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                        <h1>Maneage</h1><h2>Managing Data Lineage</h2>
                        <p>Copyright &copy; 2018-2020 Mohammad Akhlaghi <a href="&#109;&#x61;&#x69;&#x6C;&#x74;&#x6F;:&#x6D;&#111;&#104;&#97;&#x6D;&#109;a&#x64;&#64;&#x61;&#107;&#x68;&#x6C;&#x61;&#x67;&#104;&#x69;.&#x6F;&#x72;&#103;">&#x6D;&#111;&#104;&#97;&#x6D;&#109;a&#x64;&#64;&#x61;&#107;&#x68;&#x6C;&#x61;&#x67;&#104;&#x69;.&#x6F;&#x72;&#103;</a><br />
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		<hr />
		<p align="right">Next: <a href="about-tips.html">Tips for designing your project</a>, Previous: <a href="about-architecture.html">Maneage architecture</a>, Up: <a href="about.html">About</a> </p>

                <h2>Customization checklist</h2>

                <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>&gt;</code> (to write over the file),
                            the rest are <code>&gt;&gt;</code> (to append to it). If you want to avoid any other
                            set of files to be imported from Maneage into your project's branch,
                            you can follow a similar strategy. We recommend only doing it when you
                            encounter the same conflict in more than one merge and there is no
                            other change in that file. Also, don't add core Maneage Makefiles,
                            otherwise Maneage can break on the next run.</p>

                            <pre><code>echo "paper.tex merge=ours" &gt; .gitattributes
echo "tex/src/delete-me.mk merge=ours" &gt;&gt; .gitattributes
echo "tex/src/delete-me-demo.mk merge=ours" &gt;&gt; .gitattributes
echo "reproduce/analysis/make/delete-me.mk merge=ours" &gt;&gt; .gitattributes
echo "reproduce/software/config/TARGETS.conf merge=ours" &gt;&gt; .gitattributes
echo "reproduce/analysis/config/delete-me-num.conf merge=ours" &gt;&gt; .gitattributes
git add .gitattributes</code></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 &lt;existing@email.address&gt;
Copyright (C) 2020 YOUR NAME &lt;YOUR@EMAIL.ADDRESS&gt;</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>

		<p align="right">Next: <a href="about-tips.html">Tips for designing your project</a>, Previous: <a href="about-architecture.html">Maneage architecture</a>, Up: <a href="about.html">About</a> </p>





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                    <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>
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