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@@ -72,1200 +72,24 @@ </div> </div> - <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>Maneage is a <strong>fully working + template</strong> (ready to customize) for doing + reproducible research (or writing a reproducible + paper). In each of the sections below, it is discussed + in more detail. </p> + + <ol> + <li><a href="about-introduction.html">Introduction</a></li> + <li><a href="about-citation.html">Citation and published projects using Maneage</a></li> + <li><a href="about-make.html">Why Make?</a></li> + <li><a href="about-architecture.html">Maneage architecture</a></li> + <li><a href="about-customize.html">Customization checklist</a></li> + <li><a href="about-tips.html">Tips for designing your project</a></li> + <li><a href="about-future.html">Future improvements</a></li> + </ol> - <ul> - <li><a href="http://akhlaghi.org/reproducible-science.html">http://akhlaghi.org/reproducible-science.html</a></li> - </ul> - - <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> - - <ul> - <li><a href="https://en.wikipedia.org/wiki/Make_(software)">https://en.wikipedia.org/wiki/Make_(software)</a></li> - </ul> - - <p>Make is a +40 year old software that is still evolving, therefore many - implementations of Make exist. The only difference in them is some extra - features over the <a href="https://pubs.opengroup.org/onlinepubs/009695399/utilities/make.html">standard - definition</a> - (which is shared in all of them). Maneage is primarily written in GNU Make - (which it installs itself, you don't have to have it on your system). GNU - Make is the most common, most actively developed, and most advanced - implementation. Just note that Maneage downloads, builds, internally - installs, and uses its own dependencies (including GNU Make), so you don't - have to have it installed before you try it out.</p> - - <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> - - <ul> - <li><a href="https://www.gnu.org/software/make/manual/">https://www.gnu.org/software/make/manual/</a></li> - <li><a href="https://www.gnu.org/software/make/manual/make.pdf">https://www.gnu.org/software/make/manual/make.pdf</a></li> - </ul> - - <p>If you use GNU Make, you also have the whole GNU Make manual on the - command-line with the following command (you can come out of the "Info" - environment by pressing <code>q</code>).</p> - - <pre><code>info make</code></pre> - - <p>If you aren't familiar with the Info documentation format, we strongly - recommend running <code>$ info info</code> and reading along. In less than an hour, - you will become highly proficient in it (it is very simple and has a great - manual for itself). Info greatly simplifies your access (without taking - your hands off the keyboard!) to many manuals that are installed on your - system, allowing you to be much more efficient as you work. If you use the - GNU Emacs text editor (or any of its variants), you also have access to all - Info manuals while you are writing your projects (again, without taking - your hands off the keyboard!).</p> - - <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> - - <pre><code>git clone https://git.maneage.org/project.git <span class="comment"># Clone/copy the project and its history.</span> -mv project my-project <span class="comment"># Change the name to your project's name.</span> -cd my-project <span class="comment"># Go into the cloned directory.</span> -git remote rename origin origin-maneage <span class="comment"># Rename current/only remote to "origin-maneage".</span> -git checkout -b master <span class="comment"># Create and enter your own "master" branch.</span> -pwd <span class="comment"># Just to confirm where you are.</span></code></pre></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> - - <pre><code><span class="comment"># On another terminal (go to top project source directory, last command above)</span> -./project --check-config</code></pre></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> - - <pre><code>./project configure <span class="comment"># Build the project's software environment (can take an hour or so).</span> -./project make <span class="comment"># Do the processing and build paper (just a simple demo).</span> -<span class="comment"># Open 'paper.pdf' and see if everything is ok.</code></pre></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> - - <pre><code>git remote add origin XXXXXXXXXX <span class="comment"># Newly created repo is now called 'origin'.</span> -git push --set-upstream origin master <span class="comment"># Push 'master' branch to 'origin' (with tracking).</span> -git push origin maneage <span class="comment"># Push 'maneage' branch to 'origin' (no tracking).</span></code></pre></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> - <pre><code>rm tex/src/delete-me* -rm reproduce/analysis/make/delete-me* -rm reproduce/analysis/config/delete-me*</code></pre></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> - - <pre><code>./project make clean -./project make</code></pre></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> - - <pre><code>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></pre></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> - - <pre><code>Copyright (C) 2018-2020 Existing Name <existing@email.address> -Copyright (C) 2020 YOUR NAME <YOUR@EMAIL.ADDRESS></code></pre></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> - - <pre><code>git config --global user.name "YourName YourSurname" -git config --global user.email your-email@example.com -git config --global core.editor nano</code></pre></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> - - <pre><code>git status <span class="comment"># See which files you have changed.</span> -git diff <span class="comment"># Check the lines you have added/changed.</span> -./project make <span class="comment"># Make sure everything builds successfully.</span> -git add -u <span class="comment"># Put all tracked changes in staging area.</span> -git status <span class="comment"># Make sure everything is fine.</span> -git diff --cached <span class="comment"># Confirm all the changes that will be committed.</span> -git commit <span class="comment"># Your first commit: put a good description!</span> -git push <span class="comment"># Push your commit to your remote.</span></code></pre></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> - - <pre><code>grep -ir wfpc2 ./*</code></pre></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> - - <pre><code>./project make --prepare-redo</code></pre></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> - - <pre><code>info make "automatic variables"</code></pre></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. - <pre><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" > $@</code></pre> - A more advanced Make programmer will use Make's <a href="https://www.gnu.org/software/make/manual/html_node/Call-Function.html">call function</a> - to define a wrapper in <code>reproduce/analysis/make/initialize.mk</code>. This - wrapper will replace <code>$(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). - <pre><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></pre> - 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> - - <pre><code>git checkout maneage -git pull <span class="comment"># Get recent work in Maneage</span> -git log XXXXXX..XXXXXX --reverse <span class="comment"># Inspect new work (replace XXXXXXs with hashs mentioned in output of previous command).</span> -git log --oneline --graph --decorate --all <span class="comment"># General view of branches.</span> -git checkout master <span class="comment"># Go to your top working branch.</span> -git merge maneage <span class="comment"># Import all the work into master.</span></code></pre></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> - - <pre><code>git remote add origin-maneage https://git.maneage.org/project.git -git fetch origin-maneage -git checkout -b maneage --track origin-maneage/maneage</code></pre></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> - - <pre><code>git bundle create my-project-git.bundle --all</code></pre> - - <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><pre><code>git clone my-project-git.bundle</code></pre></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> - - <pre><code>/nix/store/b6gvzjyb2pg0kjfwrjmg1vfhh54ad73z-firefox-33.1/</code></pre> - - <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> <footer role="contentinfo" id="page-footer"> - <h2>Copyright information</h2> - - <p>This file is part of Maneage's core: <a href="https://git.maneage.org/project.git">https://git.maneage.org/project.git</a></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> <ul> <li><p>Maneage is currently based in the Instituto de Astrofísica de Canarias (IAC).</p></li> <li><p>Address: IAC, Calle Vía Láctea, s/n, E38205 - La Laguna (Tenerife), Spain.</p></li> |