* [patch] python-numpy, python-matplotlib and openblas update, python-cycler added
@ 2016-07-31 11:40 Pjotr Prins
2016-07-31 11:46 ` Andreas Enge
2016-08-19 6:42 ` Ricardo Wurmus
0 siblings, 2 replies; 4+ messages in thread
From: Pjotr Prins @ 2016-07-31 11:40 UTC (permalink / raw)
To: Ricardo Wurmus; +Cc: guix-devel
[-- Attachment #1: Type: text/plain, Size: 797 bytes --]
Hi Ricardo,
I ran into the eigen issue of numpy+openblas.
See https://github.com/xianyi/OpenBLAS/issues/703
The good news is that openblas now appears to have fixed eigen
support. It was broken on numpy and the upgrades fixed the segfaults.
Attached bumping of python-numpy, openblas and python-matplotlib. New
package python-cycler.
- numpy now needs setuptools
- matplotlib requires new packagen python-cycler
- matplotlib sources are now on github
- matplotlib and ipython now have a circular dependency - so I removed
one and had to disable document generation for matplotlib
We may have success getting R to work agains OpenBLAS.
Pj.
PS I thought using texlive-minimal was a good idea. Ignore those if
you think it is not supposed to be. It may be the reason the PDFs
disappeared.
[-- Attachment #2: numpy-openblas.patch --]
[-- Type: text/x-diff, Size: 8067 bytes --]
diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index b5518b0..063a6bf 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -3016,7 +3016,7 @@ writing C extensions for Python as easy as Python itself.")
(define python-numpy-bootstrap
(package
(name "python-numpy-bootstrap")
- (version "1.10.4")
+ (version "1.11.1")
(source
(origin
(method url-fetch)
@@ -3024,11 +3024,12 @@ writing C extensions for Python as easy as Python itself.")
"/numpy-" version ".tar.gz"))
(sha256
(base32
- "1bjjhvncraka5s6i4lg644jrxij6bvycxy7an20gcz3a0m11iygp"))))
+ "1kbpsnqfabpbczh3ly2d4jrwq2d1gqlshlpk5dm8bk3r77284h6w"))))
(build-system python-build-system)
(inputs
`(("python-nose" ,python-nose)
("openblas" ,openblas)
+ ("python-setuptools" ,python-setuptools)
("lapack" ,lapack)))
(native-inputs
`(("gfortran" ,gfortran)))
@@ -3130,7 +3131,7 @@ association studies (GWAS) on extremely large data sets.")
,@(package-inputs python-numpy-bootstrap)))
(native-inputs
`(("pkg-config" ,pkg-config)
- ("texlive" ,texlive)
+ ("texlive-minimal" ,texlive-minimal)
("texinfo" ,texinfo)
("perl" ,perl)
,@(package-native-inputs python-numpy-bootstrap)))
@@ -3159,10 +3160,10 @@ association studies (GWAS) on extremely large data sets.")
;; (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"))
+ ; (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))
@@ -3298,24 +3299,50 @@ transcendental functions).")
,@(alist-delete "python-numpy"
(package-propagated-inputs numexpr)))))))
+(define-public python-cycler
+ (package
+ (name "python-cycler")
+ (version "0.10.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append
+ "https://pypi.python.org/packages/c2/4b/137dea450d6e1e3d474e1d873cd1d4f7d3beed7e0dc973b06e8e10d32488/cycler-"
+ version
+ ".tar.gz"))
+ (sha256
+ (base32
+ "1n69n23fak1gjxlrbhqisi2b9pv3ckrfj98llx3p53953082syyd"))))
+ (build-system python-build-system)
+ (inputs
+ `(("python-setuptools" ,python-setuptools)
+ ("python-six" ,python-six)))
+ (home-page "http://github.com/matplotlib/cycler")
+ (synopsis "Composable style cycles")
+ (description "Composable style cycles")
+ (license bsd-3)))
+
(define-public python-matplotlib
(package
(name "python-matplotlib")
- (version "1.4.3")
+ (version "1.5.2")
(source
(origin
(method url-fetch)
- (uri (string-append "mirror://sourceforge/matplotlib/matplotlib"
- "/matplotlib-" version
- "/matplotlib-" version ".tar.gz"))
+ (uri (string-append
+ "https://github.com/matplotlib/matplotlib/archive/v"
+ version ".tar.gz"))
+ (file-name (string-append name "-" version ".tar.gz"))
(sha256
- (base32
- "1dn05cvd0g984lzhh72wa0z93psgwshbbg93fkab6slx5m3l95av"))
- (patches (search-patches "matplotlib-setupext-tk.patch"))))
+ (base32
+ "1bnr81p13l2z5kk0isngjhw458ia8jd5mg3f3qz45457rpfcad63"))
+ ; (patches (search-patches "matplotlib-setupext-tk.patch"))
+ ))
(build-system python-build-system)
(outputs '("out" "doc"))
(propagated-inputs ; the following packages are all needed at run time
- `(("python-pyparsing" ,python-pyparsing)
+ `(("python-cycler" ,python-cycler)
+ ("python-pyparsing" ,python-pyparsing)
("python-pygobject" ,python-pygobject)
("gobject-introspection" ,gobject-introspection)
("python-tkinter" ,python "tk")
@@ -3337,6 +3364,7 @@ transcendental functions).")
(inputs
`(("python-setuptools" ,python-setuptools)
("python-dateutil" ,python-dateutil-2)
+ ;; ("python-ipython" ,python-ipython) ; required for docs but circular
("python-six" ,python-six)
("python-pytz" ,python-pytz)
("python-numpy" ,python-numpy-bootstrap)
@@ -3357,7 +3385,7 @@ transcendental functions).")
("tk" ,tk)))
(native-inputs
`(("pkg-config" ,pkg-config)
- ("texlive" ,texlive)
+ ("texlive-minimal" ,texlive-minimal)
("texinfo" ,texinfo)))
(arguments
`(#:phases
@@ -3394,25 +3422,26 @@ backend = TkAgg~%"
(mkdir-p html)
(mkdir-p info)
;; The doc recommends to run the 'html' target twice.
- (system* "python" "make.py" "html")
- (system* "python" "make.py" "html")
- (copy-recursively "build/html" html)
- (system* "python" "make.py" "latex")
- (system* "python" "make.py" "texinfo")
- (symlink (string-append html "/_images")
- (string-append info "/matplotlib-figures"))
- (with-directory-excursion "build/texinfo"
- (substitute* "matplotlib.texi"
- (("@image\\{([^,]*)" all file)
- (string-append "@image{matplotlib-figures/" file)))
- (symlink (string-append html "/_images")
- "./matplotlib-figures")
- (system* "makeinfo" "--no-split"
- "-o" "matplotlib.info" "matplotlib.texi"))
- (copy-file "build/texinfo/matplotlib.info"
- (string-append info "/matplotlib.info"))
- (copy-file "build/latex/Matplotlib.pdf"
- (string-append doc "/Matplotlib.pdf")))))
+ ; (system* "python" "make.py" "html")
+ ; (system* "python" "make.py" "html")
+ ; (copy-recursively "build/html" html)
+ ; (system* "python" "make.py" "latex")
+ ; (system* "python" "make.py" "texinfo")
+ ; (symlink (string-append html "/_images")
+ ; (string-append info "/matplotlib-figures"))
+ ; (with-directory-excursion "build/texinfo"
+ ; (substitute* "matplotlib.texi"
+ ; (("@image\\{([^,]*)" all file)
+ ; (string-append "@image{matplotlib-figures/" file)))
+ ; (symlink (string-append html "/_images")
+ ; "./matplotlib-figures")
+ ; (system* "makeinfo" "--no-split"
+ ; "-o" "matplotlib.info" "matplotlib.texi"))
+ ; (copy-file "build/texinfo/matplotlib.info"
+ ; (string-append info "/matplotlib.info"))
+ ;; (copy-file "build/latex/Matplotlib.pdf"
+ ;; (string-append doc "/Matplotlib.pdf"))
+ )))
%standard-phases))))
(home-page "http://matplotlib.org")
(synopsis "2D plotting library for Python")
@@ -3535,7 +3564,7 @@ functions.")
("python-sphinx" ,python-sphinx)
("python-numpydoc" ,python-numpydoc)
("gfortran" ,gfortran)
- ("texlive" ,texlive)
+ ("texlive-minimal" ,texlive-minimal)
("perl" ,perl)))
(outputs '("out" "doc"))
(arguments
^ permalink raw reply related [flat|nested] 4+ messages in thread
* Re: [patch] python-numpy, python-matplotlib and openblas update, python-cycler added
2016-07-31 11:40 Pjotr Prins
@ 2016-07-31 11:46 ` Andreas Enge
2016-08-19 6:42 ` Ricardo Wurmus
1 sibling, 0 replies; 4+ messages in thread
From: Andreas Enge @ 2016-07-31 11:46 UTC (permalink / raw)
To: Pjotr Prins; +Cc: guix-devel
Hello,
On Sun, Jul 31, 2016 at 01:40:11PM +0200, Pjotr Prins wrote:
> PS I thought using texlive-minimal was a good idea. Ignore those if
> you think it is not supposed to be. It may be the reason the PDFs
> disappeared.
well, if the documentation does not build, then it might be a better idea
to even drop texlive altogether... Fixes to texlive-minimal (that is,
indications on what we delete from texlive-texmf while we should not)
are welcome.
Andreas
^ permalink raw reply [flat|nested] 4+ messages in thread
* [patch] python-numpy, python-matplotlib and openblas update, python-cycler added
@ 2016-07-31 13:22 Federico Beffa
0 siblings, 0 replies; 4+ messages in thread
From: Federico Beffa @ 2016-07-31 13:22 UTC (permalink / raw)
To: pjotr.public12; +Cc: Guix-devel
Pjotr Prins <pjotr.public12@thebird.nl> writes:
> Attached bumping of python-numpy, openblas and python-matplotlib. New
> package python-cycler.
>
[...]
> - matplotlib and ipython now have a circular dependency - so I removed
> one and had to disable document generation for matplotlib
We value documentation and welcome efforts to provide/keep it. An often
working workaround for circular dependencies is to use bootstrap
packages. One example is the circular dependency between python-numpy
and python-matplotlib. The former need the latter to build its
documentation, so we have an (unexported) python-numpy-bootstrap to work
around that.
Regards,
Fede
^ permalink raw reply [flat|nested] 4+ messages in thread
* Re: [patch] python-numpy, python-matplotlib and openblas update, python-cycler added
2016-07-31 11:40 Pjotr Prins
2016-07-31 11:46 ` Andreas Enge
@ 2016-08-19 6:42 ` Ricardo Wurmus
1 sibling, 0 replies; 4+ messages in thread
From: Ricardo Wurmus @ 2016-08-19 6:42 UTC (permalink / raw)
To: Pjotr Prins; +Cc: guix-devel
Pjotr Prins <pjotr.public12@thebird.nl> writes:
> Hi Ricardo,
>
> I ran into the eigen issue of numpy+openblas.
>
> See https://github.com/xianyi/OpenBLAS/issues/703
>
> The good news is that openblas now appears to have fixed eigen
> support. It was broken on numpy and the upgrades fixed the segfaults.
Thanks for the heads-up. OpenBLAS has been updated in core-updates
already.
I cannot take care of the diff you sent any time soon (busy at work and
with other patches), so if someone else would like to turn this into a
proper commit please do so.
~~ Ricardo
^ permalink raw reply [flat|nested] 4+ messages in thread
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2016-07-31 13:22 [patch] python-numpy, python-matplotlib and openblas update, python-cycler added Federico Beffa
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2016-07-31 11:40 Pjotr Prins
2016-07-31 11:46 ` Andreas Enge
2016-08-19 6:42 ` Ricardo Wurmus
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