Path: csiph.com!aioe.org!bofh.it!news.nic.it!robomod From: Peter Cock Newsgroups: linux.debian.maint.python Subject: Re: Strange encoding problem in setup.py of biopython 1.71 Date: Fri, 13 Apr 2018 13:20:01 +0200 Message-ID: References: X-Mailbox-Line: From debian-python-request@lists.debian.org Fri Apr 13 11:13:29 2018 Old-Return-Path: X-Amavis-Spam-Status: No, score=-7.779 tagged_above=-10000 required=5.3 tests=[BAYES_00=-2, DIGITS_LETTERS=1, DKIM_SIGNED=0.1, DKIM_VALID=-0.1, DKIM_VALID_AU=-0.1, FREEMAIL_FROM=0.001, LDO_WHITELIST=-5, MD5_SHA1_SUM=-1, MURPHY_DRUGS_REL8=0.02, RCVD_IN_DNSWL_LOW=-0.7] autolearn=ham autolearn_force=no X-Policyd-Weight: DYN_NJABL=SKIP(0) NOT_IN_SBL_XBL_SPAMHAUS=-1.5 BL_NJABL=SKIP(-1.5) CL_IP_EQ_HELO_IP=-2 (check from: .googlemail. - helo: .mail-qk0-x230.google. - helo-domain: .google.) FROM/MX_MATCHES_HELO(DOMAIN)=-2; rate: -7 Dkim-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=googlemail.com; s=20161025; h=mime-version:in-reply-to:references:from:date:message-id:subject:to :cc; bh=qtm7I7ZPYBiT0igSFTty1aq7irQWPrz28Q+AAEDJJMk=; b=FxM5YuFxF5xpjMUkIp38M8qm+9ACWUgDiY6D0upTGxQAbp9Ls6LJ+MzzsOqKKMX/Gs wLGAtTcKNd9wweghwFsS6NHmZTGoBcj/GU0YRMAZqCNQQNNxIj3qN5b4MJfyiopMzqY+ jTKH86ZWvVsJy/QogoSWm7NozPP79GDJu2ztaOEa8OpS1cbprKg2goyG5j0/sVcIv3cf PKqsQYsBzPj21QlNNRU8CW7NrGjurvRHKkm8zEpVeZLhrt/rvrJTmEtQeBc5Xrqyn4lY kXIhhjSAMOPpksQ2u19ifnH5Pvio8MvITUYnyfcZLOg02H1MkYbCYjD3vmN4onxHfv1s 3EWw== X-Google-Dkim-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:mime-version:in-reply-to:references:from:date :message-id:subject:to:cc; bh=qtm7I7ZPYBiT0igSFTty1aq7irQWPrz28Q+AAEDJJMk=; b=NtQavavvQQ4PX1OJwlSq2jeNC+/8mR1up+FYAe/Z5IO5/vhpikIm4kMU/g6uy+OjXS R81tVcR6H6VNs0e07OH4AGqVvPmQKtcRh47hcj9fwaJyy3ADq5048yhu43awqADceRKQ yiHP8CkMoHs28kwCFq3o5WVudi6pRpQ1L0kd52WLUGQt3vCriw2kuROL6cipdmj3wYFt Cc6pkxPl28utx5fNJESclhwfa5NZdXD0nqAp5aa9/DjpRj9HpdK5I3bJaolzvYJU5AWu wKUVX7Pv2PSZeq4p9vxr2QnWi3v15a4d2jJpBZRuTW0owVKAnPtVG3qcHzar8WWm3BFX v0jA== X-Gm-Message-State: ALQs6tCO9NxhtAGODLCtp7zbU6HYZZer7+RKtQoDAm2IlyoEGFc0MAQO FXHNIxPm1oNgV5hLQ8Bl63xZBAk7xx4/lDGBeVw= X-Google-SMTP-Source: AIpwx4/j/CG9MF0LNfGfYpqqsGJjTCvY6lMqe36ELZVTR8mDn06mg/iTbe5Rq1s8pK6YTasuaKtGplb5L0SX28yjMQE= X-Received: by 10.55.194.67 with SMTP id j3mr3870720qkm.349.1523617992289; Fri, 13 Apr 2018 04:13:12 -0700 (PDT) MIME-Version: 1.0 Content-Type: text/plain; charset="UTF-8" X-Mailing-List: archive/latest/15817 List-ID: List-URL: List-Archive: https://lists.debian.org/msgid-search/CAKVJ-_6TOqR84LTPqKtAoPguXDU=S0aoJ_reZw7-CK4-uteFUA@mail.gmail.com Approved: robomod@news.nic.it Lines: 49 Organization: linux.* mail to news gateway Sender: robomod@news.nic.it X-Original-Cc: debian-python@lists.debian.org X-Original-Date: Fri, 13 Apr 2018 12:13:11 +0100 X-Original-Message-ID: X-Original-References: <20180405141056.nsmfcwdingnmgx5d@an3as.eu> <20180405143432.xrnte6hyft7rf2vm@an3as.eu> <1eb7f5a5-711a-8dc6-a376-e4a6fd298991@gmx.de> <20180406071620.ngdzjtvqs3a4ev7m@an3as.eu> Xref: csiph.com linux.debian.maint.python:10417 I ended up doing something similar to catch any future problematic characters: https://github.com/biopython/biopython/pull/1607 Peter On Fri, Apr 6, 2018 at 10:36 AM, Peter Cock wrote: > Thanks Andreas, > > Piotr, I think your fix would be worth including in Biopython. > > Do you want to submit this as a pull request, or give me > permission to do so by email? > > We'd need you to agree to both the Biopython License Agreement > and the 3-clause BSD licence, and say if you'd like to be > acknowledged by name or not. > > Regards, > > Peter > > On Fri, Apr 6, 2018 at 8:16 AM, Andreas Tille wrote: >> Hi Peter, >> >> On Thu, Apr 05, 2018 at 04:19:50PM +0100, Peter Cock wrote: >>> >>> https://github.com/biopython/biopython/commit/6421d365a511c0de71748737ba6e1cd8518658ac >>> >>> Can you pull in that commit as a patch for the Biopython 1.71 package? >> >> Thanks. I'm using this as patch. I can confirm that this works now >> (I'm using the other patch suggested here[1] in addition to deal with >> potential other encoding issues. >> >> I'll upload soon (I had some other issues with the packaging which are >> not related). >> >> Kind regards >> >> Andreas. >> >> >> [1] https://lists.debian.org/debian-python/2018/04/msg00023.html >> >> -- >> http://fam-tille.de