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
(Manage multiple galleries)filename_pattern
andignore_pattern
(Parsing and executing examples via matching patterns)subsection_order
(Sorting gallery subsections)within_subsection_order
(Sorting gallery examples)reference_url
(Add intersphinx links to your examples)backreferences_dir
,doc_module
, andinspect_global_variables
(Add mini-galleries for API documentation)default_thumb_file
(Using a custom default thumbnail)thumbnail_size
(Setting gallery thumbnail size)line_numbers
(Adding line numbers to examples)remove_config_comments
(Removing config comments)download_all_examples
(Disabling download button of all scripts)plot_gallery
(Building without executing examples)image_scrapers
(and the deprecatedfind_mayavi_figures
) (Image scrapers)compress_images
(Compressing images)reset_modules
(Resetting modules)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)show_memory
(Showing memory consumption)binder
(Generate Binder links for gallery notebooks (experimental))first_notebook_cell
andlast_notebook_cell
(Add your own first and last notebook cell)junit
(Using JUnit XML files)log_level
(Setting log level)capture_repr
andignore_repr_types
(Controlling what output is captured)
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)# sphinx_gallery_thumbnail_path
(Providing a figure for the thumbnail image)
See also Removing config comments to hide these comments from the rendered examples.
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)
You can also use the package warnings
in the conf.py
file to prevent
warnings from being captured and included in your built documentation. For
example, to remove the specific Matplotlib agg warning, you can add:
import warnings
warnings.filterwarnings("ignore", category=UserWarning,
message='Matplotlib is currently using agg, which is a'
' non-GUI backend, so cannot show the figure.')
to your conf.py
file.
Manage 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.
Note
If your examples take a long time to run, consider looking at the execution times file that is generated for each gallery dir (as long as any examples were actually executed in that directory during the build).
Parsing and executing examples via matching patterns¶
By default, Sphinx-Gallery will parse and add all files with a .py
extension to the gallery, but only execute files beginning with plot_
.
These behaviors are controlled by the ignore_pattern
and filename_pattern
entries, which have the default values:
sphinx_gallery_conf = {
...
'filename_pattern': '/plot_',
'ignore_pattern': r'__init__\.py',
}
To omit some files from the gallery entirely (i.e., not execute, parse, or
add them), you can change the ignore_pattern
option.
To choose which of the parsed and added Python scripts are actually
executed, you can modify filename_pattern
. For example:
sphinx_gallery_conf = {
...
'filename_pattern': '/plot_compute_',
}
will build all examples starting with plot_compute_
. The key
filename_pattern
(and ignore_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 re.escape(os.sep)
instead of '/'
if they want to be agnostic to the operating system.
The filename_pattern
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': r'plot_awesome_example\.py',
}
Here, one should escape the dot r'\.'
as otherwise python regular expressions matches any character. Nevertheless, as
one is targeting a specific file, it would match the dot in the filename even without this escape character.
Note
Sphinx-gallery only re-runs examples that have changed (according to their
md5 hash). You can delete the associated MD5 files (e.g.,
./auto_examples/plot_awesome_example.py.md5
) to force a rebuild if
you have not changed the example itself between subsequent sphinx
calls.
Similarly, to build only examples in a specific directory, you can do:
sphinx_gallery_conf = {
...
'filename_pattern': '/directory/plot_',
}
Alternatively, you can skip executing 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.
Note
Remember that Sphinx allows overriding conf.py
values from the command
line, so you can for example build a single example directly via something like:
$ sphinx-build -D sphinx_gallery_conf.filename_pattern=plot_specific_example\.py ...
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.
Warning
If you create your own class for 'subsection_order'
, ensure
that the __str__
of your class is stable across runs.
Sphinx determines if the build environment has changed
(and thus if all documents should be rewritten)
by examining the config values using
md5(str(obj).encode()).hexdigest()
in
sphinx/builders/html.py
. Default class instances
in Python have their memory address in their __repr__
which
will in general change for each build. For ExplicitOrder
for example, this is fixed via:
def __repr__(self):
return '<%s: %s>' % (self.__class__.__name__, self.ordered_list)
Thus the files are only all rebuilt if the specified ordered list is changed.
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.
Add intersphinx links to your examples¶
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 Introductory example - Plotting sin.
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'
.
Add mini-galleries for API documentation¶
When documenting a given function/class, Sphinx-Gallery enables you to link to any examples that either:
Use the function/instantiate the class in the code.
Refer to that function/class using sphinx markup
:func:
/:class:
in a documentation block.
The former is useful for auto-documenting functions that are used and classes
that are explicitly instantiated. The latter is useful for classes that are
typically implicitly returned rather than explicitly instantiated (e.g.,
matplotlib.axes.Axes
which is most often instantiated only indirectly
within function calls).
For example, we can embed a small gallery of all examples that use or
refer to numpy.exp
, which 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/class granular galleries are stored
'backreferences_dir' : 'gen_modules/backreferences',
# Modules for which function/class 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 be populated with
ReStructuredText files. Each .rst file will contain a reduced version of the
gallery specific to every function/class that is used across all the examples
and belonging to the modules listed in doc_module
.
backreferences_dir
should be a string or pathlib.Path
object that is
relative to the conf.py
file, or None
. It is None
by default.
Within your sphinx documentation .rst
files, you can use easily
add this reduced version of the Gallery. For example, the rst below adds
the reduced version of the Gallery for numpy.exp
, which includes all
examples that use the specific function numpy.exp
:
.. minigallery:: numpy.exp
:add-heading:
The add-heading
option adds a heading for the mini-gallery, which will be a
default generated message if no string is provided as an argument. The example
mini-gallery shown above uses the default heading. The level of the heading
defaults to ^
, but can be changed using the heading-level
option, which
accepts a single character (e.g., -
).
You can also list multiple items, separated by spaces, which will merge all examples into a single mini-gallery, e.g.:
.. minigallery:: numpy.exp numpy.sin
:add-heading: Mini-gallery using ``numpy.exp`` or ``numpy.sin``
:heading-level: -
For such a mini-gallery, specifying a custom heading message is recommended because the default message is vague: “Examples of one of multiple objects”.
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
scrapers
py_source_parser
docs_resolv
notebook
downloads
sorting
binder
directives
.. currentmodule:: sphinx_gallery.utils
.. automodule:: sphinx_gallery.utils
:no-members:
:no-inherited-members:
:py:mod:`sphinx_gallery.utils`:
.. autosummary::
:toctree: gen_modules/
:template: module.rst
optipng
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 12-21 that parses all the functions/classes
of the module. There we have used the minigallery
directive introduced in
the previous section.
We also add a cross referencing label (on line 16) before including the
examples mini-gallery. This enables you to reference the mini-gallery for
all functions/classes of the module using
:ref:`sphx_glr_backref_<fun/class>`
, where ‘<fun/class>’ is the full path
to the function/class using dot notation (e.g.,
sphinx_gallery.backreferences.identify_names
). For example, see:
Examples using sphinx_gallery.backreferences.identify_names.
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 52 53 54 55 | {{ fullname }}
{{ underline }}
.. automodule:: {{ fullname }}
{% block functions %}
{% if functions %}
Functions
---------
{% for item in functions %}
.. autofunction:: {{ item }}
.. _sphx_glr_backref_{{fullname}}.{{item}}:
.. minigallery:: {{fullname}}.{{item}}
:add-heading:
{%- endfor %}
{% endif %}
{% endblock %}
{% block classes %}
{% if classes %}
Classes
-------
{% for item in classes %}
.. autoclass:: {{ item }}
:members:
.. _sphx_glr_backref_{{fullname}}.{{item}}:
.. minigallery:: {{fullname}}.{{item}}
:add-heading:
{%- endfor %}
{% endif %}
{% endblock %}
{% block exceptions %}
{% if exceptions %}
Exceptions
----------
.. autosummary::
{% for item in exceptions %}
{{ item }}
{%- endfor %}
{% endif %}
{% endblock %}
|
Toggling global variable inspection¶
By default, Sphinx-gallery will inspect global variables (and code objects) at the end of each code block to try to find classes of variables and method calls. It also tries to find methods called on classes. For example, this code:
lst = [1, 2]
fig, ax = plt.subplots()
ax.plot(lst)
should end up with the following links (assuming intersphinx is set up properly):
However, this feature might not work properly in all instances. Moreover, if variable names get reused in the same script to refer to different classes, it will break.
To disable this global variable introspection, you can use the configuration key:
sphinx_gallery_conf = {
...
'inspect_global_variables' : False,
}
Stylizing code links using CSS¶
Each link in the code blocks will be decorated with two or three CSS classes.
sphx-glr-backref-module-*
CSS class named after the module where the object is documented.
*
represents the module, e.g.,sphx-glr-backref-module-matplotlib-figure
.
sphx-glr-backref-type-*
CSS class named after the type of the object, where
*
represents the object type. This is a sanitized intersphinx type, e.g., apy:class
will have the CSS classsphx-glr-backref-type-py-class
.
sphx-glr-backref-instance
The third ‘optional’ class that is added only if the object is an instance of a class (rather than, e.g., a class itself, method, or function). By default, Sphinx-Gallery adds the following CSS in
gallery.css
:a.sphx-glr-backref-instance { text-decoration: none; }
This is done to reduce the visual impact of instance linking in example code. This means that for the following code:
x = Figure()
x
, an instance of a class, will have thesphx-glr-backref-instance
CSS class, and will not be decorated.Figure
however, is a class, so will not have thesphx-glr-backref-instance
CSS class, and will thus be decorated the standard way for links in the given parent styles.
These three CSS classes are meant to give fine-grained control over how
different links are decorated. For example, using CSS selectors you could
choose to avoid highlighting any sphx-glr-backref-*
links except for ones
that you whitelist (e.g., those from your own module). For example, the
following css prevents any module except for matplotlib from being decorated:
a[class^="sphx-glr-backref-module-"] {
text-decoration: none;
}
a[class^="sphx-glr-backref-module-matplotlib"] {
text-decoration: underline;
}
There are likely elements other than text-decoration
that might be worth
setting, as well.
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
Removing config comments¶
Some configurations can be done on a file-by-file basis by adding a special
comment with the pattern # sphinx_gallery_config = value
to the
example source files. By default, the source files are parsed as is and thus
the comment will appear in the example.
To remove the comment from the rendered example set the option:
sphinx_gallery_conf = {
...
'remove_config_comments': True,
}
This only removes configuration comments from code blocks, not from text blocks. However, note that technically, configuration comments will work when put in either code blocks or text blocks.
Add your own first and last notebook cell¶
Sphinx-Gallery allows you to add your own first and/or last cell to every
generated notebook. Adding a first cell can be useful for including code that
is required to run properly in the notebook, but not in a .py
file. By
default, the following first cell is added to each notebook:
.. code-block:: ipython
%matplotlib inline
Adding a last cell can be useful for performing a desired action such as reporting on the user’s environment. By default no last cell is added.
You can choose whatever text you like by modifying the first_notebook_cell
and last_notebook_cell
configuration parameters. For example, the gallery
of this documentation adds the following first cell:
.. code-block:: ipython
# This cell is added by sphinx-gallery # It can be customized to whatever you like %matplotlib inline
Which is achieved by the following configuration:
sphinx_gallery_conf = {
...
'first_notebook_cell': ("# This cell is added by sphinx-gallery\n"
"# It can be customized to whatever you like\n"
"%matplotlib inline")
}
A last cell may be added similarly by setting the last_notebook_cell
parameter:
sphinx_gallery_conf = {
...
'first_notebook_cell': ("# This cell is added by sphinx-gallery\n"
"# It can be customized to whatever you like\n"
"%matplotlib inline"),
'last_notebook_cell': "# This is the last cell",
}
If the value of first_notebook_cell
or last_notebook_cell
is set to
None
, then no extra first or last cell will be added to the notebook.
Using JUnit XML files¶
Sphinx-Gallery can create a JUnit XML file of your example run times,
successes, and failures. To create a file named e.g. junit-result.xml
in the /build
output directory, set the configuration key (path is relative
to the HTML output directory):
sphinx_gallery_conf = {
...
'junit': '../test-results/sphinx-gallery/junit.xml',
}
By default, JUnit XML file generation is disabled (by setting 'junit': ''
).
JUnit XML files are useful for example on CircleCI builds, where you can add
a line like this to get a summary of your example run times in the CircleCI GUI
(which will parse the file path
doc/_build/test-results/sphinx-gallery/junit.xml
and infer the tests
came from sphinx-gallery
based on the nested subdirectory name):
- store_test_results:
path: doc/_build/test-results
- store_artifacts:
path: doc/_build/test-results
For more information on CircleCI integration, peruse the related CircleCI doc and blog post.
Setting log level¶
Sphinx-Gallery logs output at several stages. Warnings can be generated for
code that requires case sensitivity (e.g., plt.subplot
and plt.Subplot
)
when building docs on a filesystem that does not support case sensitive
naming (e.g., Windows). In this case, by default a logger.warning
is
emitted, which will lead to a build failure when buidling with -W
.
The log level can be set with:
sphinx_gallery_conf = {
...
'log_level': {'backreference_missing': 'warning'},
}
The only valid key currently is backreference_missing
.
The valid values are 'debug'
, 'info'
, 'warning'
, and 'error'
.
Disabling download button of all scripts¶
By default Sphinx-Gallery collects all python scripts and all Jupyter
notebooks from each gallery into zip files which are made available for
download at the bottom of each gallery. To disable this behavior add to the
configuration dictionary in your conf.py
file:
sphinx_gallery_conf = {
...
'download_all_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.
Providing a figure for the thumbnail image¶
An arbitrary image can be provided to serve as a thumbnail image. To provide a
figure for the thumbnail image, add a comment to the example script to specify
the path to the figure you would like to use as the thumbnail. For example, the
following defines that the figure demo.png
in the folder _static/
should be used to create the thumbnail:
# sphinx_gallery_thumbnail_path = ``_static/demo.png``
Note that sphinx_gallery_thumbnail_number
overrules
sphinx_gallery_thumbnail_path
. See
Providing a figure for the thumbnail image for an example of
this functionality.
Generate Binder links for gallery notebooks (experimental)¶
Sphinx-Gallery automatically generates Jupyter notebooks for any examples built with the gallery. Binder makes it possible to create interactive GitHub repositories that connect to cloud resources.
If you host your documentation on a GitHub repository, it is possible to auto-generate a Binder link for each notebook. Clicking this link will take users to a live version of the Jupyter notebook where they may run the code interactively. For more information see the Binder documentation.
Warning
Binder is still beta technology, so there may be instability in the experience of users who click Binder links.
In order to enable Binder links with Sphinx-Gallery, you must specify
a few pieces of information in conf.py
. These are given as a nested
dictionary following the pattern below:
sphinx_gallery_conf = {
...
'binder': {
# Required keys
'org': '<github_org>',
'repo': '<github_repo>',
'branch': '<github_branch>', # Can be any branch, tag, or commit hash. Use a branch that hosts your docs.
'binderhub_url': '<binder_url>', # Any URL of a binderhub deployment. Must be full URL (e.g. https://mybinder.org).
'dependencies': '<list_of_paths_to_dependency_files>',
# Optional keys
'filepath_prefix': '<prefix>' # A prefix to prepend to any filepaths in Binder links.
'notebooks_dir': '<notebooks-directory-name>' # Jupyter notebooks for Binder will be copied to this directory (relative to built documentation root).
'use_jupyter_lab': <bool> # Whether Binder links should start Jupyter Lab instead of the Jupyter Notebook interface.
}
}
If a Sphinx-Gallery configuration for Binder is discovered, the following extra things will happen:
The dependency files specified in
dependencies
will be copied to abinder/
folder in your built documentation.The built Jupyter Notebooks from the documentation will be copied to a folder called
<notebooks_dir/>
at the root of your built documentation (they will follow the same folder hierarchy within the notebooks directory folder.The rST output of each Sphinx-Gallery example will now have a
launch binder
button in it.That button will point to a binder link with the following structure
<binderhub_url>/v2/gh/<org>/<repo>/<ref>?filepath=<filepath_prefix>/<notebooks_dir>/path/to/notebook.ipynb
Below is a more complete explanation of each field.
- org (type: string)
The GitHub organization where your documentation is stored.
- repo (type: string)
The GitHub repository where your documentation is stored.
- ref (type: string)
A reference to the version of your repository where your documentation exists. For example, if your built documentation is stored on a
gh-pages
branch, then this field should be set togh-pages
.- binderhub_url (type: string)
The full URL to a BinderHub deployment where you want your examples to run. One public BinderHub deployment is at
https://mybinder.org
, though if you (and your users) have access to another, this can be configured with this field.- dependencies (type: list)
A list of paths (relative to
conf.py
) to dependency files that Binder uses to infer the environment needed to run your examples. For example, arequirements.txt
file. These will be copied into a folder calledbinder/
in your built documentation folder. For a list of all the possible dependency files you can use, see the Binder configuration documentation.- filepath_prefix (type: string | None, default:
None
) A prefix to append to the filepath in the Binder links. You should use this if you will store your built documentation in a sub-folder of a repository, instead of in the root.
- notebooks_dir (type: string, default:
notebooks
) The name of a folder where the built Jupyter notebooks will be copied. This ensures that all the notebooks are in one place (though they retain their folder hierarchy) in case you’d like users to browse multiple notebook examples in one session.
- use_jupyter_lab (type: bool, default:
False
) Whether the default interface activated by the Binder link will be for Jupyter Lab or the classic Jupyter Notebook interface.
Each generated Jupyter Notebook will be copied to the folder
specified in notebooks_dir
. This will be a subfolder of the sphinx output
directory and included with your site build.
Binder links will point to these notebooks.
Note
It is not currently possible to host notebooks generated by Sphinx-Gallery with readthedocs.org, as RTD does not provide you with a GitHub repository you could link Binder to. If you’d like to use readthedocs with Sphinx-Gallery and Binder links, you should independently build your documentation and host it on a GitHub branch as well as building it with readthedocs.
See the Sphinx-Gallery Sphinx configuration file for an example that uses the public Binder server.
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) $(SOURCEDIR) $(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.
Compressing images¶
When writing PNG files (the default scraper format), sphinx-gallery can be
configured to use optipng
to optimize the PNG file sizes. Typically this
yields roughly a 50% reduction in file sizes, thus reducing the loading time
of galleries. However, it can increase build
time. The allowed values are 'images'
and 'thumbnails'
, or a
tuple/list (to optimize both), such as:
sphinx_gallery_conf = {
...
'compress_images': ('images', 'thumbnails'),
}
The default is ()
(no optimization) and a warning will be emitted if
optimization is requested but optipng
is not available. You can also pass
additional command-line options (starting with '-'
), for example to
optimize less but speed up the build time you could do:
sphinx_gallery_conf = {
...
'compress_images': ('images', 'thumbnails', '-o1'),
}
See $ optipng --help
for a complete list of options.
Image scrapers¶
Image scrapers are plugins that allow Sphinx-gallery to detect images produced
during execution of your examples, and then embed them into documentation.
Scrapers can be activated by appending scraper names to the
'image_scrapers'
tuple in your Sphinx-gallery configuration. For example,
to scrape both matplotlib and Mayavi images you can do:
sphinx_gallery_conf = {
...
'image_scrapers': ('matplotlib', 'mayavi'),
}
The default value is 'image_scrapers': ('matplotlib',)
which only scrapes
Matplotlib images. Note that this includes any images produced by packages that
are based on Matplotlib, for example Seaborn or Yellowbrick. If you want
to embed matplotlib.animation.FuncAnimation
s as animations rather
than a single static image of the animation figure, you should add:
sphinx_gallery_conf = {
...
'matplotlib_animations': True,
}
HTML embedding options can be changed by setting rcParams['animation.html']
and related options in your
matplotlib rcParams.
It’s also recommended to ensure that “imagemagick” is available as a
writer
, which you can check with
matplotlib.animation.ImageMagickWriter.isAvailable()
.
The FFmpeg writer in some light testing did not work as well for
creating GIF thumbnails for the gallery pages.
The following scrapers are supported:
- matplotlib
Sphinx-gallery maintains a scraper for
matplotlib
figures via the string'matplotlib'
.
- Mayavi
Sphinx-gallery maintains a scraper for mayavi.mlab figures via the string
'mayavi'
.
- PyVista
PyVista maintains a scraper (for PyVista >= 0.20.3) enabled by the string
'pyvista'
.
- PyGMT
See their website for more information on how to integrate with Sphinx-Gallery.
It is possible to write custom scrapers for images generated by packages outside of those listed above. This is accomplished by writing your own Python function to define how to detect and retrieve images produced by an arbitrary package. For instructions, see Write a custom image scraper. If you come up with an implementation that would be useful for general use (e.g., a custom scraper for a plotting library) feel free to add it to the list above (see discussion here)!
Resetting modules¶
Often you wish to “reset” the behavior of your visualization packages in order to ensure that any changes made to plotting behavior in one example do not propagate to the other examples.
By default, before each example file executes, Sphinx-gallery will
reset matplotlib
(by using matplotlib.pyplot.rcdefaults()
) and seaborn
(by trying to unload the module from sys.modules
). This is equivalent to the
following configuration:
sphinx_gallery_conf = {
...
'reset_modules': ('matplotlib', 'seaborn'),
}
Currently, Sphinx-gallery natively supports resetting matplotlib
and
seaborn
. However, you can also add your own custom function to
this tuple in order to define resetting behavior for other visualization libraries.
To do so, follow the instructions in Define resetting behavior (e.g., for custom libraries).
Dealing with failing Gallery example scripts¶
As your project evolves some of your example scripts might stop executing properly. Sphinx-gallery will 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.
Note
If an example is expected to fail, sphinx-gallery will error if the example runs without error.
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
parameter 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.
Showing memory consumption¶
Sphinx-Gallery can use memory_profiler
, if installed, to report the peak
memory during the run of an example. After installing memory_profiler
,
you can do:
sphinx_gallery_conf = {
...
'show_memory': True,
}
It’s also possible to use your own custom memory reporter, for example
if you would rather see the GPU memory. In that case, show_memory
must
be a callable that takes a single function to call (i.e., one generated
internally to run an individual script code block), and returns a two-element
tuple containing:
The memory used in MiB while running the function, and
The function output
A version of this that would always report 0 memory used would be:
sphinx_gallery_conf = {
...
'show_memory': lambda func: (0., func()),
}
Controlling what output is captured¶
Note
Configure capture_repr
to be an empty tuple (i.e., capture_repr: ())
to return to the output capturing behaviour prior to release v0.5.0.
The capture_repr
configuration allows the user to control what output
is captured, while executing the example .py
files, and subsequently
incorporated into the built documentation. Data directed to standard output
is always captured. The value of the last statement of each code block, if
it is an expression, can also be captured. This can be done by providing
the name of the ‘representation’ method to be captured in the capture_repr
tuple, in order of preference. The representation methods currently supported
are:
__repr__
- returns the official string representation of an object. This is what is returned when your Python shell evaluates an expression.__str__
- returns a string containing a nicely printable representation of an object. This is what is used when youprint()
an object or pass it toformat()
._repr_html_
- returns a HTML version of the object. This method is only present in some objects, for example, pandas dataframes.
The default setting is:
sphinx_gallery_conf = {
...
'capture_repr': ('_repr_html_', '__repr__'),
}
With the default setting Sphinx-Gallery would first attempt to capture the
_repr_html_
of the last statement of a code block, if it is an
expression. If this method does not exist for the expression, the second
‘representation’ method in the tuple, __repr__
, would be captured. If the
__repr__
also does not exist (unlikely for non-user defined objects),
nothing would be captured. Data directed to standard output is always
captured.
To capture only data directed to standard output, configure 'capture_repr'
to be an empty tuple: 'capture_repr': ()
. This will imitate the behaviour
of Sphinx-Gallery prior to v0.5.0.
From another perspective, take for example the following code block:
print('Hello world')
a=2
a # this is an expression
'Hello world'
would be captured for every capture_repr
setting as this
is directed to standard output. Further,
if
capture_repr
is an empty tuple, nothing else would be captured.if
capture_repr
is('__repr__')
,2
would also be captured.if
capture_repr
is('_repr_html_', '__repr__')
(the default) Sphinx-Gallery would first attempt to capture_repr_html_
. Since this does not exist fora
, it will then attempt to capture__repr__
. The__repr__
method does exist fora
, thus2
would be also captured in this case.
Matplotlib note: if the 'capture_repr'
tuple includes '__repr__'
and/or '__str__'
, code blocks which have a Matplotlib function call as the
last expression will generally produce a yellow output box in the built
documentation, as well as the figure. This is because matplotlib function calls
usually return something as well as creating/amending the plot in standard
output. For example, matplotlib.plot()
returns a list of Line2D
objects
representing the plotted data. This list has a __repr__
and a __str__
method which would thus be captured. You can prevent this by:
assigning the (last) plotting function to a temporary variable. For example:
import matplotlib.pyplot as plt _ = plt.plot([1, 2, 3, 4], [1, 4, 9, 16])
add
plt.show()
(which does not return anything) to the end of your code block. For example:import matplotlib.pyplot as plt plt.plot([1, 2, 3, 4], [1, 4, 9, 16]) plt.show()
The unwanted string output will not occur if 'capture_repr'
is an empty
tuple or does not contain __repr__
or __str__
.
Prevent capture of certain classes¶
If you wish to capture a representation of the last expression of each code
blocks unless the last expression is of a certain type, you can use
'ignore_repr_types'
. 'ignore_repr_types'
is by default an empty raw
string (r''
), meaning no types are ignored. To exclude specific type(s)
from being captured, 'ignore_repr_types'
can be set to a regular
expression matching the name(s) of the type(s) to be excluded.
For example, the configuration below would capture the __repr__
of the
last expression of each code block unless the name of the type()
of the last
expression includes the string ‘matplotlib.text’ or ‘matplotlib.axes’.
This would prevent capturing of all subclasses of ‘matplotlib.text’, e.g.
expressions of type ‘matplotlib.text.Annotation’, ‘matplotlib.text.OffsetFrom’
etc. Similarly subclasses of ‘matplotlib.axes’ (e.g. ‘matplotlib.axes.Axes’,
‘matplotlib.axes.Axes.plot’ etc.) will also not be captured.
sphinx_gallery_conf = {
...
'capture_repr': ('__repr__'),
'ignore_repr_types': r'matplotlib[text, axes]',
}