Proposed patches for the Maneage reproducible paper system. See https://git.maneage.org for the main (upstream) git repository and https://maneage.org for a general description. See https://en.wikipedia.org/wiki/Reproducibility for a wider overview.
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Boud Roukema e4499a0ba9 Revert recent reference to host system CFLAGS in basic.mk 9 months ago
reproduce Revert recent reference to host system CFLAGS in basic.mk 9 months ago
tex Maneage instead of Template in README-hacking.md and copyright notices 10 months ago
.dir-locals.el Configure step: compiler checks done before basic settings 1 year ago
.file-metadata GNU Gettext built as a dependency of Bash 9 months ago
.gitignore Configure step: compiler checks done before basic settings 1 year ago
COPYING Added generic copying/license file to top 2 years ago
README-hacking.md Astropy will no longer be installed by default 10 months ago
README.md IMPORTANT: Primary Maneage repositories are now under maneage.org 10 months ago
paper.tex IMPORTANT: Primary Maneage repositories are now under maneage.org 10 months ago
project IMPORTANT: Primary Maneage repositories are now under maneage.org 10 months ago

README.md

Reproducible source for XXXXXXXXXXXXXXXXX

Copyright (C) 2018-2020 Mohammad Akhlaghi mohammad@akhlaghi.org
See the end of the file for license conditions.

This is the reproducible project source for the paper titled "XXX XXXXX XXXXXX", by XXXXX XXXXXX, YYYYYY YYYYY and ZZZZZZ ZZZZZ that is published in XXXXX XXXXX.

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.

$ git clone XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
$ cd XXXXXXXXXXXXXXXXXX
$ ./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) [[TO AUTHORS: UPLOAD THE SOFTWARE TARBALLS WITH YOUR DATA AND PROJECT SOURCE TO ZENODO OR OTHER SIMILAR SERVICES. THEN ADD THE DOI/LINK HERE.DON'T FORGET THAT THE SOFTWARE ARE A CRITICAL PART OF YOUR WORK.]]. 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.3408481

  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.

    $ ./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)

    $ ./project make -j8
    

Source 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:

  1. If 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.

    $ arxiv=1234.56789
    $ mv $arxiv $arxiv.tar.gz
    $ mkdir $arxiv
    $ cd $arxiv
    $ tar xf ../$arxiv.tar.gz
    
  2. arXiv removes the executable flag from the files (for its own security). So before following the standard procedure of projects described in the sections above, its necessary to set the executable flag of the main project management file with this command:

    $ chmod +x project
    
  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.

    $ ls
    COPYING  paper.tex  project  README-hacking.md  README.md  reproduce  tex
    
  4. To build the figures from scratch, you need to make the following corrections to the LaTeX source files below.

    4.1: paper.tex: uncomment (remove the starting %) of the line containing \newcommand{\makepdf}{}. See the comments above it for more information.

    4.2: tex/src/preamble-pgfplots.tex: set the tikzsetexternalprefix variable value to tikz/, so it looks like this: \tikzsetexternalprefix{tikz/}.

  5. In order to let arXiv build the LaTeX paper without bothering to run the analysis pipeline it was necessary to create and fill the two tex/build and tex/tikz subdirectories. But to do a clean build of the project, it is necessary for these to be symbolic links to the build directory. So when you are first configuring the project, run it with --clean-texdir (only once is enough, they will be deleted permanently after that), for example:

    $ ./project configure --clean-texdir
    

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 https://www.gnu.org/licenses/.