bug#70276: closed ([PATCH] gnu: python-deeptools: Update to 3.5.5.)

[GNU bug Tracking System]

Your message dated Tue, 09 Apr 2024 18:15:21 +0100
with message-id <87h6gacv9y.fsf@cbaines.net>
and subject line Re: [bug#70276] [PATCH] gnu: python-deeptools: Update to 3.5.5.
has caused the debbugs.gnu.org bug report #70276,
regarding [PATCH] gnu: python-deeptools: Update to 3.5.5.
to be marked as done.

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-- 
70276: https://debbugs.gnu.org/cgi/bugreport.cgi?bug=70276
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> --- Begin Message ---
>
>
>
> Subject: 
>
> [PATCH] gnu: python-deeptools: Update to 3.5.5.
>
>
>
>
> Date: 
>
> Mon,  8 Apr 2024 14:49:56 +0200
>
>
>
>
> * gnu/packages/bioinformatics.scm (python-deeptools): Update to 3.5.5.
> [build-system]: Replace by pyproject-build-system.
> [arguments]: Add phase that fixes 'test/test_tools.py'.
>
> Change-Id: Ibb51939275c96df2c4a1e248a03d683f2f4904ac
> ---
>  gnu/packages/bioinformatics.scm | 23 +++++++++++++++++++----
>  1 file changed, 19 insertions(+), 4 deletions(-)
>
> diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
> index 7861987704..452ec1d829 100644
> --- a/gnu/packages/bioinformatics.scm
> +++ b/gnu/packages/bioinformatics.scm
> @@ -4615,7 +4615,7 @@ (define-public python-deeptoolsintervals
>  (define-public python-deeptools
>    (package
>      (name "python-deeptools")
> -    (version "3.4.3")
> +    (version "3.5.5")
>      (source (origin
>                (method git-fetch)
>                (uri (git-reference
> @@ -4624,8 +4624,23 @@ (define-public python-deeptools
>                (file-name (git-file-name name version))
>                (sha256
>                 (base32
> -                "0l09vyynz6s6w7fnyd94rpys4a6aja6kp4gli64pngdxdz3md1nl"))))
> -    (build-system python-build-system)
> +                "0mgcs03amrd5157drbm6ikdg0m0szrn9xbflariz2zrrnqpsai6s"))))
> +    (build-system pyproject-build-system)
> +    (arguments
> +     (list
> +      #:phases
> +      #~(modify-phases %standard-phases
> +          (add-after 'unpack 'fix-test
> +            (lambda _
> +              (substitute* "deeptools/test/test_tools.py"
> +                (("e_ver = _p")
> +                 "e_ver = \".\" + _p + \"-real\""))
> +              (substitute* "deeptools/multiBigwigSummary.py"
> +                (("version='multiBigwigSummary")
> +                 "version='%(prog)s"))
> +              (substitute* "deeptools/plotCoverage.py"
> +                (("version='plotCoverage")
> +                 "version='%(prog)s")))))))
>      (native-inputs
>       (list python-mock python-nose))
>      (propagated-inputs
> @@ -4637,7 +4652,7 @@ (define-public python-deeptools
>             python-pysam
>             python-scipy
>             python-deeptoolsintervals
> -           python-plotly-2.4.1))
> +           python-plotly))
>      (home-page "https://pypi.org/project/deepTools/";)
>      (synopsis "Useful tools for exploring deep sequencing data")
>      (description "This package addresses the challenge of handling large 
> amounts
>
> base-commit: cd45294d576975a3bff2f755764a3f46f09ea6f9
> -- 
> 2.41.0
>
>
>
>
> --- End Message ---

--- Begin Message --- Subject: Re: [bug#70276] [PATCH] gnu: python-deeptools: Update to 3.5.5. Date: Tue, 09 Apr 2024 18:15:21 +0100 User-agent: mu4e 1.12.2; emacs 29.3

Simon Tournier <zimon.toutoune@gmail.com> writes:

> * gnu/packages/bioinformatics.scm (python-deeptools): Update to 3.5.5.
> [build-system]: Replace by pyproject-build-system.
> [arguments]: Add phase that fixes 'test/test_tools.py'.
>
> Change-Id: Ibb51939275c96df2c4a1e248a03d683f2f4904ac
> ---
>  gnu/packages/bioinformatics.scm | 23 +++++++++++++++++++----
>  1 file changed, 19 insertions(+), 4 deletions(-)

Looks good to me, I've pushed this to master as
cf29c427e90bd82556addf67885c276e067ce121.

Chris

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