GNU bug report logs - #44613
[PATCH] Fix build for bedtools

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From: zimoun <zimon.toutoune <at> gmail.com>
To: Marius Bakke <marius <at> gnu.org>, Roel Janssen <roel <at> gnu.org>, 44613 <at> debbugs.gnu.org
Subject: [bug#44613] what “guix build -S” should return?
Date: Fri, 13 Nov 2020 16:51:46 +0100

Hi Marius,

Thank you for the explanations.


On Fri, 13 Nov 2020 at 16:08, Marius Bakke <marius <at> gnu.org> wrote:
> zimoun <zimon.toutoune <at> gmail.com> writes:
>
>> PS:
>> I am always confused if the removal should be done in ’origin’ or in the
>> ’add-after 'unpack’ phase; especially when the bundle is free software.
>> Other said, what should an user expect when fetching with “guix build -S”?
>> Anyway! :-)
>
> Unbundling is always better to do in a snippet.  It leads to less
> bandwidth usage, and users can more easily inspect the (actual) code.

Well, I do not know.  For example, I could do this workflow:

 guix environment bedtools
 tar -xvf $(guix build -S bedtools)
 make

which probably fails because removing the bundles often needs some extra
tweaks.  Concretely, see python-pysam for instance:

--8<---------------cut here---------------start------------->8---
              (snippet '(begin
                          ;; Drop bundled htslib. TODO: Also remove samtools
                          ;; and bcftools.
                          (delete-file-recursively "htslib")
                          #t))))
[...]
       #:phases
       (modify-phases %standard-phases
         (add-before 'build 'set-flags
           (lambda* (#:key inputs #:allow-other-keys)
             (setenv "HTSLIB_MODE" "external")
             (setenv "HTSLIB_LIBRARY_DIR"
                     (string-append (assoc-ref inputs "htslib") "/lib"))
             (setenv "HTSLIB_INCLUDE_DIR"
                     (string-append (assoc-ref inputs "htslib") "/include"))
--8<---------------cut here---------------end--------------->8---

Then, I am not convince that:

  guix build bedtools --with-git-url=http://example.org

works too.  Or ’--with-source=’ as well.  I remember a discussion
initiated by Mark and Maxim about this: snippet vs phases but I am not
able to reach it.


> For other kinds of patching the boundary is less clear.  Generally,
> Guix-specific tweaks should be in a phase, but "universal" bug fixes may
> well be in a snippet.

I agree that non-free and bug fixes should go to snippet.  Then I am
still confused and my feelings are mixed about Guix specific tweaks.


> I sometimes imagine a downstream distribution that use Guix sources, but
> not the build scripts, to draw the line.

It seems a good criteria to draw the line.  And in the case of bedtools
or python-pysam or many others, ’snippet’ removes (free software)
bundles because of an implicit and non-uniform Guix policy that a
downstream distribution could choose differently.

Well, my mind is not clear about this topic. :-)

All the best,
simon

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