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bug#25834: [PATCH] Update scipy stack.
|
From: |
Thomas Danckaert |
|
Subject: |
bug#25834: [PATCH] Update scipy stack. |
|
Date: |
Mon, 27 Feb 2017 10:54:36 +0100 (CET) |
Hi,
here's a new and improved patch series, on top of the python-tests
branch. It also needs python-cycler, which is currently only in
master (cherry-picked commit included here for convenience).
some comments:
1) matplotlib-documentation/numpy-documentation: I decided not to use
“(inherits ...)” because
- it got messy for matplotlib, where I think the “python2-variant”
of
the base matplotlib package interfered when trying to
(package-with-python2 matplotlib-documentation), and
- all of the input fields need to be rewritten anyway (the
documentation packages only need a number of native inputs).
2) Building the latex version of scipy's documentation now fails due
to missing unicode characters and a lot of unescaped inline math
formulas, which are upstream issues IMO (I'll submit an issue on
their github page).
3)
From: Marius Bakke <address@hidden>
Date: Thu, 23 Feb 2017 14:21:30 +0100
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append
+ "https://pypi.python.org/packages/ec/9c/";
+
"368086faa9c016efce5da3e0e13ba392c9db79e3ab740b763fe28620b18b/"
+ "backports.shutil_get_terminal_size-" version
".tar.gz"))
Is it possible to use 'pypi-uri' here?
I couldn't find a working pypi-uri, having tried all sorts of
combinations of “backports.shutil-get-terminal-size” or
“backports-shutil-get-terminal-size” (is there some sort of trick to
find these? These simple urls are never listed on pypi, is my
impression.).
4) I removed the patch related to the Matplotlib Tk backend, because
it now seems to work just fine without it. But maybe I misunderstand
the reason the patch was there... comments?
cheers,
Thomas
From 556764c10272b412b0b1aad26429be563bc711e3 Mon Sep 17 00:00:00 2001
From: Marius Bakke <address@hidden>
Date: Thu, 19 Jan 2017 18:35:18 +0100
Subject: [PATCH 1/9] gnu: Add python-cycler.
* gnu/packages/python.scm (python-cycler, python2-cycler): New variables.
---
gnu/packages/python.scm | 30 ++++++++++++++++++++++++++++++
1 file changed, 30 insertions(+)
diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index e26e442e5..9d1996314 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -3733,6 +3733,36 @@ transcendental functions).")
(define-public python2-numexpr
(package-with-python2 python-numexpr))
+(define-public python-cycler
+ (package
+ (name "python-cycler")
+ (version "0.10.0")
+ (source (origin
+ (method url-fetch)
+ (uri (pypi-uri "cycler" version))
+ (sha256
+ (base32
+ "1n69n23fak1gjxlrbhqisi2b9pv3ckrfj98llx3p53953082syyd"))))
+ (build-system python-build-system)
+ (arguments
+ ;; XXX: The current version requires 'coveralls' which we don't have.
+ ;; Enable this for the next release which uses 'python-pytest'.
+ '(#:tests? #f))
+ (propagated-inputs
+ `(("python-six" ,python-six)))
+ (home-page "http://matplotlib.org/cycler/";)
+ (synopsis "Composable keyword argument iterator")
+ (description
+ "When using @code{matplotlib} and plotting more than one line, it is
+common to want to be able to want to be able to cycle over one or more artist
+styles; but the plotting logic can quickly become involved.
+To address this and enable easy cycling over arbitrary @code{kwargs}, the
address@hidden class was developed.")
+ (license license:bsd-3)))
+
+(define-public python2-cycler
+ (package-with-python2 python-cycler))
+
(define-public python-matplotlib
(package
(name "python-matplotlib")
--
2.11.1
From 9f229fce352b60c194c7300d9efe65d5e73e60f5 Mon Sep 17 00:00:00 2001
From: Thomas Danckaert <address@hidden>
Date: Tue, 21 Feb 2017 13:33:20 +0100
Subject: [PATCH 2/9] gnu: Add python2-backports-shutil-get-terminal-size.
* gnu/packages/python.scm (python2-backports-shutil-get-terminal-size): New
variable.
---
gnu/packages/python.scm | 29 ++++++++++++++++++++++++++++-
1 file changed, 28 insertions(+), 1 deletion(-)
diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 9d1996314..54c870d63 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -33,7 +33,7 @@
;;; Copyright © 2016 Arun Isaac <address@hidden>
;;; Copyright © 2016, 2017 Julien Lepiller <address@hidden>
;;; Copyright © 2016, 2017 Tobias Geerinckx-Rice <address@hidden>
-;;; Copyright © 2016 Thomas Danckaert <address@hidden>
+;;; Copyright © 2016, 2017 Thomas Danckaert <address@hidden>
;;; Copyright © 2017 Carlo Zancanaro <address@hidden>
;;; Copyright © 2017 Frederick M. Muriithi <address@hidden>
;;;
@@ -6024,6 +6024,33 @@ connection to each user.")
(define-public python2-backports-abc
(package-with-python2 python-backports-abc))
+(define-public python2-backports-shutil-get-terminal-size
+ (package
+ (name "python2-backports-shutil-get-terminal-size")
+ (version "1.0.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append
+ "https://pypi.python.org/packages/ec/9c/";
+ "368086faa9c016efce5da3e0e13ba392c9db79e3ab740b763fe28620b18b/"
+ "backports.shutil_get_terminal_size-" version ".tar.gz"))
+ (sha256
+ (base32
+ "107cmn7g3jnbkp826zlj8rrj19fam301qvaqf0f3905f5217lgki"))))
+ (build-system python-build-system)
+ (arguments
+ `(#:python ,python-2))
+ (home-page
+ "https://github.com/chrippa/backports.shutil_get_terminal_size";)
+ (synopsis
+ "Backport of Python 3.3's shutil.get_terminal_size")
+ (description
+ "A backport of the @code{get_terminal_size function} from Python 3.3's
@code{shutil}.
+Unlike the original version it is written in pure Python rather than C, so it
+might be a tiny bit slower.")
+ (license license:expat)))
+
(define-public python-waf
(package
(name "python-waf")
--
2.11.1
From 49cc81a88f80b2e48ee248221b1b290f6bfaf64a Mon Sep 17 00:00:00 2001
From: Thomas Danckaert <address@hidden>
Date: Tue, 21 Feb 2017 21:33:02 +0100
Subject: [PATCH 3/9] gnu: Add python-colorspacious.
* gnu/packages/python.scm (python-colorspacious, python2-colorspacious): New
variables.
---
gnu/packages/python.scm | 25 +++++++++++++++++++++++++
1 file changed, 25 insertions(+)
diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 54c870d63..bab5f85e4 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -3763,6 +3763,31 @@ To address this and enable easy cycling over arbitrary
@code{kwargs}, the
(define-public python2-cycler
(package-with-python2 python-cycler))
+(define-public python-colorspacious
+ (package
+ (name "python-colorspacious")
+ (version "1.1.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append
+ "https://github.com/njsmith/colorspacious/archive/v";
+ version ".tar.gz"))
+ (file-name (string-append name "-" version))
+ (sha256
+ (base32 "1vflh5jm32qb0skza2i8pjacv09w6gq84fqpp2nj77s0rbmzgr4k"))))
+ (build-system python-build-system)
+ (propagated-inputs
+ `(("python-numpy" ,python-numpy)))
+ (home-page "https://github.com/njsmith/colorspacious";)
+ (synopsis "Python library for colorspace conversions")
+ (description "Colorspacious is a Python library that lets you easily convert
+between colorspaces like sRGB, XYZ, CIEL*a*b*, CIECAM02, CAM02-UCS, etc.")
+ (license license:expat)))
+
+(define-public python2-colorspacious
+ (package-with-python2 python-colorspacious))
+
(define-public python-matplotlib
(package
(name "python-matplotlib")
--
2.11.1
From 70f5cbbab305dbf13a8c1c6215dd24e99bb62684 Mon Sep 17 00:00:00 2001
From: Thomas Danckaert <address@hidden>
Date: Tue, 21 Feb 2017 20:28:27 +0100
Subject: [PATCH 4/9] gnu: python-numpy: Update to 1.12.0.
* 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 | 148 +++++++++++++++++++++++++++---------------------
1 file changed, 82 insertions(+), 66 deletions(-)
diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index bab5f85e4..4f1359324 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -3402,24 +3402,26 @@ 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
@@ -3468,8 +3470,8 @@ 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
@@ -3526,69 +3528,83 @@ 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
+ (name "python-numpy-documentation")
+ (version (package-version python-numpy))
+ (source (package-source python-numpy))
+ (build-system python-build-system)
(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)))))))
+ ("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)
+ (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 "." ".*")))))
+ #t)))))
+ (home-page (package-home-page python-numpy))
+ (synopsis "Documentation for the python-numpy package")
+ (description (package-description python-numpy))
+ (license (package-license python-numpy))))
-(define-public python2-numpy
- (package-with-python2 python-numpy))
+(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
@@ -3810,7 +3826,7 @@ between colorspaces like sRGB, XYZ, CIEL*a*b*, CIECAM02,
CAM02-UCS, etc.")
("gobject-introspection" ,gobject-introspection)
("python-tkinter" ,python "tk")
("python-dateutil" ,python-dateutil)
- ("python-numpy" ,python-numpy-bootstrap)
+ ("python-numpy" ,python-numpy)
("python-pillow" ,python-pillow)
("python-pytz" ,python-pytz)
("python-six" ,python-six)
--
2.11.1
From c766e974d5e785b0940a588687986de79f98fede Mon Sep 17 00:00:00 2001
From: Thomas Danckaert <address@hidden>
Date: Tue, 21 Feb 2017 22:18:45 +0100
Subject: [PATCH 5/9] gnu: python-matplotlib: Update to 2.0.0.
* gnu/packages/python.scm (python-matplotlib): Update to 2.0.0.
[source]: Remove Tk backend patch, use Github instead of Sourceforge.
[outputs]: Remove "doc" output.
[inputs]: Add python-pyqt.
[propagated-inputs]: Add python-cycler.
[native-inputs]: Remove python-sphinx, python-numpydoc, texlive and texinfo.
(python-matplotlib-documentation, python2-matplotlib-documentation): New
variables.
* gnu/packages/patches/matplotlib-setupext-tk.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Remove patch.
---
gnu/local.mk | 1 -
gnu/packages/patches/matplotlib-setupext-tk.patch | 34 -------
gnu/packages/python.scm | 118 ++++++++++++----------
3 files changed, 67 insertions(+), 86 deletions(-)
delete mode 100644 gnu/packages/patches/matplotlib-setupext-tk.patch
diff --git a/gnu/local.mk b/gnu/local.mk
index 899dc06b8..b2a176d45 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -747,7 +747,6 @@ dist_patch_DATA =
\
%D%/packages/patches/make-impure-dirs.patch \
%D%/packages/patches/mars-install.patch \
%D%/packages/patches/mars-sfml-2.3.patch \
- %D%/packages/patches/matplotlib-setupext-tk.patch \
%D%/packages/patches/maxima-defsystem-mkdir.patch \
%D%/packages/patches/mcron-install.patch \
%D%/packages/patches/mcrypt-CVE-2012-4409.patch \
diff --git a/gnu/packages/patches/matplotlib-setupext-tk.patch
b/gnu/packages/patches/matplotlib-setupext-tk.patch
deleted file mode 100644
index 37c3d686e..000000000
--- a/gnu/packages/patches/matplotlib-setupext-tk.patch
+++ /dev/null
@@ -1,34 +0,0 @@
-Use 'pkg-config' instead of heuristics to find 'tk' flags.
-
---- matplotlib-1.4.3/setupext.py.orig 2015-12-01 14:21:19.554417453 +0100
-+++ matplotlib-1.4.3/setupext.py 2015-12-02 10:39:47.282363530 +0100
-@@ -1457,7 +1457,7 @@
- p = subprocess.Popen(
- '. %s ; eval echo ${%s}' % (file, varname),
- shell=True,
-- executable="/bin/sh",
-+ executable="sh",
- stdout=subprocess.PIPE)
- result = p.communicate()[0]
- return result.decode('ascii')
-@@ -1601,8 +1601,19 @@
- # of distros.
-
- # Query Tcl/Tk system for library paths and version string
-+ def getoutput(s):
-+ ret = os.popen(s).read().strip()
-+ return ret
- try:
-- tcl_lib_dir, tk_lib_dir, tk_ver = self.query_tcltk()
-+ pkg_config_libs = getoutput('pkg-config --libs-only-L
tk').split()
-+ # drop '-L' part of strings
-+ pkg_config_libs = [s[2:] for s in pkg_config_libs]
-+ pkg_config_ver = getoutput('pkg-config --modversion tk')
-+ tk_ver = re.match(r"(\d+.\d+)[\d.]*", pkg_config_ver).group(1)
-+ tcl_lib_dir = next(s for s in pkg_config_libs
-+ if re.match(r".*-tcl-.*", s)) + '/tcl' +
tk_ver
-+ tk_lib_dir = next(s for s in pkg_config_libs
-+ if re.match(r".*-tk-.*", s)) + '/tk' +
tk_ver
- except:
- tk_ver = ''
- result = self.hardcoded_tcl_config()
diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 4f1359324..78a7cf1f0 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -89,6 +89,7 @@
#:use-module (gnu packages perl)
#:use-module (gnu packages pkg-config)
#:use-module (gnu packages protobuf)
+ #:use-module (gnu packages qt)
#:use-module (gnu packages readline)
#:use-module (gnu packages sdl)
#:use-module (gnu packages shells)
@@ -3807,21 +3808,20 @@ between colorspaces like sRGB, XYZ, CIEL*a*b*,
CIECAM02, CAM02-UCS, etc.")
(define-public python-matplotlib
(package
(name "python-matplotlib")
- (version "1.4.3")
+ (version "2.0.0")
(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"))))
+ "0w3k5m5qb3wsd7yhvmg042xddvligklvcq2visk2c5wnph3hhsln"))))
(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")
@@ -3853,17 +3853,13 @@ between colorspaces like sRGB, XYZ, CIEL*a*b*,
CIECAM02, CAM02-UCS, etc.")
("glib" ,glib)
;; FIXME: Add backends when available.
;("python-wxpython" ,python-wxpython)
- ;("python-pyqt" ,python-pyqt)
+ ("python-pyqt" ,python-pyqt)
("tcl" ,tcl)
("tk" ,tk)))
(native-inputs
`(("pkg-config" ,pkg-config)
- ("python-sphinx" ,python-sphinx-1.2.3)
- ("python-numpydoc" ,python-numpydoc)
("python-nose" ,python-nose)
- ("python-mock" ,python-mock)
- ("texlive" ,texlive)
- ("texinfo" ,texinfo)))
+ ("python-mock" ,python-mock)))
(arguments
`(#:phases
(modify-phases %standard-phases
@@ -3882,26 +3878,66 @@ between colorspaces like sRGB, XYZ, CIEL*a*b*,
CIECAM02, CAM02-UCS, etc.")
basedirlist = ~a,~a~%
[rc_options]~%
backend = TkAgg~%"
- (assoc-ref inputs "tcl")
- (assoc-ref inputs "tk"))))
- #t)))
- (add-after 'install 'install-doc
+ (assoc-ref inputs "tcl")
+ (assoc-ref inputs "tk")))))
+ #t)))))
+ (home-page "http://matplotlib.org";)
+ (synopsis "2D plotting library for Python")
+ (description
+ "Matplotlib is a Python 2D plotting library which produces publication
+quality figures in a variety of hardcopy formats and interactive environments
+across platforms. Matplotlib can be used in Python scripts, the python and
+ipython shell, web application servers, and six graphical user interface
+toolkits.")
+ (license license:psfl)
+ (properties `((python2-variant . ,(delay python2-matplotlib))))))
+
+(define-public python2-matplotlib
+ (let ((matplotlib (package-with-python2
+ (strip-python2-variant python-matplotlib))))
+ (package (inherit matplotlib)
+ ;; Make sure to use special packages for Python 2 instead
+ ;; of those automatically rewritten by package-with-python2.
+ (propagated-inputs
+ `(("python2-pycairo" ,python2-pycairo)
+ ("python2-pygobject-2" ,python2-pygobject-2)
+ ("python2-tkinter" ,python-2 "tk")
+ ,@(fold alist-delete (package-propagated-inputs matplotlib)
+ '("python-pycairo" "python-pygobject" "python-tkinter")))))))
+
+(define-public python-matplotlib-documentation
+ (package
+ (name "python-matplotlib-documentation")
+ (version (package-version python-matplotlib))
+ (source (package-source python-matplotlib))
+ (build-system python-build-system)
+ (native-inputs
+ `(("python-matplotlib" ,python-matplotlib)
+ ("python-colorspacious" ,python-colorspacious)
+ ("python-sphinx" ,python-sphinx)
+ ("python-numpydoc" ,python-numpydoc)
+ ("python-ipython" ,python-ipython)
+ ("texlive" ,texlive)
+ ("texinfo" ,texinfo)
+ ,@(package-native-inputs python-matplotlib)))
+ (arguments
+ `(#:tests? #f ; we're only generating documentation
+ #:phases
+ (modify-phases %standard-phases
+ (delete 'build)
+ (replace 'install
(lambda* (#:key inputs outputs #:allow-other-keys)
- (let* ((data (string-append (assoc-ref outputs "doc") "/share"))
+ (let* ((data (string-append (assoc-ref outputs "out") "/share"))
(doc (string-append data "/doc/" ,name "-" ,version))
(info (string-append data "/info"))
(html (string-append doc "/html")))
;; Make installed package available for building the
;; documentation
- (add-installed-pythonpath inputs outputs)
(with-directory-excursion "doc"
;; Produce pdf in 'A4' format.
(substitute* (find-files "." "conf\\.py")
(("latex_paper_size = 'letter'")
"latex_paper_size = 'a4'"))
- (substitute* "users/intro.rst"
- ;; Fix reST markup error (see
<https://github.com/sphinx-doc/sphinx/issues/3044>)
- (("[[][*][]]") "[#]"))
(mkdir-p html)
(mkdir-p info)
;; The doc recommends to run the 'html' target twice.
@@ -3923,35 +3959,15 @@ backend = TkAgg~%"
(copy-file "build/texinfo/matplotlib.info"
(string-append info "/matplotlib.info"))
(copy-file "build/latex/Matplotlib.pdf"
- (string-append doc "/Matplotlib.pdf")))
- #t))))))
- (home-page "http://matplotlib.org";)
- (synopsis "2D plotting library for Python")
- (description
- "Matplotlib is a Python 2D plotting library which produces publication
-quality figures in a variety of hardcopy formats and interactive environments
-across platforms. Matplotlib can be used in Python scripts, the python and
-ipython shell, web application servers, and six graphical user interface
-toolkits.")
- (license license:psfl)
- (properties `((python2-variant . ,(delay python2-matplotlib))))))
+ (string-append doc "/Matplotlib.pdf"))))
+ #t)))))
+ (home-page (package-home-page python-matplotlib))
+ (synopsis "Documentation for the python-matplotlib package")
+ (description (package-description python-matplotlib))
+ (license (package-license python-matplotlib))))
-(define-public python2-matplotlib
- (let ((matplotlib (package-with-python2
- (strip-python2-variant python-matplotlib))))
- (package (inherit matplotlib)
- ;; Make sure to use special packages for Python 2 instead
- ;; of those automatically rewritten by package-with-python2.
- (native-inputs
- `(("python2-sphinx" ,python2-sphinx-1.2.3)
- ,@(fold alist-delete (package-native-inputs matplotlib)
- '("python-sphinx"))))
- (propagated-inputs
- `(("python2-pycairo" ,python2-pycairo)
- ("python2-pygobject-2" ,python2-pygobject-2)
- ("python2-tkinter" ,python-2 "tk")
- ,@(fold alist-delete (package-propagated-inputs matplotlib)
- '("python-pycairo" "python-pygobject" "python-tkinter")))))))
+(define-public python2-matplotlib-documentation
+ (package-with-python2 python-matplotlib-documentation))
(define-public python2-pysnptools
(package
--
2.11.1
From dca7c6aab5a15eb2064287c2c355ed4fc19fde39 Mon Sep 17 00:00:00 2001
From: Thomas Danckaert <address@hidden>
Date: Fri, 24 Feb 2017 17:07:27 +0100
Subject: [PATCH 6/9] gnu: python-testpath: Fix library location for python2
version.
* gnu/packages/python.scm (python-testpath)[arguments]: Install module in the
proper
"lib/pythonx.y" location for all Python versions.
---
gnu/packages/python.scm | 26 ++++++++++++++++----------
1 file changed, 16 insertions(+), 10 deletions(-)
diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 78a7cf1f0..d8948d1c5 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -5153,20 +5153,26 @@ installing @code{kernelspec}s for use with Jupyter
frontends.")
(build-system python-build-system)
(arguments
`(#:tests? #f ; this package does not even have a setup.py
+ #:modules ((guix build python-build-system)
+ (guix build utils)
+ (srfi srfi-1))
+ #:imported-modules (,@%python-build-system-modules
+ (srfi srfi-1))
#:phases
(modify-phases %standard-phases
(delete 'install)
(replace 'build
- (lambda* (#:key inputs outputs #:allow-other-keys)
- (let ((dir (string-append
- (assoc-ref outputs "out")
- "/lib/python"
- (string-take (string-take-right
- (assoc-ref inputs "python") 5) 3)
- "/site-packages/testpath")))
- (mkdir-p dir)
- (copy-recursively "testpath" dir))
- #t)))))
+ (lambda* (#:key inputs outputs #:allow-other-keys)
+ (let* ((version (last
+ (string-split (assoc-ref inputs "python") #\-)))
+ (x.y (string-join (take (string-split version #\.) 2)
+ "."))
+ (dir (string-append
+ (assoc-ref outputs "out")
+ "/lib/python" x.y "/site-packages/testpath")))
+ (mkdir-p dir)
+ (copy-recursively "testpath" dir))
+ #t)))))
(home-page "https://github.com/takluyver/testpath";)
(synopsis "Test utilities for code working with files and commands")
(description
--
2.11.1
From 0dde6387dfb61f111e86331064fb30340ed3d972 Mon Sep 17 00:00:00 2001
From: Thomas Danckaert <address@hidden>
Date: Tue, 21 Feb 2017 12:41:09 +0100
Subject: [PATCH 7/9] gnu: python-ipython: Update to 5.2.2.
* gnu/packages/python.scm (python-ipython): Update to 5.2.2.
[propagated-inputs]: Add pyhon-prompt-toolkit and python-nbformat.
(python2-ipython) [arguments]: Enable tests.
[propagated-inputs]: Add python2-backports-shutil-get-terminal-size.
---
gnu/packages/python.scm | 22 ++++++++++++++--------
1 file changed, 14 insertions(+), 8 deletions(-)
diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index d8948d1c5..691e11757 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -5187,17 +5187,18 @@ tools for mocking system commands and recording calls
to those.")
(define-public python-ipython
(package
(name "python-ipython")
- (version "4.0.3")
+ (version "5.2.2")
(source
(origin
(method url-fetch)
(uri (pypi-uri "ipython" version ".tar.gz"))
(sha256
- (base32 "1h2gp1p06sww9rzfkfzqy489bh47gj3910y2b1wdk3dcx1cqz4is"))))
+ (base32 "1qhjwa9cyz1np7rhv3p4ip13lkgbqsad62l24xkwiq1ic2gwiqbf"))))
(build-system python-build-system)
(outputs '("out" "doc"))
(propagated-inputs
`(("python-pyzmq" ,python-pyzmq)
+ ("python-prompt-toolkit" ,python-prompt-toolkit)
("python-terminado" ,python-terminado)
("python-matplotlib" ,python-matplotlib)
("python-numpy" ,python-numpy)
@@ -5210,6 +5211,7 @@ tools for mocking system commands and recording calls to
those.")
("python-jsonschema" ,python-jsonschema)
("python-traitlets" ,python-traitlets)
("python-ipykernel" ,python-ipykernel)
+ ("python-nbformat" ,python-nbformat)
("python-pygments" ,python-pygments)))
(inputs
`(("readline" ,readline)
@@ -5220,6 +5222,7 @@ tools for mocking system commands and recording calls to
those.")
("python-testpath" ,python-testpath)
("python-nose" ,python-nose)
("python-sphinx" ,python-sphinx)
+ ("python-shpinx-rtd-theme" ,python-sphinx-rtd-theme)
("texlive" ,texlive)
("texinfo" ,texinfo)))
(arguments
@@ -5233,15 +5236,16 @@ tools for mocking system commands and recording calls
to those.")
(html (string-append doc "/html"))
(man1 (string-append data "/man/man1"))
(info (string-append data "/info"))
- (examples (string-append doc "/examples")))
+ (examples (string-append doc "/examples"))
+ (python-arg (string-append "PYTHON=" (which "python"))))
(setenv "LANG" "en_US.utf8")
;; Make installed package available for running the tests
(add-installed-pythonpath inputs outputs)
(with-directory-excursion "docs"
;; FIXME: pdf fails to build
;;(system* "make" "pdf" "PAPER=a4")
- (system* "make" "html")
- (system* "make" "info"))
+ (system* "make" python-arg "html")
+ (system* "make" python-arg "info"))
(copy-recursively "docs/man" man1)
(copy-recursively "examples" examples)
(copy-recursively "docs/build/html" html)
@@ -5291,10 +5295,12 @@ computing.")
(let ((ipython (package-with-python2 (strip-python2-variant
python-ipython))))
(package
(inherit ipython)
- ;; FIXME: some tests are failing
- (arguments
- `(#:tests? #f ,@(package-arguments ipython)))
;; FIXME: add pyreadline once available.
+ (propagated-inputs
+ `(("python2-backports-shutil-get-terminal-size"
+ ,python2-backports-shutil-get-terminal-size)
+ ("python2-pathlib2" ,python2-pathlib2)
+ ,@(package-propagated-inputs ipython)))
(native-inputs
`(("python2-mock" ,python2-mock)
,@(package-native-inputs ipython))))))
--
2.11.1
From 1a4c6d3f1f18c696809b2987abac428c429beb5f Mon Sep 17 00:00:00 2001
From: Thomas Danckaert <address@hidden>
Date: Tue, 21 Feb 2017 11:45:06 +0100
Subject: [PATCH 8/9] gnu: python-scipy: Update to 0.18.1.
* 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 | 104 ++++++++++++++++++++++--------------------------
1 file changed, 48 insertions(+), 56 deletions(-)
diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 691e11757..f164fff13 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -4049,16 +4049,16 @@ 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)
@@ -4068,21 +4068,16 @@ functions.")
`(("lapack" ,lapack)
("openblas" ,openblas)))
(native-inputs
- `(("python-nose" ,python-nose)
- ("python-sphinx" ,python-sphinx-1.2.3)
+ `(("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
(modify-phases %standard-phases
- (add-after 'unpack 'fix-tests
- (lambda _
- (substitute* "scipy/integrate/tests/test_quadpack.py"
- (("libm.so") "libm.so.6"))
- #t))
(add-before 'build 'configure-openblas
(lambda* (#:key inputs #:allow-other-keys)
(call-with-output-file "site.cfg"
@@ -4102,40 +4097,44 @@ atlas_libs = openblas
(assoc-ref inputs "openblas")
(assoc-ref inputs "openblas"))))
#t))
- (delete 'check)
- (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)
- (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 "." ".*"))))
- #t)))
- (add-after 'install-doc 'check
- (lambda _
- ;; Tests can only be run after the library has been installed
and not
- ;; within the source directory.
- (with-directory-excursion "/tmp"
- (zero? (system* "python" "-c" "import scipy;
scipy.test()"))))))))
+ (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 "." ".*")))))
+ #t))
+ (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 "/tmp"
+ (zero? (system* "python" "-c"
+ "import scipy; scipy.test('full')")))
+ #t)))))
(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
@@ -4145,15 +4144,8 @@ routines such as routines for numerical integration and
optimization.")
(license license:bsd-3)))
(define-public python2-scipy
- (let ((scipy (package-with-python2
- (strip-python2-variant python-scipy))))
- (package (inherit scipy)
- ;; Make sure to use special packages for Python 2 instead
- ;; of those automatically rewritten by package-with-python2.
- (native-inputs
- `(("python2-sphinx" ,python2-sphinx-1.2.3)
- ,@(fold alist-delete (package-native-inputs scipy)
- '("python-sphinx")))))))
+ (package-with-python2
+ (strip-python2-variant python-scipy)))
(define-public python-socksipy-branch
(package
--
2.11.1
From f48c4ae867e21f0843bd1487a9c1cc54bd2d78d6 Mon Sep 17 00:00:00 2001
From: Thomas Danckaert <address@hidden>
Date: Sat, 25 Feb 2017 23:35:22 +0100
Subject: [PATCH 9/9] gnu: Remove python-sphinx-1.2.3.
* gnu/packages/python.scm (python-sphinx-1.2.3, python2-sphinx-1.2.3): Remove
variables.
---
gnu/packages/python.scm | 18 ------------------
1 file changed, 18 deletions(-)
diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index f164fff13..22c4d7aae 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -3029,24 +3029,6 @@ sources.")
(propagated-inputs `(("python2-pytz" ,python2-pytz)
,@(package-propagated-inputs base))))))
-;; This is needed for address@hidden and address@hidden, at least.
-;; Try removing this when they are updated.
-(define-public python-sphinx-1.2.3
- (package (inherit python-sphinx)
- (version "1.2.3")
- (source (origin
- (method url-fetch)
- (uri (pypi-uri "Sphinx" version))
- (sha256
- (base32
-
"011xizm3jnmf4cvs5i6kgf6c5nn046h79i8j0vd0f27yw9j3p4wl"))))
- ;; XXX: "'NoneType' object has no attribute 'split'".
- (arguments '(#:tests? #f))))
-
-(define-public python2-sphinx-1.2.3
- (package (inherit (package-with-python2
- (strip-python2-variant python-sphinx-1.2.3)))))
-
(define-public python-sphinx-rtd-theme
(package
(name "python-sphinx-rtd-theme")
--
2.11.1
- bug#25834: [PATCH 3/7] gnu: python-sphinx: Update to 1.5.2., (continued)
bug#25834: [PATCH 7/7] gnu: python-scipy: Update to 0.18.1., Thomas Danckaert, 2017/02/22
bug#25834: [PATCH 5/7] gnu: python-matplotlib: Update to 2.0.0., Thomas Danckaert, 2017/02/22
bug#25834: [PATCH 4/7] gnu: python-numpy: Update to 1.12.0., Thomas Danckaert, 2017/02/22
bug#25834: [PATCH 2/7] gnu: Add python-colorspacious., Thomas Danckaert, 2017/02/22
bug#25834: [PATCH 6/7] gnu: python-ipython: Update to 5.2.2., Thomas Danckaert, 2017/02/22
bug#25834: [PATCH 1/7] gnu: Add python2-backports-shutil-get-terminal-size., Marius Bakke, 2017/02/23