Documentation How To#
Documentation building#
Generating the HTML docs for Gammapy is straight-forward:
make docs-sphinx
make docs-show
Or one can equivalently use tox:
tox -e build_docs
Generating the PDF docs is more complex. This should work:
# build the latex file
cd docs
python -m sphinx . _build/latex -b latex -j auto
# first generation of pdf file
cd _build/latex
pdflatex -interaction=nonstopmode gammapy.tex
# final generation of pdf file
pdflatex -interaction=nonstopmode gammapy.tex
# clean the git repo
git reset --hard
# open the pdf file
open gammapy.pdf
You need a bunch or LaTeX stuff, specifically texlive-fonts-extra is needed.
Check Python code#
Code in RST files#
Most of the documentation of Gammapy is present in RST files that are converted into HTML pages using
Sphinx during the build documentation process. You may include snippets of Python code in these RST files
within blocks labelled with .. code-block:: python Sphinx directive. However, this code could not be
tested, and it will not be possible to know if it fails in following versions of Gammapy. That’s why we
recommend using the .. testcode:: directive to enclose code that will be tested against the results
present in a block labelled with .. testoutput:: directive. If not .. testoutput:: directive is provided,
only execution tests will be performed.
For example, we could check that the code below does not fail, since it does not provide any output.
.. testcode::
from gammapy.astro import source
from gammapy.astro import population
from gammapy.astro import darkmatter
On the contrary, we could check the execution of the following code as well as the output values produced.
.. testcode::
from astropy.time import Time
time = Time(['1999-01-01T00:00:00.123456789', '2010-01-01T00:00:00'])
print(time.mjd)
.. testoutput::
[51179.00000143 55197. ]
In order to perform tests of these snippets of code present in RST files, you may run the following command.
pytest --doctest-glob="*.rst" docs/
Code in docstrings in Python files#
It is also advisable to add code snippets within the docstrings of the classes and functions present in Python files. These snippets show how to use the function or class that is documented, and are written in the docstrings using the following syntax.
Examples
--------
>>> from astropy.units import Quantity
>>> from gammapy.data import EventList
>>> event_list = EventList.read('events.fits') # doctest: +SKIP
In the case above, we could check the execution of the first two lines importing the Quantity and EventList
modules, whilst the third line will be skipped. On the contrary, in the example below we could check the execution of
the code as well as the output value produced.
Examples
--------
>>> from regions import Regions
>>> regions = Regions.parse("galactic;circle(10,20,3)", format="ds9")
>>> print(regions[0])
Region: CircleSkyRegion
center: <SkyCoord (Galactic): (l, b) in deg
(10., 20.)>
radius: 3.0 deg
To allow the code block to be placed correctly over multiple lines utilise the “…”:
Examples
--------
>>> from gammapy.maps import WcsGeom, MapAxis
>>> energy_axis_true = MapAxis.from_energy_bounds(
... 0.5, 20, 10, unit="TeV", name="energy_true"
... )
For a larger code block it is also possible to utilise the following syntax.
Examples
--------
.. testcode::
from gammapy.maps import MapAxis
from gammapy.irf import EnergyDispersion2D
filename = '$GAMMAPY_DATA/hess-dl3-dr1/data/hess_dl3_dr1_obs_id_020136.fits.gz'
edisp2d = EnergyDispersion2D.read(filename, hdu="EDISP")
In order to perform tests of these snippets of code present in the docstrings of the Python files, you may run the following command.
pytest --doctest-modules --ignore-glob=*/tests gammapy
If you get a zsh error try using putting to ignore block inside quotes
pytest --doctest-modules "--ignore-glob=*/tests" gammapy
It is also important to check that you have correctly formatted your docstring. An easy way to check this is with the following for your specific file, i.e.:
pydocstyle gammapy/data/event_list.py
Sphinx gallery extension#
The documentation built-in process uses the sphinx-gallery
extension to build galleries of illustrated examples on how to use Gammapy (i.e.
Model gallery). The Python scripts used to produce the model gallery are placed in
examples/models and examples/tutorials. The configuration of the sphinx-gallery module is done in docs/conf.py.
The tutorials are order using a python dictionary stored in docs/sphinxext.py.
Choose a thumbnail and tooltip for the tutorial gallery#
The Gammapy Tutorials are Python scripts in the Sphinx Gallery format. They are displayed as a gallery with picture thumbnails and tooltips. You can choose the thumbnail for the tutorial by adding a comment before the plot:
# The next line sets the thumbnail for the second figure in the gallery
# (plot with negative exponential in orange)
# sphinx_gallery_thumbnail_number = 2
plt.figure()
plt.plot(x, -np.exp(-x), color='orange', linewidth=4)
plt.xlabel('$x$')
plt.ylabel(r'$-\exp(-x)$')
# To avoid matplotlib text output
plt.show()
The example is taken from the sphinx-gallery documentation, please refer to it for more details.
The tooltip is the text that appears when you hover over the thumbnail. It is taken from the first line of the docstring of the tutorial. You can change it by editing the docstring. See e.g. Analysis 1 Tutorial.
Dealing with links#
Links in tutorials are just handled via normal RST syntax.
Links to other tutorials#
From docstrings and RST documentation files in Gammapy you can link to other tutorials and gallery examples by using RST syntax like this:
:doc:`/tutorials/starting/analysis_2`
This will link to the tutorial Low level API from the tutorial base folder. The file suffix will be automatically inferred by Sphinx.
Links to documentation#
To make a reference to a heading within an RST file, first you need to define an explicit target for the heading:
.. _datasets:
Datasets (DL4)
==============
The reference is the rendered as datasets.
To link to this in the documentation you can use:
:ref:`datasets`
API Links#
Links to Gammapy API are handled via normal Sphinx syntax in comments:
# Create an `~gammapy.analysis.AnalysisConfig` object and edit it to
# define the analysis configuration:
config = AnalysisConfig()
This will resolve to a link to the AnalysisConfig class in the API documentation.
Check broken links#
To check for broken external links you can use tox:
tox -e linkcheck
Include png files as images#
In the RST files#
Gammapy has a gp-image directive to include an image from $GAMMAPY_DATA/figures/,
use the gp-image directive instead of the usual Sphinx image directive like this:
.. gp-image:: detect/fermi_ts_image.png
:scale: 100%
More info on the image directive.
Documentation guidelines#
Like almost all Python projects, the Gammapy documentation is written in a format called restructured text (RST) and built using Sphinx. We mostly follow the Astropy documentation guidelines, which are based on the Numpy docstring standard, which is what most scientific Python packages use.
There’s a few details that are not easy to figure out by browsing the Numpy or Astropy documentation guidelines, or that we actually do differently in Gammapy. These are listed here so that Gammapy developers have a reference.
Usually the quickest way to figure out how something should be done is to browse the Astropy or Gammapy code a bit (either locally with your editor or online on GitHub or via the HTML docs), or search the Numpy or Astropy documentation guidelines mentioned above. If that doesn’t quickly turn up something useful, please ask by putting a comment on the issue or pull request you’re working on GitHub, or email the Gammapy mailing list.
Correct format for bullet point list#
To correctly add a bullet point list to the docstring, the following can be implemented:
"""
Docstring explanation.
Parameters
----------
parameter_name : parameter_type
Description of the parameter with entries:
* option1 : description1
* option2 : description2
* option3 : description3 over more than
one line.
"""
Functions or class methods that return a single object#
For functions or class methods that return a single object, following the
Numpy docstring standard and adding a Returns section usually means
that you duplicate the one-line description and repeat the function name as
return variable name.
See w or sidereal_time
as examples in the Astropy codebase. Here’s a simple example:
def circle_area(radius):
"""Circle area.
Parameters
----------
radius : `~astropy.units.Quantity`
Circle radius
Returns
-------
area : `~astropy.units.Quantity`
Circle area
"""
return 3.14 * (radius ** 2)
In these cases, the following shorter format omitting the Returns section is recommended:
def circle_area(radius):
"""Circle area (`~astropy.units.Quantity`).
Parameters
----------
radius : `~astropy.units.Quantity`
Circle radius
"""
return 3.14 * (radius ** 2)
Usually the parameter description doesn’t fit on the one line, so it’s recommended to always keep this in the Parameters section.
A common case where the short format is appropriate are class properties,
because they always return a single object.
As an example see radec, which is reproduced here:
@property
def radec(self):
"""Event RA / DEC sky coordinates (`~astropy.coordinates.SkyCoord`)."""
lon, lat = self['RA'], self['DEC']
return SkyCoord(lon, lat, unit='deg', frame='icrs')
Class attributes#
Class attributes (data members) and properties are currently a bit of a mess. Attributes are listed in an Attributes section because I’ve listed them in a class-level docstring attributes section as recommended here. Properties are listed in separate Attributes summary and Attributes Documentation sections, which is confusing to users (“what’s the difference between attributes and properties?”).
One solution is to always use properties, but that can get very verbose if we have to write so many getters and setters. We could start using descriptors.
TODO: make a decision on this and describe the issue / solution here.