GNU bug report logs - #25834
Update scientific Python packages

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From: help-debbugs <at> gnu.org (GNU bug Tracking System)
To: Marius Bakke <mbakke <at> fastmail.com>
Cc: tracker <at> debbugs.gnu.org
Subject: bug#25705: closed ([PATCH] gnu: python-matplotlib: Don't
 propagate python-numpy-bootstrap.)
Date: Mon, 06 Mar 2017 22:54:02 +0000

[Message part 1 (text/plain, inline)]

Your message dated Mon, 06 Mar 2017 23:53:42 +0100
with message-id <87y3wi2f0p.fsf <at> kirby.i-did-not-set--mail-host-address--so-tickle-me>
and subject line Re: bug#25834: [PATCH] Update scipy stack.
has caused the debbugs.gnu.org bug report #25834,
regarding [PATCH] gnu: python-matplotlib: Don't propagate python-numpy-bootstrap.
to be marked as done.

(If you believe you have received this mail in error, please contact
help-debbugs <at> gnu.org.)


-- 
25834: http://debbugs.gnu.org/cgi/bugreport.cgi?bug=25834
GNU Bug Tracking System
Contact help-debbugs <at> gnu.org with problems

[Message part 2 (message/rfc822, inline)]

From: Thomas Danckaert <post <at> thomasdanckaert.be>
To: guix-patches <at> gnu.org
Subject: Re: [PATCH] gnu: python-matplotlib: Don't propagate
 python-numpy-bootstrap.
Date: Mon, 13 Feb 2017 10:57:06 +0100 (CET)

[Message part 3 (text/plain, inline)]

(continuing the discussion from 
https://lists.gnu.org/archive/html/guix-devel/2017-01/msg02239.html)

From: Marius Bakke <mbakke <at> fastmail.com>
Subject: Re: [PATCH] gnu: python-matplotlib: Don't propagate 
python-numpy-bootstrap.
Date: Fri, 27 Jan 2017 20:57:12 +0100

>> This patch works around it by creating an intermediate
>> python-matplotlib-bootstrap package as well, which is then used as 
>> a
>> native input to generate the documentation of python-numpy.
>> python-numpy is then used as a propagated input of 
>> python-matplotlib,
>> so python-numpy-bootstrap doesn't appear in user's profiles 
>> anymore.
>>
>> What do you think?
>
> This sounds sensible. Does numpy not require any matplotlib 
> functions at
> runtime?

No. It's just used for the documentation.  With the attached patch, 
the dependency chain is this:

matplotlib -> numpy -> matplotlib-bootstrap -> numpy-bootstrap 
(=“numpy-without-docs”)

> If so, this patch LGTM. The new matplotlib-bootstrap variables
> should have an explaining comment though :)

I've added a comment and fixed some long lines.

Thomas

[0001-gnu-python-matplotlib-Don-t-propagate-python-numpy-b.patch (text/x-patch, inline)]

From 8a9584dd196dae3520fe2ac4b050a9e0c88503f8 Mon Sep 17 00:00:00 2001
From: Thomas Danckaert <thomas.danckaert <at> gmail.com>
Date: Fri, 27 Jan 2017 12:12:42 +0100
Subject: [PATCH] gnu: python-matplotlib: Don't propagate
 python-numpy-bootstrap.

* gnu/packages/python.scm (python-matplotlib-bootstrap,python2-matplotlib-bootstrap):
  New variables.
  (python-matplotlib, python2-matplotlib) [propagated-inputs]: Use
  python-numpy instead of python-numpy-bootstrap.
  (python-numpy, python2-numpy) [propagated-inputs,native-inputs]: Replace
  matplotlib by native inputs matplotlib-bootstrap.
---
 gnu/packages/python.scm | 26 ++++++++++++++++++++------
 1 file changed, 20 insertions(+), 6 deletions(-)

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 81f9200..14d2e23 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -33,7 +33,7 @@
 ;;; Copyright © 2016 Arun Isaac <arunisaac <at> systemreboot.net>
 ;;; Copyright © 2016 Julien Lepiller <julien <at> lepiller.eu>
 ;;; Copyright © 2016, 2017 Tobias Geerinckx-Rice <me <at> tobias.gr>
-;;; Copyright © 2016 Thomas Danckaert <post <at> thomasdanckaert.be>
+;;; Copyright © 2016, 2017 Thomas Danckaert <post <at> thomasdanckaert.be>
 ;;; Copyright © 2017 Carlo Zancanaro <carlo <at> zancanaro.id.au>
 ;;;
 ;;; This file is part of GNU Guix.
@@ -3404,11 +3404,11 @@ association studies (GWAS) on extremely large data sets.")
      `(("which" ,which)
        ,@(package-inputs python-numpy-bootstrap)))
     (propagated-inputs
-     `(("python-matplotlib" ,python-matplotlib)
-       ("python-pyparsing" ,python-pyparsing)
+     `(("python-pyparsing" ,python-pyparsing)
        ,@(package-propagated-inputs python-numpy-bootstrap)))
     (native-inputs
      `(("pkg-config" ,pkg-config)
+       ("python-matplotlib" ,python-matplotlib-bootstrap) ; to build documentation
        ("python-sphinx" ,python-sphinx)
        ("python-numpydoc" ,python-numpydoc)
        ("texlive" ,texlive)
@@ -3458,7 +3458,11 @@ association studies (GWAS) on extremely large data sets.")
               ,phases)))))))
 
 (define-public python2-numpy
-  (package-with-python2 python-numpy))
+  (let ((numpy (package-with-python2 python-numpy)))
+    (package (inherit numpy)
+             (native-inputs
+              `(("python-matplotlib" ,python2-matplotlib-bootstrap)
+                ,@(alist-delete "python-matplotlib" (package-native-inputs numpy)))))))
 
 (define-public python-pygit2
   (package
@@ -3623,7 +3627,7 @@ transcendental functions).")
        ("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)
@@ -3740,8 +3744,18 @@ toolkits.")
        `(("python2-pycairo" ,python2-pycairo)
          ("python2-pygobject-2" ,python2-pygobject-2)
          ("python2-tkinter" ,python-2 "tk")
+         ("python2-numpy" ,python2-numpy)
          ,@(fold alist-delete (package-propagated-inputs matplotlib)
-                 '("python-pycairo" "python-pygobject" "python-tkinter")))))))
+                 '("python-pycairo" "python-pygobject" "python-tkinter"
+                   "python-numpy")))))))
+
+;; Use `bootstrap` versions of matplotlib to build numpy documentation.
+(define python-matplotlib-bootstrap
+  ((package-input-rewriting `((,python-numpy . ,python-numpy-bootstrap)))
+   python-matplotlib))
+(define python2-matplotlib-bootstrap
+  ((package-input-rewriting `((,python2-numpy . ,python2-numpy-bootstrap)))
+   python2-matplotlib))
 
 (define-public python2-pysnptools
   (package
-- 
2.7.4

[Message part 5 (message/rfc822, inline)]

From: Marius Bakke <mbakke <at> fastmail.com>
To: Thomas Danckaert <post <at> thomasdanckaert.be>
Cc: dannym <at> scratchpost.org, 25834-done <at> debbugs.gnu.org
Subject: Re: bug#25834: [PATCH] Update scipy stack.
Date: Mon, 06 Mar 2017 23:53:42 +0100

[Message part 6 (text/plain, inline)]

Thomas Danckaert <post <at> thomasdanckaert.be> writes:

> From: Marius Bakke <mbakke <at> fastmail.com>
> Subject: Re: bug#25834: [PATCH] Update scipy stack.
> Date: Mon, 06 Mar 2017 14:25:26 +0100
>
>> Please pay attention during the 'check' phase of Python packages -- 
>> both
>> colorspacious and the shutils backport prints 'Ran 0 tests in...'.
>> Usually this is a sign that they require some other command than 
>> 'python
>> setup.py test', which is the default of python-build-system.
>>
>> I pushed a fix for python2-backports-shutil-get-terminal-size that 
>> I had
>> in my queue, but it would be nice to enable tests on colorspacious 
>> as
>> well. Any takers? :)
>
> I've attached an attempt (now runs 34 tests).  Am I right that 
> running “nosetests colorspacious/*.py” is the only way to make it run 
> the tests in this case?

Thanks! By adding "--all-modules" to the "nosetests" invocation, it was
able to discover the tests without having to add them as arguments.

Pushed! Closing this bug now, wahoo!

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