bug#48862: closed ([PATCH] gnu: python-hic2cool: Update to 0.8.3.)

[GNU bug Tracking System]

Your message dated Mon, 7 Jun 2021 10:40:08 +0300
with message-id <YL3NWLGIW7WewgjQ@3900XT>
and subject line Re: [bug#48862] [PATCH] gnu: python-hic2cool: Update to 0.8.3.
has caused the debbugs.gnu.org bug report #48862,
regarding [PATCH] gnu: python-hic2cool: Update to 0.8.3.
to be marked as done.

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-- 
48862: http://debbugs.gnu.org/cgi/bugreport.cgi?bug=48862
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> --- Begin Message ---
>
>
>
> Subject: 
>
> [PATCH] gnu: python-hic2cool: Update to 0.8.3.
>
>
>
>
> Date: 
>
> Sun, 6 Jun 2021 07:14:07 +0200
>
>
>
>
> * gnu/packages/bioinformatics.scm (python-hic2cool): Update to 0.8.3.
> ---
>  gnu/packages/bioinformatics.scm | 28 ++++++++++++++++++++++------
>  1 file changed, 22 insertions(+), 6 deletions(-)
>
> diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
> index dab097381a..66e69ff2c8 100644
> --- a/gnu/packages/bioinformatics.scm
> +++ b/gnu/packages/bioinformatics.scm
> @@ -11892,18 +11892,34 @@ pyGenomeTracks can make plots with or without Hi-C 
> data.")
>  (define-public python-hic2cool
>    (package
>      (name "python-hic2cool")
> -    (version "0.4.2")
> +    (version "0.8.3")
> +    ;; pypi sources do not contain the test_data directory and no test can be
> +    ;; run
>      (source
>       (origin
> -       (method url-fetch)
> -       (uri (pypi-uri "hic2cool" version))
> +       (method git-fetch)
> +       (uri (git-reference
> +             (url "https://github.com/4dn-dcic/hic2cool";)
> +             (commit version)))
> +       (file-name (git-file-name name version))
>         (sha256
>          (base32
> -         "0xy6mhfns2lzib1kcr6419jjp6pmh0qx8z8na55lmiwn0ds8q9cl"))))
> +         "0dlnf0qfcp4jrc1nyya32a035c13xicyq16bwfnwhbb9s47mz7gl"))))
>      (build-system python-build-system)
> -    (arguments '(#:tests? #f)) ; no tests included
> +    (arguments
> +     `(#:phases
> +       (modify-phases %standard-phases
> +         ;;two of the test-data files need to be writable
> +         (add-after 'unpack 'patch-test-data
> +           (lambda* (#:key inputs outputs #:allow-other-keys)
> +             (chmod "test_data/hic2cool_0.4.2_single_res.cool" #o600)
> +             (chmod "test_data/hic2cool_0.7.0_multi_res.mcool" #o600))))))
>      (propagated-inputs
> -     `(("python-cooler" ,python-cooler)))
> +     `(("python-cooler" ,python-cooler)
> +       ("python-h5py" ,python-h5py)
> +       ("python-numpy" ,python-numpy)
> +       ("python-pandas" ,python-pandas)
> +       ("python-scipy" ,python-scipy)))
>      (home-page "https://github.com/4dn-dcic/hic2cool";)
>      (synopsis "Converter for .hic and .cool files")
>      (description
> -- 
> 2.31.1
>
>
>
>
> --- End Message ---

--- Begin Message --- Subject: Re: [bug#48862] [PATCH] gnu: python-hic2cool: Update to 0.8.3. Date: Mon, 7 Jun 2021 10:40:08 +0300

I made a few changes before pushing the patch.

On Sun, Jun 06, 2021 at 07:14:07AM +0200, Mădălin Ionel Patrașcu wrote:
> * gnu/packages/bioinformatics.scm (python-hic2cool): Update to 0.8.3.

I mentioned that the download changed to use git-fetch, the added phase
and enabled tests, and the added inputs.

> ---
>  gnu/packages/bioinformatics.scm | 28 ++++++++++++++++++++++------
>  1 file changed, 22 insertions(+), 6 deletions(-)
> 
> diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
> index dab097381a..66e69ff2c8 100644
> --- a/gnu/packages/bioinformatics.scm
> +++ b/gnu/packages/bioinformatics.scm
> @@ -11892,18 +11892,34 @@ pyGenomeTracks can make plots with or without Hi-C 
> data.")
>  (define-public python-hic2cool
>    (package
>      (name "python-hic2cool")
> -    (version "0.4.2")
> +    (version "0.8.3")
> +    ;; pypi sources do not contain the test_data directory and no test can be
> +    ;; run
>      (source
>       (origin
> -       (method url-fetch)
> -       (uri (pypi-uri "hic2cool" version))
> +       (method git-fetch)
> +       (uri (git-reference
> +             (url "https://github.com/4dn-dcic/hic2cool";)
> +             (commit version)))
> +       (file-name (git-file-name name version))
>         (sha256
>          (base32
> -         "0xy6mhfns2lzib1kcr6419jjp6pmh0qx8z8na55lmiwn0ds8q9cl"))))
> +         "0dlnf0qfcp4jrc1nyya32a035c13xicyq16bwfnwhbb9s47mz7gl"))))
>      (build-system python-build-system)
> -    (arguments '(#:tests? #f)) ; no tests included
> +    (arguments
> +     `(#:phases
> +       (modify-phases %standard-phases
> +         ;;two of the test-data files need to be writable
> +         (add-after 'unpack 'patch-test-data
> +           (lambda* (#:key inputs outputs #:allow-other-keys)
> +             (chmod "test_data/hic2cool_0.4.2_single_res.cool" #o600)
> +             (chmod "test_data/hic2cool_0.7.0_multi_res.mcool" #o600))))))

I changed this one to be 'lambda _' and I changed the chmods to
make-file-writable.

>      (propagated-inputs
> -     `(("python-cooler" ,python-cooler)))
> +     `(("python-cooler" ,python-cooler)
> +       ("python-h5py" ,python-h5py)
> +       ("python-numpy" ,python-numpy)
> +       ("python-pandas" ,python-pandas)
> +       ("python-scipy" ,python-scipy)))
>      (home-page "https://github.com/4dn-dcic/hic2cool";)
>      (synopsis "Converter for .hic and .cool files")
>      (description
> -- 
> 2.31.1
> 
> 
> 
> 

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Efraim Flashner   <efraim@flashner.co.il>   אפרים פלשנר
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