bug#66847: closed ([PATCH] gnu: python-baltica: Update to 1.1.2.)

[GNU bug Tracking System]

Your message dated Tue, 31 Oct 2023 22:05:29 +0100
with message-id <875y2mv6wz.fsf@elephly.net>
and subject line [PATCH] gnu: python-baltica: Update to 1.1.2.
has caused the debbugs.gnu.org bug report #66847,
regarding [PATCH] gnu: python-baltica: Update to 1.1.2.
to be marked as done.

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-- 
66847: https://debbugs.gnu.org/cgi/bugreport.cgi?bug=66847
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> --- Begin Message ---
>
>
>
> Subject: 
>
> [PATCH] gnu: python-baltica: Update to 1.1.2.
>
>
>
>
> Date: 
>
> Tue, 31 Oct 2023 14:01:22 +0000
>
>
>
>
> * gnu/packages/bioinformatics.scm (python-baltica): Update to 1.1.2.
> [propagated-inputs]: Add r-yaml, r-rsamtools, r-biocmanager, r-here, 
> r-genomicranges,
> r-readr, r-tidyr, r-stringr, r-optparse, r-openxlsx, r-dplyr, and
> r-upsetr.
>
> Change-Id: I8c1bb556048b406b95e081155a46da17a6be5676
> ---
>  gnu/packages/bioinformatics.scm | 76 +++++++++++++++++++--------------
>  1 file changed, 43 insertions(+), 33 deletions(-)
>
> diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
> index a47e84bc33..66d1a21ffe 100644
> --- a/gnu/packages/bioinformatics.scm
> +++ b/gnu/packages/bioinformatics.scm
> @@ -5130,47 +5130,57 @@ (define-public python-baltica
>    (package
>      (name "python-baltica")
>      (version "1.1.2")
> -    (source (origin
> -              (method git-fetch)
> -              (uri (git-reference
> -                    (url "https://github.com/dieterich-lab/Baltica";)
> -                    (commit (string-append "v" version))))
> -              (file-name (git-file-name name version))
> -              (sha256
> -               (base32
> -                "001ac03v9pbqqzf9pv7v8gf0296ksa4f0v3wdmpa6m9701skqi4r"))))
> +    (source
> +     (origin
> +       (method git-fetch)
> +       (uri (git-reference
> +             (url "https://github.com/dieterich-lab/Baltica";)
> +             (commit (string-append "v" version))))
> +       (file-name (git-file-name name version))
> +       (sha256
> +        (base32 "001ac03v9pbqqzf9pv7v8gf0296ksa4f0v3wdmpa6m9701skqi4r"))))
>      (build-system pyproject-build-system)
>      (arguments
>       (list
> -      #:phases
> -      '(modify-phases %standard-phases
> -         (replace 'check
> -           (lambda* (#:key tests? #:allow-other-keys)
> -             (when tests?
> -               ;; The tests need to be run from elsewhere...
> -               (mkdir-p "/tmp/test")
> -               (copy-recursively ".tests" "/tmp/test")
> -               (with-directory-excursion "/tmp/test"
> -                 (invoke "pytest" "-v" "--doctest-modules"))))))))
> -    (propagated-inputs
> -     (list gunicorn
> -           python-anndata
> -           python-click
> -           python-flask
> -           python-flask-wtf
> -           python-h5py
> -           python-numpy
> -           python-psutil
> -           python-pysam
> -           python-pyyaml
> -           python-scipy
> -           snakemake-7))
> +      #:phases '(modify-phases %standard-phases
> +                  (replace 'check
> +                    (lambda* (#:key tests? #:allow-other-keys)
> +                      (when tests?
> +                        ;; The tests need to be run from elsewhere...
> +                        (mkdir-p "/tmp/test")
> +                        (copy-recursively ".tests" "/tmp/test")
> +                        (with-directory-excursion "/tmp/test"
> +                          (invoke "pytest" "-v" "--doctest-modules"))))))))
> +    (propagated-inputs (list gunicorn
> +                             python-anndata
> +                             python-click
> +                             python-flask
> +                             python-flask-wtf
> +                             python-h5py
> +                             python-numpy
> +                             python-psutil
> +                             python-pysam
> +                             python-pyyaml
> +                             python-scipy
> +                             r-yaml
> +                             r-rsamtools
> +                             r-biocmanager
> +                             r-here
> +                             r-genomicranges
> +                             r-readr
> +                             r-tidyr
> +                             r-stringr
> +                             r-optparse
> +                             r-openxlsx
> +                             r-dplyr
> +                             r-upsetr
> +                             snakemake-7))
>      (native-inputs (list python-cython python-pyfakefs python-pytest))
>      (home-page "https://github.com/dieterich-lab/Baltica";)
>      (synopsis "Integrated splice junction usage analysis")
>      (description
>       "This framework facilitates the execution of @dfn{differential junction
> -usage} (DJU) methods. Additionally, it enables the integration of results from
> +usage} (DJU) methods.  Additionally, it enables the integration of results from
>  multiple DJU methods.")
>      (license license:expat)))
>  
>
> base-commit: c0895371c5759c7d9edb330774e90f192cc4cf2c
> -- 
> 2.34.1
>
>
>
>
> --- End Message ---
> --- Begin Message ---
>
>
>
> Subject: 
>
> [PATCH] gnu: python-baltica: Update to 1.1.2.
>
>
>
>
> Date: 
>
> Tue, 31 Oct 2023 22:05:29 +0100
>
>
>
>
> User-agent: 
>
> mu4e 1.10.7; emacs 29.1
>
>
>
>
> Thanks for the patch.  I changed the commit message and reduced the
> number of changes to the essential.
>
> Pushed!
>
> -- 
> Ricardo
>
>
> --- End Message ---