README.md
Reproducible source for paper introducing Maneage (MANaging data linEAGE)
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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 "**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.
```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
```
### 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.
```shell
$ 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:
```shell
$ 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.
```shell
$ 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:
```shell
$ ./project configure --clean-texdir
```
### 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 <https://www.gnu.org/licenses/>.
