diff options
| author | Mohammad Akhlaghi <mohammad@akhlaghi.org> | 2020-11-28 23:16:13 +0000 |
|---|---|---|
| committer | Mohammad Akhlaghi <mohammad@akhlaghi.org> | 2020-11-28 23:16:13 +0000 |
| commit | 604880c08186ce88e9e4b2d289bddf8df2899d22 (patch) | |
| tree | 5440b0cbfb94dc3c2262fc90bd924e5ece8c3bf1 | |
| parent | ba25a9ca0b065f44509daf6e983aa09e66159dcd (diff) | |
Figure added for showing file architecture
In the initial version of the paper, we had this nice figure to show
the file structure of Maneage, so I thought its good to put it in the
page describing Maneage's file architecture.
Also, the long copyright at the end of the page was summarized into
one line and a link to the GPL has been added.
| -rw-r--r-- | about-architecture.html | 573 | ||||
| -rw-r--r-- | about-citation.html | 31 | ||||
| -rw-r--r-- | about-customize.html | 31 | ||||
| -rw-r--r-- | about-future.html | 31 | ||||
| -rw-r--r-- | about-introduction.html | 31 | ||||
| -rw-r--r-- | about-make.html | 31 | ||||
| -rw-r--r-- | about-tips.html | 31 | ||||
| -rw-r--r-- | about.html | 14 | ||||
| -rw-r--r-- | img/maneage-file-structure.png | bin | 0 -> 190455 bytes | |||
| -rw-r--r-- | index.html | 25 | ||||
| -rw-r--r-- | tutorial.html | 33 |
11 files changed, 407 insertions, 424 deletions
diff --git a/about-architecture.html b/about-architecture.html index db5653c..8138c49 100644 --- a/about-architecture.html +++ b/about-architecture.html @@ -81,238 +81,366 @@ <h2>Project architecture</h2> - <p>In order to customize Maneage to your research, it is important to first - understand its architecture so you can navigate your way in the directories - and understand how to implement your research project within its framework: - where to add new files and which existing files to modify for what - purpose. 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>In order to customize Maneage to your research, it + is important to first understand its architecture so + you can navigate your way in the directories and + understand how to implement your research project + within its framework: where to add new files and which + existing files to modify for what purpose. </p> <p>The project has two top-level directories: <code>reproduce</code> and - <code>tex</code>. <code>reproduce</code> hosts all the software building and analysis - steps. <code>tex</code> contains all the final paper's components to be compiled into - a PDF using LaTeX.</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>tex</code>. <code>reproduce</code> hosts all the + software building and analysis steps. <code>tex</code> + contains all the final paper's components to be + compiled into a PDF using LaTeX. The image below shows + the directory and file structure in a hypothetical + project using Maneage. Files are shown with small, + green boxes that have a suffix in their names (for + example <code>format.mk</code> or + <code>download.tex</code>). Directories (containing + multiple files) are shown as large, brown boxes, where + the name ends in a slash (<code>/</code>). + Directories with dashed lines and no files (just a + description) are symbolic links that are created after + building the project, pointing to commonly needed + built directories. Symbolic links and their contents + are not considered part of the source and are not + under version control. Files and directories are + shown within their parent directory. For example the + full address of <code>format.mk</code> from the top + project directory is + <code>reproduce/analysis/make/format.mk</code>.</p> + + <img class="center" src="img/maneage-file-structure.png" width="90%" /> + <p> </p> + + <p>As shown above, the <code>reproduce</code> + directory has two + sub-directories: <code>software</code> and + <code>analysis</code>. As the name says, the former + contains all the instructions to download, build and + install (independent of the host operating system) the + necessary software (these are called by + the <code>./project configure</code> command). The + latter contains instructions on how to use those + software to do your project's analysis.</p> + + <p>After it finishes, <code>./project configure</code> + will create the following symbolic links in the + project's top source directory: <code>.build</code> + which points to the top build directory + and <code>.local</code> for easy access to the custom + built software installation directory. With these you + can easily access the build directory and + project-specific software from your top source + directory. For example if you + run <code>.local/bin/ls</code> you will be using + the <code>ls</code> of Maneage, which is probably + different from your system's <code>ls</code> (run them + both with <code>--version</code> to check).</p> - <p>Once the project is configured for your system, <code>./project make</code> will do - the basic preparations and run the project's analysis with the custom - version of software. The <code>project</code> script is just a wrapper, and with the + <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 + <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 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 + <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 + <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 + <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>$(mtexdir)/project.tex</code> is <em>the connection</em> between the - processing/analysis steps of the project, and the steps to build the final + <p>The <code>reproduce/analysis/make/paper.mk</code> + Makefile must be the final Makefile that is + included. This workhorse Makefile ends with the rule + to build + <code>paper.pdf</code> (final target of the whole + project). If you look in it, you will notice that this + Makefile starts with a rule to create + <code>$(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 + <p>During the research, it often happens that you want + to test a step that is not a prerequisite of any + higher-level operation. In such cases, you can + (temporarily) define that processing as a rule in the + most relevant workhorse-Makefile and set its target as + a prerequisite of its TeX macro. If your test gives a + promising result and you want to include it in your + research, set it as prerequisites to other rules and + remove it from the list of prerequisites for TeX macro + file. In fact, this is how a project is designed to + grow in this framework.</p> + + <h3>File modification dates (meta data)</h3> + + <p>While Git does an excellent job at keeping a + history of the contents of files, it makes no effort + in keeping the file meta data, and in particular the + dates of files. Therefore when you checkout to a + different branch, files that are re-written by Git + will have a newer date than the other project + files. However, file dates are important in the + current design of Maneage: Make checks the dates of + the prerequisite files and target files to see if the + target should be re-built.</p> + + <p>To fix this problem, for Maneage we use a forked + version of + <a href="https://github.com/mohammad-akhlaghi/metastore">Metastore</a>. Metastore + use a binary database file (which is + called <code>.file-metadata</code>) to keep the + modification dates of all the files under version + control. This file is also under version control, but + is hidden (because it shouldn't be modified by + hand). During the project's configuration, Maneage + installs to Git hooks to run Metastore 1) before + making a commit to update its database with the file + dates in a branch, and 2) after doing a checkout, to + reset the file-dates after the checkout is complete + and re-set the file dates back to what they were.</p> + + <p>In practice, Metastore should work almost fully + invisibly within your project. The only place you + might notice its presence is that you'll see + <code>.file-metadata</code> in the list of + modified/staged files (commonly after merging your + branches). Since its a binary file, Git also won't + show you the changed contents. In a merge, you can + simply accept any changes with + <code>git add -u</code>. But if Git is telling you + that it has changed without a merge (for example if + you started a commit, but canceled it in the middle), + you can just do <code>git checkout + .file-metadata</code> and set it back to its original state.</p> - <h2>Summary</h2> + <h3>Summary</h3> - <p>Based on the explanation above, some major design points you should have in - mind are listed below.</p> + <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 + <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>$(mtexdir)/project.tex</code>, which is the bridge between the - processing steps and PDF-building steps of the project.</p></li> + + <li><p>Do not use any constant numbers (or + important names like filter names) in the + workhorse-Makefiles or paper's LaTeX + source. Define such constants as + logically-grouped, separate + configuration-Makefiles in + <code>reproduce/analysis/config/XXXXX.conf</code>. Then + set this configuration-Makefiles file as a + prerequisite to any rule that uses the + variable defined in it.</p></li> + + <li><p>Through any number of intermediate + prerequisites, all processing steps should end + in (be a prerequisite + of) <code>$(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> @@ -322,32 +450,13 @@ <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> + <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>Contact: with <a href="https://savannah.nongnu.org/support/?func=additem&group=reproduce">this form</a>, or project PI (<a href="http://akhlaghi.org">Mohammad Akhlaghi</a>).</p></li> <li><p>Copyright © 2020 Maneage volunteers</p></li> - <li><p>All logos are copyrighted by the respective institutions</p></li> - </ul> + <li>This page is distributed under GNU General Public License (<a href="https://www.gnu.org/licenses/gpl-3.0.en.html">GPL</a>).</li> + </ul> </footer> - </div> - </body> +</body> +</html> diff --git a/about-citation.html b/about-citation.html index 6129e14..1482b17 100644 --- a/about-citation.html +++ b/about-citation.html @@ -177,32 +177,13 @@ <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> + <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>Contact: with <a href="https://savannah.nongnu.org/support/?func=additem&group=reproduce">this form</a>, or project PI (<a href="http://akhlaghi.org">Mohammad Akhlaghi</a>).</p></li> <li><p>Copyright © 2020 Maneage volunteers</p></li> - <li><p>All logos are copyrighted by the respective institutions</p></li> - </ul> + <li>This page is distributed under GNU General Public License (<a href="https://www.gnu.org/licenses/gpl-3.0.en.html">GPL</a>).</li> + </ul> </footer> - </div> - </body> +</body> +</html> diff --git a/about-customize.html b/about-customize.html index d978072..3d195a5 100644 --- a/about-customize.html +++ b/about-customize.html @@ -413,32 +413,13 @@ git push <span class="comment"># Push your commit to your remo <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> + <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>Contact: with <a href="https://savannah.nongnu.org/support/?func=additem&group=reproduce">this form</a>, or project PI (<a href="http://akhlaghi.org">Mohammad Akhlaghi</a>).</p></li> <li><p>Copyright © 2020 Maneage volunteers</p></li> - <li><p>All logos are copyrighted by the respective institutions</p></li> - </ul> + <li>This page is distributed under GNU General Public License (<a href="https://www.gnu.org/licenses/gpl-3.0.en.html">GPL</a>).</li> + </ul> </footer> - </div> - </body> +</body> +</html> diff --git a/about-future.html b/about-future.html index 80958c1..35f35e2 100644 --- a/about-future.html +++ b/about-future.html @@ -129,32 +129,13 @@ <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> + <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>Contact: with <a href="https://savannah.nongnu.org/support/?func=additem&group=reproduce">this form</a>, or project PI (<a href="http://akhlaghi.org">Mohammad Akhlaghi</a>).</p></li> <li><p>Copyright © 2020 Maneage volunteers</p></li> - <li><p>All logos are copyrighted by the respective institutions</p></li> - </ul> + <li>This page is distributed under GNU General Public License (<a href="https://www.gnu.org/licenses/gpl-3.0.en.html">GPL</a>).</li> + </ul> </footer> - </div> - </body> +</body> +</html> diff --git a/about-introduction.html b/about-introduction.html index b2598ad..5e58fd7 100644 --- a/about-introduction.html +++ b/about-introduction.html @@ -146,32 +146,13 @@ <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> + <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>Contact: with <a href="https://savannah.nongnu.org/support/?func=additem&group=reproduce">this form</a>, or project PI (<a href="http://akhlaghi.org">Mohammad Akhlaghi</a>).</p></li> <li><p>Copyright © 2020 Maneage volunteers</p></li> - <li><p>All logos are copyrighted by the respective institutions</p></li> - </ul> + <li>This page is distributed under GNU General Public License (<a href="https://www.gnu.org/licenses/gpl-3.0.en.html">GPL</a>).</li> + </ul> </footer> - </div> - </body> +</body> +</html> diff --git a/about-make.html b/about-make.html index 4474075..248992c 100644 --- a/about-make.html +++ b/about-make.html @@ -190,32 +190,13 @@ <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> + <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>Contact: with <a href="https://savannah.nongnu.org/support/?func=additem&group=reproduce">this form</a>, or project PI (<a href="http://akhlaghi.org">Mohammad Akhlaghi</a>).</p></li> <li><p>Copyright © 2020 Maneage volunteers</p></li> - <li><p>All logos are copyrighted by the respective institutions</p></li> - </ul> + <li>This page is distributed under GNU General Public License (<a href="https://www.gnu.org/licenses/gpl-3.0.en.html">GPL</a>).</li> + </ul> </footer> - </div> - </body> +</body> +</html> diff --git a/about-tips.html b/about-tips.html index b7c90e8..070969d 100644 --- a/about-tips.html +++ b/about-tips.html @@ -411,32 +411,13 @@ git checkout -b maneage --track origin-maneage/maneage</code></pre></li> <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> + <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>Contact: with <a href="https://savannah.nongnu.org/support/?func=additem&group=reproduce">this form</a>, or project PI (<a href="http://akhlaghi.org">Mohammad Akhlaghi</a>).</p></li> <li><p>Copyright © 2020 Maneage volunteers</p></li> - <li><p>All logos are copyrighted by the respective institutions</p></li> - </ul> + <li>This page is distributed under GNU General Public License (<a href="https://www.gnu.org/licenses/gpl-3.0.en.html">GPL</a>).</li> + </ul> </footer> - </div> - </body> +</body> +</html> @@ -89,17 +89,17 @@ </ol> + + + <footer role="contentinfo" id="page-footer"> - <ul> + <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>Contact: with <a href="https://savannah.nongnu.org/support/?func=additem&group=reproduce">this form</a>, or project PI (<a href="http://akhlaghi.org">Mohammad Akhlaghi</a>).</p></li> <li><p>Copyright © 2020 Maneage volunteers</p></li> - <li><p>All logos are copyrighted by the respective institutions</p></li> - </ul> + <li>This page is distributed under GNU General Public License (<a href="https://www.gnu.org/licenses/gpl-3.0.en.html">GPL</a>).</li> + </ul> </footer> </div> </body> diff --git a/img/maneage-file-structure.png b/img/maneage-file-structure.png Binary files differnew file mode 100644 index 0000000..24fa023 --- /dev/null +++ b/img/maneage-file-structure.png @@ -139,17 +139,20 @@ git branch -b my-fix</code></pre> <div id="logo-mext"><a href="https://www.mext.go.jp/en"><img src="./img/mext-compressed.svg"></a></div> </div> </section> - <footer role="contentinfo"> - <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</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 role="contentinfo" id="page-footer"> + <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> + <li><p>Contact: with <a href="https://savannah.nongnu.org/support/?func=additem&group=reproduce">this form</a>, or project PI (<a href="http://akhlaghi.org">Mohammad Akhlaghi</a>).</p></li> + <li><p>Copyright © 2020 Maneage volunteers</p></li> + <li>This page is distributed under GNU General Public License (<a href="https://www.gnu.org/licenses/gpl-3.0.en.html">GPL</a>).</li> + <li><p>All logos are copyrighted by the respective institutions</p></li> + </ul> </footer> </div> </body> diff --git a/tutorial.html b/tutorial.html index 1878ddd..2c6de32 100644 --- a/tutorial.html +++ b/tutorial.html @@ -682,33 +682,18 @@ The linear fitting is $y=a*x+b$, with the following parameters: $a=\afitparam$ a tutorial and now you are able to use <code>Maneage</code> for making your exciting research in a reproducible way!</p> - <footer role="contentinfo" id="page-footer"> - <h2>Copyright information</h2> - <p>This file is part of the reproducible paper template - <a href="http://savannah.nongnu.org/projects/reproduce">http://savannah.nongnu.org/projects/reproduce</a></p> - <p>This template 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>This template 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 Template. 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 role="contentinfo" id="page-footer"> + <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> + <li><p>Contact: with <a href="https://savannah.nongnu.org/support/?func=additem&group=reproduce">this form</a>, or project PI (<a href="http://akhlaghi.org">Mohammad Akhlaghi</a>).</p></li> + <li><p>Copyright © 2020 Maneage volunteers</p></li> + <li>This page is distributed under GNU General Public License (<a href="https://www.gnu.org/licenses/gpl-3.0.en.html">GPL</a>).</li> + </ul> </footer> </body> +</html> |
