SunPy Documentation Rules

Overview

All code must be documented and we follow these style conventions described here:

We recommend familiarizing yourself with these references.

Differences

The current differences we have are as follows:

We backtick each type in the documentation strings so that they are interlinked by our documentation builder:

"""
Parameters
----------
x : `type`
   Description of parameter x.
"""

SunPy-Specific Rules

  • For all RST files, we enforce a one sentence per line rule and ignore the line length.

  • Standards on docstring length and style are enforced using docformatter:

$ docformatter -r -i  --pre-summary-newline --make-summary-multi-line

Documenting Data Sources

Subclasses of GenericMap or TimeSeries must provide a detailed docstring providing an overview of the data source that the object represents. In order to maintain consistency and completeness, the following information must be provided by a data source docstring, if available, and preferably in the following order:

  • the name of the mission and instrument and the institution that built it

  • short description of the instrument (e.g. Cassegrain reflector, Wolter-1 grazing incidence x-ray, coronagraph) including the type of detector

  • description of the platform (e.g. satellite in 28 deg inclined orbit, a telescope on the summit of Mauna Kea in Hawaii)

  • description of the primary purpose or science goals of the instrument.

  • list of all wavelength(s) or passbands in appropriate units

  • description of the emission processes which dominate in those passbands

  • appropriate measurement properties such as field of view, angular resolution, time resolution

  • description of the operational concept (e.g. operates 24/7, observes from 7 am to 5 pm UT) including mention of unusual operations scenarios (e.g. calibration seasons, eclipse seasons)

  • the start and end of the data set

In addition, a reference section must be provided with links to the following resources, if available,

  • the mission web page

  • the instrument web page

  • relevant wikipedia page(s)

  • relevant user guide(s)

  • the mission paper and instrument paper

  • information to interpret metadata keywords such as FITS header reference

  • the data archive

An example docstring can be found in the Writing a new Instrument Map Class guide.

Sphinx

All of the SunPy documentation (like this page) is built by Sphinx, which is a tool especially well-suited for documenting Python projects. Sphinx works by parsing files written using a a Mediawiki-like syntax called reStructuredText. In addition to parsing static files of reStructuredText, Sphinx can also be told to parse code comments. In fact, in addition to what you are reading right now, the Python documentation was also created using Sphinx.

Usage

All of the SunPy documentation is contained in the “docs” folder and code documentation strings. The examples from the example gallery can be found in the “examples” folder.

In the root directory run:

$ tox -e build_docs

This will generate HTML documentation for SunPy in the “docs/_build/html” directory. You can open the “index.html” file to browse the final product. The gallery examples are located under “docs/_build/html/generated/gallery”. Sphinx builds documentation iteratively, only adding things that have changed.

If you want to build the documentation without building the gallery, i.e. to reduce build times while working on other sections of the documentation you can run:

$ tox -e build_docs -- -D plot_gallery=0

If you’d like to start from scratch (i.e., remove the tox cache) then run:

$ tox -e build_docs -- -aE

To build the documentation in your current python environment you must have all the dependencies specified in setup.cfg installed (pip install -e .[docs]). Then change to the docs/ directory and run:

$ make html

For more information on how to use Sphinx, consult the Sphinx documentation.

SunPy-Specific Additions

minigallery directive

Sphinx will automatically record which functions, classes, etc. are used in each gallery example. In the documentation, you can insert a mini-gallery of the subset of the gallery examples that uses a particular function, class, etc. For example, the following RST block:

.. minigallery:: sunpy.coordinates.RotatedSunFrame

produces this mini-gallery:

If you want to specify more than one object, separate them by spaces. This is particularly useful if you need to cover multiple namespaces in which an object may be accessed, e.g.:

.. minigallery:: sunpy.coordinates.RotatedSunFrame sunpy.coordinates.metaframes.RotatedSunFrame

generate directive

In rare circumstances, one may want to insert “raw” HTML directly into the pages written by Sphinx. For HTML that is statically available (i.e., already written in some form), one can use the “raw” directive. For HTML that is generated by Python code, SunPy provides the custom directive generate. Here’s an example RST block:

.. generate:: html
    :html_border:

    import os
    from sunpy.data.sample import file_dict
    print("<table>")
    for key, value in file_dict.items():
        print(f"<tr><th>{key}</th><td>{os.path.basename(value)}</td></tr>")
    print("</table>")

to insert the following HTML table:

GBM_TIMESERIESglg_cspec_n5_110607_v00.pha
AIA_193_CUTOUT03_IMAGEAIA20110607_064555_0193_cutout.fits
HMI_LOS_IMAGEHMI20110607_063211_los_lowres.fits
AIA_193_IMAGEAIA20110607_063307_0193_lowres.fits
CALLISTO_SPECTRUMBIR_20110607_062400_10.fit
AIA_131_IMAGEAIA20110607_063301_0131_lowres.fits
RHESSI_TIMESERIEShsi_obssumm_20110607_025.fits
AIA_193_CUTOUT01_IMAGEAIA20110607_063307_0193_cutout.fits
LYRA_LEVEL3_TIMESERIESlyra_20110607-000000_lev3_std.fits
AIA_193_CUTOUT05_IMAGEAIA20110607_065843_0193_cutout.fits
AIA_171_IMAGEAIA20110607_063302_0171_lowres.fits
GOES_XRS_TIMESERIESgo1520110607.fits
AIA_1600_IMAGEAIA20110607_063305_1600_lowres.fits
NORH_TIMESERIEStca110607.fits
AIA_211_IMAGEAIA20110607_063302_0211_lowres.fits
AIA_094_IMAGEAIA20110607_063305_0094_lowres.fits
AIA_193_CUTOUT04_IMAGEAIA20110607_065219_0193_cutout.fits
EIT_195_IMAGEeit_l1_20110607_203753.fits
AIA_193_CUTOUT02_IMAGEAIA20110607_063931_0193_cutout.fits
AIA_171_ROLL_IMAGEaiacalibim5.fits.gz
RHESSI_IMAGEhsi_image_20110607_063300.fits
SWAP_LEVEL1_IMAGEswap_lv1_20110607_063329.fits
AIA_335_IMAGEAIA20110607_063303_0335_lowres.fits
EVE_TIMESERIES20110607_EVE_L0CS_DIODES_1m.txt

Troubleshooting

Sphinx can be very particular about formatting, and the warnings and errors aren’t always obvious.

Below are some commonly-encountered warning/error messages along with a human-readable translation:

WARNING: Duplicate explicit target name: “xxx”.

If you reference the same URL, etc more than once in the same document sphinx will complain. To avoid, use double-underscores instead of single ones after the URL.

ERROR: Malformed table. Column span alignment problem at line offset n

Make sure there is a space before and after each colon in your class and function docs (e.g. attribute : type, instead of attribute: type). Also, for some sections (e.g. Attributes) numpydoc seems to complain when a description spans more than one line, particularly if it is the first attribute listed.

WARNING: Block quote ends without a blank line; unexpected unindent.

Lists should be indented one level from their parents.

ERROR: Unknown target name: “xxx”

In addition to legitimate errors of this type, this error will also occur when variables have a trailing underscore, e.g., xxx_.

WARNING: Explicit markup ends without a blank line; unexpected unindent.

This usually occurs when the text following a directive is wrapped to the next line without properly indenting a multi-line text block.

WARNING: toctree references unknown document ‘…’ / WARNING: toctree contains reference to nonexisting document

This pair of errors is due to the way numpydoc scrapes class members.