unofficial mirror of guix-patches@gnu.org 
 help / color / mirror / code / Atom feed
From: Ricardo Wurmus <rekado@elephly.net>
To: "Mădălin Ionel Patrașcu" <madalinionel.patrascu@mdc-berlin.de>
Cc: 60997@debbugs.gnu.org
Subject: [bug#60997] [PATCH 1/4] gnu: Add python-cmseq.
Date: Tue, 24 Jan 2023 09:36:39 +0100	[thread overview]
Message-ID: <87lelse36h.fsf@elephly.net> (raw)
In-Reply-To: <20230122004951.119277-1-madalinionel.patrascu@mdc-berlin.de>


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




      parent reply	other threads:[~2023-01-24  8:41 UTC|newest]

Thread overview: 8+ messages / expand[flat|nested]  mbox.gz  Atom feed  top
2023-01-22  0:44 [bug#60997] [patch] gnu: Add python-cmseq, python-cmseq, python-phylophlan and python-metaphlan MadalinIonel.Patrascu
2023-01-22  0:49 ` [bug#60997] [PATCH 1/4] gnu: Add python-cmseq Mădălin Ionel Patrașcu
2023-01-22  0:49   ` [bug#60997] [PATCH 2/4] gnu: Add python-hclust2 Mădălin Ionel Patrașcu
2023-01-22  0:49   ` [bug#60997] [PATCH 3/4] gnu: Add python-phylophlan Mădălin Ionel Patrașcu
2023-01-24  9:10     ` Ricardo Wurmus
2023-01-22  0:49   ` [bug#60997] [PATCH 4/4] gnu: Add python-metaphlan Mădălin Ionel Patrașcu
2023-01-24  9:11     ` Ricardo Wurmus
2023-01-24  8:36   ` Ricardo Wurmus [this message]

Reply instructions:

You may reply publicly to this message via plain-text email
using any one of the following methods:

* Save the following mbox file, import it into your mail client,
  and reply-to-all from there: mbox

  Avoid top-posting and favor interleaved quoting:
  https://en.wikipedia.org/wiki/Posting_style#Interleaved_style

  List information: https://guix.gnu.org/

* Reply using the --to, --cc, and --in-reply-to
  switches of git-send-email(1):

  git send-email \
    --in-reply-to=87lelse36h.fsf@elephly.net \
    --to=rekado@elephly.net \
    --cc=60997@debbugs.gnu.org \
    --cc=madalinionel.patrascu@mdc-berlin.de \
    /path/to/YOUR_REPLY

  https://kernel.org/pub/software/scm/git/docs/git-send-email.html

* If your mail client supports setting the In-Reply-To header
  via mailto: links, try the mailto: link
Be sure your reply has a Subject: header at the top and a blank line before the message body. 
Code repositories for project(s) associated with this public inbox

	https://git.savannah.gnu.org/cgit/guix.git

This is a public inbox, see mirroring instructions
for how to clone and mirror all data and code used for this inbox;
as well as URLs for read-only IMAP folder(s) and NNTP newsgroup(s).