From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from mp1 ([2001:41d0:2:4a6f::]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits)) by ms0.migadu.com with LMTPS id NQfNEfYXQGE1IgAAgWs5BA (envelope-from ) for ; Tue, 14 Sep 2021 05:33:10 +0200 Received: from aspmx1.migadu.com ([2001:41d0:2:4a6f::]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits)) by mp1 with LMTPS id 0PPeDPYXQGGNMgAAbx9fmQ (envelope-from ) for ; Tue, 14 Sep 2021 03:33:10 +0000 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (No client certificate requested) by aspmx1.migadu.com (Postfix) with ESMTPS id A0639BF12 for ; Tue, 14 Sep 2021 05:33:08 +0200 (CEST) Received: from localhost ([::1]:40560 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1mPzBz-0008Ba-Au for larch@yhetil.org; Mon, 13 Sep 2021 23:33:07 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:54074) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1mPzBu-0008BQ-CN for guix-patches@gnu.org; Mon, 13 Sep 2021 23:33:02 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:35654) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1mPzBu-00057x-5I for guix-patches@gnu.org; Mon, 13 Sep 2021 23:33:02 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1mPzBu-0002JK-3c for guix-patches@gnu.org; Mon, 13 Sep 2021 23:33:02 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#33032] Update Resent-From: Sarah Morgensen Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Tue, 14 Sep 2021 03:33:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 33032 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch moreinfo To: Andreas Enge Cc: 33032@debbugs.gnu.org Received: via spool by 33032-submit@debbugs.gnu.org id=B33032.16315903728864 (code B ref 33032); Tue, 14 Sep 2021 03:33:02 +0000 Received: (at 33032) by debbugs.gnu.org; 14 Sep 2021 03:32:52 +0000 Received: from localhost ([127.0.0.1]:47200 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1mPzBk-0002Iu-Ao for submit@debbugs.gnu.org; Mon, 13 Sep 2021 23:32:52 -0400 Received: from out0.migadu.com ([94.23.1.103]:65193) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1mPzBh-0002Ij-8G for 33032@debbugs.gnu.org; Mon, 13 Sep 2021 23:32:50 -0400 X-Report-Abuse: Please report any abuse attempt to abuse@migadu.com and include these headers. DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=mgsn.dev; s=key1; t=1631590362; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc:cc:mime-version:mime-version:content-type:content-type: in-reply-to:in-reply-to:references:references; bh=pXHFC+eb/Rwdqa6dv+etc/fhlFiqUeQjXovoUT8iXO0=; b=MCNMXbyHBIJ6KqJVpWprIbGNY84j8452/0boGFr8yb60ZaV3YaOZNXAkRkis8VB26LWCpW EL48ibgrt85xmWucLN6grcyhJ9AWrAfr6HXOhkn+6hAEL9n9mxiLIX15r7OvuPdBqC0+5B zLf6aqAm+vegXVygFXtOQHlDDjeJRVw= From: Sarah Morgensen References: <20181013034945.9545-1-brettg@posteo.net> <20200905203639.GA24538@jurong> Date: Mon, 13 Sep 2021 20:32:40 -0700 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)") Message-ID: <86o88vj0h3.fsf@mgsn.dev> MIME-Version: 1.0 Content-Type: text/plain X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-BeenThere: guix-patches@gnu.org List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-patches-bounces+larch=yhetil.org@gnu.org Sender: "Guix-patches" X-Migadu-Flow: FLOW_IN ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=yhetil.org; s=key1; t=1631590390; h=from:from:sender:sender:reply-to:subject:subject:date:date: message-id:message-id:to:to:cc:cc:mime-version:mime-version: content-type:content-type:resent-cc:resent-from:resent-sender: resent-message-id:in-reply-to:in-reply-to:references:references: list-id:list-help:list-unsubscribe:list-subscribe:list-post: dkim-signature; bh=pXHFC+eb/Rwdqa6dv+etc/fhlFiqUeQjXovoUT8iXO0=; b=bgxEz4liyH7/+v6lifR81beAbwSWqSNnkQFQMuIZ9SzTaPAzq0PO+oMY59/QS7rmaXLpl1 g4MxkP/znzxkZG34y2PdKIhbjIkeocJ6AulC33Lv9O0hxq4b8FdnGYqpJB90L4hkpa5rF6 ZiNCxYg/4cfPUcp81UkBdW87RG+eW+VjfD8LI1G+k41gHsn6kY8LyqTol/O8hEABMGsqnk qdigzbF2magg0MX3nbuteWZCA5G+QEasvQAYZ04YivNG07Pm1LZis8lI1HTDGLweW5/FJY 4YOOlphWyi30RizmyROUPe5huBj53hi+W3aM9FeSbeCeCX4763gU0GU8e1yDxA== ARC-Seal: i=1; s=key1; d=yhetil.org; t=1631590390; a=rsa-sha256; cv=none; b=Cl3ZZQxCSQhIV2XVwOLJgwMQ4Zb8L343rXalnlp7fSqcPL6G9Psbgs2PKvTNiw1ffb64fq I5YguC5uPoGqVz8pWwh6xZ8ZyPOR3slAOkSKcg1FIYTNXvAg+M9RJRBrPbwKEgI8QiKm+d adVorAaXjz0VjEK+56tXWXnnXCYYrg7a1QLydSYk7w8XvtMuqHpuRFLxiLXbjreBdHdwmm 58SKcj0EPCEUpVWO3XQhFutxo9gosX+yS71ZwWxhjfE+DvZbL7Vy6X2sUJGwkWzEE3WPjP 8wqjA7yXDl53SMJU9XyHcfqbKgYgG/QbxOLr/ZtlEPw7rGpfz3To893sJ0c76g== ARC-Authentication-Results: i=1; aspmx1.migadu.com; dkim=fail ("headers rsa verify failed") header.d=mgsn.dev header.s=key1 header.b=MCNMXbyH; dmarc=fail reason="SPF not aligned (relaxed)" header.from=mgsn.dev (policy=none); spf=pass (aspmx1.migadu.com: domain of guix-patches-bounces@gnu.org designates 209.51.188.17 as permitted sender) smtp.mailfrom=guix-patches-bounces@gnu.org X-Migadu-Spam-Score: 0.20 Authentication-Results: aspmx1.migadu.com; dkim=fail ("headers rsa verify failed") header.d=mgsn.dev header.s=key1 header.b=MCNMXbyH; dmarc=fail reason="SPF not aligned (relaxed)" header.from=mgsn.dev (policy=none); spf=pass (aspmx1.migadu.com: domain of guix-patches-bounces@gnu.org designates 209.51.188.17 as permitted sender) smtp.mailfrom=guix-patches-bounces@gnu.org X-Migadu-Queue-Id: A0639BF12 X-Spam-Score: 0.20 X-Migadu-Scanner: scn0.migadu.com X-TUID: YKh3lBvZKsfp Hello, Andreas Enge 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