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<h1>Maneage</h1><h2>Managing Data Lineage</h2>
<p>Copyright © 2018-2022 Mohammad Akhlaghi <a href="mailto:mohammad@akhlaghi.org">mohammad@akhlaghi.org</a><br />
Copyright © 2020-2022 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-customize.html">Customization checklist</a>, Previous: <a href="about-make.html">Why Make?</a>, Up: <a href="about.html">About</a> </p>
<h2>Project architecture</h2>
<p>In order to customize Maneage to your research, it
is important to first understand its architecture so
you can navigate your way in the directories and
understand how to implement your research project
within its framework: where to add new files and which
existing files to modify for what purpose. </p>
<p>The project has two top-level directories: <code>reproduce</code> and
<code>tex</code>. <code>reproduce</code> hosts all the
software building and analysis steps. <code>tex</code>
contains all the final paper's components to be
compiled into a PDF using LaTeX. The image below shows
the directory and file structure in a hypothetical
project using Maneage. Files are shown with small,
green boxes that have a suffix in their names (for
example <code>format.mk</code> or
<code>download.tex</code>). Directories (containing
multiple files) are shown as large, brown boxes, where
the name ends in a slash (<code>/</code>).
Directories with dashed lines and no files (just a
description) are symbolic links that are created after
building the project, pointing to commonly needed
built directories. Symbolic links and their contents
are not considered part of the source and are not
under version control. Files and directories are
shown within their parent directory. For example the
full address of <code>format.mk</code> from the top
project directory is
<code>reproduce/analysis/make/format.mk</code>.</p>
<img class="center" src="img/maneage-file-structure.png" width="90%" />
<p> </p>
<p>As shown above, the <code>reproduce</code>
directory has two
sub-directories: <code>software</code> and
<code>analysis</code>. As the name says, the former
contains all the instructions to download, build and
install (independent of the host operating system) the
necessary software (these are called by
the <code>./project configure</code> command). The
latter contains instructions on how to use those
software to do your project's analysis.</p>
<p>After it finishes, <code>./project configure</code>
will create the following symbolic links in the
project's top source directory: <code>.build</code>
which points to the top build directory
and <code>.local</code> for easy access to the custom
built software installation directory. With these you
can easily access the build directory and
project-specific software from your top source
directory. For example if you
run <code>.local/bin/ls</code> you will be using
the <code>ls</code> of Maneage, which is probably
different from your system's <code>ls</code> (run them
both with
<code>--version</code> to check).</p>
<p>Once the project is configured for your
system, <code>./project make</code> will do the basic
preparations and run the project's analysis with the
custom version of software. The <code>project</code>
script is just a wrapper, and with the
<code>make</code> argument, it will first call <code>top-prepare.mk</code> and <code>top-make.mk</code>
(both are in the <code>reproduce/analysis/make</code> directory).</p>
<p>In terms of
organization, <code>top-prepare.mk</code>
and <code>top-make.mk</code> have an identical design,
only minor differences. So, let's continue Maneage's
architecture with <code>top-make.mk</code>. Once you
understand that, you'll clearly
understand <code>top-prepare.mk</code> also. These
very high-level files are relatively short and heavily
commented so hopefully the descriptions in each
comment will be enough to understand the general
details. As you read this section, please also look at
the contents of the mentioned files and directories to
fully understand what is going on.</p>
<p>Before starting to look into the
top <code>top-make.mk</code>, it is important to
recall that Make defines dependencies by
files. Therefore, the input/prerequisite and output of
every step/rule must be a file. Also recall that Make
will use the modification date of the prerequisite(s)
and target files to see if the target must be re-built
or not. Therefore during the processing, <em>many</em>
intermediate files will be created (see the tips
section below on a good strategy to deal with
large/huge files).</p>
<p>To keep the source and (intermediate) built files
separate, the user <em>must</em> define a top-level
build directory variable (or <code>$(BDIR)</code>) to
host all the intermediate files (you defined it
during <code>./project configure</code>). This
directory doesn't need to be version controlled or
even synchronized, or backed-up in other servers: its
contents are all products, and can be easily
re-created any time. As you define targets for your
new rules, it is thus important to place them all
under sub-directories of <code>$(BDIR)</code>. As
mentioned above, you always have fast access to this
"build"-directory with the <code>.build</code>
symbolic link. Also, beware to <em>never</em> make any
manual change in the files of the build-directory,
just delete them (so they are re-built).</p>
<p>In this architecture, we have two types of
Makefiles that are loaded into the
top <code>Makefile</code>: <em>configuration-Makefiles</em>
(only independent variables/configurations)
and <em>workhorse-Makefiles</em> (Makefiles that
actually contain analysis/processing rules).</p>
<p>The configuration-Makefiles are those that satisfy
these two wildcards:
<code>reproduce/software/config/*.conf</code> (for
building the necessary software when you
run <code>./project configure</code>)
and <code>reproduce/analysis/config/*.conf</code> (for
the high-level analysis, when you run <code>./project
make</code>). These Makefiles don't actually have any
rules, they just have values for various free
parameters throughout the configuration or
analysis. Open a few of them to see for
yourself. These Makefiles must only contain raw Make
variables (project configurations). By "raw" we mean
that the Make variables in these files must not depend
on variables in any other configuration-Makefile. This
is because we don't want to assume any order in
reading them. It is also very important
to <em>not</em> define any rule, or other Make
construct, in these configuration-Makefiles.</p>
<p>Following this rule-of-thumb enables you to set
these configure-Makefiles as a prerequisite to any
target that depends on their variable
values. Therefore, if you change any of their values,
all targets that depend on those values will be
re-built. This is very convenient as your project
scales up and gets more complex.</p>
<p>The workhorse-Makefiles are those satisfying this wildcard
<code>reproduce/software/make/*.mk</code>
and <code>reproduce/analysis/make/*.mk</code>. They
contain the details of the processing steps (Makefiles
containing rules). Therefore, in this phase <em>order
is important</em>, because the prerequisites of most
rules will be the targets of other rules that will be
defined prior to them (not a fixed name
like <code>paper.pdf</code>). The lower-level rules
must be imported into Make before the higher-level
ones.</p>
<p>All processing steps are assumed to ultimately
(usually after many rules) end up in some number,
image, figure, or table that will be included in the
paper. The writing of these results into the final
report/paper is managed through separate LaTeX files
that only contain macros (a name given to a
number/string to be used in the LaTeX source, which
will be replaced when compiling it to the final
PDF). So the last target in a workhorse-Makefile is
a <code>.tex</code> file (with the same base-name as
the Makefile, but
in <code>$(BDIR)/tex/macros</code>). As a result, if
the targets in a workhorse-Makefile aren't directly a
prerequisite of other workhorse-Makefile targets, they
can be a prerequisite of that intermediate LaTeX macro
file and thus be called when necessary. Otherwise,
they will be ignored by Make.</p>
<p>Maneage also has a mode to share the build
directory between several users of a Unix group (when
working on large computer clusters). In this scenario,
each user can have their own cloned project source,
but share the large built files between each other. To
do this, it is necessary for all built files to give
full permission to group members while not allowing
any other users access to the contents. Therefore
the <code>./project configure</code> and
<code>./project make</code> steps must be called with
special conditions which are managed in
the <code>--group</code> option.</p>
<p>Let's see how this design is implemented. Please
open and inspect
<code>top-make.mk</code> it as we go along here. The
first step (un-commented line) is to import the local
configuration (your answers to the questions of
<code>./project configure</code>). They are defined in
the configuration-Makefile
<code>reproduce/software/config/LOCAL.conf</code>
which was also built by <code>./project
configure</code> (based on
the <code>LOCAL.conf.in</code> template of the
same directory).</p>
<p>The next non-commented set of the
top <code>Makefile</code> defines the ultimate target
of the whole project (<code>paper.pdf</code>). But to
avoid mistakes, a sanity check is necessary to see if
Make is being run with the same group settings as the
configure script (for example when the project is
configured for group access using
the <code>./for-group</code> script, but Make
isn't). Therefore we use a Make conditional to define
the <code>all</code> target based on the group
permissions.</p>
<p>Having defined the top/ultimate target, our next
step is to include all the other necessary
Makefiles. However, order matters in the importing of
workhorse-Makefiles and each must also have a TeX
macro file with the same base name (without a
suffix). Therefore, the next step in the top-level
Makefile is to define the <code>makesrc</code>
variable to keep the base names (without
a <code>.mk</code> suffix) of the workhorse-Makefiles
that must be imported, in the proper order.</p>
<p>Finally, we import all the necessary remaining
Makefiles: 1) All the analysis configuration-Makefiles
with a wildcard. 2) The software
configuration-Makefile that contains their version
(just in case its necessary). 3) All
workhorse-Makefiles in the proper order using a Make
<code>foreach</code> loop.</p>
<p>In short, to keep things modular, readable and
manageable, follow these recommendations: 1) Set
clear-to-understand names for the
configuration-Makefiles, and workhorse-Makefiles, 2)
Only import other Makefiles from top Makefile. These
will let you know/remember generally which step you
are taking before or after another. Projects will
scale up very fast. Thus if you don't start and
continue with a clean and robust convention like this,
in the end it will become very dirty and hard to
manage/understand (even for yourself). As a general
rule of thumb, break your rules into as many
logically-similar but independent steps as
possible.</p>
<p>The <code>reproduce/analysis/make/paper.mk</code>
Makefile must be the final Makefile that is
included. This workhorse Makefile ends with the rule
to build
<code>paper.pdf</code> (final target of the whole
project). If you look in it, you will notice that this
Makefile starts with a rule to create
<code>$(mtexdir)/project.tex</code>
(<code>mtexdir</code> is just a shorthand name for
<code>$(BDIR)/tex/macros</code> mentioned before). As
you see, the only dependency of
<code>$(mtexdir)/project.tex</code>
is <code>$(mtexdir)/verify.tex</code> (which is the
last analysis step: it verifies all the generated
results). Therefore,
<code>$(mtexdir)/project.tex</code> is <em>the
connection</em> between the processing/analysis steps
of the project, and the steps to build the final
PDF.</p>
<p>During the research, it often happens that you want
to test a step that is not a prerequisite of any
higher-level operation. In such cases, you can
(temporarily) define that processing as a rule in the
most relevant workhorse-Makefile and set its target as
a prerequisite of its TeX macro. If your test gives a
promising result and you want to include it in your
research, set it as prerequisites to other rules and
remove it from the list of prerequisites for TeX macro
file. In fact, this is how a project is designed to
grow in this framework.</p>
<h3>File modification dates (meta data)</h3>
<p>While Git does an excellent job at keeping a
history of the contents of files, it makes no effort
in keeping the file meta data, and in particular the
dates of files. Therefore when you checkout to a
different branch, files that are re-written by Git
will have a newer date than the other project
files. However, file dates are important in the
current design of Maneage: Make checks the dates of
the prerequisite files and target files to see if the
target should be re-built.</p>
<p>To fix this problem, for Maneage we use a forked
version of
<a href="https://github.com/mohammad-akhlaghi/metastore">Metastore</a>. Metastore
use a binary database file (which is
called <code>.file-metadata</code>) to keep the
modification dates of all the files under version
control. This file is also under version control, but
is hidden (because it shouldn't be modified by
hand). During the project's configuration, Maneage
installs to Git hooks to run Metastore 1) before
making a commit to update its database with the file
dates in a branch, and 2) after doing a checkout, to
reset the file-dates after the checkout is complete
and re-set the file dates back to what they were.</p>
<p>In practice, Metastore should work almost fully
invisibly within your project. The only place you
might notice its presence is that you'll see
<code>.file-metadata</code> in the list of
modified/staged files (commonly after merging your
branches). Since its a binary file, Git also won't
show you the changed contents. In a merge, you can
simply accept any changes with
<code>git add -u</code>. But if Git is telling you
that it has changed without a merge (for example if
you started a commit, but canceled it in the middle),
you can just do <code>git checkout
.file-metadata</code> and set it back to its original
state.</p>
<h3>Summary</h3>
<p>Based on the explanation above, some major design
points you should have in mind are listed below.</p>
<ul>
<li><p>Define
new <code>reproduce/analysis/make/XXXXXX.mk</code>
workhorse-Makefile(s) with good and
human-friendly name(s)
replacing <code>XXXXXX</code>.</p></li>
<li><p>Add <code>XXXXXX</code>, as a new line, to
the values in <code>makesrc</code> of the
top-level
<code>Makefile</code>.</p></li>
<li><p>Do not use any constant numbers (or
important names like filter names) in the
workhorse-Makefiles or paper's LaTeX
source. Define such constants as
logically-grouped, separate
configuration-Makefiles in
<code>reproduce/analysis/config/XXXXX.conf</code>. Then
set this configuration-Makefiles file as a
prerequisite to any rule that uses the
variable defined in it.</p></li>
<li><p>Through any number of intermediate
prerequisites, all processing steps should end
in (be a prerequisite
of) <code>$(mtexdir)/verify.tex</code>
(defined in
<code>reproduce/analysis/make/verify.mk</code>). <code>$(mtexdir)/verify.tex</code>
is the sole dependency
of <code>$(mtexdir)/project.tex</code>, which
is the bridge between the processing steps and
PDF-building steps of the project.</p></li>
</ul>
<p align="right">Next: <a href="about-customize.html">Customization checklist</a>, Previous: <a href="about-make.html">Why Make?</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 project PI (<a href="http://akhlaghi.org">Mohammad Akhlaghi</a>).</p></li>
<li><p>Copyright © 2020-2022 Maneage volunteers</p></li>
<li>This page is distributed under GNU General Public License (<a href="https://www.gnu.org/licenses/gpl-3.0.en.html">GPL</a>).</li>
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