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diff --git a/about.html b/about.html new file mode 100644 index 0000000..fbfc83c --- /dev/null +++ b/about.html @@ -0,0 +1,1240 @@ +<h1>Maneage: managing data lineage</h1> + +<p>Copyright (C) 2018-2020 Mohammad Akhlaghi <a href="mailto:mohammad@akhlaghi.org">mohammad@akhlaghi.org</a>\ +Copyright (C) 2020 Raul Infante-Sainz <a href="mailto:infantesainz@gmail.com">infantesainz@gmail.com</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&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&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 & 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 & 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>></code> (to write over the file), + the rest are <code>>></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" > .gitattributes + $ echo "tex/src/delete-me.mk merge=ours" >> .gitattributes + $ echo "tex/src/delete-me-demo.mk merge=ours" >> .gitattributes + $ echo "reproduce/analysis/make/delete-me.mk merge=ours" >> .gitattributes + $ echo "reproduce/software/config/TARGETS.conf merge=ours" >> .gitattributes + $ echo "reproduce/analysis/config/delete-me-num.conf merge=ours" >> .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 <existing@email.address> + Copyright (C) 2020 YOUR NAME <YOUR@EMAIL.ADDRESS> +</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>$@</code> instead of the target's name, <code>$<</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 $< 2 + --output=$(subst .txt,,$@) + echo "done" > $@ +large2.fits.txt: large1.fits.txt + astarithmetic $(subst .txt,,$<) 2 - --output=$(subst .txt,,$@) + rm $(subst .txt,,$<) + echo "done" > $@ +</code> +A more advanced Make programmer will use Make's <a href="https://www.gnu.org/software/make/manual/html_node/Call-Function.html">call +function</a> +to define a wrapper in <code>reproduce/analysis/make/initialize.mk</code>. This +wrapper will replace <code>$(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=$$(mktemp $(shm-maneage)) + astarithmetic $< 2 + --output=$$out.fits + echo "$$out" > $@ +large2.txt: large1.txt + input=$$(cat $<) + out=$$(mktemp $(shm-maneage)) + astarithmetic $$input.fits 2 - --output=$$out.fits + rm $$input.fits $$input + echo "$$out" > $@ +mean-std.txt: large2.txt + input=$$(cat $<) + aststatistics $$input.fits --mean --std > $@ + 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> |