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<h1>Maneage</h1><h2>Managing Data Lineage</h2>
<p>Copyright © 2018-2023 Mohammad Akhlaghi <a href="mailto:mohammad@akhlaghi.org">mohammad@akhlaghi.org</a><br />
Copyright © 2020-2023 Raul Infante-Sainz <a href="mailto:infantesainz@gmail.com">infantesainz@gmail.com</a><br />
<a href="#page-footer">License Conditions</a></p>
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<hr />
<p align="right">Next: <a href="about-architecture.html">Maneage architecture</a>, Previous: <a href="about-citation.html">Citation and published papers</a>, Up: <a href="about.html">About</a> </p>
<h2>Why Make?</h2>
<p>When batch processing is necessary (no manual intervention, as in a
reproducible project), shell scripts are usually the first solution that
come to mind. However, the inherent complexity and non-linearity of
progress in a scientific project (where experimentation is key) make it
hard to manage the script(s) as the project evolves. For example, a script
will start from the top/start every time it is run. So if you have already
completed 90% of a research project and want to run the remaining 10% that
you have newly added, you have to run the whole script from the start
again. Only then will you see the effects of the last new steps (to find
possible errors, or better solutions and etc).</p>
<p>It is possible to manually ignore/comment parts of a script to only do a
special part. However, such checks/comments will only add to the complexity
of the script and will discourage you to play-with/change an already
completed part of the project when an idea suddenly comes up. It is also
prone to very serious bugs in the end (when trying to reproduce from
scratch). Such bugs are very hard to notice during the work and frustrating
to find in the end.</p>
<p>The Make paradigm, on the other hand, starts from the end: the final
<em>target</em>. It builds a dependency tree internally, and finds where it should
start each time the project is run. Therefore, in the scenario above, a
researcher that has just added the final 10% of steps of her research to
her Makefile, will only have to run those extra steps. With Make, it is
also trivial to change the processing of any intermediate (already written)
<em>rule</em> (or step) in the middle of an already written analysis: the next
time Make is run, only rules that are affected by the changes/additions
will be re-run, not the whole analysis/project.</p>
<p>This greatly speeds up the processing (enabling creative changes), while
keeping all the dependencies clearly documented (as part of the Make
language), and most importantly, enabling full reproducibility from scratch
with no changes in the project code that was working during the
research. This will allow robust results and let the scientists get to what
they do best: experiment and be critical to the methods/analysis without
having to waste energy and time on technical problems that come up as a
result of that experimentation in scripts.</p>
<p>Since the dependencies are clearly demarcated in Make, it can identify
independent steps and run them in parallel. This further speeds up the
processing. Make was designed for this purpose. It is how huge projects
like all Unix-like operating systems (including GNU/Linux or Mac OS
operating systems) and their core components are built. Therefore, Make is
a highly mature paradigm/system with robust and highly efficient
implementations in various operating systems perfectly suited for a complex
non-linear research project.</p>
<p>Make is a small language with the aim of defining <em>rules</em> containing
<em>targets</em>, <em>prerequisites</em> and <em>recipes</em>. It comes with some nice features
like functions or automatic-variables to greatly facilitate the management
of text (filenames for example) or any of those constructs. For a more
detailed (yet still general) introduction see the article on Wikipedia:</p>
<ul>
<li><a href="https://en.wikipedia.org/wiki/Make_(software)">https://en.wikipedia.org/wiki/Make_(software)</a></li>
</ul>
<p>Make is a +40 year old software that is still evolving, therefore many
implementations of Make exist. The only difference in them is some extra
features over the <a href="https://pubs.opengroup.org/onlinepubs/009695399/utilities/make.html">standard
definition</a>
(which is shared in all of them). Maneage is primarily written in GNU Make
(which it installs itself, you don't have to have it on your system). GNU
Make is the most common, most actively developed, and most advanced
implementation. Just note that Maneage downloads, builds, internally
installs, and uses its own dependencies (including GNU Make), so you don't
have to have it installed before you try it out.</p>
<h3>How can I learn Make?</h3>
<p>The GNU Make book/manual (links below) is arguably the best place to learn
Make. It is an excellent and non-technical book to help get started (it is
only non-technical in its first few chapters to get you started easily). It
is freely available and always up to date with the current GNU Make
release. It also clearly explains which features are specific to GNU Make
and which are general in all implementations. So the first few chapters
regarding the generalities are useful for all implementations.</p>
<p>The first link below points to the GNU Make manual in various formats and
in the second, you can download it in PDF (which may be easier for a first
time reading).</p>
<ul>
<li><a href="https://www.gnu.org/software/make/manual/">https://www.gnu.org/software/make/manual/</a></li>
<li><a href="https://www.gnu.org/software/make/manual/make.pdf">https://www.gnu.org/software/make/manual/make.pdf</a></li>
</ul>
<p>If you use GNU Make, you also have the whole GNU Make manual on the
command-line with the following command (you can come out of the "Info"
environment by pressing <code>q</code>).</p>
<pre><code>info make</code></pre>
<p>If you aren't familiar with the Info documentation format, we strongly
recommend running <code>$ info info</code> and reading along. In less than an hour,
you will become highly proficient in it (it is very simple and has a great
manual for itself). Info greatly simplifies your access (without taking
your hands off the keyboard!) to many manuals that are installed on your
system, allowing you to be much more efficient as you work. If you use the
GNU Emacs text editor (or any of its variants), you also have access to all
Info manuals while you are writing your projects (again, without taking
your hands off the keyboard!).</p>
<p align="right">Next: <a href="about-architecture.html">Maneage architecture</a>, Previous: <a href="about-citation.html">Citation and published papers</a>, Up: <a href="about.html">About</a> </p>
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<li><p>Maneage is currently based in the Centro de Estudios de Física del Cosmos de Aragón (CEFCA).</p></li>
<li><p>Address: CEFCA, Plaza San Juan 1, Planta 2, Teruel, Spain, 44001.</p></li>
<li><p>Contact: with <a href="https://savannah.nongnu.org/support/?func=additem&group=reproduce">this form</a>, or <a href="https://app.element.io/#/room/#maneage-general:matrix.org">#maneage-general:matrix.org</a>, or project PI (<a href="http://akhlaghi.org">Mohammad Akhlaghi</a>).</p></li>
<li><p>Copyright © 2020-2023 Maneage volunteers</p></li>
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