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<section class="tex2jax_ignore mathjax_ignore" id="developing-petsc-documentation">
<h1>Developing PETSc Documentation<a class="headerlink" href="#developing-petsc-documentation" title="Link to this heading">#</a></h1>
<div class="toctree-wrapper compound">
</div>
<section id="general-guidelines">
<h2>General Guidelines<a class="headerlink" href="#general-guidelines" title="Link to this heading">#</a></h2>
<ul class="simple">
<li><p>Good documentation should be like a bonsai tree: alive, on display, frequently tended, and as small as possible (adapted from <a class="reference external" href="https://github.com/google/styleguide/blob/gh-pages/docguide/best_practices.md">these best practices</a>).</p></li>
<li><p>Wrong, irrelevant, or confusing documentation is worse than no documentation.</p></li>
</ul>
</section>
<section id="documentation-with-sphinx">
<span id="sphinx-documentation"></span><h2>Documentation with Sphinx<a class="headerlink" href="#documentation-with-sphinx" title="Link to this heading">#</a></h2>
<p>We use <a class="reference external" href="https://www.sphinx-doc.org/en/master/">Sphinx</a> to build our web pages and documentation. Most content is written using <a class="reference external" href="https://www.sphinx-doc.org/en/master/usage/restructuredtext/basics.html">reStructuredText</a>, a simple markup language.</p>
<p><a class="reference external" href="https://gitlab.com/psanan/petsc-sphinx-slides">These slides</a> contain an overview of Sphinx and how we use(d) it, as of October 2020.</p>
<section id="building-the-html-docs-locally">
<span id="sec-local-html-docs"></span><h3>Building the HTML docs locally<a class="headerlink" href="#building-the-html-docs-locally" title="Link to this heading">#</a></h3>
<p>We use a <a class="reference external" href="https://docs.python.org/3/tutorial/venv.html">Python 3 virtual environment</a> to build the documentation since not all developers can trivially install the needed Python modules directly.</p>
<div class="highlight-console notranslate"><div class="highlight"><pre><span></span><span class="gp">$ </span><span class="nb">cd</span><span class="w"> </span><span class="nv">$PETSC_DIR</span>
<span class="gp">$ </span>make<span class="w"> </span>docs
<span class="gp">$ </span>open<span class="w"> </span>doc/_build/html/index.html<span class="w"> </span><span class="c1"># in a browser</span>
</pre></div>
</div>
<p>or</p>
<div class="highlight-console notranslate"><div class="highlight"><pre><span></span><span class="gp">$ </span><span class="nb">cd</span><span class="w"> </span><span class="nv">$PETSC_DIR</span>/doc
<span class="gp">$ </span>make<span class="w"> </span>sphinxhtml
<span class="gp">$ </span>open<span class="w"> </span>_build/html/index.html
</pre></div>
</div>
</section>
<section id="building-the-manual-locally-as-a-pdf-via-latex">
<span id="sec-local-docs-latex"></span><h3>Building the manual locally as a PDF via LaTeX<a class="headerlink" href="#building-the-manual-locally-as-a-pdf-via-latex" title="Link to this heading">#</a></h3>
<div class="admonition-note admonition">
<p class="admonition-title">Note</p>
<p>Before following these instructions, you need to have a working
local LaTeX installation and the ability to install additional packages,
if need be, to resolve LaTeX errors.</p>
</div>
<p>Set up your local Python environment (e.g., ref:<code class="docutils notranslate"><span class="pre">as</span> <span class="pre">above</span> <span class="pre"><sec_local_html_docs></span></code>), then</p>
<div class="highlight-console notranslate"><div class="highlight"><pre><span></span><span class="gp">$ </span><span class="nb">cd</span><span class="w"> </span>doc
<span class="gp">$ </span>make<span class="w"> </span>sphinxpdf
<span class="gp">$ </span>open<span class="w"> </span>_build/latex/manual.pdf<span class="w"> </span><span class="c1"># in PDF viewer</span>
</pre></div>
</div>
</section>
<section id="sphinx-documentation-guidelines">
<span id="sphinx-guidelines"></span><h3>Sphinx Documentation Guidelines<a class="headerlink" href="#sphinx-documentation-guidelines" title="Link to this heading">#</a></h3>
<p>Refer to Sphinx’s <a class="reference external" href="https://https://www.sphinx-doc.org">own documentation</a> for general information on how to use Sphinx, and note the following additional guidelines.</p>
<ul>
<li><p>Use the <a class="reference external" href="https://www.sphinx-doc.org/en/master/usage/restructuredtext/directives.html#directive-literalinclude">literalinclude directive</a> to directly include pieces of source code. Use a path beginning with <code class="docutils notranslate"><span class="pre">/</span></code>, relative to the root for the Sphinx docs (where <code class="docutils notranslate"><span class="pre">conf.py</span></code> is found).</p>
<div class="highlight-rst notranslate"><div class="highlight"><pre><span></span><span class="p">..</span> <span class="ow">literalinclude</span><span class="p">::</span> /../src/sys/error/err.c
<span class="nc">:start-at:</span> <a href="../manualpages/Sys/PetscErrorCode.html">PetscErrorCode</a> <a href="../manualpages/Sys/PetscError.html">PetscError</a>(
<span class="nc">:end-at:</span> <a href="../manualpages/Sys/PetscFunctionReturn.html">PetscFunctionReturn</a>(<a href="../manualpages/Sys/PetscErrorCode.html">PETSC_SUCCESS</a>)
<span class="nc">:append:</span> }
</pre></div>
</div>
<p>For robustness to changes in the source files, Use <code class="docutils notranslate"><span class="pre">:start-at:</span></code> and related options when possible, noting that you can also use (positive) values of <code class="docutils notranslate"><span class="pre">:lines:</span></code> relative to this. Use the <code class="docutils notranslate"><span class="pre">:language:</span></code> option to appropriately highlight languages other than C.</p>
</li>
<li><p>Any invocable command line statements longer than a few words should be in
<code class="docutils notranslate"><span class="pre">..</span> <span class="pre">code-block::</span></code> sections. Double backticks must enclose any such statements not in code-block statements”``”. For example <code class="docutils notranslate"><span class="pre">make</span> <span class="pre">all</span></code> is acceptable but</p>
<div class="highlight-console notranslate"><div class="highlight"><pre><span></span><span class="gp">$ </span>make<span class="w"> </span><span class="nv">PETSC_DIR</span><span class="o">=</span>/my/path/to/petsc<span class="w"> </span><span class="nv">PETSC_ARCH</span><span class="o">=</span>my-petsc-arch<span class="w"> </span>all
</pre></div>
</div>
<p>should be in a <code class="docutils notranslate"><span class="pre">..</span> <span class="pre">code-block::</span></code>.</p>
</li>
<li><p>All code blocks showing command line invocation must use the “console” block
directive. E.g.</p>
<div class="highlight-rst notranslate"><div class="highlight"><pre><span></span><span class="p">..</span> <span class="ow">code-block</span><span class="p">::</span> <span class="k">console</span>
<span class="gp">$ </span><span class="nb">cd</span><span class="w"> </span><span class="nv">$PETSC_DIR</span>/src/snes/interface
<span class="gp">$ </span>./someprog
<span class="go">output1</span>
<span class="go">output2</span>
</pre></div>
</div>
<p>The only exception to this is when displaying raw output, i.e., with no preceding
commands. Then one may use just the “::” directive to improve visibility, e.g.,</p>
<div class="highlight-rst notranslate"><div class="highlight"><pre><span></span><span class="se">::</span>
<span class="s"> output1</span>
<span class="s"> output2</span>
</pre></div>
</div>
</li>
<li><p>Any code blocks that show command line invocations must be preceded by <code class="docutils notranslate"><span class="pre">$</span></code>, e.g.</p>
<div class="highlight-rst notranslate"><div class="highlight"><pre><span></span><span class="p">..</span> <span class="ow">code-block</span><span class="p">::</span> <span class="k">console</span>
<span class="gp">$ </span>./configure<span class="w"> </span>--some-args
<span class="gp">$ </span>make<span class="w"> </span>libs
<span class="gp">$ </span>make<span class="w"> </span>./ex1
<span class="gp">$ </span>./ex1<span class="w"> </span>--some-args
</pre></div>
</div>
</li>
<li><p>Environment variables such as <code class="docutils notranslate"><span class="pre">$PETSC_DIR</span></code> or <code class="docutils notranslate"><span class="pre">$PATH</span></code> must be preceded by
<code class="docutils notranslate"><span class="pre">$</span></code> and be enclosed in double backticks, e.g.</p>
<div class="highlight-rst notranslate"><div class="highlight"><pre><span></span>Set <span class="s">``$PETSC_DIR``</span> and <span class="s">``$PETSC_ARCH``</span>
</pre></div>
</div>
</li>
<li><p>For internal links, use explicit labels, e.g</p>
<div class="highlight-rst notranslate"><div class="highlight"><pre><span></span><span class="p">..</span> <span class="nt">_sec_short_name:</span>
<span class="gh">Section name</span>
<span class="gh">============</span>
</pre></div>
</div>
<p>and elsewhere (in any document),</p>
<div class="highlight-rst notranslate"><div class="highlight"><pre><span></span>See <span class="na">:ref:</span><span class="nv">`link text <sec_short_name>`</span>
</pre></div>
</div>
</li>
<li><p>For internal links in the manual with targets outside the manual, always provide alt text
so that the text will be properly formatted in the <a class="reference internal" href="#sec-local-docs-latex"><span class="std std-ref">standalone PDF manual</span></a>, e.g.</p>
<blockquote>
<div><div class="highlight-rst notranslate"><div class="highlight"><pre><span></span>PETSc has <span class="na">:doc:</span><span class="nv">`mailing lists </community/mailing>`</span>.
</pre></div>
</div>
</div></blockquote>
</li>
<li><p>We use the <a class="reference external" href="https://sphinxcontrib-bibtex.readthedocs.io/en/latest/">sphinxcontrib-bibtex extension</a>
to include citations from BibTeX files.
You must include <code class="docutils notranslate"><span class="pre">..</span> <span class="pre">bibliography::</span></code> blocks at the bottom of a page, including citations (<a class="reference external" href="https://gitlab.com/petsc/petsc/-/raw/main/doc/manual/ksp.rst">example</a>).
To cite the same reference on more than one page, use <a class="reference external" href="https://sphinxcontrib-bibtex.readthedocs.io/en/latest/usage.html#key-prefixing">this workaround</a> on one of them (<a class="reference external" href="https://gitlab.com/petsc/petsc/-/raw/main/doc/developers/articles.rst">example</a>) <a class="footnote-reference brackets" href="#bibtex-footnote" id="id1" role="doc-noteref"><span class="fn-bracket">[</span>1<span class="fn-bracket">]</span></a>.</p></li>
<li><p>See special instructions on <a class="reference internal" href="#docs-images"><span class="std std-ref">Images</span></a>.</p></li>
<li><p>Prefer formatting styles that are easy to modify and maintain. In particular, the use of <a class="reference external" href="https://docutils.sourceforge.io/docs/ref/rst/directives.html#list-table">list-table</a> is recommended.</p></li>
<li><p>When using external links with inline URLs, prefer to use <a class="reference external" href="https://docutils.sourceforge.io/docs/ref/rst/restructuredtext.html#anonymous-hyperlinks">anonymous hyperlink references</a> with two trailing underscores, e.g.</p>
<div class="highlight-rst notranslate"><div class="highlight"><pre><span></span><span class="s">`link text </span><span class="si"><https://external.org></span><span class="s">`__</span>
</pre></div>
</div>
</li>
<li><p>To pluralize something with inline markup, e.g. <code class="docutils notranslate"><span class="pre"><a href="../manualpages/DM/DM.html">DM</a></span></code>s, escape the trailing character to avoid <code class="docutils notranslate"><span class="pre">WARNING:</span> <span class="pre">Inline</span> <span class="pre">literal</span> <span class="pre">start-string</span> <span class="pre">without</span> <span class="pre">end-string</span></code>.</p>
<div class="highlight-rst notranslate"><div class="highlight"><pre><span></span><span class="s">``<a href="../manualpages/DM/DM.html">DM</a>``\s</span>
</pre></div>
</div>
</li>
<li><p>Use restraint in adding new Sphinx extensions, in particular, those which aren’t
widely used and well-supported, or those with hidden system dependencies.</p></li>
</ul>
</section>
</section>
<section id="other-petsc-repositories">
<span id="petsc-repositories"></span><h2>Other PETSc repositories<a class="headerlink" href="#other-petsc-repositories" title="Link to this heading">#</a></h2>
<p>In addition to the <a class="reference external" href="https://gitlab.com/petsc/petsc">PETSc repository</a>, there are three other PETSc repositories which contain large data
files that are unnecessary for most PETSc usages and thus are not stored in the main repository.</p>
<ul class="simple">
<li><p><a class="reference external" href="https://gitlab.com/petsc/images">Images</a> contains images that are used in the PETSc documentation or have other uses. See <a class="reference internal" href="#docs-images"><span class="std std-ref">Images</span></a>
for details on its use.</p></li>
<li><p><a class="reference external" href="https://gitlab.com/petsc/annual-meetings">Annual-Meetings</a> contains various documents from the <a class="reference internal" href="../community/meetings/meeting.html#meetings"><span class="std std-ref">PETSc Annual User Meetings</span></a>. See <a class="reference internal" href="#docs-meetings"><span class="std std-ref">Annual meetings website</span></a>.</p></li>
<li><p><a class="reference external" href="https://gitlab.com/petsc/datafiles">Datafiles</a> contains large matrices, meshes, and various other data files that
are used in the <a class="reference internal" href="testing.html#test-harness-data"><span class="std std-ref">PETSc CI</span></a>.</p></li>
<li><p>[Tutorials]((https://gitlab.com/petsc/annual-meetings) contains slides from <a class="reference internal" href="../tutorials/in_person.html#tutorials"><span class="std std-ref">In-Person Tutorials</span></a>. See <a class="reference internal" href="#docs-tutorials"><span class="std std-ref">Tutorials website</span></a>.</p></li>
</ul>
<p>Other repositories containing software PETSc uses are located at <a class="reference external" href="https://gitlab.com/petsc/">GitLab</a>
and <a class="reference external" href="https://bitbucket.org/petsc/workspace/repositories">BitBucket</a>. The BitBucket location is used for historical reasons,
there are many links on the web to these locations thus the repositories have not been migrated to GitLab.</p>
</section>
<section id="images">
<span id="docs-images"></span><h2>Images<a class="headerlink" href="#images" title="Link to this heading">#</a></h2>
<p>PETSc’s documentation is tightly coupled to the source code and tests and
is tracked in the primary PETSc Git repository. However, image files are
too large to track directly this way (especially because they persist in the integration branches’ histories). Thus we do not put images
into the PETSc git repository.</p>
<p>Therefore, we store image files in a separate Git repository, <a class="reference external" href="https://gitlab.com/petsc/petsc">Images</a>. This repository is automatically cloned
(if not already available) and updated when building the documentation. It can also be cloned by running
<code class="docutils notranslate"><span class="pre">make</span> <span class="pre">images</span></code> in the <code class="docutils notranslate"><span class="pre">doc/</span></code> directory.
Any new images required must be added to the currently-used branch of this repository.</p>
<section id="image-guidelines">
<h3>Image Guidelines<a class="headerlink" href="#image-guidelines" title="Link to this heading">#</a></h3>
<ul class="simple">
<li><p>Whenever possible, use SVG files. SVG is a web-friendly vector format and will be automatically converted to PDF using <code class="docutils notranslate"><span class="pre">rsvg-convert</span></code> <a class="footnote-reference brackets" href="#svg-footnote" id="id2" role="doc-noteref"><span class="fn-bracket">[</span>2<span class="fn-bracket">]</span></a></p></li>
<li><p>Avoid large files and large numbers of images.</p></li>
<li><p>Do not add movies or other non-image files.</p></li>
</ul>
</section>
<section id="adding-new-images">
<h3>Adding new images<a class="headerlink" href="#adding-new-images" title="Link to this heading">#</a></h3>
<ul class="simple">
<li><p>Decide where in <code class="docutils notranslate"><span class="pre">doc/images</span></code> a new image should go. Use the structure of the <code class="docutils notranslate"><span class="pre">doc/</span></code> tree as a guide.</p></li>
<li><p>Create a Merge Request to the currently-used branch of the upstream images repository, adding this image <a class="footnote-reference brackets" href="#maintainer-fast-image-footnote" id="id3" role="doc-noteref"><span class="fn-bracket">[</span>3<span class="fn-bracket">]</span></a>.</p></li>
<li><p>Once this Merge Request is merged, you may make a MR on the main PETSc Git repository relying on the new image(s).</p></li>
</ul>
<p>It may be helpful to place working copies of the new image(s) in your local <code class="docutils notranslate"><span class="pre">doc/images</span></code>
while iterating on documentation; don’t forget to update the upstream images repository.</p>
</section>
<section id="removing-renaming-moving-or-updating-images">
<h3>Removing, renaming, moving, or updating images<a class="headerlink" href="#removing-renaming-moving-or-updating-images" title="Link to this heading">#</a></h3>
<p>Do not directly move, rename, or update images in the images repository.
Simply add a logically-numbered new version of the image.</p>
<p>If an image is not used in <em>any</em> <a class="reference internal" href="contributing/developingmr.html#sec-integration-branches"><span class="std std-ref">integration branch</span></a> (<code class="docutils notranslate"><span class="pre">main</span></code> or <code class="docutils notranslate"><span class="pre">release</span></code>),
add it to the top-level list of files to delete in the images repository.</p>
</section>
<section id="cleaning-up-the-images-repository-maintainers-only">
<span id="docs-images-cleanup"></span><h3>Cleaning up the images repository (maintainers only)<a class="headerlink" href="#cleaning-up-the-images-repository-maintainers-only" title="Link to this heading">#</a></h3>
<p>If the size of the image repository grows too large,</p>
<ul class="simple">
<li><p>Create a new branch <code class="docutils notranslate"><span class="pre">main-X</span></code>, where <code class="docutils notranslate"><span class="pre">X</span></code> increments the current value</p></li>
<li><p>Create a new commit deleting all files in the to-delete list and clearing the list</p></li>
<li><p>Reset the new <code class="docutils notranslate"><span class="pre">main-X</span></code> to a single commit with this new, cleaned-up state</p></li>
<li><p>Set <code class="docutils notranslate"><span class="pre">main-X</span></code> as the “default” branch on GitLab.</p></li>
<li><p>Update both <code class="docutils notranslate"><span class="pre">release</span></code> and <code class="docutils notranslate"><span class="pre">main</span></code> in the primary PETSc repository to clone this new branch</p></li>
</ul>
</section>
</section>
<section id="annual-meetings-website">
<span id="docs-meetings"></span><h2>Annual meetings website<a class="headerlink" href="#annual-meetings-website" title="Link to this heading">#</a></h2>
<p>Like <a class="reference internal" href="#docs-images"><span class="std std-ref">Images</span></a> the material (slides, etc.) for the PETSc annual meetings is too large to store in the primary PETSc Git repository.
It is stored in <a class="reference external" href="https://gitlab.com/petsc/annual-meetings">Annual-Meetings</a> repository and linked from <a class="reference internal" href="../community/meetings/meeting.html#meetings"><span class="std std-ref">PETSc Annual User Meetings</span></a>.</p>
<p>The files are all in the public directory of the repository so that the <code class="docutils notranslate"><span class="pre">.gitlab-ci.yml</span></code> file for the repository
automatically displays all the files at https://petsc.gitlab.io/annual-meetings. Thus, all one needs to do is add files into
<a class="reference external" href="https://gitlab.com/petsc/annual-meetings">Annual-Meetings</a> and provide appropriate links within that repository or from <a class="reference internal" href="../community/meetings/meeting.html#meetings"><span class="std std-ref">PETSc Annual User Meetings</span></a>
in the primary PETSc Git repository.</p>
</section>
<section id="tutorials-website">
<span id="docs-tutorials"></span><h2>Tutorials website<a class="headerlink" href="#tutorials-website" title="Link to this heading">#</a></h2>
<p>Like <a class="reference internal" href="#docs-meetings"><span class="std std-ref">Annual meetings website</span></a> the material (slides, etc.) for the PETSc tutorials is too large to store in the primary PETSc Git repository.
It is stored in <a class="reference external" href="https://gitlab.com/petsc/tutorials">Tutorials</a> repository and linked from <a class="reference internal" href="../tutorials/in_person.html#tutorials"><span class="std std-ref">In-Person Tutorials</span></a>.</p>
<p>The files are all in the public directory of the repository so that the <code class="docutils notranslate"><span class="pre">.gitlab-ci.yml</span></code> file for the repository
automatically displays all the files at https://petsc.gitlab.io/tutorials. Thus, all one needs to do is add files into
<a class="reference external" href="https://gitlab.com/petsc/tutorials">Tutorials</a> and provide appropriate links within that repository or from <a class="reference internal" href="../tutorials/in_person.html#tutorials"><span class="std std-ref">In-Person Tutorials</span></a>
in the primary PETSc Git repository.</p>
</section>
<section id="building-manual-pages-and-c2html-files">
<span id="manpages-c2html-build"></span><h2>Building Manual Pages and C2HTML Files<a class="headerlink" href="#building-manual-pages-and-c2html-files" title="Link to this heading">#</a></h2>
<p>The manual pages and C2HTML-generated file as built in a process described below using the documentation tools listed below, which are
automatically downloaded and installed if needed while building the PETSc documentation./</p>
<ul class="simple">
<li><p><a class="reference external" href="https://bitbucket.org/petsc/pkg-sowing">Sowing</a>: Developed by Bill Gropp, this produces the PETSc manual pages; see the <a class="reference external" href="http://wgropp.cs.illinois.edu/projects/software/sowing/doctext/doctext.htm">Sowing documentation</a> and <a class="reference internal" href="style.html#manual-page-format"><span class="std std-ref">Manual Page Format</span></a>.</p></li>
<li><p><a class="reference external" href="https://gitlab.com/petsc/pkg-c2html">C2html</a>: This generates the HTML versions of all the source code.</p></li>
</ul>
<p>Sowing and C2html are build tools that do not use the compilers specified to PETSc’s <code class="docutils notranslate"><span class="pre">configure</span></code>, as they
need to work in cross-compilation environments. Thus, they default to using <code class="docutils notranslate"><span class="pre">gcc</span></code>, <code class="docutils notranslate"><span class="pre">g++</span></code>, and <code class="docutils notranslate"><span class="pre">flex</span></code> from
the user’s environment (or <code class="docutils notranslate"><span class="pre">configure</span></code> options like <code class="docutils notranslate"><span class="pre">--download-sowing-cxx</span></code>). Microsoft Windows users must install <code class="docutils notranslate"><span class="pre">gcc</span></code>
etc., from Cygwin in order to be able to build the documentation.</p>
<p class="rubric">Footnotes</p>
</section>
</section>
<hr class="footnotes docutils" />
<aside class="footnote-list brackets">
<aside class="footnote brackets" id="bibtex-footnote" role="doc-footnote">
<span class="label"><span class="fn-bracket">[</span><a role="doc-backlink" href="#id1">1</a><span class="fn-bracket">]</span></span>
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