From: Sarah Morgensen <iskarian@mgsn.dev>
To: Andreas Enge <andreas@enge.fr>
Cc: 33032@debbugs.gnu.org
Subject: [bug#33032] Update
Date: Mon, 13 Sep 2021 20:32:40 -0700 [thread overview]
Message-ID: <86o88vj0h3.fsf@mgsn.dev> (raw)
In-Reply-To: <20200905203639.GA24538@jurong> (Andreas Enge's message of "Sat, 5 Sep 2020 22:36:39 +0200 (1 year, 1 week, 1 day ago)")
Hello,
Andreas Enge <andreas@enge.fr> writes:
> Hello,
>
> I just updated seqmagick to 0.8.0.
>
> Then I tried to update python-biopython to the latest version, 1.78. With it,
> seqmagick fails to compile with the following message:
>
> mportError: cannot import name 'triefind' from 'Bio'
> (/gnu/store/9cr6885z39yb5x3pbanva5h9nacmlkvz-python-biopython-1.78/lib/python3.8/site-packages/Bio/__init__.py)
>
> ======================================================================
> ERROR: Failure: ImportError (Bio.Alphabet has been removed from Biopython. In
> many cases, the alphabet can simply be ignored and removed from scripts. In a
> few cases, you may need to specify the ``molecule_type`` as an annotation on a
> SeqRecord for your script to work correctly. Please see
> https://biopython.org/wiki/Alphabet for more information.)
I think this may be fixed by updating seqmagick to 0.8.1 (current
release 0.8.4) and packaging its new dependency, pygtrie, which provides
that removed functionality.
--
Sarah
next prev parent reply other threads:[~2021-09-14 3:33 UTC|newest]
Thread overview: 5+ messages / expand[flat|nested] mbox.gz Atom feed top
2018-10-13 3:49 [bug#33032] [PATCH] gnu: update python-biopython to 1.72 Brett Gilio
2018-10-21 21:40 ` Ludovic Courtès
2020-09-05 20:36 ` [bug#33032] Update Andreas Enge
2021-09-14 3:32 ` Sarah Morgensen [this message]
2022-04-07 12:03 ` bug#33032: [PATCH] gnu: update python-biopython to 1.72 zimoun
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
* Reply using the --to, --cc, and --in-reply-to
switches of git-send-email(1):
git send-email \
--in-reply-to=86o88vj0h3.fsf@mgsn.dev \
--to=iskarian@mgsn.dev \
--cc=33032@debbugs.gnu.org \
--cc=andreas@enge.fr \
/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 external index
https://git.savannah.gnu.org/cgit/guix.git
This is an external index of several public inboxes,
see mirroring instructions on how to clone and mirror
all data and code used by this external index.