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+<h1>Maneage: managing data lineage</h1>
+
+<p>Copyright (C) 2018-2020 Mohammad Akhlaghi <a href="&#109;&#x61;&#x69;&#x6C;&#x74;&#x6F;:&#x6D;&#111;&#104;&#97;&#x6D;&#109;a&#x64;&#64;&#x61;&#107;&#x68;&#x6C;&#x61;&#x67;&#104;&#x69;.&#x6F;&#x72;&#103;">&#x6D;&#111;&#104;&#97;&#x6D;&#109;a&#x64;&#64;&#x61;&#107;&#x68;&#x6C;&#x61;&#x67;&#104;&#x69;.&#x6F;&#x72;&#103;</a>\
+Copyright (C) 2020 Raul Infante-Sainz <a href="m&#x61;&#105;&#108;t&#111;:&#x69;&#x6E;&#x66;&#x61;&#x6E;&#116;&#101;&#115;&#97;&#x69;n&#122;&#64;&#103;&#x6D;&#x61;&#x69;&#x6C;&#x2E;&#x63;&#111;&#x6D;">&#x69;&#x6E;&#x66;&#x61;&#x6E;&#116;&#101;&#115;&#97;&#x69;n&#122;&#64;&#103;&#x6D;&#x61;&#x69;&#x6C;&#x2E;&#x63;&#111;&#x6D;</a>\
+See the end of the file for license conditions.</p>
+
+<p>Maneage is a <strong>fully working template</strong> for doing reproducible research (or
+writing a reproducible paper) as defined in the link below. If the link
+below is not accessible at the time of reading, please see the appendix at
+the end of this file for a portion of its introduction. Some
+<a href="http://akhlaghi.org/pdf/reproducible-paper.pdf">slides</a> are also available
+to help demonstrate the concept implemented here.</p>
+
+<p>http://akhlaghi.org/reproducible-science.html</p>
+
+<p>Maneage is created with the aim of supporting reproducible research by
+making it easy to start a project in this framework. As shown below, it is
+very easy to customize Maneage for any particular (research) project and
+expand it as it starts and evolves. It can be run with no modification (as
+described in <code>README.md</code>) as a demonstration and customized for use in any
+project as fully described below.</p>
+
+<p>A project designed using Maneage will download and build all the necessary
+libraries and programs for working in a closed environment (highly
+independent of the host operating system) with fixed versions of the
+necessary dependencies. The tarballs for building the local environment are
+also collected in a <a href="http://git.maneage.org/tarballs-software.git/tree/">separate
+repository</a>. The final
+output of the project is <a href="http://git.maneage.org/output-raw.git/plain/paper.pdf">a
+paper</a>. Notice the
+last paragraph of the Acknowledgments where all the necessary software are
+mentioned with their versions.</p>
+
+<p>Below, we start with a discussion of why Make was chosen as the high-level
+language/framework for project management and how to learn and master Make
+easily (and freely). The general architecture and design of the project is
+then discussed to help you navigate the files and their contents. This is
+followed by a checklist for the easy/fast customization of Maneage to your
+exciting research. We continue with some tips and guidelines on how to
+manage or extend your project as it grows based on our experiences with it
+so far. The main body concludes with a description of possible future
+improvements that are planned for Maneage (but not yet implemented). As
+discussed above, we end with a short introduction on the necessity of
+reproducible science in the appendix.</p>
+
+<p>Please don't forget to share your thoughts, suggestions and
+criticisms. Maintaining and designing Maneage is itself a separate project,
+so please join us if you are interested. Once it is mature enough, we will
+describe it in a paper (written by all contributors) for a formal
+introduction to the community.</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>
+
+<p>https://en.wikipedia.org/wiki/Make_(software)</p>
+
+<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>
+
+<h2>How can I learn Make?</h2>
+
+<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>
+
+<p>https://www.gnu.org/software/make/manual/</p>
+
+<p>https://www.gnu.org/software/make/manual/make.pdf</p>
+
+<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>
+
+<p><code>shell
+ $ info make
+</code></p>
+
+<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>
+
+<h2>Published works using Maneage</h2>
+
+<p>The list below shows some of the works that have already been published
+with (earlier versions of) Maneage. Previously it was simply called
+"Reproducible paper template". Note that Maneage is evolving, so some
+details may be different in them. The more recent ones can be used as a
+good working example.</p>
+
+<ul>
+<li><p>Infante-Sainz et
+al. (<a href="https://ui.adsabs.harvard.edu/abs/2020MNRAS.491.5317I">2020</a>,
+MNRAS, 491, 5317): The version controlled project source is available
+<a href="https://gitlab.com/infantesainz/sdss-extended-psfs-paper">on GitLab</a>
+and is also archived on Zenodo with all the necessary software tarballs:
+<a href="https://zenodo.org/record/3524937">zenodo.3524937</a>.</p></li>
+<li><p>Akhlaghi (<a href="https://arxiv.org/abs/1909.11230">2019</a>, IAU Symposium
+355). The version controlled project source is available <a href="https://gitlab.com/makhlaghi/iau-symposium-355">on
+GitLab</a> and is also
+archived on Zenodo with all the necessary software tarballs:
+<a href="https://doi.org/10.5281/zenodo.3408481">zenodo.3408481</a>.</p></li>
+<li><p>Section 7.3 of Bacon et
+al. (<a href="http://adsabs.harvard.edu/abs/2017A%26A...608A...1B">2017</a>, A&amp;A
+608, A1): The version controlled project source is available <a href="https://gitlab.com/makhlaghi/muse-udf-origin-only-hst-magnitudes">on
+GitLab</a>
+and a snapshot of the project along with all the necessary input
+datasets and outputs is available in
+<a href="https://doi.org/10.5281/zenodo.1164774">zenodo.1164774</a>.</p></li>
+<li><p>Section 4 of Bacon et
+al. (<a href="http://adsabs.harvard.edu/abs/2017A%26A...608A...1B">2017</a>, A&amp;A,
+608, A1): The version controlled project is available <a href="https://gitlab.com/makhlaghi/muse-udf-photometry-astrometry">on
+GitLab</a> and
+a snapshot of the project along with all the necessary input datasets is
+available in <a href="https://doi.org/10.5281/zenodo.1163746">zenodo.1163746</a>.</p></li>
+<li><p>Akhlaghi &amp; Ichikawa
+(<a href="http://adsabs.harvard.edu/abs/2015ApJS..220....1A">2015</a>, ApJS, 220,
+1): The version controlled project is available <a href="https://gitlab.com/makhlaghi/NoiseChisel-paper">on
+GitLab</a>. This is the
+very first (and much less mature!) incarnation of Maneage: the history
+of Maneage started more than two years after this paper was
+published. It is a very rudimentary/initial implementation, thus it is
+only included here for historical reasons. However, the project source
+is complete, accurate and uploaded to arXiv along with the paper.</p></li>
+</ul>
+
+<h2>Citation</h2>
+
+<p>A paper to fully describe Maneage has been submitted. Until then, if you
+used it in your work, please cite the paper that implemented its first
+version: Akhlaghi &amp; Ichikawa
+(<a href="http://adsabs.harvard.edu/abs/2015ApJS..220....1A">2015</a>, ApJS, 220, 1).</p>
+
+<p>Also, when your paper is published, don't forget to add a notice in your
+own paper (in coordination with the publishing editor) that the paper is
+fully reproducible and possibly add a sentence or paragraph in the end of
+the paper shortly describing the concept. This will help spread the word
+and encourage other scientists to also manage and publish their projects in
+a reproducible manner.</p>
+
+<h1>Project architecture</h1>
+
+<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. But if this the first time you are using Maneage, before reading
+this theoretical discussion, please run Maneage once from scratch without
+any changes (described in <code>README.md</code>). You will see how it works (note that
+the configure step builds all necessary software, so it can take long, but
+you can continue reading while its working).</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.</p>
+
+<p>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>
+
+<h2>File modification dates (meta data)</h2>
+
+<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>
+
+<h2>Summary</h2>
+
+<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>
+
+<h1>Customization checklist</h1>
+
+<p>Take the following steps to fully customize Maneage for your research
+project. After finishing the list, be sure to run <code>./project configure</code> and
+<code>project make</code> to see if everything works correctly. If you notice anything
+missing or any in-correct part (probably a change that has not been
+explained here), please let us know to correct it.</p>
+
+<p>As described above, the concept of reproducibility (during a project)
+heavily relies on <a href="https://en.wikipedia.org/wiki/Version_control">version
+control</a>. Currently Maneage
+uses Git as its main version control system. If you are not already
+familiar with Git, please read the first three chapters of the <a href="https://git-scm.com/book/en/v2">ProGit
+book</a> which provides a wonderful practical
+understanding of the basics. You can read later chapters as you get more
+advanced in later stages of your work.</p>
+
+<h2>First custom commit</h2>
+
+<ol>
+<li><p><strong>Get this repository and its history</strong> (if you don't already have it):
+ Arguably the easiest way to start is to clone Maneage and prepare for
+ your customizations as shown below. After the cloning first you rename
+ the default <code>origin</code> remote server to specify that this is Maneage's
+ remote server. This will allow you to use the conventional <code>origin</code>
+ name for your own project as shown in the next steps. Second, you will
+ create and go into the conventional <code>master</code> branch to start
+ committing in your project later.</p>
+
+<p><code>shell
+ $ git clone https://git.maneage.org/project.git # Clone/copy the project and its history.
+ $ mv project my-project # Change the name to your project's name.
+ $ cd my-project # Go into the cloned directory.
+ $ git remote rename origin origin-maneage # Rename current/only remote to "origin-maneage".
+ $ git checkout -b master # Create and enter your own "master" branch.
+ $ pwd # Just to confirm where you are.
+</code></p></li>
+<li><p><strong>Prepare to build project</strong>: The <code>./project configure</code> command of the
+ next step will build the different software packages within the
+ "build" directory (that you will specify). Nothing else on your system
+ will be touched. However, since it takes long, it is useful to see
+ what it is being built at every instant (its almost impossible to tell
+ from the torrent of commands that are produced!). So open another
+ terminal on your desktop and navigate to the same project directory
+ that you cloned (output of last command above). Then run the following
+ command. Once every second, this command will just print the date
+ (possibly followed by a non-existent directory notice). But as soon as
+ the next step starts building software, you'll see the names of
+ software get printed as they are being built. Once any software is
+ installed in the project build directory it will be removed. Again,
+ don't worry, nothing will be installed outside the build directory.</p>
+
+<p><code>shell
+ # On another terminal (go to top project source directory, last command above)
+ $ ./project --check-config
+</code></p></li>
+<li><p><strong>Test Maneage</strong>: Before making any changes, it is important to test it
+ and see if everything works properly with the commands below. If there
+ is any problem in the <code>./project configure</code> or <code>./project make</code> steps,
+ please contact us to fix the problem before continuing. Since the
+ building of dependencies in configuration can take long, you can take
+ the next few steps (editing the files) while its working (they don't
+ affect the configuration). After <code>./project make</code> is finished, open
+ <code>paper.pdf</code>. If it looks fine, you are ready to start customizing the
+ Maneage for your project. But before that, clean all the extra Maneage
+ outputs with <code>make clean</code> as shown below.</p>
+
+<p>```shell
+ $ ./project configure # Build the project's software environment (can take an hour or so).
+ $ ./project make # Do the processing and build paper (just a simple demo).</p>
+
+<p># Open 'paper.pdf' and see if everything is ok.
+ ```</p></li>
+<li><p><strong>Setup the remote</strong>: You can use any <a href="https://en.wikipedia.org/wiki/Comparison_of_source_code_hosting_facilities">hosting
+ facility</a>
+ that supports Git to keep an online copy of your project's version
+ controlled history. We recommend <a href="https://gitlab.com">GitLab</a> because
+ it is <a href="https://www.gnu.org/software/repo-criteria-evaluation.html">more ethical (although not
+ perfect)</a>,
+ and later you can also host GitLab on your own server. Anyway, create
+ an account in your favorite hosting facility (if you don't already
+ have one), and define a new project there. Please make sure <em>the newly
+ created project is empty</em> (some services ask to include a <code>README</code> in
+ a new project which is bad in this scenario, and will not allow you to
+ push to it). It will give you a URL (usually starting with <code>git@</code> and
+ ending in <code>.git</code>), put this URL in place of <code>XXXXXXXXXX</code> in the first
+ command below. With the second command, "push" your <code>master</code> branch to
+ your <code>origin</code> remote, and (with the <code>--set-upstream</code> option) set them
+ to track/follow each other. However, the <code>maneage</code> branch is currently
+ tracking/following your <code>origin-maneage</code> remote (automatically set
+ when you cloned Maneage). So when pushing the <code>maneage</code> branch to your
+ <code>origin</code> remote, you <em>shouldn't</em> use <code>--set-upstream</code>. With the last
+ command, you can actually check this (which local and remote branches
+ are tracking each other).</p>
+
+<p><code>shell
+ git remote add origin XXXXXXXXXX # Newly created repo is now called 'origin'.
+ git push --set-upstream origin master # Push 'master' branch to 'origin' (with tracking).
+ git push origin maneage # Push 'maneage' branch to 'origin' (no tracking).
+</code></p></li>
+<li><p><strong>Title</strong>, <strong>short description</strong> and <strong>author</strong>: The title and basic
+ information of your project's output PDF paper should be added in
+ <code>paper.tex</code>. You should see the relevant place in the preamble (prior
+ to <code>\begin{document}</code>. After you are done, run the <code>./project make</code>
+ command again to see your changes in the final PDF, and make sure that
+ your changes don't cause a crash in LaTeX. Of course, if you use a
+ different LaTeX package/style for managing the title and authors (in
+ particular a specific journal's style), please feel free to use it
+ your own methods after finishing this checklist and doing your first
+ commit.</p></li>
+<li><p><strong>Delete dummy parts</strong>: Maneage contains some parts that are only for
+ the initial/test run, mainly as a demonstration of important steps,
+ which you can use as a reference to use in your own project. But they
+ not for any real analysis, so you should remove these parts as
+ described below:</p>
+
+<ul>
+<li><p><code>paper.tex</code>: 1) Delete the text of the abstract (from
+<code>\includeabstract{</code> to <code>\vspace{0.25cm}</code>) and write your own (a
+single sentence can be enough now, you can complete it later). 2)
+Add some keywords under it in the keywords part. 3) Delete
+everything between <code>%% Start of main body.</code> and <code>%% End of main
+body.</code>. 4) Remove the notice in the "Acknowledgments" section (in
+<code>\new{}</code>) and Acknowledge your funding sources (this can also be
+done later). Just don't delete the existing acknowledgment
+statement: Maneage is possible thanks to funding from several
+grants. Since Maneage is being used in your work, it is necessary to
+acknowledge them in your work also.</p></li>
+<li><p><code>reproduce/analysis/make/top-make.mk</code>: Delete the <code>delete-me</code> line
+in the <code>makesrc</code> definition. Just make sure there is no empty line
+between the <code>download \</code> and <code>verify \</code> lines (they should be
+directly under each other).</p></li>
+<li><p><code>reproduce/analysis/make/verify.mk</code>: In the final recipe, under the
+commented line <code>Verify TeX macros</code>, remove the full line that
+contains <code>delete-me</code>, and set the value of <code>s</code> in the line for
+<code>download</code> to <code>XXXXX</code> (any temporary string, you'll fix it in the
+end of your project, when its complete).</p></li>
+<li><p>Delete all <code>delete-me*</code> files in the following directories:</p>
+
+<p><code>shell
+$ rm tex/src/delete-me*
+$ rm reproduce/analysis/make/delete-me*
+$ rm reproduce/analysis/config/delete-me*
+</code></p></li>
+<li><p>Disable verification of outputs by removing the <code>yes</code> from
+<code>reproduce/analysis/config/verify-outputs.conf</code>. Later, when you are
+ready to submit your paper, or publish the dataset, activate
+verification and make the proper corrections in this file (described
+under the "Other basic customizations" section below). This is a
+critical step and only takes a few minutes when your project is
+finished. So DON'T FORGET to activate it in the end.</p></li>
+<li><p>Re-make the project (after a cleaning) to see if you haven't
+introduced any errors.</p>
+
+<p><code>shell
+$ ./project make clean
+$ ./project make
+</code></p></li>
+</ul></li>
+<li><p><strong>Don't merge some files in future updates</strong>: As described below, you
+ can later update your infra-structure (for example to fix bugs) by
+ merging your <code>master</code> branch with <code>maneage</code>. For files that you have
+ created in your own branch, there will be no problem. However if you
+ modify an existing Maneage file for your project, next time its
+ updated on <code>maneage</code> you'll have an annoying conflict. The commands
+ below show how to fix this future problem. With them, you can
+ configure Git to ignore the changes in <code>maneage</code> for some of the files
+ you have already edited and deleted above (and will edit below). Note
+ that only the first <code>echo</code> command has a <code>&gt;</code> (to write over the file),
+ the rest are <code>&gt;&gt;</code> (to append to it). If you want to avoid any other
+ set of files to be imported from Maneage into your project's branch,
+ you can follow a similar strategy. We recommend only doing it when you
+ encounter the same conflict in more than one merge and there is no
+ other change in that file. Also, don't add core Maneage Makefiles,
+ otherwise Maneage can break on the next run.</p>
+
+<p><code>shell
+ $ echo "paper.tex merge=ours" &gt; .gitattributes
+ $ echo "tex/src/delete-me.mk merge=ours" &gt;&gt; .gitattributes
+ $ echo "tex/src/delete-me-demo.mk merge=ours" &gt;&gt; .gitattributes
+ $ echo "reproduce/analysis/make/delete-me.mk merge=ours" &gt;&gt; .gitattributes
+ $ echo "reproduce/software/config/TARGETS.conf merge=ours" &gt;&gt; .gitattributes
+ $ echo "reproduce/analysis/config/delete-me-num.conf merge=ours" &gt;&gt; .gitattributes
+ $ git add .gitattributes
+</code></p></li>
+<li><p><strong>Copyright and License notice</strong>: It is necessary that <em>all</em> the
+ "copyright-able" files in your project (those larger than 10 lines)
+ have a copyright and license notice. Please take a moment to look at
+ several existing files to see a few examples. The copyright notice is
+ usually close to the start of the file, it is the line starting with
+ <code>Copyright (C)</code> and containing a year and the author's name (like the
+ examples below). The License notice is a short description of the
+ copyright license, usually one or two paragraphs with a URL to the
+ full license. Don't forget to add these <em>two</em> notices to <em>any new
+ file</em> you add in your project (you can just copy-and-paste). When you
+ modify an existing Maneage file (which already has the notices), just
+ add a copyright notice in your name under the existing one(s), like
+ the line with capital letters below. To start with, add this line with
+ your name and email address to <code>paper.tex</code>,
+ <code>tex/src/preamble-header.tex</code>, <code>reproduce/analysis/make/top-make.mk</code>,
+ and generally, all the files you modified in the previous step.</p>
+
+<p><code>
+ Copyright (C) 2018-2020 Existing Name &lt;existing@email.address&gt;
+ Copyright (C) 2020 YOUR NAME &lt;YOUR@EMAIL.ADDRESS&gt;
+</code></p></li>
+<li><p><strong>Configure Git for fist time</strong>: If this is the first time you are
+ running Git on this system, then you have to configure it with some
+ basic information in order to have essential information in the commit
+ messages (ignore this step if you have already done it). Git will
+ include your name and e-mail address information in each commit. You
+ can also specify your favorite text editor for making the commit
+ (<code>emacs</code>, <code>vim</code>, <code>nano</code>, and etc.).</p>
+
+<p><code>shell
+ $ git config --global user.name "YourName YourSurname"
+ $ git config --global user.email your-email@example.com
+ $ git config --global core.editor nano
+</code></p></li>
+<li><p><strong>Your first commit</strong>: You have already made some small and basic
+ changes in the steps above and you are in your project's <code>master</code>
+ branch. So, you can officially make your first commit in your
+ project's history and push it. But before that, you need to make sure
+ that there are no problems in the project. This is a good habit to
+ always re-build the system before a commit to be sure it works as
+ expected.</p>
+
+<p><code>shell
+ $ git status # See which files you have changed.
+ $ git diff # Check the lines you have added/changed.
+ $ ./project make # Make sure everything builds successfully.
+ $ git add -u # Put all tracked changes in staging area.
+ $ git status # Make sure everything is fine.
+ $ git diff --cached # Confirm all the changes that will be committed.
+ $ git commit # Your first commit: put a good description!
+ $ git push # Push your commit to your remote.
+</code></p></li>
+<li><p><strong>Start your exciting research</strong>: You are now ready to add flesh and
+ blood to this raw skeleton by further modifying and adding your
+ exciting research steps. You can use the "published works" section in
+ the introduction (above) as some fully working models to learn
+ from. Also, don't hesitate to contact us if you have any
+ questions.</p></li>
+</ol>
+
+<h2>Other basic customizations</h2>
+
+<ul>
+<li><p><strong>High-level software</strong>: Maneage installs all the software that your
+ project needs. You can specify which software your project needs in
+ <code>reproduce/software/config/TARGETS.conf</code>. The necessary software are
+ classified into two classes: 1) programs or libraries (usually written
+ in C/C++) which are run directly by the operating system. 2) Python
+ modules/libraries that are run within Python. By default
+ <code>TARGETS.conf</code> only has GNU Astronomy Utilities (Gnuastro) as one
+ scientific program and Astropy as one scientific Python module. Both
+ have many dependencies which will be installed into your project
+ during the configuration step. To see a list of software that are
+ currently ready to be built in Maneage, see
+ <code>reproduce/software/config/versions.conf</code> (which has their versions
+ also), the comments in <code>TARGETS.conf</code> describe how to use the software
+ name from <code>versions.conf</code>. Currently the raw pipeline just uses
+ Gnuastro to make the demonstration plots. Therefore if you don't need
+ Gnuastro, go through the analysis steps in <code>reproduce/analysis</code> and
+ remove all its use cases (clearly marked).</p></li>
+<li><p><strong>Input dataset</strong>: The input datasets are managed through the
+ <code>reproduce/analysis/config/INPUTS.conf</code> file. It is best to gather all
+ the information regarding all the input datasets into this one central
+ file. To ensure that the proper dataset is being downloaded and used
+ by the project, it is also recommended get an <a href="https://en.wikipedia.org/wiki/MD5">MD5
+ checksum</a> of the file and include
+ that in <code>INPUTS.conf</code> so the project can check it automatically. The
+ preparation/downloading of the input datasets is done in
+ <code>reproduce/analysis/make/download.mk</code>. Have a look there to see how
+ these values are to be used. This information about the input datasets
+ is also used in the initial <code>configure</code> script (to inform the users),
+ so also modify that file. You can find all occurrences of the demo
+ dataset with the command below and replace it with your input's
+ dataset.</p>
+
+<p><code>shell
+ $ grep -ir wfpc2 ./*
+</code></p></li>
+<li><p><strong><code>README.md</code></strong>: Correct all the <code>XXXXX</code> place holders (name of your
+ project, your own name, address of your project's online/remote
+ repository, link to download dependencies and etc). Generally, read
+ over the text and update it where necessary to fit your project. Don't
+ forget that this is the first file that is displayed on your online
+ repository and also your colleagues will first be drawn to read this
+ file. Therefore, make it as easy as possible for them to start
+ with. Also check and update this file one last time when you are ready
+ to publish your project's paper/source.</p></li>
+<li><p><strong>Verify outputs</strong>: During the initial customization checklist, you
+ disabled verification. This is natural because during the project you
+ need to make changes all the time and its a waste of time to enable
+ verification every time. But at significant moments of the project
+ (for example before submission to a journal, or publication) it is
+ necessary. When you activate verification, before building the paper,
+ all the specified datasets will be compared with their respective
+ checksum and if any file's checksum is different from the one recorded
+ in the project, it will stop and print the problematic file and its
+ expected and calculated checksums. First set the value of
+ <code>verify-outputs</code> variable in
+ <code>reproduce/analysis/config/verify-outputs.conf</code> to <code>yes</code>. Then go to
+ <code>reproduce/analysis/make/verify.mk</code>. The verification of all the files
+ is only done in one recipe. First the files that go into the
+ plots/figures are checked, then the LaTeX macros. Validation of the
+ former (inputs to plots/figures) should be done manually. If its the
+ first time you are doing this, you can see two examples of the dummy
+ steps (with <code>delete-me</code>, you can use them if you like). These two
+ examples should be removed before you can run the project. For the
+ latter, you just have to update the checksums. The important thing to
+ consider is that a simple checksum can be problematic because some
+ file generators print their run-time date in the file (for example as
+ commented lines in a text table). When checking text files, this
+ Makefile already has this function:
+ <code>verify-txt-no-comments-leading-space</code>. As the name suggests, it will
+ remove comment lines and empty lines before calculating the MD5
+ checksum. For FITS formats (common in astronomy, fortunately there is
+ a <code>DATASUM</code> definition which will return the checksum independent of
+ the headers. You can use the provided function(s), or define one for
+ your special formats.</p></li>
+<li><p><strong>Feedback</strong>: As you use Maneage you will notice many things that if
+ implemented from the start would have been very useful for your
+ work. This can be in the actual scripting and architecture of Maneage,
+ or useful implementation and usage tips, like those below. In any
+ case, please share your thoughts and suggestions with us, so we can
+ add them here for everyone's benefit.</p></li>
+<li><p><strong>Re-preparation</strong>: Automatic preparation is only run in the first run
+ of the project on a system, to re-do the preparation you have to use
+ the option below. Here is the reason for this: when its necessary, the
+ preparation process can be slow and will unnecessarily slow down the
+ whole project while the project is under development (focus is on the
+ analysis that is done after preparation). Because of this, preparation
+ will be done automatically for the first time that the project is run
+ (when <code>.build/software/preparation-done.mk</code> doesn't exist). After the
+ preparation process completes once, future runs of <code>./project make</code>
+ will not do the preparation process anymore (will not call
+ <code>top-prepare.mk</code>). They will only call <code>top-make.mk</code> for the
+ analysis. To manually invoke the preparation process after the first
+ attempt, the <code>./project make</code> script should be run with the
+ <code>--prepare-redo</code> option, or you can delete the special file above.</p>
+
+<p><code>shell
+ $ ./project make --prepare-redo
+</code></p></li>
+<li><p><strong>Pre-publication</strong>: add notice on reproducibility**: Add a notice
+ somewhere prominent in the first page within your paper, informing the
+ reader that your research is fully reproducible. For example in the
+ end of the abstract, or under the keywords with a title like
+ "reproducible paper". This will encourage them to publish their own
+ works in this manner also and also will help spread the word.</p></li>
+</ul>
+
+<h1>Tips for designing your project</h1>
+
+<p>The following is a list of design points, tips, or recommendations that
+have been learned after some experience with this type of project
+management. Please don't hesitate to share any experience you gain after
+using it with us. In this way, we can add it here (with full giving credit)
+for the benefit of others.</p>
+
+<ul>
+<li><p><strong>Modularity</strong>: Modularity is the key to easy and clean growth of a
+ project. So it is always best to break up a job into as many
+ sub-components as reasonable. Here are some tips to stay modular.</p>
+
+<ul>
+<li><p><em>Short recipes</em>: if you see the recipe of a rule becoming more than a
+handful of lines which involve significant processing, it is probably
+a good sign that you should break up the rule into its main
+components. Try to only have one major processing step per rule.</p></li>
+<li><p><em>Context-based (many) Makefiles</em>: For maximum modularity, this design
+allows easy inclusion of many Makefiles: in
+<code>reproduce/analysis/make/*.mk</code> for analysis steps, and
+<code>reproduce/software/make/*.mk</code> for building software. So keep the
+rules for closely related parts of the processing in separate
+Makefiles.</p></li>
+<li><p><em>Descriptive names</em>: Be very clear and descriptive with the naming of
+the files and the variables because a few months after the
+processing, it will be very hard to remember what each one was
+for. Also this helps others (your collaborators or other people
+reading the project source after it is published) to more easily
+understand your work and find their way around.</p></li>
+<li><p><em>Naming convention</em>: As the project grows, following a single standard
+or convention in naming the files is very useful. Try best to use
+multiple word filenames for anything that is non-trivial (separating
+the words with a <code>-</code>). For example if you have a Makefile for
+creating a catalog and another two for processing it under models A
+and B, you can name them like this: <code>catalog-create.mk</code>,
+<code>catalog-model-a.mk</code> and <code>catalog-model-b.mk</code>. In this way, when
+listing the contents of <code>reproduce/analysis/make</code> to see all the
+Makefiles, those related to the catalog will all be close to each
+other and thus easily found. This also helps in auto-completions by
+the shell or text editors like Emacs.</p></li>
+<li><p><em>Source directories</em>: If you need to add files in other languages for
+example in shell, Python, AWK or C, keep the files in the same
+language in a separate directory under <code>reproduce/analysis</code>, with the
+appropriate name.</p></li>
+<li><p><em>Configuration files</em>: If your research uses special programs as part
+of the processing, put all their configuration files in a devoted
+directory (with the program's name) within
+<code>reproduce/software/config</code>. Similar to the
+<code>reproduce/software/config/gnuastro</code> directory (which is put in
+Maneage as a demo in case you use GNU Astronomy Utilities). It is
+much cleaner and readable (thus less buggy) to avoid mixing the
+configuration files, even if there is no technical necessity.</p></li>
+</ul></li>
+<li><p><strong>Contents</strong>: It is good practice to follow the following
+ recommendations on the contents of your files, whether they are source
+ code for a program, Makefiles, scripts or configuration files
+ (copyrights aren't necessary for the latter).</p>
+
+<ul>
+<li><p><em>Copyright</em>: Always start a file containing programming constructs
+with a copyright statement like the ones that Maneage starts with
+(for example in the top level <code>Makefile</code>).</p></li>
+<li><p><em>Comments</em>: Comments are vital for readability (by yourself in two
+months, or others). Describe everything you can about why you are
+doing something, how you are doing it, and what you expect the result
+to be. Write the comments as if it was what you would say to describe
+the variable, recipe or rule to a friend sitting beside you. When
+writing the project it is very tempting to just steam ahead with
+commands and codes, but be patient and write comments before the
+rules or recipes. This will also allow you to think more about what
+you should be doing. Also, in several months when you come back to
+the code, you will appreciate the effort of writing them. Just don't
+forget to also read and update the comment first if you later want to
+make changes to the code (variable, recipe or rule). As a general
+rule of thumb: first the comments, then the code.</p></li>
+<li><p><em>File title</em>: In general, it is good practice to start all files with
+a single line description of what that particular file does. If
+further information about the totality of the file is necessary, add
+it after a blank line. This will help a fast inspection where you
+don't care about the details, but just want to remember/see what that
+file is (generally) for. This information must of course be commented
+(its for a human), but this is kept separate from the general
+recommendation on comments, because this is a comment for the whole
+file, not each step within it.</p></li>
+</ul></li>
+<li><p><strong>Make programming</strong>: Here are some experiences that we have come to
+ learn over the years in using Make and are useful/handy in research
+ contexts.</p>
+
+<ul>
+<li><p><em>Environment of each recipe</em>: If you need to define a special
+environment (or aliases, or scripts to run) for all the recipes in
+your Makefiles, you can use a Bash startup file
+<code>reproduce/software/shell/bashrc.sh</code>. This file is loaded before every
+Make recipe is run, just like the <code>.bashrc</code> in your home directory is
+loaded every time you start a new interactive, non-login terminal. See
+the comments in that file for more.</p></li>
+<li><p><em>Automatic variables</em>: These are wonderful and very useful Make
+constructs that greatly shrink the text, while helping in
+read-ability, robustness (less bugs in typos for example) and
+generalization. For example even when a rule only has one target or
+one prerequisite, always use <code>$@</code> instead of the target's name, <code>$&lt;</code>
+instead of the first prerequisite, <code>$^</code> instead of the full list of
+prerequisites and etc. You can see the full list of automatic
+variables
+<a href="https://www.gnu.org/software/make/manual/html_node/Automatic-Variables.html">here</a>. If
+you use GNU Make, you can also see this page on your command-line:</p>
+
+<p><code>shell
+$ info make "automatic variables"
+</code></p></li>
+<li><p><em>Debug</em>: Since Make doesn't follow the common top-down paradigm, it
+can be a little hard to get accustomed to why you get an error or
+un-expected behavior. In such cases, run Make with the <code>-d</code>
+option. With this option, Make prints a full list of exactly which
+prerequisites are being checked for which targets. Looking
+(patiently) through this output and searching for the faulty
+file/step will clearly show you any mistake you might have made in
+defining the targets or prerequisites.</p></li>
+<li><p><em>Large files</em>: If you are dealing with very large files (thus having
+multiple copies of them for intermediate steps is not possible), one
+solution is the following strategy (Also see the next item on "Fast
+access to temporary files"). Set a small plain text file as the
+actual target and delete the large file when it is no longer needed
+by the project (in the last rule that needs it). Below is a simple
+demonstration of doing this. In it, we use Gnuastro's Arithmetic
+program to add all pixels of the input image with 2 and create
+<code>large1.fits</code>. We then subtract 2 from <code>large1.fits</code> to create
+<code>large2.fits</code> and delete <code>large1.fits</code> in the same rule (when its no
+longer needed). We can later do the same with <code>large2.fits</code> when it
+is no longer needed and so on.
+<code>
+large1.fits.txt: input.fits
+ astarithmetic $&lt; 2 + --output=$(subst .txt,,$@)
+ echo "done" &gt; $@
+large2.fits.txt: large1.fits.txt
+ astarithmetic $(subst .txt,,$&lt;) 2 - --output=$(subst .txt,,$@)
+ rm $(subst .txt,,$&lt;)
+ echo "done" &gt; $@
+</code>
+A more advanced Make programmer will use Make's <a href="https://www.gnu.org/software/make/manual/html_node/Call-Function.html">call
+function</a>
+to define a wrapper in <code>reproduce/analysis/make/initialize.mk</code>. This
+wrapper will replace <code>$(subst .txt,,XXXXX)</code>. Therefore, it will be
+possible to greatly simplify this repetitive statement and make the
+code even more readable throughout the whole project.</p></li>
+<li><p><em>Fast access to temporary files</em>: Most Unix-like operating systems
+will give you a special shared-memory device (directory): on systems
+using the GNU C Library (all GNU/Linux system), it is <code>/dev/shm</code>. The
+contents of this directory are actually in your RAM, not in your
+persistence storage like the HDD or SSD. Reading and writing from/to
+the RAM is much faster than persistent storage, so if you have enough
+RAM available, it can be very beneficial for large temporary files to
+be put there. You can use the <code>mktemp</code> program to give the temporary
+files a randomly-set name, and use text files as targets to keep that
+name (as described in the item above under "Large files") for later
+deletion. For example, see the minimal working example Makefile below
+(which you can actually put in a <code>Makefile</code> and run if you have an
+<code>input.fits</code> in the same directory, and Gnuastro is installed).
+<code>
+.ONESHELL:
+.SHELLFLAGS = -ec
+all: mean-std.txt
+shm-maneage := /dev/shm/$(shell whoami)-maneage-XXXXXXXXXX
+large1.txt: input.fits
+ out=$$(mktemp $(shm-maneage))
+ astarithmetic $&lt; 2 + --output=$$out.fits
+ echo "$$out" &gt; $@
+large2.txt: large1.txt
+ input=$$(cat $&lt;)
+ out=$$(mktemp $(shm-maneage))
+ astarithmetic $$input.fits 2 - --output=$$out.fits
+ rm $$input.fits $$input
+ echo "$$out" &gt; $@
+mean-std.txt: large2.txt
+ input=$$(cat $&lt;)
+ aststatistics $$input.fits --mean --std &gt; $@
+ rm $$input.fits $$input
+</code>
+The important point here is that the temporary name template
+(<code>shm-maneage</code>) has no suffix. So you can add the suffix
+corresponding to your desired format afterwards (for example
+<code>$$out.fits</code>, or <code>$$out.txt</code>). But more importantly, when <code>mktemp</code>
+sets the random name, it also checks if no file exists with that name
+and creates a file with that exact name at that moment. So at the end
+of each recipe above, you'll have two files in your <code>/dev/shm</code>, one
+empty file with no suffix one with a suffix. The role of the file
+without a suffix is just to ensure that the randomly set name will
+not be used by other calls to <code>mktemp</code> (when running in parallel) and
+it should be deleted with the file containing a suffix. This is the
+reason behind the <code>rm $$input.fits $$input</code> command above: to make
+sure that first the file with a suffix is deleted, then the core
+random file (note that when working in parallel on powerful systems,
+in the time between deleting two files of a single <code>rm</code> command, many
+things can happen!). When using Maneage, you can put the definition
+of <code>shm-maneage</code> in <code>reproduce/analysis/make/initialize.mk</code> to be
+usable in all the different Makefiles of your analysis, and you won't
+need the three lines above it. <strong>Finally, BE RESPONSIBLE:</strong> after you
+are finished, be sure to clean up any possibly remaining files (due
+to crashes in the processing while you are working), otherwise your
+RAM may fill up very fast. You can do it easily with a command like
+this on your command-line: <code>rm -f /dev/shm/$(whoami)-*</code>.</p></li>
+</ul></li>
+<li><p><strong>Software tarballs and raw inputs</strong>: It is critically important to
+ document the raw inputs to your project (software tarballs and raw
+ input data):</p>
+
+<ul>
+<li><p><em>Keep the source tarball of dependencies</em>: After configuration
+finishes, the <code>.build/software/tarballs</code> directory will contain all
+the software tarballs that were necessary for your project. You can
+mirror the contents of this directory to keep a backup of all the
+software tarballs used in your project (possibly as another version
+controlled repository) that is also published with your project. Note
+that software web-pages are not written in stone and can suddenly go
+offline or not be accessible in some conditions. This backup is thus
+very important. If you intend to release your project in a place like
+Zenodo, you can upload/keep all the necessary tarballs (and data)
+there with your
+project. <a href="https://doi.org/10.5281/zenodo.1163746">zenodo.1163746</a> is
+one example of how the data, Gnuastro (main software used) and all
+major Gnuastro's dependencies have been uploaded with the project's
+source. Just note that this is only possible for free and open-source
+software.</p></li>
+<li><p><em>Keep your input data</em>: The input data is also critical to the
+project's reproducibility, so like the above for software, make sure
+you have a backup of them, or their persistent identifiers (PIDs).</p></li>
+</ul></li>
+<li><p><strong>Version control</strong>: Version control is a critical component of
+ Maneage. Here are some tips to help in effectively using it.</p>
+
+<ul>
+<li><p><em>Regular commits</em>: It is important (and extremely useful) to have the
+history of your project under version control. So try to make commits
+regularly (after any meaningful change/step/result).</p></li>
+<li><p><em>Keep Maneage up-to-date</em>: In time, Maneage is going to become more
+and more mature and robust (thanks to your feedback and the feedback
+of other users). Bugs will be fixed and new/improved features will be
+added. So every once and a while, you can run the commands below to
+pull new work that is done in Maneage. If the changes are useful for
+your work, you can merge them with your project to benefit from
+them. Just pay <strong>very close attention</strong> to resolving possible
+<strong>conflicts</strong> which might happen in the merge (updated settings that
+you have customized in Maneage).</p>
+
+<p><code>shell
+$ git checkout maneage
+$ git pull # Get recent work in Maneage
+$ git log XXXXXX..XXXXXX --reverse # Inspect new work (replace XXXXXXs with hashs mentioned in output of previous command).
+$ git log --oneline --graph --decorate --all # General view of branches.
+$ git checkout master # Go to your top working branch.
+$ git merge maneage # Import all the work into master.
+</code></p></li>
+<li><p><em>Adding Maneage to a fork of your project</em>: As you and your colleagues
+continue your project, it will be necessary to have separate
+forks/clones of it. But when you clone your own project on a
+different system, or a colleague clones it to collaborate with you,
+the clone won't have the <code>origin-maneage</code> remote that you started the
+project with. As shown in the previous item above, you need this
+remote to be able to pull recent updates from Maneage. The steps
+below will setup the <code>origin-maneage</code> remote, and a local <code>maneage</code>
+branch to track it, on the new clone.</p>
+
+<p><code>shell
+$ git remote add origin-maneage https://git.maneage.org/project.git
+$ git fetch origin-maneage
+$ git checkout -b maneage --track origin-maneage/maneage
+</code></p></li>
+<li><p><em>Commit message</em>: The commit message is a very important and useful
+aspect of version control. To make the commit message useful for
+others (or yourself, one year later), it is good to follow a
+consistent style. Maneage already has a consistent formatting
+(described below), which you can also follow in your project if you
+like. You can see many examples by running <code>git log</code> in the <code>maneage</code>
+branch. If you intend to push commits to Maneage, for the consistency
+of Maneage, it is necessary to follow these guidelines. 1) No line
+should be more than 75 characters (to enable easy reading of the
+message when you run <code>git log</code> on the standard 80-character
+terminal). 2) The first line is the title of the commit and should
+summarize it (so <code>git log --oneline</code> can be useful). The title should
+also not end with a point (<code>.</code>, because its a short single sentence,
+so a point is not necessary and only wastes space). 3) After the
+title, leave an empty line and start the body of your message
+(possibly containing many paragraphs). 4) Describe the context of
+your commit (the problem it is trying to solve) as much as possible,
+then go onto how you solved it. One suggestion is to start the main
+body of your commit with "Until now ...", and continue describing the
+problem in the first paragraph(s). Afterwards, start the next
+paragraph with "With this commit ...".</p></li>
+<li><p><em>Project outputs</em>: During your research, it is possible to checkout a
+specific commit and reproduce its results. However, the processing
+can be time consuming. Therefore, it is useful to also keep track of
+the final outputs of your project (at minimum, the paper's PDF) in
+important points of history. However, keeping a snapshot of these
+(most probably large volume) outputs in the main history of the
+project can unreasonably bloat it. It is thus recommended to make a
+separate Git repo to keep those files and keep your project's source
+as small as possible. For example if your project is called
+<code>my-exciting-project</code>, the name of the outputs repository can be
+<code>my-exciting-project-output</code>. This enables easy sharing of the output
+files with your co-authors (with necessary permissions) and not
+having to bloat your email archive with extra attachments also (you
+can just share the link to the online repo in your
+communications). After the research is published, you can also
+release the outputs repository, or you can just delete it if it is
+too large or un-necessary (it was just for convenience, and fully
+reproducible after all). For example Maneage's output is available
+for demonstration in <a href="http://git.maneage.org/output-raw.git/">a
+separate</a> repository.</p></li>
+<li><p><em>Full Git history in one file</em>: When you are publishing your project
+(for example to Zenodo for long term preservation), it is more
+convenient to have the whole project's Git history into one file to
+save with your datasets. After all, you can't be sure that your
+current Git server (for example GitLab, Github, or Bitbucket) will be
+active forever. While they are good for the immediate future, you
+can't rely on them for archival purposes. Fortunately keeping your
+whole history in one file is easy with Git using the following
+commands. To learn more about it, run <code>git help bundle</code>.</p>
+
+<ul>
+<li>"bundle" your project's history into one file (just don't forget to
+change <code>my-project-git.bundle</code> to a descriptive name of your
+project):</li>
+</ul>
+
+<p><code>shell
+$ git bundle create my-project-git.bundle --all
+</code></p>
+
+<ul>
+<li>You can easily upload <code>my-project-git.bundle</code> anywhere. Later, if
+you need to un-bundle it, you can use the following command.</li>
+</ul>
+
+<p><p><p><code>shell
+$ git clone my-project-git.bundle
+</code></p></li>
+</ul></p></li>
+</ul></p>
+
+<h1>Future improvements</h1>
+
+<p>This is an evolving project and as time goes on, it will evolve and become
+more robust. Some of the most prominent issues we plan to implement in the
+future are listed below, please join us if you are interested.</p>
+
+<h2>Package management</h2>
+
+<p>It is important to have control of the environment of the project. Maneage
+currently builds the higher-level programs (for example GNU Bash, GNU Make,
+GNU AWK and domain-specific software) it needs, then sets <code>PATH</code> so the
+analysis is done only with the project's built software. But currently the
+configuration of each program is in the Makefile rules that build it. This
+is not good because a change in the build configuration does not
+automatically cause a re-build. Also, each separate project on a system
+needs to have its own built tools (that can waste a lot of space).</p>
+
+<p>A good solution is based on the <a href="https://nixos.org/nix/about.html">Nix package
+manager</a>: a separate file is present for
+each software, containing all the necessary info to build it (including its
+URL, its tarball MD5 hash, dependencies, configuration parameters, build
+steps and etc). Using this file, a script can automatically generate the
+Make rules to download, build and install program and its dependencies
+(along with the dependencies of those dependencies and etc).</p>
+
+<p>All the software are installed in a "store". Each installed file (library
+or executable) is prefixed by a hash of this configuration (and the OS
+architecture) and the standard program name. For example (from the Nix
+webpage):</p>
+
+<p><code>
+/nix/store/b6gvzjyb2pg0kjfwrjmg1vfhh54ad73z-firefox-33.1/
+</code></p>
+
+<p>The important thing is that the "store" is <em>not</em> in the project's search
+path. After the complete installation of the software, symbolic links are
+made to populate each project's program and library search paths without a
+hash. This hash will be unique to that particular software and its
+particular configuration. So simply by searching for this hash in the
+installed directory, we can find the installed files of that software to
+generate the links.</p>
+
+<p>This scenario has several advantages: 1) a change in a software's build
+configuration triggers a rebuild. 2) a single "store" can be used in many
+projects, thus saving space and configuration time for new projects (that
+commonly have large overlaps in lower-level programs).</p>
+
+<h1>Appendix: Necessity of exact reproduction in scientific research</h1>
+
+<p>In case <a href="http://akhlaghi.org/reproducible-science.html">the link above</a> is
+not accessible at the time of reading, here is a copy of the introduction
+of that link, describing the necessity for a reproducible project like this
+(copied on February 7th, 2018):</p>
+
+<p>The most important element of a "scientific" statement/result is the fact
+that others should be able to falsify it. The Tsunami of data that has
+engulfed astronomers in the last two decades, combined with faster
+processors and faster internet connections has made it much more easier to
+obtain a result. However, these factors have also increased the complexity
+of a scientific analysis, such that it is no longer possible to describe
+all the steps of an analysis in the published paper. Citing this
+difficulty, many authors suffice to describing the generalities of their
+analysis in their papers.</p>
+
+<p>However, It is impossible to falsify (or even study) a result if you can't
+exactly reproduce it. The complexity of modern science makes it vitally
+important to exactly reproduce the final result. Because even a small
+deviation can be due to many different parts of an analysis. Nature is
+already a black box which we are trying so hard to comprehend. Not letting
+other scientists see the exact steps taken to reach a result, or not
+allowing them to modify it (do experiments on it) is a self-imposed black
+box, which only exacerbates our ignorance.</p>
+
+<p>Other scientists should be able to reproduce, check and experiment on the
+results of anything that is to carry the "scientific" label. Any result
+that is not reproducible (due to incomplete information by the author) is
+not scientific: the readers have to have faith in the subjective experience
+of the authors in the very important choice of configuration values and
+order of operations: this is contrary to the scientific spirit.</p>
+
+<h2>Copyright information</h2>
+
+<p>This file is part of Maneage's core: https://git.maneage.org/project.git</p>
+
+<p>Maneage 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.</p>
+
+<p>Maneage 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.</p>
+
+<p>You should have received a copy of the GNU General Public License along
+with Maneage. If not, see <a href="https://www.gnu.org/licenses/">https://www.gnu.org/licenses/</a>.</p>