GNU bug report logs - #25705
[PATCH] gnu: python-matplotlib: Don't propagate python-numpy-bootstrap.

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Message #5 received at submit <at> debbugs.gnu.org (full text, mbox):

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 1 (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 #8 received at 25705 <at> debbugs.gnu.org (full text, mbox):

From: Marius Bakke <mbakke <at> fastmail.com>
To: Thomas Danckaert <post <at> thomasdanckaert.be>, 25705 <at> debbugs.gnu.org
Subject: Re: bug#25705: [PATCH] gnu: python-matplotlib: Don't
 propagate	python-numpy-bootstrap.
Date: Mon, 13 Feb 2017 21:48:09 +0100

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

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

> (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.

Hi Thomas,

Thanks for the reminder. I'm not comfortable pushing this while we don't
notice python test failures[0], but will add this as soon as the
'python-tests' branch is merged.

There are a few unresolved failures still in [1], I will work on the
list (from the bottom) over the next few days.

[0] https://debbugs.gnu.org/cgi/bugreport.cgi?bug=25177
[1] https://hydra.gnu.org/eval/109444?full=1&compare=master#tabs-now-fail

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Message #11 received at 25705 <at> debbugs.gnu.org (full text, mbox):

From: Thomas Danckaert <post <at> thomasdanckaert.be>
To: mbakke <at> fastmail.com
Cc: 25705 <at> debbugs.gnu.org
Subject: Re: bug#25705: [PATCH] gnu: python-matplotlib: Don't propagate
 python-numpy-bootstrap.
Date: Tue, 14 Feb 2017 09:51:17 +0100 (CET)

From: Marius Bakke <mbakke <at> fastmail.com>
Subject: Re: bug#25705: [PATCH] gnu: python-matplotlib: Don't 
propagate python-numpy-bootstrap.
Date: Mon, 13 Feb 2017 21:48:09 +0100

> Hi Thomas,
>
> Thanks for the reminder. I'm not comfortable pushing this while we 
> don't
> notice python test failures[0], but will add this as soon as the
> 'python-tests' branch is merged.

Yes, I thought that had something to do with it.

By the way, as another solution, we could create a separate 
python-numpy-documentation package (not to be confused with 
python-numpydoc, which is something different...), instead of a 
python-numpy:doc output.  This way, we could end up with a much 
simpler dependency graph, which doesn't require any bootstrap 
packages:

python-numpy <- python-matplotlib <- python-numpy-documentation

But I suppose the preference in guix is to work with multiple outputs?

Thomas

Message #14 received at 25705 <at> debbugs.gnu.org (full text, mbox):

From: Marius Bakke <mbakke <at> fastmail.com>
To: Thomas Danckaert <post <at> thomasdanckaert.be>
Cc: 25705 <at> debbugs.gnu.org
Subject: Re: bug#25705: [PATCH] gnu: python-matplotlib: Don't propagate
 python-numpy-bootstrap.
Date: Tue, 14 Feb 2017 15:51:44 +0100

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

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

> From: Marius Bakke <mbakke <at> fastmail.com>
> Subject: Re: bug#25705: [PATCH] gnu: python-matplotlib: Don't 
> propagate python-numpy-bootstrap.
> Date: Mon, 13 Feb 2017 21:48:09 +0100
>
>> Hi Thomas,
>>
>> Thanks for the reminder. I'm not comfortable pushing this while we 
>> don't
>> notice python test failures[0], but will add this as soon as the
>> 'python-tests' branch is merged.
>
> Yes, I thought that had something to do with it.
>
> By the way, as another solution, we could create a separate 
> python-numpy-documentation package (not to be confused with 
> python-numpydoc, which is something different...), instead of a 
> python-numpy:doc output.  This way, we could end up with a much 
> simpler dependency graph, which doesn't require any bootstrap 
> packages:
>
> python-numpy <- python-matplotlib <- python-numpy-documentation
>
> But I suppose the preference in guix is to work with multiple outputs?

That depends. I tried updating scipy, numpy and matplotlib recently, but
ran into a circular dependency (can't remember which). Something like
this might help.

I think we should do a 'python-updates' branch as soon as 'python-tests'
is ready, where we can address this problem. Would you like to try
updating the trio and resolving the dependency conflict? :-)

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Message #17 received at 25705 <at> debbugs.gnu.org (full text, mbox):

From: Thomas Danckaert <post <at> thomasdanckaert.be>
To: mbakke <at> fastmail.com
Cc: 25705 <at> debbugs.gnu.org
Subject: Re: bug#25705: [PATCH] gnu: python-matplotlib: Don't propagate
 python-numpy-bootstrap.
Date: Tue, 14 Feb 2017 21:07:35 +0100 (CET)

From: Marius Bakke <mbakke <at> fastmail.com>
Subject: Re: bug#25705: [PATCH] gnu: python-matplotlib: Don't 
propagate python-numpy-bootstrap.
Date: Tue, 14 Feb 2017 15:51:44 +0100

> I think we should do a 'python-updates' branch as soon as 
> 'python-tests'
> is ready, where we can address this problem. Would you like to try
> updating the trio and resolving the dependency conflict? :-)

challenge accepted ;-)

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