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Reproducible source for XXXXXXXXXXXXXXXXX
=========================================
Copyright (C) 2018-2019 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).
```shell
$ git clone XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
$ ./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, please
see the [principles of reproducible
science](http://akhlaghi.org/reproducible-science.html), and a
[reproducible paper
template](https://gitlab.com/makhlaghi/reproducible-paper) that is based on
it.
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.
```shell
$ ./project configure
```
3. Run the following command (local build of the Make software) 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
```
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/>.
|
