bug#69011: closed ([PATCH] gnu: Add python-pdbfixer.)

[GNU bug Tracking System]

Your message dated Sat, 10 Feb 2024 11:21:39 +0100
with message-id <87ttmgsjom.fsf@elephly.net>
and subject line [PATCH] gnu: Add python-pdbfixer.
has caused the debbugs.gnu.org bug report #69011,
regarding [PATCH] gnu: Add python-pdbfixer.
to be marked as done.

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-- 
69011: https://debbugs.gnu.org/cgi/bugreport.cgi?bug=69011
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> --- Begin Message ---
>
>
>
> Subject: 
>
> [PATCH] gnu: Add python-pdbfixer.
>
>
>
>
> Date: 
>
> Sat, 10 Feb 2024 10:14:48 +0000
>
>
>
>
> * gnu/packages/bioinformatics.scm (python-pdbfixer): New variable.
>
> Change-Id: I2894a08ab3eed463f052b9df6372d4016b718d1a
> ---
>  gnu/packages/bioinformatics.scm | 31 +++++++++++++++++++++++++++++++
>  1 file changed, 31 insertions(+)
>
> diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
> index 56709c0332..2c1917be95 100644
> --- a/gnu/packages/bioinformatics.scm
> +++ b/gnu/packages/bioinformatics.scm
> @@ -2244,6 +2244,37 @@ (define-public python-parabam
>  defined rule on an input file.")
>      (license license:gpl3)))
>  
> +(define-public python-pdbfixer
> +  (package
> +    (name "python-pdbfixer")
> +    (version "1.9")
> +    (source
> +     (origin
> +       (method git-fetch)
> +       (uri (git-reference
> +             (url "https://github.com/openmm/pdbfixer";)
> +             (commit version)))
> +       (file-name (git-file-name name version))
> +       (sha256
> +        (base32 "1zjhb19q5dclkwvzh8n29p31n1vzkhlmmzwqllimi89jsis1cx35"))))
> +    (build-system pyproject-build-system)
> +    (arguments
> +     (list
> +      #:test-flags '(list "-k"
> +                          ;; These tests fail because they require internet 
> access.
> +                          (string-append "not test_build_and_simulate.py"
> +                                         " and not test_cli.py"
> +                                         " and not test_mutate.py"))))
> +    (propagated-inputs (list python-numpy openmm))
> +    (native-inputs (list python-pytest))
> +    (home-page "https://github.com/openmm/pdbfixer";)
> +    (synopsis "Application for fixing problems in Protein Data Bank")
> +    (description
> +     "PDBFixer is designed to rectify issues in Protein Data Bank files.
> +Its intuitive interface simplifies the process of resolving problems
> +encountered in PDB files prior to simulation tasks.")
> +    (license license:expat)))
> +
>  (define-public python-peaks2utr
>    (package
>      (name "python-peaks2utr")
>
> base-commit: 10dba10fd6551ab480a38d00301e6f102def674d
> prerequisite-patch-id: 3a59afadab83198b19921e19197e26925523b4a3
> prerequisite-patch-id: 116b12264d1713957eef349460a71f04b0757a9e
> -- 
> 2.34.1
>
>
>
>
> --- End Message ---
> --- Begin Message ---
>
>
>
> Subject: 
>
> [PATCH] gnu: Add python-pdbfixer.
>
>
>
>
> Date: 
>
> Sat, 10 Feb 2024 11:21:39 +0100
>
>
>
>
> User-agent: 
>
> mu4e 1.10.8; emacs 29.1
>
>
>
>
> Thanks for the patch.  I’ve applied it and pushed with commit
> ca4c9062c4a04a3550fdcf67cb2b41daa13627d8.
>
> -- 
> Ricardo
>
>
> --- End Message ---