-bootstrap, python2-numpy-bootstrap): Remove variables.
(python-numpy-documentation, python2-numpy-documentation): New variables.
---
gnu/packages/python.scm | 146 ++++++++++++++++++++++++++----------------------
1 file changed, 79 insertions(+), 67 deletions(-)
diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 95cea0e89..c45cc9db4 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -3278,24 +3278,26 @@ between language specification and implementation aspects.")
;; This version of numpy is missing the documentation and is only used to
;; build matplotlib which is required to build numpy's documentation.
-(define python-numpy-bootstrap
+(define-public python-numpy
(package
- (name "python-numpy-bootstrap")
- (version "1.10.4")
+ (name "python-numpy")
+ (version "1.12.0")
(source
(origin
(method url-fetch)
- (uri (string-append "mirror://sourceforge/numpy/NumPy/" version
- "/numpy-" version ".tar.gz"))
+ (uri (string-append
+ "https://github.com/numpy/numpy/archive/v" version ".tar.gz"))
+ (file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
- "1bjjhvncraka5s6i4lg644jrxij6bvycxy7an20gcz3a0m11iygp"))))
+ "025d4j4aakcp8w5i5diqh812cbbjgac7jszx1j56ivrbi1i8vv7d"))))
(build-system python-build-system)
(inputs
`(("openblas" ,openblas)
("lapack" ,lapack)))
(native-inputs
- `(("python-nose" ,python-nose)
+ `(("python-cython" ,python-cython)
+ ("python-nose" ,python-nose)
("gfortran" ,gfortran)))
(arguments
`(#:phases
@@ -3344,8 +3346,8 @@ and Fortran code, useful linear algebra, Fourier transform, and random number
capabilities.")
(license license:bsd-3)))
-(define python2-numpy-bootstrap
- (package-with-python2 python-numpy-bootstrap))
+(define-public python2-numpy
+ (package-with-python2 python-numpy))
(define-public python-munch
(package
@@ -3401,69 +3403,79 @@ Models, is a program for performing both single-SNP and SNP-set genome-wide
association studies (GWAS) on extremely large data sets.")
(license license:asl2.0)))
-(define-public python-numpy
- (package (inherit python-numpy-bootstrap)
- (name "python-numpy")
- (outputs '("out" "doc"))
- (inputs
- `(("which" ,which)
- ,@(package-inputs python-numpy-bootstrap)))
- (propagated-inputs
- `(("python-matplotlib" ,python-matplotlib)
- ("python-pyparsing" ,python-pyparsing)
- ,@(package-propagated-inputs python-numpy-bootstrap)))
+(define-public python-numpy-documentation
+ (package (inherit python-numpy)
+ (name "python-numpy-documentation")
(native-inputs
- `(("pkg-config" ,pkg-config)
+ `(("python-matplotlib" ,python-matplotlib)
+ ("python-numpy" ,python-numpy)
+ ("pkg-config" ,pkg-config)
("python-sphinx" ,python-sphinx)
("python-numpydoc" ,python-numpydoc)
("texlive" ,texlive)
("texinfo" ,texinfo)
("perl" ,perl)
- ,@(package-native-inputs python-numpy-bootstrap)))
- (arguments
- `(,@(substitute-keyword-arguments
- (package-arguments python-numpy-bootstrap)
- ((#:phases phases)
- `(alist-cons-after
- 'install 'install-doc
- (lambda* (#:key inputs outputs #:allow-other-keys)
- ;; Make installed package available for building the
- ;; documentation
- (add-installed-pythonpath inputs outputs)
- (let* ((data (string-append (assoc-ref outputs "doc") "/share"))
- (doc (string-append
- data "/doc/" ,name "-"
- ,(package-version python-numpy-bootstrap)))
- (info (string-append data "/info"))
- (html (string-append doc "/html"))
- (pyver ,(string-append "PYVER=")))
- (with-directory-excursion "doc"
- (mkdir-p html)
- (system* "make" "html" pyver)
- (system* "make" "latex" "PAPER=a4" pyver)
- (system* "make" "-C" "build/latex"
- "all-pdf" "PAPER=a4" pyver)
- ;; FIXME: Generation of the info file fails.
- ;; (system* "make" "info" pyver)
- ;; (mkdir-p info)
- ;; (copy-file "build/texinfo/numpy.info"
- ;; (string-append info "/numpy.info"))
- (for-each (lambda (file)
- (copy-file (string-append "build/latex" file)
- (string-append doc file)))
- '("/numpy-ref.pdf" "/numpy-user.pdf"))
- (with-directory-excursion "build/html"
- (for-each (lambda (file)
- (let* ((dir (dirname file))
- (tgt-dir (string-append html "/" dir)))
- (unless (equal? "." dir)
- (mkdir-p tgt-dir))
- (install-file file html)))
- (find-files "." ".*"))))))
- ,phases)))))))
-
-(define-public python2-numpy
- (package-with-python2 python-numpy))
+ ("scipy-sphinx-theme"
+ ,(origin ; The build script expects scipy-sphinx-theme as a git submodule
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/scipy/scipy-sphinx-theme.git")
+ (commit "c466764e22")))
+ (sha256
+ (base32
+ "0q2y87clwlsgc7wvlsn9pzyssybcq10plwhq2w1ydykfsyyqbmkl"))))
+ ,@(package-native-inputs python-numpy)))
+ (arguments
+ `(#:tests? #f ; we're only generating the documentation
+ #:phases
+ (modify-phases %standard-phases
+ (delete 'build)
+ (replace 'install
+ (lambda* (#:key inputs outputs #:allow-other-keys)
+ ;; Make installed package available for building the
+ ;; documentation
+ (add-installed-pythonpath inputs outputs)
+ (let* ((data (string-append (assoc-ref outputs "out") "/share"))
+ (doc (string-append
+ data "/doc/" ,name "-"
+ ,(package-version python-numpy)))
+ (info-reader (string-append data "/info"))
+ (html (string-append doc "/html"))
+ (scipy-sphinx-theme "scipy-sphinx-theme")
+ (sphinx-theme-checkout (assoc-ref inputs scipy-sphinx-theme))
+ (pyver ,(string-append "PYVER=")))
+ (with-directory-excursion "doc"
+ (copy-recursively sphinx-theme-checkout scipy-sphinx-theme)
+ (mkdir-p html)
+ (system* "make" "html" pyver)
+ (system* "make" "latex" "PAPER=a4" pyver)
+ (system* "make" "-C" "build/latex"
+ "all-pdf" "PAPER=a4" pyver)
+ ;; FIXME: Generation of the info file fails.
+ ;; (system* "make" "info" pyver)
+ ;; (mkdir-p info)
+ ;; (copy-file "build/texinfo/numpy.info"
+ ;; (string-append info "/numpy.info"))
+ (for-each (lambda (file)
+ (copy-file (string-append "build/latex" file)
+ (string-append doc file)))
+ '("/numpy-ref.pdf" "/numpy-user.pdf"))
+ (with-directory-excursion "build/html"
+ (for-each (lambda (file)
+ (let* ((dir (dirname file))
+ (tgt-dir (string-append html "/" dir)))
+ (unless (equal? "." dir)
+ (mkdir-p tgt-dir))
+ (install-file file html)))
+ (find-files "." ".*"))))))))))
+ (synopsis "Documentation for the python-numpy package")))
+
+(define-public python2-numpy-documentation
+ (let ((numpy-documentation (package-with-python2 python-numpy-documentation)))
+ (package
+ (inherit numpy-documentation)
+ (native-inputs `(("python2-functools32" ,python2-functools32)
+ ,@(package-native-inputs numpy-documentation))))))
(define-public python-pygit2
(package
@@ -3682,7 +3694,7 @@ between colorspaces like sRGB, XYZ, CIEL*a*b*, CIECAM02, CAM02-UCS, etc.")
("gobject-introspection" ,gobject-introspection)
("python-tkinter" ,python "tk")
("python-dateutil" ,python-dateutil-2)
- ("python-numpy" ,python-numpy-bootstrap)
+ ("python-numpy" ,python-numpy)
("python-pillow" ,python-pillow)
("python-pytz" ,python-pytz)
("python-six" ,python-six)
--
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1997,2003 nCipher Corporation Ltd,
1994-97 Ian Jackson.