GNU bug report logs - #60997
[patch] gnu: Add python-cmseq, python-cmseq, python-phylophlan and python-metaphlan.

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Message #20 received at 60997 <at> debbugs.gnu.org (full text, mbox):

From: Ricardo Wurmus <rekado <at> elephly.net>
To: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
Cc: 60997 <at> debbugs.gnu.org
Subject: Re: [bug#60997] [PATCH 1/4] gnu: Add python-cmseq.
Date: Tue, 24 Jan 2023 09:36:39 +0100

Hi Mădălin,

> * gnu/packages/bioinformatics.scm (python-cmseq): New variable.

Thanks for the patch.

Unfortunately, this is incomplete:

- The tool calls out to samtools (see cmseq/cmseq.py), so it needs
  samtools as an input and the call needs to be patched.

- The README says that biopython <= 1.76 is needed for polymut.py.
  You’re using 1.80.

> +    (build-system python-build-system)

Please consider using the pyproject-build-system.

> +    (arguments
> +     (list #:tests? #f )) ;pypi no tests

Apparantly, there are no tests anywhere.  It’s not a pypi problem.
Please update the comment and remove that extra space after #f.

> +    (home-page "http://github.com/SegataLab/cmseq/")

Please use HTTPS.  “guix lint” informs you about the redirect.

-- 
Ricardo

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