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Reply-To: bug#34456 <34456@debbugs.gnu.org> Date: Mon, 23 Jun 2025 05:42:55 +0000 retitle 34456 [PATCH] gnu: python-pybedtools: Update to 0.8.0 and fix build. reassign 34456 guix-patches submitter 34456 Maxim Cournoyer severity 34456 normal tag 34456 patch thanks From debbugs-submit-bounces@debbugs.gnu.org Tue Feb 12 10:32:27 2019 Received: (at submit) by debbugs.gnu.org; 12 Feb 2019 15:32:27 +0000 Received: from localhost ([127.0.0.1]:45035 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1gta2o-0004aG-Ao for submit@debbugs.gnu.org; Tue, 12 Feb 2019 10:32:27 -0500 Received: from eggs.gnu.org ([209.51.188.92]:33223) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1gta2i-0004Zy-UQ for submit@debbugs.gnu.org; Tue, 12 Feb 2019 10:32:20 -0500 Received: from lists.gnu.org ([209.51.188.17]:39841) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32) (Exim 4.71) (envelope-from ) id 1gta2d-0000ai-Md for submit@debbugs.gnu.org; Tue, 12 Feb 2019 10:32:11 -0500 Received: from eggs.gnu.org ([209.51.188.92]:47598) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1gta2c-00056S-3V for guix-patches@gnu.org; Tue, 12 Feb 2019 10:32:11 -0500 X-Spam-Checker-Version: SpamAssassin 3.3.2 (2011-06-06) on eggs.gnu.org X-Spam-Level: X-Spam-Status: No, score=0.8 required=5.0 tests=BAYES_50,FREEMAIL_FROM, URIBL_BLOCKED autolearn=disabled version=3.3.2 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1gta2a-0000X2-FQ for guix-patches@gnu.org; Tue, 12 Feb 2019 10:32:10 -0500 Received: from mail-qk1-x72c.google.com ([2607:f8b0:4864:20::72c]:46183) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1gta2a-0000VS-8c for guix-patches@gnu.org; Tue, 12 Feb 2019 10:32:08 -0500 Received: by mail-qk1-x72c.google.com with SMTP id i5so4203747qkd.13 for ; Tue, 12 Feb 2019 07:32:08 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=from:to:subject:date:message-id:user-agent:mime-version :content-disposition:content-transfer-encoding; bh=DlIJjaJd+lgTy7xBsMRbc7AWKzFXQ2XH2ltDFiR1H78=; b=JHwBn24ay3CeB5mKcbcQOf5hDAigqFqkjLwznONGGAY4wgv0GplfVQnDZq2kqA5guP 9f6SoWsQtqbdS98AljlP0uSbxG8oaCGaaFGiyAiw32ooXR0Xbq5glBjLn7DSyyKk0SOd 1/iBiitzXMVerAqhE02ip9cMOq82/SAkMV7MCldx1iJRFdzR1D+cX3wS/kOD8tYw6TvF yzQH5AkqQos4CcdfVo5K5ldrfJ7Fkl1S0xXZmgnuEbJaV/mfqV+4fuJdPVR+3sfLYpzQ E4RJq3sjv8adftFNEftT55dlf+X5FxJIhbehCkrvi63gYVKTsSkkJYEXC285ikJ7aOvR qdPA== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:from:to:subject:date:message-id:user-agent :mime-version:content-disposition:content-transfer-encoding; bh=DlIJjaJd+lgTy7xBsMRbc7AWKzFXQ2XH2ltDFiR1H78=; b=KRmabP3npbff054DqzX5MhJDCWKzAy/TrvXLb9FvEaK2io3dEriLCDJ5qSEm9/4Bdv klhGKJZRWYEJTAzAxucf/hDHyWJ89rH4V6wfBUrDZpmaDaoo1rnzdI5W7swrpnZYn+DE WVKhVHP2O/ELq4ps3rlOy+KF93V0sfA0DxAodQqTHFf6dNtvkWbhyf4RCYkXaBHfbt1Q TBg6eB2gGCZ0hNtT8OMVyQVO6u/Cpd9GlXwxa9hljDFFqejxK2L+PwadGooe2kENdzQx ALAd6KXR1xx387/d1FFiC9UrKu9xsOWE+ZD6oPmPOQWGmx7CnxQ5amNcy2xgc6/qfDPV FQ4A== X-Gm-Message-State: AHQUAuZzQzVwN8vhukgJ96o2Ovso3NsIjju4WrYRZfIhgjfFROoZV1jc XZ5haTOdKtcI6gfS9pANLjMunHX6 X-Google-Smtp-Source: AHgI3Ibej//EoBQ6avqDJROe91JJUoVxUNoIuQjuiBhumtH5SOSfWxKVmQRQj1AWh0SIFKl07O3E4g== X-Received: by 2002:a37:9d56:: with SMTP id g83mr2993150qke.351.1549985527220; Tue, 12 Feb 2019 07:32:07 -0800 (PST) Received: from kwak (mtl.savoirfairelinux.net. [208.88.110.46]) by smtp.gmail.com with ESMTPSA id c9sm11142140qkj.61.2019.02.12.07.32.06 for (version=TLS1_2 cipher=ECDHE-RSA-CHACHA20-POLY1305 bits=256/256); Tue, 12 Feb 2019 07:32:06 -0800 (PST) From: Maxim Cournoyer To: guix-patches Subject: [PATCH] gnu: python-pybedtools: Update to 0.8.0 and fix build. Date: Tue, 12 Feb 2019 10:32:03 -0500 Message-ID: <87d0nx10r0.fsf@gmail.com> User-Agent: Gnus/5.13 (Gnus v5.13) Emacs/26.1 (gnu/linux) MIME-Version: 1.0 Content-Type: text/x-patch; charset=utf-8 Content-Disposition: attachment; filename=0001-gnu-python-pybedtools-Update-to-0.8.0-and-fix-build.patch Content-Transfer-Encoding: quoted-printable X-detected-operating-system: by eggs.gnu.org: Genre and OS details not recognized. X-Received-From: 2607:f8b0:4864:20::72c X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.6.x X-Spam-Score: 1.0 (+) X-Debbugs-Envelope-To: submit X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -0.0 (/) >From 40db2b4eae5ca61a3134cdaf7b156ed1ae9f7415 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Sun, 10 Feb 2019 23:39:25 -0500 Subject: [PATCH] gnu: python-pybedtools: Update to 0.8.0 and fix build. * gnu/packages/bioinformatics.scm (python-pybedtools): Update to 0.8.0. [phases]{disable-broken-tests}: Do not disable "test_issue_157" and "test_to_dataframe" tests. Disable the "test_getting_example_beds". {remove-cython-generated-files}: Add phase. {generate-cython-extensions}: Add phase. {check}: Move from python2-pybedtools to here. Add a scripts subdirectory of the build directory to the PATH, so that the tests can call them. Invoke pytest rather than nosetests. [modules]: Move from python2-pybedtools to here. [propagated-inputs]: Depend on the current BEDTOOLS rather than version 1.2= 6. [native-inputs]: Replace python-nose by python-pytest and add python-psutil. --- gnu/packages/bioinformatics.scm | 114 +++++++++++++++++++------------- 1 file changed, 67 insertions(+), 47 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.= scm index 279d52ae9..d6db02188 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -12,6 +12,7 @@ ;;; Copyright =C2=A9 2018 Joshua Sierles, Nextjournal ;;; Copyright =C2=A9 2018 G=C3=A1bor Boskovits ;;; Copyright =C2=A9 2018 M=C4=83d=C4=83lin Ionel Patra=C8=99cu +;;; Copyright =C2=A9 2019 Maxim Cournoyer ;;; ;;; This file is part of GNU Guix. ;;; @@ -612,16 +613,22 @@ intended to behave exactly the same as the original B= WK awk.") (define-public python-pybedtools (package (name "python-pybedtools") - (version "0.7.10") + (version "0.8.0") (source (origin (method url-fetch) (uri (pypi-uri "pybedtools" version)) (sha256 (base32 - "0l2b2wrnj85azfqgr0zwr60f7j58vlla1hcgxvr9rwikpl8j72ji")))) + "1xl454ijvd4dzfvqgfahad49b49j7qy710fq9xh1rvk42z6x5ssf")))) (build-system python-build-system) (arguments - `(#:phases + `(#:modules ((ice-9 ftw) + (srfi srfi-1) + (srfi srfi-26) + (guix build utils) + (guix build python-build-system)) + ;; See https://github.com/daler/pybedtools/issues/192 + #:phases (modify-phases %standard-phases ;; See https://github.com/daler/pybedtools/issues/261 (add-after 'unpack 'disable-broken-tests @@ -631,21 +638,59 @@ intended to behave exactly the same as the original B= WK awk.") (substitute* "pybedtools/test/test_scripts.py" (("def test_venn_mpl") "def _do_not_test_venn_mpl")) - ;; Requires internet access. (substitute* "pybedtools/test/test_helpers.py" + ;; Requires internet access. (("def test_chromsizes") - "def _do_not_test_chromsizes")) - ;; FIXME: these two fail for no good reason. - (substitute* "pybedtools/test/test1.py" - (("def test_issue_157") - "def _do_not_test_issue_157") - (("def test_to_dataframe") - "def _do_not_test_to_dataframe")) - #t))))) - (propagated-inputs - ;; Tests don't pass with Bedtools 2.27.1. - ;; See https://github.com/daler/pybedtools/issues/260 - `(("bedtools" ,bedtools-2.26) + "def _do_not_test_chromsizes") + ;; Broken as a result of the workaround used in the check p= hase + ;; (see: https://github.com/daler/pybedtools/issues/192). + (("def test_getting_example_beds") + "def _do_not_test_getting_example_beds")) + #t)) + ;; TODO: Remove phase after it's part of PYTHON-BUILD-SYSTEM. + ;; build system. + ;; Force the Cythonization of C++ files to guard against compilat= ion + ;; problems. + (add-after 'unpack 'remove-cython-generated-files + (lambda _ + (let ((cython-sources (map (cut string-drop-right <> 4) + (find-files "." "\\.pyx$"))) + (c/c++-files (find-files "." "\\.(c|cpp|cxx)$"))) + (define (strip-extension filename) + (string-take filename (string-index-right filename #\.))) + (define (cythonized? c/c++-file) + (member (strip-extension c/c++-file) cython-sources)) + (for-each delete-file (filter cythonized? c/c++-files)) + #t))) + (add-after 'remove-cython-generated-files 'generate-cython-extens= ions + (lambda _ + (invoke "python" "setup.py" "cythonize"))) + (replace 'check + (lambda _ + (let* ((cwd (getcwd)) + (build-root-directory (string-append cwd "/build/")) + (build (string-append + build-root-directory + (find (cut string-prefix? "lib" <>) + (scandir (string-append + build-root-directory))))) + (scripts (string-append + build-root-directory + (find (cut string-prefix? "scripts" <>) + (scandir build-root-directory))))) + (setenv "PYTHONPATH" + (string-append build ":" (getenv "PYTHONPATH"))) + ;; Executable scripts such as 'intron_exon_reads.py' must be + ;; available in the PATH. + (setenv "PATH" + (string-append scripts ":" (getenv "PATH")))) + ;; The tests need to be run from elsewhere... + (mkdir-p "/tmp/test") + (copy-recursively "pybedtools/test" "/tmp/test") + (with-directory-excursion "/tmp/test" + (invoke "pytest"))))))) + (propagated-inputs + `(("bedtools" ,bedtools) ("samtools" ,samtools) ("python-matplotlib" ,python-matplotlib) ("python-pysam" ,python-pysam) @@ -654,9 +699,11 @@ intended to behave exactly the same as the original BW= K awk.") `(("python-numpy" ,python-numpy) ("python-pandas" ,python-pandas) ("python-cython" ,python-cython) - ("python-nose" ,python-nose) - ("kentutils" ,kentutils) ; for bedGraphToBigWig - ("python-six" ,python-six))) + ("kentutils" ,kentutils) ; for bedGraphToBigWig + ("python-six" ,python-six) + ;; For the test suite. + ("python-pytest" ,python-pytest) + ("python-psutil" ,python-psutil))) (home-page "https://pythonhosted.org/pybedtools/") (synopsis "Python wrapper for BEDtools programs") (description @@ -667,34 +714,7 @@ Python.") (license license:gpl2+))) =20 (define-public python2-pybedtools - (let ((pkg (package-with-python2 python-pybedtools))) - (package (inherit pkg) - (arguments - `(#:modules ((ice-9 ftw) - (srfi srfi-1) - (srfi srfi-26) - (guix build utils) - (guix build python-build-system)) - ;; See https://github.com/daler/pybedtools/issues/192 - ,@(substitute-keyword-arguments (package-arguments pkg) - ((#:phases phases) - `(modify-phases ,phases - (replace 'check - (lambda _ - (let ((cwd (getcwd))) - (setenv "PYTHONPATH" - (string-append cwd "/build/" - (find (cut string-prefix? "l= ib" <>) - (scandir (string-appen= d cwd "/build"))) - ":" (getenv "PYTHONPATH")))) - ;; The tests need to be run from elsewhere... - (mkdir-p "/tmp/test") - (copy-recursively "pybedtools/test" "/tmp/test") - (with-directory-excursion "/tmp/test" - (invoke "nosetests" - ;; This test fails for unknown reasons - "--exclude=3D.*test_getting_example_beds")) - #t)))))))))) + (package-with-python2 python-pybedtools)) =20 (define-public python-biom-format (package --=20 2.20.1 From debbugs-submit-bounces@debbugs.gnu.org Tue Feb 12 11:18:58 2019 Received: (at 34456-done) by debbugs.gnu.org; 12 Feb 2019 16:18:58 +0000 Received: from localhost ([127.0.0.1]:45062 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1gtalu-0005iJ-57 for submit@debbugs.gnu.org; Tue, 12 Feb 2019 11:18:58 -0500 Received: from sender-of-o51.zoho.com ([135.84.80.216]:21111) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1gtalq-0005hp-9O for 34456-done@debbugs.gnu.org; Tue, 12 Feb 2019 11:18:56 -0500 ARC-Seal: i=1; a=rsa-sha256; t=1549988320; cv=none; d=zoho.com; s=zohoarc; b=kqDjGJFQYyz8WQ1NkOyAZm1fJqy1HGBDdyrVKossO7Rei0V7WnW+XaEFkmqJa/R7VUrU4dQ3UrK/TQqqeNQcM8vUrCVNVP9zJPY7mwn1OkYmF31BUx9z6aZs8KDLCXOzz+hf2yd2qLrAmCD5i07l7yiEvBYTBvSOeZv3AbyB2jA= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zoho.com; s=zohoarc; t=1549988320; h=Content-Type:Cc:Date:From:In-Reply-To:MIME-Version:Message-ID:References:Subject:To:ARC-Authentication-Results; bh=llq3lQfrdwyuMe8y7RAIQc7sL90qzE/Sog9Fw++4KPI=; b=dvCk15hGZ4afuLEVCdFKHp4ubqAXclF8gaW63f0DuvVGUlBKJ+Iqh1mRKxPSjMn00IGT5YYJxuYyoKlIgGeLiJyqwR82D/MgNAjc6A7qgjY/SfJOBvWb2spyXVz9hHb1Gl33xGiSqOaPPjoyZOzDRNpXVF6S5uS6Oujb61amPeY= ARC-Authentication-Results: i=1; mx.zoho.com; dkim=pass header.i=elephly.net; spf=pass smtp.mailfrom=rekado@elephly.net; dmarc=pass header.from= header.from= DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; t=1549988320; s=zoho; d=elephly.net; i=rekado@elephly.net; h=References:From:To:Cc:Subject:In-reply-to:Date:Message-ID:MIME-Version:Content-Type; l=509; bh=llq3lQfrdwyuMe8y7RAIQc7sL90qzE/Sog9Fw++4KPI=; b=LRMRBLd7gxZwgNzpDSkg4oy3kqTBF91R/HzHlycJaySn53DqmB0dEXFg3KwQcMsx DAY+MTpq5r1LXRB1GjNM8UOFI0ak6Z2fO7ICzK2YJ6VCYO0jsQDLpHBQPET/MfdWbCG O4t5FmcWeTQEzqHUGeN3Ryzgh9DZJDEPP0UJfYf8= Received: from localhost (141.80.247.226 [141.80.247.226]) by mx.zohomail.com with SMTPS id 1549988317836212.4241045910369; Tue, 12 Feb 2019 08:18:37 -0800 (PST) References: <87d0nx10r0.fsf@gmail.com> User-agent: mu4e 1.0; emacs 26.1 From: Ricardo Wurmus To: Maxim Cournoyer Subject: Re: [bug#34456] [PATCH] gnu: python-pybedtools: Update to 0.8.0 and fix build. In-reply-to: <87d0nx10r0.fsf@gmail.com> X-URL: https://elephly.net X-PGP-Key: https://elephly.net/rekado.pubkey X-PGP-Fingerprint: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC Date: Tue, 12 Feb 2019 17:18:34 +0100 Message-ID: <87bm3hj7z9.fsf@elephly.net> MIME-Version: 1.0 Content-Type: text/plain X-ZohoMailClient: External X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 34456-done Cc: 34456-done@debbugs.gnu.org X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.0 (-) Hi Maxim, > From 40db2b4eae5ca61a3134cdaf7b156ed1ae9f7415 Mon Sep 17 00:00:00 2001 > From: Maxim Cournoyer > Date: Sun, 10 Feb 2019 23:39:25 -0500 > Subject: [PATCH] gnu: python-pybedtools: Update to 0.8.0 and fix build. Thank you, pushed to master with 155194d97. (I should have checked the commit message before pushing. The From, Date, and Subject headers made it into the commit message. This is the second time this has happened to me. Sorry!) -- Ricardo From debbugs-submit-bounces@debbugs.gnu.org Tue Feb 12 12:47:58 2019 Received: (at 34456-done) by debbugs.gnu.org; 12 Feb 2019 17:47:58 +0000 Received: from localhost ([127.0.0.1]:45137 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1gtcA1-0001d1-QR for submit@debbugs.gnu.org; Tue, 12 Feb 2019 12:47:58 -0500 Received: from mail-qt1-f194.google.com ([209.85.160.194]:45538) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1gtc9z-0001cl-PI for 34456-done@debbugs.gnu.org; Tue, 12 Feb 2019 12:47:56 -0500 Received: by mail-qt1-f194.google.com with SMTP id e5so3903485qtr.12 for <34456-done@debbugs.gnu.org>; Tue, 12 Feb 2019 09:47:55 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=from:to:cc:subject:references:date:in-reply-to:message-id :user-agent:mime-version; bh=UwXWgnozNhWdExeZRf3sIQlmxZpnQIkiDV0e8hgLVHY=; b=CEb1L4hMISW64AvEyGFXYNkibXV9gQpaqjeCUD/4C8RmEUBkZcngUQWnzaoaWFFjNb 5wPA0sobTgU5mXvQxh/byc/wpC8qU0gohqkBlmlYFNDSQPGmMGsIMiDqgJKhD7VGdDIJ Tu7OzJvXRieoMhWY685HnT6anoQ2RvS7ASp7pROgorPcE4P3YHPCndkgquAzeqgCmlCQ X7U4TL/8Fa3OkWZKouuUl1Iqtg5HgJU7MrYhVOtIOb8o9lFGZgv2NE3Ff22O793ln0Wd /VB89detPQbyfdA+wqJq5sQrVpqHvpmeQcDv/oc0CaAASx7I1EDcdPOAmR26sP9LYOwF zDUg== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:from:to:cc:subject:references:date:in-reply-to :message-id:user-agent:mime-version; bh=UwXWgnozNhWdExeZRf3sIQlmxZpnQIkiDV0e8hgLVHY=; b=hnUWQkXxOk+BpBdoSELwrj3M9i+FcdBxs30C/scU/4z/Mk7giFZoOMb4NfYAabWxD+ Z6y/NSslD8UflL89IuhiYRQb7ib7Ko9vy57AdvOvdv6cWwWuyLaCrS4d/b7DSvG6dWth o6g7QsoACqpnwibJWs0E8GZ+LED9bCrvJRmqnz8ry+FISWq1oUXsonV3nyre9yu3Nv34 fcpohSkFbnS76k61Pyjjjm+GUWldaP3DtDZsJwZH6LQ5VL0BCli91J9SsYTLj9iQWI0C uA8rzWeQiyrUCzQRpD/6GoDUIGVSmmfpNCtv6sIS2DqyCcQOMukclxeXm+9g+ClRrDn0 Er8w== X-Gm-Message-State: AHQUAubobCOrMfrkitvXg3VPOcN4hVxDcXxMmQRPMRIRopQfFfIsvuQi sZk+DlwBGVXaB+uFc9ecUIEZgLNe X-Google-Smtp-Source: AHgI3IZdMJkOFnn6e8oz8TgptrDIQX7xtymRRXP3KQvVjKCy/JljfKsBLPjPdP32CiJeLFiRNT20jg== X-Received: by 2002:aed:3783:: with SMTP id j3mr3964444qtb.16.1549993670004; Tue, 12 Feb 2019 09:47:50 -0800 (PST) Received: from kwak (mtl.savoirfairelinux.net. [208.88.110.46]) by smtp.gmail.com with ESMTPSA id c9sm11626061qkj.61.2019.02.12.09.47.48 (version=TLS1_2 cipher=ECDHE-RSA-CHACHA20-POLY1305 bits=256/256); Tue, 12 Feb 2019 09:47:49 -0800 (PST) From: Maxim Cournoyer To: Ricardo Wurmus Subject: Re: [bug#34456] [PATCH] gnu: python-pybedtools: Update to 0.8.0 and fix build. References: <87d0nx10r0.fsf@gmail.com> <87bm3hj7z9.fsf@elephly.net> Date: Tue, 12 Feb 2019 12:47:47 -0500 In-Reply-To: <87bm3hj7z9.fsf@elephly.net> (Ricardo Wurmus's message of "Tue, 12 Feb 2019 17:18:34 +0100") Message-ID: <878syk2918.fsf@gmail.com> User-Agent: Gnus/5.13 (Gnus v5.13) Emacs/26.1 (gnu/linux) MIME-Version: 1.0 Content-Type: text/plain X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 34456-done Cc: 34456-done@debbugs.gnu.org X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.0 (-) Hello Ricardo, Ricardo Wurmus writes: > Hi Maxim, > >> From 40db2b4eae5ca61a3134cdaf7b156ed1ae9f7415 Mon Sep 17 00:00:00 2001 >> From: Maxim Cournoyer >> Date: Sun, 10 Feb 2019 23:39:25 -0500 >> Subject: [PATCH] gnu: python-pybedtools: Update to 0.8.0 and fix build. > > Thank you, pushed to master with 155194d97. > > (I should have checked the commit message before pushing. The From, > Date, and Subject headers made it into the commit message. This is the > second time this has happened to me. Sorry!) No problem, and thanks for the prompt review! Maxim From unknown Sun Jun 22 22:42:55 2025 Received: (at fakecontrol) by fakecontrolmessage; To: internal_control@debbugs.gnu.org From: Debbugs Internal Request Subject: Internal Control Message-Id: bug archived. Date: Wed, 13 Mar 2019 11:24:10 +0000 User-Agent: Fakemail v42.6.9 # This is a fake control message. # # The action: # bug archived. thanks # This fakemail brought to you by your local debbugs # administrator