Configuration¶
Configuration and customization of sphinx-gallery is done primarily with a
dictionary specified in your conf.py
file. A list of the possible
keys are listed below and explained in
greater detail in subsequent sections.
List of config options¶
Most sphinx-gallery configuration options are set in the Sphinx conf.py
file:
examples_dirs
andgallery_dirs
(Managing multiple galleries)filename_pattern
(Building examples matching a pattern)subsection_order
(Sorting gallery subsections)within_subsection_order
(Sorting gallery examples)reference_url
(Linking to documentation)backreferences_dir
anddoc_module
(Adding references to examples)default_thumb_file
(Using a custom default thumbnail)thumbnail_size
(Setting gallery thumbnail size)line_numbers
(Adding line numbers to examples)download_section_examples
(Disabling joint download of scripts)plot_gallery
(Building without executing examples)find_mayavi_figures
(Finding Mayavi figures)abort_on_example_error
(Abort build on first fail)expected_failing_examples
(Don’t fail the build on exit)min_reported_time
(Minimal reported time)
Some options can also be set or overridden on a file-by-file basis:
# sphinx_gallery_line_numbers
(Adding line numbers to examples)# sphinx_gallery_thumbnail_number
(Choosing the thumbnail image)
Some options can be set during the build execution step, e.g. using a Makefile:
make html-noplot
(Building without executing examples)make html_abort_on_example_error
(Abort build on first fail)
And some things can be tweaked directly in CSS:
.sphx-glr-thumbcontainer
(Setting gallery thumbnail size)
Managing multiple galleries¶
Sphinx-Gallery only supports up to sub-folder level in its gallery directories.
This might be a limitation for you. Or you might want to have separate
galleries for different purposes, an examples gallery and a tutorials gallery.
For this you use in your Sphinx conf.py
file a list of directories in
the sphinx configuration dictionary:
sphinx_gallery_conf = {
...
'examples_dirs': ['../examples', '../tutorials'],
'gallery_dirs': ['auto_examples', 'tutorials'],
}
Keep in mind that both lists have to be of the same length.
Building examples matching a pattern¶
By default, Sphinx-Gallery execute only examples beginning with plot
. However,
if this naming convention does not suit your project, you can modify this pattern
in your Sphinx conf.py
. For example:
sphinx_gallery_conf = {
...
'filename_pattern': '/plot_compute_',
}
will build all examples starting with plot_compute_
. The key filename_pattern
accepts
regular expressions which will be matched with the full path of the example. This is the reason
the leading '/'
is required. Users are advised to use os.sep
instead of '/'
if
they want to be agnostic to the operating system.
This option is also useful if you want to build only a subset of the examples. For example, you may want to build only one example so that you can link it in the documentation. In that case, you would do:
sphinx_gallery_conf = {
...
'filename_pattern': 'plot_awesome_example.py',
}
Here, one should escape the dot '\.'
as otherwise python regular expressions matches any character. Nevertheless, as
one is targeting a specific file, it is most certainly going to match the dot in the filename.
Similarly, to build only examples in a specific directory, you can do:
sphinx_gallery_conf = {
...
'filename_pattern': '/directory/plot_',
}
Alternatively, you can skip some examples. For example, to skip building examples
starting with plot_long_examples_
, you would do:
sphinx_gallery_conf = {
...
'filename_pattern': '/plot_(?!long_examples)',
}
As the patterns are parsed as regular expressions, users are advised to consult the regular expressions module for more details.
Sorting gallery subsections¶
Gallery subsections are sorted by default alphabetically by their folder name, and as such you can always organize them by changing your folder names. An alternative option is to use a sortkey to organize those subsections. We provide an explicit order sortkey where you have to define the order of all subfolders in your galleries:
from sphinx_gallery.sorting import ExplicitOrder
sphinx_gallery_conf = {
...
'examples_dirs': ['../examples','../tutorials'],
'subsection_order': ExplicitOrder(['../examples/sin_func',
'../examples/no_output',
'../tutorials/seaborn']),
}
Here we build 2 main galleries examples and tutorials, each of them
with subsections. To specify their order explicitly in the gallery we
import sphinx_gallery.sorting.ExplicitOrder
and initialize it with
the list of all subfolders with their paths relative to conf.py in the
order you prefer them to appear. Keep in mind that we use a single sort key
for all the galleries that are built, thus we include the prefix of each
gallery in the corresponding subsection folders. One does not define a
sortkey per gallery. You can use Linux paths, and if your documentation is
built in a Windows system, paths will be transformed to work accordingly,
the converse does not hold.
If you so desire you can implement your own sorting key. It will be provided the relative paths to conf.py of each sub gallery folder.
Sorting gallery examples¶
Within a given gallery (sub)section, the example files are ordered by
using the standard sorted()
function with the key
argument by default
set to
NumberOfCodeLinesSortKey(src_dir)
,
which sorts the files based on the number of code lines:
from sphinx_gallery.sorting import NumberOfCodeLinesSortKey
sphinx_gallery_conf = {
...
'within_subsection_order': NumberOfCodeLinesSortKey,
}
In addition, multiple convenience classes are provided for use with
within_subsection_order
:
sphinx_gallery.sorting.NumberOfCodeLinesSortKey
(default) to sort by the number of code lines.sphinx_gallery.sorting.FileSizeSortKey
to sort by file size.sphinx_gallery.sorting.FileNameSortKey
to sort by file name.sphinx_gallery.sorting.ExampleTitleSortKey
to sort by example title.
Linking to documentation¶
Sphinx-Gallery enables you to add hyperlinks in your example scripts so that you can link the used functions to their matching online documentation. As such code snippets within the gallery appear like this
y = np.sin(x)
Have a look at this in full action in our example Sphinx-Gallery introduction.
To make this work in your documentation you need to include to the configuration
dictionary within your Sphinx conf.py
file:
sphinx_gallery_conf = {
...
'reference_url': {
# The module you locally document uses None
'sphinx_gallery': None,
}
}
To link to external modules, if you use the Sphinx extension
sphinx.ext.intersphinx
, no additional changes are necessary,
as the intersphinx
inventory will automatically be used.
If you do not use intersphinx
, then you should add entries that
point to the directory containing searchindex.js
, such as
'matplotlib': 'https://matplotlib.org'
.
Adding references to examples¶
Sphinx-Gallery enables you, when documenting your modules, to
reference to the examples that use a particular function. For example
if we are documenting the numpy.exp()
function its possible to embed
a small gallery of examples that is specific to this function and
looks like this:
Examples using numpy.exp
¶
For such behavior to be available, you have to activate it in your
Sphinx-Gallery configuration conf.py
file with:
sphinx_gallery_conf = {
...
# directory where function granular galleries are stored
'backreferences_dir' : 'gen_modules/backreferences',
# Modules for which function level galleries are created. In
# this case sphinx_gallery and numpy in a tuple of strings.
'doc_module' : ('sphinx_gallery', 'numpy')}
The path you specify in backreferences_dir
, here we choose
gen_modules/backreferences
will get populated with
ReStructuredText files, each of which contains a reduced version of the
gallery specific to every function used across all the examples
galleries and belonging to the modules listed in doc_module
. Keep
in mind that the path set in backreferences_dir
is relative to the
conf.py
file.
Then within your sphinx documentation .rst
files you write these
lines to include this reduced version of the Gallery, which has
examples in use of a specific function, in this case numpy.exp
:
.. include:: gen_modules/backreferences/numpy.exp.examples
.. raw:: html
<div style='clear:both'></div>
The include
directive takes a path relative to the rst
file it is called from. In the case of this documentation file (which
is in the same directory as conf.py
) we directly use the path
declared in backreferences_dir
followed by the function whose
examples we want to show and the file has the .examples
extension.
Auto-documenting your API with links to examples¶
The previous feature can be automated for all your modules combining
it with the standard sphinx extensions autodoc and autosummary. First enable them in your
conf.py
extensions list:
import sphinx_gallery
extensions = [
...
'sphinx.ext.autodoc',
'sphinx.ext.autosummary',
'sphinx_gallery.gen_gallery',
]
# generate autosummary even if no references
autosummary_generate = True
autodoc and autosummary are very powerful
extensions please read about them. In this example we’ll explain how
the Sphinx-Gallery API Reference is automatically generated. The
documentation is done at the module level. We first start with the
reference.rst
file
.. _sphx_glr_api_reference:
Sphinx-Gallery API Reference
============================
The complete Sphinx-Gallery project is automatically documented for
every module.
.. currentmodule:: sphinx_gallery
.. automodule:: sphinx_gallery
:no-members:
:no-inherited-members:
:py:mod:`sphinx_gallery`:
.. autosummary::
:toctree: gen_modules/
:template: module.rst
gen_gallery
backreferences
gen_rst
py_source_parser
docs_resolv
notebook
downloads
docs_resolv
sorting
The important directives are currentmodule
where we specify which
module we are documenting, for our purpose is sphinx_gallery
. The
autosummary
directive is responsible for generating the rst
files documenting each module. autosummary
takes the option
toctree which is where the rst
files are saved and template
which is the file that describes how the module rst
documentation
file is to be constructed, finally we write the modules we wish to
document, in this case all modules of Sphinx-Gallery.
The template file module.rst
for the autosummary
directive has
to be saved in the path _templates/module.rst
. We present our
configuration in the following block. The most relevant part is the
loop defined between lines 12-22 that parses all the functions of
the module. There we have included the snippet introduced in the
previous section. Keep in mind that the include directive is
relative to the file location, and module documentation files are
saved in the directory we specified in the toctree option of the
autosummary
directive used before in the reference.rst
file.
The files we are including are from the backreferences_dir
configuration option setup for Sphinx-Gallery.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 | {{ fullname }}
{{ underline }}
.. automodule:: {{ fullname }}
{% block functions %}
{% if functions %}
Functions
---------
{% for item in functions %}
.. autofunction:: {{ item }}
.. include:: backreferences/{{fullname}}.{{item}}.examples
.. raw:: html
<div style='clear:both'></div>
{%- endfor %}
{% endif %}
{% endblock %}
{% block classes %}
{% if classes %}
Classes
-------
{% for item in classes %}
.. autoclass:: {{ item }}
:members:
{%- endfor %}
{% endif %}
{% endblock %}
{% block exceptions %}
{% if exceptions %}
Exceptions
----------
.. autosummary::
{% for item in exceptions %}
{{ item }}
{%- endfor %}
{% endif %}
{% endblock %}
|
Using a custom default thumbnail¶
In case you want to use your own image for the thumbnail of examples that do
not generate any plot, you can specify it by editing your Sphinx conf.py
file. You need to add to the configuration dictionary a key called
default_thumb_file. For example:
sphinx_gallery_conf = {
...
'default_thumb_file': 'path/to/thumb/file.png',
}
Adding line numbers to examples¶
Line numbers can be displayed in listings by adding the global line_numbers
setting:
sphinx_gallery_conf = {
...
'line_numbers': True,
}
or by adding a comment to the example script, which overrides any global setting:
# sphinx_gallery_line_numbers = True
Note that for Sphinx < 1.3, the line numbers will not be consistent with the original file.
Disabling joint download of scripts¶
By default Sphinx-Gallery prepares zip files of all python scripts and
all Jupyter notebooks for each gallery section and makes them
available for download at the end of each section. To disable this
behavior add to the configuration dictionary in your conf.py
file:
sphinx_gallery_conf = {
...
'download_section_examples': False,
}
Choosing the thumbnail image¶
For examples that generate multiple figures, the default behavior will use the first figure created in each as the thumbnail image displayed in the gallery. To change the thumbnail image to a figure generated later in an example script, add a comment to the example script to specify the number of the figure you would like to use as the thumbnail. For example, to use the 2nd figure created as the thumbnail:
# sphinx_gallery_thumbnail_number = 2
The default behavior is sphinx_gallery_thumbnail_number = 1
. See
Choosing the thumbnail figure for an example
of this functionality.
Building without executing examples¶
Sphinx-Gallery can parse all your examples and build the gallery
without executing any of the scripts. This is just for speed
visualization processes of the gallery and the size it takes your
website to display, or any use you can imagine for it. To achieve this you
need to pass the no plot option in the build process by modifying
your Makefile
with:
html-noplot:
$(SPHINXBUILD) -D plot_gallery=0 -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
@echo
@echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
Remember that for Makefile
white space is significant and the indentation are tabs
and not spaces.
Alternatively, you can add the plot_gallery
option to the
sphinx_gallery_conf
dictionary inside your conf.py
to have it as
a default:
sphinx_gallery_conf = {
...
'plot_gallery': False,
}
The highest precedence is always given to the -D flag of the
sphinx-build
command.
Finding Mayavi figures¶
By default, Sphinx-gallery will only look for matplotlib.pyplot
figures
when building. However, extracting figures generated by mayavi.mlab
is
also supported. To enable this feature, you can do:
sphinx_gallery_conf = {
...
'find_mayavi_figures': True,
}
Dealing with failing Gallery example scripts¶
As your project evolves some of your example scripts might stop executing properly. Sphinx-Gallery assist you in the discovery process of those bugged examples. The default behavior is to replace the thumbnail of those examples in the gallery with the broken thumbnail. That allows you to find with a quick glance of the gallery which examples failed. Broken examples remain accessible in the html view of the gallery and the traceback message is written for the failing code block. Refer to example Example that fails to execute to view the default behavior.
The build is also failed exiting with code 1 and giving you a summary of the failed examples with their respective traceback. This way you are aware of failing examples right after the build and can find them easily.
There are some additional options at your hand to deal with broken examples.
Abort build on first fail¶
Sphinx-Gallery provides the early fail option. In
this mode the gallery build process breaks as soon as an exception
occurs in the execution of the examples scripts. To activate this
behavior you need to pass a flag at the build process. It can be done
by including in your Makefile
:
html_abort_on_example_error:
$(SPHINXBUILD) -D abort_on_example_error=1 -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
@echo
@echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
Remember that for Makefile
white space is significant and the indentation are tabs
and not spaces.
Alternatively, you can add the abort_on_example_error
option to
the sphinx_gallery_conf
dictionary inside your conf.py
configuration file to have it as a default:
sphinx_gallery_conf = {
...
'abort_on_example_error': True,
}
The highest precedence is always given to the -D flag of
the sphinx-build
command.
Don’t fail the build on exit¶
It might be the case that you want to keep the gallery even with failed examples. Thus you can configure Sphinx-Gallery to allow certain examples to fail and still exit with a 0 exit code. For this you need to list all the examples you want to allow to fail during build. Change your conf.py accordingly:
sphinx_gallery_conf = {
...
'expected_failing_examples': ['../examples/plot_raise.py']
}
Here you list the examples you allow to fail during the build process, keep in mind to specify the full relative path from your conf.py to the example script.
Setting gallery thumbnail size¶
By default Sphinx-gallery will generate thumbnails at size (400, 280)
,
and add pillarboxes or letterboxes as necessary to scale the image while
maintaining the original aspect ratio. This size can be controlled with the
thumbnail_size
entry as, e.g.:
sphinx_gallery_conf = {
...
'thumbnail_size': (250, 250),
}
The gallery uses various CSS classes to display these thumbnails, which default to maximum 160x160px. To change this, e.g. to display the images at 250x250px, you can modify the default CSS with something like the following in your own site’s CSS file:
.sphx-glr-thumbcontainer {
min-height: 320px !important;
margin: 20px !important;
}
.sphx-glr-thumbcontainer .figure {
width: 250px !important;
}
.sphx-glr-thumbcontainer img {
max-height: 250px !important;
width: 250px !important;
}
.sphx-glr-thumbcontainer a.internal {
padding: 270px 10px 0 !important;
}
Minimal reported time¶
By default, Sphinx-gallery logs and embeds in the html output the time it took to run each script. If the majority of your examples runs quickly, you may not need this information.
The min_reported_time
configuration can be set to a number of seconds. The
duration of scripts that ran faster than that amount will not be logged nor
embedded in the html output.