Reproducible source for Akhlaghi et al. (2020, arXiv:2006.03018) ---------------------------------------------------------------- Copyright (C) 2018-2020 Mohammad Akhlaghi \ See the end of the file for license conditions. This is the reproducible project source for the paper titled "**Towards Long-term and Archivable Reproducibility**", by Mohammad Akhlaghi, Raúl Infante-Sainz, Boudewijn F. Roukema, David Valls-Gabaud, Roberto Baena-Gallé. To reproduce the results and final paper, the only dependency is a minimal Unix-based building environment including a C compiler (already available on your system if you have ever built and installed a software from source) and a downloader (Wget or cURL). Note that **Git is not mandatory**: if you don't have Git to run the first command below, go to the URL given in the command on your browser, and download the project's source (there is a button to download a compressed tarball of the project). If you have received this source from arXiv, please see the respective section below. *IMPORTANT NOTE*: If you want to build using a distributed tarball that isn't under Git's version control, see the points below under building project tarball, a few minor modifications need to be made before starting the project configuration and build. ```shell $ git clone https://gitlab.com/makhlaghi/maneage-paper $ cd maneage-paper $ ./project configure $ ./project make ``` To learn more about the purpose, principles and technicalities of this reproducible paper, please see `README-hacking.md`. For a general introduction to reproducible science as implemented in this project (through Maneage), please see Maneage project's webpage at https://maneage.org. ### Building the project This project was designed to have as few dependencies as possible without requiring root/administrator permissions. 1. Necessary dependencies: 1.1: Minimal software building tools like C compiler, Make, and other tools found on any Unix-like operating system (GNU/Linux, BSD, Mac OS, and others). All necessary dependencies will be built from source (for use only within this project) by the `./project configure` script (next step). 1.2: (OPTIONAL) Tarball of dependencies. If they are already present (in a directory given at configuration time), they will be used. Otherwise, a downloader (`wget` or `curl`) will be necessary to download any necessary tarball. The necessary tarballs are also collected in the archived project on Zenodo (link below). Just unpack that tarball, and when `./project configure` asks for the "software tarball directory", give the address of the unpacked directory that has all the tarballs. https://doi.org/10.5281/zenodo.3872248 2. Configure the environment (top-level directories in particular) and build all the necessary software for use in the next step. It is recommended to set directories outside the current directory. Please read the description of each necessary input clearly and set the best value. Note that the configure script also downloads, builds and locally installs (only for this project, no root privileges necessary) many programs (project dependencies). So it may take a while to complete. ```shell $ ./project configure ``` 3. Run the following command to reproduce all the analysis and build the final `paper.pdf` on `8` threads. If your CPU has a different number of threads, change the number (you can see the number of threads available to your operating system by running `./.local/bin/nproc`) ```shell $ ./project make -j8 ``` ### Building project tarball (possibly from arXiv) If the paper is also published on arXiv, it is highly likely that the authors also uploaded/published the full project there along with the LaTeX sources. If you have downloaded (or plan to download) this source from arXiv, some minor extra steps are necessary as listed below. This is because this tarball is mainly tailored to automatic creation of the final PDF without actually using the './project' command! You can directly run 'latex' on this directory and the paper will be built with no analysis (all necessary built products are already included). #### Only building PDF using tarball (no analysis) 1. If you got the tarball from arXiv and the arXiv code for the paper is 1234.56789, then the downloaded source will be called `1234.56789` (no special identification suffix). However, it is actually a `.tar.gz` file. So take these steps to unpack it to see its contents. ```shell $ arxiv=1234.56789 $ mv $arxiv $arxiv.tar.gz $ mkdir $arxiv $ cd $arxiv $ tar xf ../$arxiv.tar.gz ``` 2. No matter how you got the tarball, if you just want to build the PDF paper from the tarball, simply run the command below. Note that this won't actually install any software or do any analysis, it will just use your host operating system to build the PDF and assums you already have all the necessary LaTeX packages. ```shell $ make # Build PDF in tarball without doing analysis ``` 3. If you want to re-build the figures from scratch, you need to make the following corrections to the paper's main LaTeX source (`paper.tex`): uncomment (remove the starting `%`) of the line containing `\newcommand{\makepdf}{}`. See the comments above it for more information. #### Building full project from tarball (custom software and analysis) Since the tarball is mainly geared to only building only the final PDF, a few small tweaks are necessary to build the full project from scratch (download necessary software and data, build them and run the analysis and finally create the final paper). 1. If you got the tarball from arXiv, before following the standard procedure of projects described at the top of the file above (using the './project' script), its necessary to set its executable flag. arXiv removes the executable flag from the files (for its own security). ```shell $ chmod +x project ``` 2. Make the following change in two of the LaTeX files so LaTeX attempts to build the figures from scratch (to make the tarball, it was configured to avoid building the figures, just using the ones that came with the tarball). - `paper.tex`: uncomment (remove the starting `%`) of the line containing `\newcommand{\makepdf}{}`. See the comments above it for more information. - `tex/src/preamble-pgfplots.tex`: set the `tikzsetexternalprefix` variable value to `tikz/`, so it looks like this: `\tikzsetexternalprefix{tikz/}`. 3. Remove extra files. In order to make sure arXiv can build the paper (resolve conflicts due to different versions of LaTeX packages), it is sometimes necessary to copy raw LaTeX package files in the tarball uploaded to arXiv. Later, we will implement a feature to automatically delete these extra files, but for now, the project's top directory should only have the following contents (where `reproduce` and `tex` are directories). You can safely remove any other file/directory. ```shell $ ls COPYING paper.tex project README-hacking.md README.md reproduce tex ``` ### Copyright information This file and `.file-metadata` (a binary file, used by Metastore to store file dates when doing Git checkouts) are part of the reproducible project mentioned above and share the same copyright notice (at the start of this file) and license notice (below). This project is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. This project is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this project. If not, see .