bug#66064: closed ([PATCH] gnu: python-plastid: Patch it for python 3.10.)

[GNU bug Tracking System]

Your message dated Mon, 18 Sep 2023 10:33:37 +0200
with message-id <87led3yj6c.fsf@elephly.net>
and subject line Re: [bug#66064] [PATCH] gnu: python-plastid: Patch it for 
python 3.10.
has caused the debbugs.gnu.org bug report #66064,
regarding [PATCH] gnu: python-plastid: Patch it for python 3.10.
to be marked as done.

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-- 
66064: https://debbugs.gnu.org/cgi/bugreport.cgi?bug=66064
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> --- Begin Message ---
>
>
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> Subject: 
>
> [PATCH] gnu: python-plastid: Patch it for python 3.10.
>
>
>
>
> Date: 
>
> Mon, 18 Sep 2023 05:39:20 +0200
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>
>
>
> * gnu/packages/bioinformatics.scm (python-plastid)[arguments]: Add
> new phase patch-for-python-3.10.
> ---
>  gnu/packages/bioinformatics.scm | 7 +++++++
>  1 file changed, 7 insertions(+)
>
> diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
> index c78f017a24..d7a9697c6e 100644
> --- a/gnu/packages/bioinformatics.scm
> +++ b/gnu/packages/bioinformatics.scm
> @@ -3787,6 +3787,13 @@ (define-public python-plastid
>                        "-xf" (assoc-ref inputs "test-data"))
>                ;; This one requires bowtie-build
>                (delete-file "plastid/test/functional/test_crossmap.py")))
> +          (add-after 'unpack 'patch-for-python-3.10
> +              (lambda _
> +                ;; Some classes were moved from collections to collections.abc
> +                ;; in Python 3.10.
> +                (substitute* "plastid/readers/bigbed.pyx"
> +                  ((", Iterable")
> +                   "\nfrom collections.abc import Iterable"))))
>            (add-before 'check 'build-extensions
>              (lambda _
>                ;; Cython extensions have to be built before running the tests.
>
> base-commit: 1d30ec935126f316187dfc26446347bc7de9868b
> -- 
> 2.41.0
>
>
>
>
> --- End Message ---
> --- Begin Message ---
>
>
>
> Subject: 
>
> Re: [bug#66064] [PATCH] gnu: python-plastid: Patch it for python 3.10.
>
>
>
>
> Date: 
>
> Mon, 18 Sep 2023 10:33:37 +0200
>
>
>
>
> User-agent: 
>
> mu4e 1.10.5; emacs 28.2
>
>
>
>
> Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de> writes:
>
> > * gnu/packages/bioinformatics.scm (python-plastid)[arguments]: Add
> > new phase patch-for-python-3.10.
>
> Applied, thanks!
>
> -- 
> Ricardo
>
>
> --- End Message ---