From mboxrd@z Thu Jan 1 00:00:00 1970 From: Brett Viren Subject: Re: Open Peer-Review Reproducible Publication with Org and GRASS Date: Fri, 03 Jun 2016 10:57:55 -0400 Message-ID: References: Mime-Version: 1.0 Content-Type: multipart/signed; boundary="=-=-="; micalg=pgp-sha512; protocol="application/pgp-signature" Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:58549) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1b8qXc-0000ul-Bz for emacs-orgmode@gnu.org; Fri, 03 Jun 2016 10:57:41 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1b8qXZ-0002aa-4j for emacs-orgmode@gnu.org; Fri, 03 Jun 2016 10:57:40 -0400 Received: from smtpgw.bnl.gov ([2620:10a:0:3::30]:35570 helo=iron4.sec.bnl.local) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1b8qXY-0002aH-VV for emacs-orgmode@gnu.org; Fri, 03 Jun 2016 10:57:37 -0400 In-Reply-To: (Ken Mankoff's message of "Fri, 03 Jun 2016 10:19:07 -0400") List-Id: "General discussions about Org-mode." List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: emacs-orgmode-bounces+geo-emacs-orgmode=m.gmane.org@gnu.org Sender: "Emacs-orgmode" To: Ken Mankoff Cc: 'grass-user grass-user' , Org Mode --=-=-= Content-Type: text/plain Content-Transfer-Encoding: quoted-printable Thanks for your example. A few ideas: =2D When you begin developing your paper, or sometime before submission, make a break from your personal ~/.emacs.d/ environment and begin processing the .org in an explicitly configured Emacs session. Submit the needed, minimal, paper-specific Emacs setup as part of the supplementary material. =2D Bundle the document building into a shell script which calls Emacs so that you can assure that personal ~/.emacs.d/ is excluded and only the paper-specific Emacs setup is used. It also helps users to rebuild the paper, especially if they may not yet be Emacs aficionados. =2D Instead of multi-GB VM image, provide a few kB Dockerfile which can be used to build a Linux container with base OS and all required applications needed to run the Babel code blocks. =2D The Dockerfile could go so far as to create a user account, get the supplementary material from a repository or the publisher's web page, unpack and run the shell script which calls Emacs to build the document. If you go this far then in principle just this Dockerfile is enough to reproduce the paper - but this will rely on some binaries to remain available (Docker base OS images and OS packages). The reliance on long-term availability of the Docker base OS image and binary packages is problematic for long term automated reproducibility. However, even after those bits disappear from the 'net the Dockerfile serves as a concise and explicit recipe for future humans to follow. =2DBrett. Ken Mankoff writes: > Hi Org and GRASS lists, > > I just wanted to let these two lists know that I've just posted a > paper written in Org and using GRASS (text-mode) and Python for the > analysis. My goal was to create not just an open access publication, > but a fully reproducible publication. This is an early announcement, > and the paper may not pass peer review. > > The Supplemental Material is the Org file with all the code to > generate the document, beginning with downloading the 3rd party data > that is input to our analysis, the GRASS code to perform the analysis, > and the Python code to regenerate the figures. > > I don't think I did a great job on the reproducible part because I > have a highly customized .emacs, etc. All the information necessary to > replicate the work should be in the Supplemental Material, but it > might not be easy to do so. Anyway, I think it is a step in the right > direction. > > To make it easier to reproduce... including my emacs.org seems > overkill. Including a Virtual Machine that contains everything, > including my ~/.emacs.d/ and all the software and data seems like the > right thing to do, but journals don't want to host a 20 GB VM with the > publication. > > Thanks to people on these two lists who have developed the software and h= elped me use it. > > -k. >=20=20=20=20 > http://www.the-cryosphere-discuss.net/tc-2016-113/ --=-=-= Content-Type: application/pgp-signature; name="signature.asc" -----BEGIN PGP SIGNATURE----- iQIcBAEBCgAGBQJXUZrzAAoJEFsAceCXpRtHIeIP/i/pVGWVjvXD5KIcjgI5f2S/ YmDmcx8UCXq3rsTfEosJpVarcwQR0zAdsGaUJaeztzzQ5h9WHop+c7Fbc6wGjFrg wr+zvN4zPbCBoMEubD2G21ZELMYPLqQL490THoi62dku2FXg5vndmh8YRXOBJk3O uv4gdBqke9uotsNxlOyDLOwtZhhgkq4Zdji2a2bHW9C5YSDDgsUokbtf7XGyGqxM ToQ6kDp4IOY2ISTCPsqsSM3MyfagfARB1DFkKB+ky0+1T1DQUOS0Q7YScFSMZxxS WtyvxNdA0ChMvzcWXtV8aDkG76bdUEdaE/VmOWnUBHUu7oTC876yYdjPulVdby5k jeNMSrXNeFDGSp/fSrZPa1G7YBwpTIN7P9/thrQKjPey8/h91v0uxo1V7opSQYUE PG20U+MHh+ZAk2rhsp13/jywV8QXfBoXKC74QEeof/xLWVQVw6S2G6SLesfpLSXI CbGB89FD+VAtwcRfF8cQbTDDqCZ/N0RnLMgl+7bGhOfpKIlyt2bDld7owJpxocjp oesr9Rlzb2d46PVujRjWXk//i7FmLju+gvLH/GJMWH99ZuD+VxjeKHYSsTrZ2fW7 uxZk7iy+oB3rdLPb2S2tXsg+SDjchK395jVe+D4GdWEtgfUlvOiSsgnmWGmyfnfC rZMfNTRsMYe5LSSkqmuC =2fkG -----END PGP SIGNATURE----- --=-=-=--