Developing PETSc Documentation

General Guidelines

  • Good documentation should be like a bonsai tree: alive, on display, frequently tended, and as small as possible (adapted from these best practices).

  • Wrong, irrelevant, or confusing documentation is worse than no documentation.

Documentation with Sphinx

Sphinx is a well-documented and widely-used set of Python-based tools for building documentation. Most content is written using reStructuredText, a simple markup language.

We use Sphinx to coordinate building the documentation for our web page, as well as a PDF of the Users Manual. To create this PDF, you must have a working LaTeX installation.

These slides contain an overview of Sphinx and how we use(d) it, as of October, 2020.

The documentation build with Sphinx involves configuring a minimal build of PETSc and building some of the classic docs.

Building the HTML docs locally

We suggest using a Python 3 virtual environment.

> cd $PETSC_DIR
> python3 -m venv petsc-doc-env
> . petsc-doc-env/bin/activate
> pip install -r doc/requirements.txt
> cd doc
> make html  # may take several minutes

Then open _build/html/index.html with your browser.

Notes:

  • The above assumes that python3 is Python 3.3 or later. Check with python3 --version.

  • You may need to install a package like python3-venv.

Sphinx Documentation Guidelines

  • Use the .. code-block:: directive instead of the .. code:: directive for any example code that is not included literally using .. literalinclude::. See below for more details on .. literalinclude.

  • Any invocable command line statements longer than a few words should be in .. code-block:: sections. Any such statements not in code-block statements must be enclosed by double backticks “``”. For example make all is acceptable but

    > make PETSC_DIR=/my/path/to/petsc PETSC_ARCH=my-petsc-arch all
    

    should be in a block.

  • All code blocks showing invocation of command line must use the “console” block directive. E.g.

    .. code-block:: console
    
       > cd $PETSC_DIR/src/snes/interface
       > ./someprog
       output1
       output2
    

    The only exception of this is when displaying raw output, i.e. with no preceding commands. Then one may use just the “::” directive to improve visibility E.g.

    ::
    
       output1
       output2
    

    which renders as

    output1
    output2
    

    Notice that now “output1” and “output2” are not greyed out as previously.

  • Any code blocks that show command line invocations must be preceded by the “>” character. E.g.

    .. code-block:: console
    
       > ./configure --some-args
       > make libs
       > make ./ex1
       > ./ex1 --some-args
    
  • All environment variables such as $PETSC_DIR or $PATH must be preceded by the “$” character and be enclosed in double backticks “``”. E.g.

    Lorem ipsum dolor sit ``$PETSC_DIR``, consectetur adipiscing ``$PETSC_ARCH``...
    
  • When referring to configuration of PETSc, specifically the $PETSC_DIR/configure script in plain text (not code blocks), it should always be lower-case, enclosed in double backticks “``” and not include “./”. E.g.

    Lorem ipsum dolor sit ``configure``, consectetur adipiscing elit...
    
  • If using internal section links to to jump to other places within the documentation, use explicit labels and namespace them appropriately. Do not use autosectionlabel extension, and do not use implicit links. E.g.

    .. _doc_mydoc:
    
    ======================
    Start Document Heading
    ======================
    
    .. _doc_mydoc_internalheadline:
    
    Internal Headline
    =================
    

    And in some other file

    .. _tut_mytutorial:
    
    ======================
    Start Tutorial Heading
    ======================
    
    A link- :ref:`my link name <doc_mydoc_internalheadline>`
    
  • Use the literalinclude directive to directly include pieces of source code, as in the following example. Note that an “absolute” path has been used, which means relative to the root for the Sphinx docs (where conf.py is found).

    .. literalinclude:: /../src/sys/error/err.c
       :start-at: PetscErrorCode PetscError(
       :end-at: PetscFunctionReturn(0)
       :append: }
    

    For robustness to changes in the source files, Use :start-at: and related options when possible, noting that you can also use (positive) values of :lines: relative to this. For languages other than C, use the :language: option to appropriately highlight.

  • We use the sphinxcontrib-bibtex extension to include citations from BibTeX files. You must include .. bibliography:: blocks at the bottom of a page including citations (example). To cite the same reference in more than one page, use this workaround on one of them (example) 1.

  • Do not check in large images (or PDFs), more than a few KB, since they will be downloaded every time the repository is cloned. When possible, please use SVG for images. SVG is web-friendly and will be automatically converted to PDF using rsvg-convert (installable with your package manager, e.g., librsvg2-bin on Debian/Ubuntu systems).

  • Prefer formatting styles that are easy to modify and maintain. In particular, use of list-table is recommended.

  • When using external links with inline URLs, prefer to use anonymous hyperlink references with two trailing underscores, e.g.

    `link text <https://external.org>`__
    
  • Use restraint in adding new Sphinx extensions, in particular those which aren’t widely-used and well-supported, or those with hidden system dependencies.

Building Classic Documentation

Some of the documentation is built by a “classic” process as described below.

The documentation tools listed below can be automatically downloaded and installed by configure.

Note: Sowing and c2html have additional dependencies like gcc, g++, and flex and do not use compilers specified to PETSc configure. [Windows users please install the corresponding cygwin packages]

> make alldoc LOC=${PETSC_DIR}

To get a quick preview of manual pages from a single source directory (mainly to debug the manual page syntax):

> cd $PETSC_DIR/src/snes/interface
> make LOC=$PETSC_DIR manualpages_buildcite
> browse $PETSC_DIR/docs/manualpages/SNES/SNESCreate.html  # or suitable command to open the HTML page in a browser

Footnotes

1

The extensions’s development branch supports our use case better (:footcite:), which can be investigated if a release is ever made.