From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from mp2 ([2001:41d0:2:4a6f::]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits)) by ms11 with LMTPS id IM0XCshz717ZdAAA0tVLHw (envelope-from ) for ; Sun, 21 Jun 2020 14:50:48 +0000 Received: from aspmx1.migadu.com ([2001:41d0:2:4a6f::]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits)) by mp2 with LMTPS id 6H/xBchz717KQAAAB5/wlQ (envelope-from ) for ; Sun, 21 Jun 2020 14:50:48 +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 96C95940144 for ; Sun, 21 Jun 2020 14:50:47 +0000 (UTC) Received: from localhost ([::1]:55398 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1jn1J0-0004ol-9u for larch@yhetil.org; Sun, 21 Jun 2020 10:50:46 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:37774) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1jn1Ik-0004oU-KL for guix-devel@gnu.org; Sun, 21 Jun 2020 10:50:30 -0400 Received: from forward5-smtp.messagingengine.com ([66.111.4.239]:57581) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1jn1If-0001hW-MX; Sun, 21 Jun 2020 10:50:28 -0400 Received: from compute3.internal (compute3.nyi.internal [10.202.2.43]) by mailforward.nyi.internal (Postfix) with ESMTP id 21ECF194122E; Sun, 21 Jun 2020 10:50:21 -0400 (EDT) Received: from mailfrontend2 ([10.202.2.163]) by compute3.internal (MEProxy); Sun, 21 Jun 2020 10:50:21 -0400 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d= messagingengine.com; h=cc:content-transfer-encoding:content-type :date:from:in-reply-to:message-id:mime-version:references :subject:to:x-me-proxy:x-me-proxy:x-me-sender:x-me-sender :x-sasl-enc; s=fm3; bh=pMii8gbYvuTFw4szSft5kTDizITxoDnzgxlI8wFOR ss=; b=c2g0f62kBjcV3Wzil7Dr7QICHUditZ1tzNdPaIEnAyh6DVzvupizTqBJ/ G8p5ZPW43oCkQ7ERz4n1CgTq1/lnwKEUgt5WvSfKKCXIJGkchg+LtfRPpBgD0Ube Irl7WxFQWDkOi57hV7jAvv3z7w3h+3PCc03zxK6PSui8ZPoJvyFSjSX1AktOQ/FX FNR983r6H9W+Wz0+8PEvwfTgtyPBs9d2Sc+XJuKMNW2DVRmLxHZd+IXjIj+D9okd ROSTUcKbNR35E5W4o0kSJfZwEG8RfaOX/U7XXWmftpvlBOPLoGAqdGfZGic0JDTO Fvpo0vkxU8+mTrBi51NwgkSFYEovQ== X-ME-Sender: X-ME-Proxy-Cause: gggruggvucftvghtrhhoucdtuddrgeduhedrudektddgkeefucetufdoteggodetrfdotf fvucfrrhhofhhilhgvmecuhfgrshhtofgrihhlpdfqfgfvpdfurfetoffkrfgpnffqhgen uceurghilhhouhhtmecufedttdenucesvcftvggtihhpihgvnhhtshculddquddttddmne cujfgurhephffvufgjfhffkfggtgfgsehtqhertddttdejnecuhfhrohhmpefmohhnrhgr ugcujfhinhhsvghnuceokhhonhhrrggurdhhihhnshgvnhestghnrhhsrdhfrheqnecugg ftrfgrthhtvghrnhepgfelueffkefftddtffduffetieduveekkeegvdfhgffgleeiteet heeuheelleevnecuffhomhgrihhnpehgihhthhhusgdrtghomhdptghnrhhsqdhorhhlvg grnhhsrdhfrhdpohhrtghiugdrohhrghenucfkphepkeeirddvfeekrddufeejrdduleef necuvehluhhsthgvrhfuihiivgeptdenucfrrghrrghmpehmrghilhhfrhhomhepkhhonh hrrggurdhhihhnshgvnhestghnrhhsrdhfrh X-ME-Proxy: Received: from khs-macbook.home (lfbn-idf2-1-906-193.w86-238.abo.wanadoo.fr [86.238.137.193]) by mail.messagingengine.com (Postfix) with ESMTPA id 7CC1F3066DCA; Sun, 21 Jun 2020 10:50:17 -0400 (EDT) From: Konrad Hinsen To: Ludovic =?utf-8?Q?Court=C3=A8s?= , zimoun Subject: Re: =?utf-8?Q?=E2=80=9CReproducible?= research articles, from source code to =?utf-8?Q?PDF=E2=80=9D?= In-Reply-To: References: <87d05ztcxj.fsf@inria.fr> <864kraxjau.fsf@gmail.com> <87k104omnv.fsf@inria.fr> <87r1ucmwh5.fsf@inria.fr> <86lfkkwn0l.fsf@gmail.com> <87h7v8le1l.fsf@inria.fr> Date: Sun, 21 Jun 2020 16:50:16 +0200 Message-ID: MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable Received-SPF: softfail client-ip=66.111.4.239; envelope-from=konrad.hinsen@cnrs.fr; helo=forward5-smtp.messagingengine.com X-detected-operating-system: by eggs.gnu.org: First seen = 2020/06/21 10:12:20 X-ACL-Warn: Detected OS = Linux 2.2.x-3.x [generic] [fuzzy] X-Spam_score_int: -18 X-Spam_score: -1.9 X-Spam_bar: - X-Spam_report: (-1.9 / 5.0 requ) BAYES_00=-1.9, DKIM_SIGNED=0.1, DKIM_VALID=-0.1, RCVD_IN_DNSWL_LOW=-0.7, SPF_HELO_PASS=-0.001, SPF_SOFTFAIL=0.665, URIBL_BLOCKED=0.001 autolearn=_AUTOLEARN X-Spam_action: no action X-BeenThere: guix-devel@gnu.org X-Mailman-Version: 2.1.23 Precedence: list List-Id: "Development of GNU Guix and the GNU System distribution." List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Cc: guix-devel , guix-hpc@gnu.org Errors-To: guix-devel-bounces+larch=yhetil.org@gnu.org Sender: "Guix-devel" X-Scanner: scn0 Authentication-Results: aspmx1.migadu.com; dkim=pass header.d=messagingengine.com header.s=fm3 header.b=c2g0f62k; dmarc=none; spf=pass (aspmx1.migadu.com: domain of guix-devel-bounces@gnu.org designates 209.51.188.17 as permitted sender) smtp.mailfrom=guix-devel-bounces@gnu.org X-Spam-Score: -1.21 X-TUID: jvnoh9aMjFu3 Konrad Hinsen writes: > Sounds fine. I am not much of a hackathon expert, so I don't propose > myself for organizing this, but I can make a preselection of suitable > submissions to the ReScience challenge (no proprietary software etc.) > with comments about the specific challenges. Here is my list of candidate projects. There are three general categories: 1) Package old software that is of sufficiently wide interest (i.e. add to guix-past) - g77 (used in https://github.com/ReScience/submissions/issues/41) - SciPy ecosystem from 2007 (at least Python, NumPy, matplotlib) (used in https://github.com/ReScience/submissions/issues/14) 2) Package highly specialized research software These programs are too specialized for the Guix distribution, so "packaging" means writing a guix.scm. The long-term goal is to learn how to make this kind of packaging easier, to the point that scientists are willing to do it themselves. This means it must be doable with minimal Guile competence, ideally by modifying templates provided by experts. I have picked four cases, listed by increasing level of difficulty: a) https://github.com/ReScience/submissions/issues/42 A rather standard Fortran code, with only the popular BLAS and LAPACK libraries as dependencies. Instructions are given for manual compilation. b) https://github.com/ReScience/submissions/issues/36 A medium-sized Fortran program with a Makefile. c) https://github.com/ReScience/submissions/issues/41 A mixed C-Fortran code from 2008, built with autotools. Looks simple, but the author did not succeed in compiling it on a modern machine because it requires the abandoned g77 compiler. d) https://github.com/ReScience/submissions/issues/20 A medium-sized Fortran library with a Makefile. Tricky because it adds its own wrappers around the Fortran compiler. 3) Fully automated reproductions of results (typically figures) There is only one case (other than Ludo's which already uses Guix): - https://github.com/ReScience/submissions/issues/39 A fully reproducible reproduction of two Open Source simulation software packages (C/C++), based on Debian and its debuerreotype system. The challenge is to demonstrate how Guix can do it better! Cheers, Konrad --=20 --------------------------------------------------------------------- Konrad Hinsen Centre de Biophysique Mol=C3=A9culaire, CNRS Orl=C3=A9ans Synchrotron Soleil - Division Exp=C3=A9riences Saint Aubin - BP 48 91192 Gif sur Yvette Cedex, France Tel. +33-1 69 35 97 15 E-Mail: konrad DOT hinsen AT cnrs DOT fr http://dirac.cnrs-orleans.fr/~hinsen/ ORCID: https://orcid.org/0000-0003-0330-9428 Twitter: @khinsen ---------------------------------------------------------------------