diff options
| author | Mohammad Akhlaghi <mohammad@akhlaghi.org> | 2020-11-26 03:45:54 +0000 |
|---|---|---|
| committer | Mohammad Akhlaghi <mohammad@akhlaghi.org> | 2020-11-26 03:45:54 +0000 |
| commit | 6b87843fc38c1646615ab0342a703f7ab3caf1cb (patch) | |
| tree | ea11daebe93d93f7e549fe9e3404248d850026f7 /about-architecture.html | |
| parent | 56779683e1abd996f50d1e66055f4f5540a7d61c (diff) | |
The long about.hml is now broken up into smaller pages
The "About" page ('about.html') was effectively a full copy of
Maneage's 'README-hacking.md', so it was very long. To help in
readability it has now been broken down into smaller pages (one for
each section).
Also the indentation of Make recipes was corrected, both in the about
pages, and also in the tutorial.
Diffstat (limited to 'about-architecture.html')
| -rw-r--r-- | about-architecture.html | 353 |
1 files changed, 353 insertions, 0 deletions
diff --git a/about-architecture.html b/about-architecture.html new file mode 100644 index 0000000..915b45f --- /dev/null +++ b/about-architecture.html @@ -0,0 +1,353 @@ +<!DOCTYPE html> +<!-- Copyright notes are just below the head and before body --> + + <html lang="en-US"> + + <!-- HTML Header --> + <head> + <!-- Title of the page. --> + <title>Maneage -- Managing data lineage</title> + + <!-- Enable UTF-8 encoding to easily use non-ASCII charactes --> + <meta charset="UTF-8"> + <meta http-equiv="Content-type" content="text/html; charset=UTF-8"> + + <!-- Put logo beside the address bar --> + <link rel="shortcut icon" href="./img/favicon.svg" /> + + <!-- The viewport meta tag is placed mainly for mobile browsers + that are pre-configured in different ways (for example setting the + different widths for the page than the actual width of the device, + or zooming to different values. Without this the CSS media + solutions might not work properly on all mobile browsers.--> + <meta name="viewport" + content="width=device-width, initial-scale=1"> + + <!-- Basic styles --> + <link rel="stylesheet" href="css/base.css" /> + </head> + + <!-- + Webpage of Maneage: a framework for managing data lineage + + Copyright (C) 2020, Pedram Ashofteh Ardakani <pedramardakani@pm.me> + Copyright (C) 2020, Mohammad Akhlaghi <mohammad@akhlaghi.org> + + This file is part of Maneage. 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. + + 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. See + <http://www.gnu.org/licenses/>. --> + + <!-- Start the main body. --> + <body> + <div id="container"> + <header role="banner"> + <!-- global navigation --> + <nav role="navigation" id="nav-hamburger-wrapper"> + <input type="checkbox" id="nav-hamburger-input"/> + <label for="nav-hamburger-input">|||</label> + <div id="nav-hamburger-items" class="button"> + <a href="index.html">Home</a> + <a href="about.html">About</a> + <a href="http://git.maneage.org/project.git/">Git</a> + <a href="tutorial.html">Tutorial</a> + </div> + </nav> + </header> + <div class="banner"> + <div> + <a href="index.html"><img src="img/maneage-logo.svg" /></a> + </div> + <div> + <h1>Maneage</h1><h2>Managing Data Lineage</h2> + <p>Copyright © 2018-2020 Mohammad Akhlaghi <a href="mailto:mohammad@akhlaghi.org">mohammad@akhlaghi.org</a><br /> + Copyright © 2020 Raul Infante-Sainz <a href="mailto:infantesainz@gmail.com">infantesainz@gmail.com</a><br /> + <a href="#page-footer">License Conditions</a></p> + </div> + </div> + + + + + + <hr /> + <p align="right">Next: <a href="about-customize.html">Customization checklist</a>, Previous: <a href="about-make.html">Why Make?</a>, Up: <a href="about.html">About</a> </p> + + <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> + + <p align="right">Next: <a href="about-customize.html">Customization checklist</a>, Previous: <a href="about-make.html">Why Make?</a>, Up: <a href="about.html">About</a> </p> + + + + + + <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> + <!-- The people page will be added later + <li><p>People [page will be added later]</p></li> + --> + <li><p>Contact: with <a href="https://savannah.nongnu.org/support/?func=additem&group=reproduce">this form.</a></p></li> + <li><p>Copyright © 2020 Maneage volunteers</p></li> + <li><p>All logos are copyrighted by the respective institutions</p></li> + </ul> + </footer> + </div> + </body> |