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# scikit-learn documentation build configuration file, created by
# sphinx-quickstart on Fri Jan 8 09:13:42 2010.
#
# This file is execfile()d with the current directory set to its containing
# dir.
#
# Note that not all possible configuration values are present in this
# autogenerated file.
#
# All configuration values have a default; values that are commented out
# serve to show the default.
import os
import re
import sys
import warnings
from datetime import datetime
from io import StringIO
from pathlib import Path
from sklearn.externals._packaging.version import parse
from sklearn.utils._testing import turn_warnings_into_errors
# If extensions (or modules to document with autodoc) are in another
# directory, add these directories to sys.path here. If the directory
# is relative to the documentation root, use os.path.abspath to make it
# absolute, like shown here.
sys.path.insert(0, os.path.abspath("sphinxext"))
import sphinx_gallery
from github_link import make_linkcode_resolve
from sphinx_gallery.notebook import add_code_cell, add_markdown_cell
from sphinx_gallery.sorting import ExampleTitleSortKey
try:
# Configure plotly to integrate its output into the HTML pages generated by
# sphinx-gallery.
import plotly.io as pio
pio.renderers.default = "sphinx_gallery"
except ImportError:
# Make it possible to render the doc when not running the examples
# that need plotly.
pass
# -- General configuration ---------------------------------------------------
# Add any Sphinx extension module names here, as strings. They can be
# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
extensions = [
"sphinx.ext.autodoc",
"sphinx.ext.autosummary",
"numpydoc",
"sphinx.ext.linkcode",
"sphinx.ext.doctest",
"sphinx.ext.intersphinx",
"sphinx.ext.imgconverter",
"sphinx_gallery.gen_gallery",
"sphinx_issues",
"add_toctree_functions",
"sphinx-prompt",
"sphinx_copybutton",
"sphinxext.opengraph",
"doi_role",
"allow_nan_estimators",
"matplotlib.sphinxext.plot_directive",
]
# Specify how to identify the prompt when copying code snippets
copybutton_prompt_text = r">>> |\.\.\. "
copybutton_prompt_is_regexp = True
copybutton_exclude = "style"
try:
import jupyterlite_sphinx # noqa: F401
extensions.append("jupyterlite_sphinx")
with_jupyterlite = True
except ImportError:
# In some cases we don't want to require jupyterlite_sphinx to be installed,
# e.g. the doc-min-dependencies build
warnings.warn(
"jupyterlite_sphinx is not installed, you need to install it "
"if you want JupyterLite links to appear in each example"
)
with_jupyterlite = False
# Produce `plot::` directives for examples that contain `import matplotlib` or
# `from matplotlib import`.
numpydoc_use_plots = True
# Options for the `::plot` directive:
# https://matplotlib.org/stable/api/sphinxext_plot_directive_api.html
plot_formats = ["png"]
plot_include_source = True
plot_html_show_formats = False
plot_html_show_source_link = False
# this is needed for some reason...
# see https://github.com/numpy/numpydoc/issues/69
numpydoc_class_members_toctree = False
# For maths, use mathjax by default and svg if NO_MATHJAX env variable is set
# (useful for viewing the doc offline)
if os.environ.get("NO_MATHJAX"):
extensions.append("sphinx.ext.imgmath")
imgmath_image_format = "svg"
mathjax_path = ""
else:
extensions.append("sphinx.ext.mathjax")
mathjax_path = "file:///usr/share/javascript/mathjax/MathJax.js?config=TeX-AMS_CHTML"
autodoc_default_options = {"members": True, "inherited-members": True}
# Add any paths that contain templates here, relative to this directory.
templates_path = ["templates"]
# generate autosummary even if no references
autosummary_generate = True
# The suffix of source filenames.
source_suffix = ".rst"
# The encoding of source files.
# source_encoding = 'utf-8'
# The main toctree document.
root_doc = "contents"
# General information about the project.
project = "scikit-learn"
copyright = f"2007 - {datetime.now().year}, scikit-learn developers (BSD License)"
# The version info for the project you're documenting, acts as replacement for
# |version| and |release|, also used in various other places throughout the
# built documents.
#
# The short X.Y version.
import sklearn
parsed_version = parse(sklearn.__version__)
version = ".".join(parsed_version.base_version.split(".")[:2])
# The full version, including alpha/beta/rc tags.
# Removes post from release name
if parsed_version.is_postrelease:
release = parsed_version.base_version
else:
release = sklearn.__version__
# The language for content autogenerated by Sphinx. Refer to documentation
# for a list of supported languages.
# language = None
# There are two options for replacing |today|: either, you set today to some
# non-false value, then it is used:
# today = ''
# Else, today_fmt is used as the format for a strftime call.
# today_fmt = '%B %d, %Y'
# List of patterns, relative to source directory, that match files and
# directories to ignore when looking for source files.
exclude_patterns = ["_build", "templates", "includes", "themes"]
# The reST default role (used for this markup: `text`) to use for all
# documents.
default_role = "literal"
# If true, '()' will be appended to :func: etc. cross-reference text.
add_function_parentheses = False
# If true, the current module name will be prepended to all description
# unit titles (such as .. function::).
# add_module_names = True
# If true, sectionauthor and moduleauthor directives will be shown in the
# output. They are ignored by default.
# show_authors = False
# The name of the Pygments (syntax highlighting) style to use.
pygments_style = "sphinx"
# A list of ignored prefixes for module index sorting.
# modindex_common_prefix = []
# -- Options for HTML output -------------------------------------------------
# The theme to use for HTML and HTML Help pages. Major themes that come with
# Sphinx are currently 'default' and 'sphinxdoc'.
html_theme = "scikit-learn-modern"
# Theme options are theme-specific and customize the look and feel of a theme
# further. For a list of options available for each theme, see the
# documentation.
html_theme_options = {
"legacy_google_analytics": True,
"analytics": False,
"mathjax_path": mathjax_path,
"link_to_live_contributing_page": not parsed_version.is_devrelease,
}
# Add any paths that contain custom themes here, relative to this directory.
html_theme_path = ["themes"]
# The name for this set of Sphinx documents. If None, it defaults to
# "<project> v<release> documentation".
# html_title = None
# A shorter title for the navigation bar. Default is the same as html_title.
html_short_title = "scikit-learn"
# The name of an image file (relative to this directory) to place at the top
# of the sidebar.
html_logo = "logos/scikit-learn-logo-small.png"
# The name of an image file (within the static path) to use as favicon of the
# docs. This file should be a Windows icon file (.ico) being 16x16 or 32x32
# pixels large.
html_favicon = "logos/favicon.ico"
# Add any paths that contain custom static files (such as style sheets) here,
# relative to this directory. They are copied after the builtin static files,
# so a file named "default.css" will overwrite the builtin "default.css".
html_static_path = ["images"]
# If not '', a 'Last updated on:' timestamp is inserted at every page bottom,
# using the given strftime format.
# html_last_updated_fmt = '%b %d, %Y'
# Custom sidebar templates, maps document names to template names.
# html_sidebars = {}
# Additional templates that should be rendered to pages, maps page names to
# template names.
html_additional_pages = {"index": "index.html"}
# If false, no module index is generated.
html_domain_indices = False
# If false, no index is generated.
html_use_index = False
# If true, the index is split into individual pages for each letter.
# html_split_index = False
# If true, links to the reST sources are added to the pages.
# html_show_sourcelink = True
# If true, an OpenSearch description file will be output, and all pages will
# contain a <link> tag referring to it. The value of this option must be the
# base URL from which the finished HTML is served.
# html_use_opensearch = ''
# If nonempty, this is the file name suffix for HTML files (e.g. ".xhtml").
# html_file_suffix = ''
# Output file base name for HTML help builder.
htmlhelp_basename = "scikit-learndoc"
# If true, the reST sources are included in the HTML build as _sources/name.
html_copy_source = True
# Adds variables into templates
html_context = {}
# finds latest release highlights and places it into HTML context for
# index.html
release_highlights_dir = Path("..") / "examples" / "release_highlights"
# Finds the highlight with the latest version number
latest_highlights = sorted(release_highlights_dir.glob("plot_release_highlights_*.py"))[
-1
]
latest_highlights = latest_highlights.with_suffix("").name
html_context["release_highlights"] = (
f"auto_examples/release_highlights/{latest_highlights}"
)
# get version from highlight name assuming highlights have the form
# plot_release_highlights_0_22_0
highlight_version = ".".join(latest_highlights.split("_")[-3:-1])
html_context["release_highlights_version"] = highlight_version
# redirects dictionary maps from old links to new links
redirects = {
"documentation": "index",
"auto_examples/feature_selection/plot_permutation_test_for_classification": (
"auto_examples/model_selection/plot_permutation_tests_for_classification"
),
"modules/model_persistence": "model_persistence",
"auto_examples/linear_model/plot_bayesian_ridge": (
"auto_examples/linear_model/plot_ard"
),
"auto_examples/model_selection/grid_search_text_feature_extraction.py": (
"auto_examples/model_selection/plot_grid_search_text_feature_extraction.py"
),
"auto_examples/miscellaneous/plot_changed_only_pprint_parameter": (
"auto_examples/miscellaneous/plot_estimator_representation"
),
"auto_examples/decomposition/plot_beta_divergence": (
"auto_examples/applications/plot_topics_extraction_with_nmf_lda"
),
"auto_examples/ensemble/plot_adaboost_hastie_10_2": (
"auto_examples/ensemble/plot_adaboost_multiclass"
),
"auto_examples/decomposition/plot_pca_3d": (
"auto_examples/decomposition/plot_pca_iris"
),
"auto_examples/exercises/plot_cv_digits.py": (
"auto_examples/model_selection/plot_nested_cross_validation_iris.py"
),
}
html_context["redirects"] = redirects
for old_link in redirects:
html_additional_pages[old_link] = "redirects.html"
# Not showing the search summary makes the search page load faster.
html_show_search_summary = True
# The "summary-anchor" IDs will be overwritten via JavaScript to be unique.
# See `doc/theme/scikit-learn-modern/static/js/details-permalink.js`.
rst_prolog = """
.. |details-start| raw:: html
<details id="summary-anchor">
<summary class="btn btn-light">
.. |details-split| raw:: html
<span class="tooltiptext">Click for more details</span>
<a class="headerlink" href="#summary-anchor" title="Permalink to this heading">ΒΆ</a>
</summary>
<div class="card">
.. |details-end| raw:: html
</div>
</details>
"""
# -- Options for LaTeX output ------------------------------------------------
latex_elements = {
# The paper size ('letterpaper' or 'a4paper').
# 'papersize': 'letterpaper',
# The font size ('10pt', '11pt' or '12pt').
# 'pointsize': '10pt',
# Additional stuff for the LaTeX preamble.
"preamble": r"""
\usepackage{amsmath}\usepackage{amsfonts}\usepackage{bm}
\usepackage{morefloats}\usepackage{enumitem} \setlistdepth{10}
\let\oldhref\href
\renewcommand{\href}[2]{\oldhref{#1}{\hbox{#2}}}
"""
}
# Grouping the document tree into LaTeX files. List of tuples
# (source start file, target name, title, author, documentclass
# [howto/manual]).
latex_documents = [
(
"contents",
"user_guide.tex",
"scikit-learn user guide",
"scikit-learn developers",
"manual",
),
]
# The name of an image file (relative to this directory) to place at the top of
# the title page.
latex_logo = "logos/scikit-learn-logo.png"
# Documents to append as an appendix to all manuals.
# latex_appendices = []
# If false, no module index is generated.
latex_domain_indices = False
trim_doctests_flags = True
# intersphinx configuration
intersphinx_mapping = {
"python": ("/usr/share/doc/python3/html/", None),
"numpy": ("/usr/share/doc/python-numpy/html/", None),
"scipy": ("/usr/share/doc/python-scipy-doc/html/", None),
"matplotlib": ("/usr/share/doc/python-matplotlib/html/", None),
"pandas": ("/usr/share/doc/python-pandas-doc/html/", None),
}
v = parse(release)
if v.release is None:
raise ValueError(
"Ill-formed version: {!r}. Version should follow PEP440".format(version)
)
if v.is_devrelease:
binder_branch = "main"
else:
major, minor = v.release[:2]
binder_branch = "{}.{}.X".format(major, minor)
class SubSectionTitleOrder:
"""Sort example gallery by title of subsection.
Assumes README.txt exists for all subsections and uses the subsection with
dashes, '---', as the adornment.
"""
def __init__(self, src_dir):
self.src_dir = src_dir
self.regex = re.compile(r"^([\w ]+)\n-", re.MULTILINE)
def __repr__(self):
return "<%s>" % (self.__class__.__name__,)
def __call__(self, directory):
src_path = os.path.normpath(os.path.join(self.src_dir, directory))
# Forces Release Highlights to the top
if os.path.basename(src_path) == "release_highlights":
return "0"
readme = os.path.join(src_path, "README.txt")
try:
with open(readme, "r") as f:
content = f.read()
except FileNotFoundError:
return directory
title_match = self.regex.search(content)
if title_match is not None:
return title_match.group(1)
return directory
class SKExampleTitleSortKey(ExampleTitleSortKey):
"""Sorts release highlights based on version number."""
def __call__(self, filename):
title = super().__call__(filename)
prefix = "plot_release_highlights_"
# Use title to sort if not a release highlight
if not str(filename).startswith(prefix):
return title
major_minor = filename[len(prefix) :].split("_")[:2]
version_float = float(".".join(major_minor))
# negate to place the newest version highlights first
return -version_float
def notebook_modification_function(notebook_content, notebook_filename):
notebook_content_str = str(notebook_content)
warning_template = "\n".join(
[
"<div class='alert alert-{message_class}'>",
"",
"# JupyterLite warning",
"",
"{message}",
"</div>",
]
)
message_class = "warning"
message = (
"Running the scikit-learn examples in JupyterLite is experimental and you may"
" encounter some unexpected behavior.\n\nThe main difference is that imports"
" will take a lot longer than usual, for example the first `import sklearn` can"
" take roughly 10-20s.\n\nIf you notice problems, feel free to open an"
" [issue](https://github.com/scikit-learn/scikit-learn/issues/new/choose)"
" about it."
)
markdown = warning_template.format(message_class=message_class, message=message)
dummy_notebook_content = {"cells": []}
add_markdown_cell(dummy_notebook_content, markdown)
code_lines = []
if "seaborn" in notebook_content_str:
code_lines.append("%pip install seaborn")
if "plotly.express" in notebook_content_str:
code_lines.append("%pip install plotly")
if "skimage" in notebook_content_str:
code_lines.append("%pip install scikit-image")
if "fetch_" in notebook_content_str:
code_lines.extend(
[
"%pip install pyodide-http",
"import pyodide_http",
"pyodide_http.patch_all()",
]
)
# always import matplotlib and pandas to avoid Pyodide limitation with
# imports inside functions
code_lines.extend(["import matplotlib", "import pandas"])
if code_lines:
code_lines = ["# JupyterLite-specific code"] + code_lines
code = "\n".join(code_lines)
add_code_cell(dummy_notebook_content, code)
notebook_content["cells"] = (
dummy_notebook_content["cells"] + notebook_content["cells"]
)
default_global_config = sklearn.get_config()
def reset_sklearn_config(gallery_conf, fname):
"""Reset sklearn config to default values."""
sklearn.set_config(**default_global_config)
sphinx_gallery_conf = {
"doc_module": "sklearn",
"backreferences_dir": os.path.join("modules", "generated"),
"show_memory": False,
"reference_url": {"sklearn": None},
"examples_dirs": ["../examples"],
"gallery_dirs": ["auto_examples"],
"subsection_order": SubSectionTitleOrder("../examples"),
"within_subsection_order": SKExampleTitleSortKey,
# avoid generating too many cross links
"inspect_global_variables": False,
"remove_config_comments": True,
"plot_gallery": "True",
"reset_modules": ("matplotlib", "seaborn", reset_sklearn_config),
}
if with_jupyterlite:
sphinx_gallery_conf["jupyterlite"] = {
"notebook_modification_function": notebook_modification_function
}
# The following dictionary contains the information used to create the
# thumbnails for the front page of the scikit-learn home page.
# key: first image in set
# values: (number of plot in set, height of thumbnail)
carousel_thumbs = {"sphx_glr_plot_classifier_comparison_001.png": 600}
# enable experimental module so that experimental estimators can be
# discovered properly by sphinx
from sklearn.experimental import enable_iterative_imputer # noqa
from sklearn.experimental import enable_halving_search_cv # noqa
def make_carousel_thumbs(app, exception):
"""produces the final resized carousel images"""
if exception is not None:
return
print("Preparing carousel images")
image_dir = os.path.join(app.builder.outdir, "_images")
for glr_plot, max_width in carousel_thumbs.items():
image = os.path.join(image_dir, glr_plot)
if os.path.exists(image):
c_thumb = os.path.join(image_dir, glr_plot[:-4] + "_carousel.png")
sphinx_gallery.gen_rst.scale_image(image, c_thumb, max_width, 190)
def filter_search_index(app, exception):
if exception is not None:
return
# searchindex only exist when generating html
if app.builder.name != "html":
return
print("Removing methods from search index")
searchindex_path = os.path.join(app.builder.outdir, "searchindex.js")
with open(searchindex_path, "r") as f:
searchindex_text = f.read()
searchindex_text = re.sub(r"{__init__.+?}", "{}", searchindex_text)
searchindex_text = re.sub(r"{__call__.+?}", "{}", searchindex_text)
with open(searchindex_path, "w") as f:
f.write(searchindex_text)
def generate_min_dependency_table(app):
"""Generate min dependency table for docs."""
from sklearn._min_dependencies import dependent_packages
# get length of header
package_header_len = max(len(package) for package in dependent_packages) + 4
version_header_len = len("Minimum Version") + 4
tags_header_len = max(len(tags) for _, tags in dependent_packages.values()) + 4
output = StringIO()
output.write(
" ".join(
["=" * package_header_len, "=" * version_header_len, "=" * tags_header_len]
)
)
output.write("\n")
dependency_title = "Dependency"
version_title = "Minimum Version"
tags_title = "Purpose"
output.write(
f"{dependency_title:<{package_header_len}} "
f"{version_title:<{version_header_len}} "
f"{tags_title}\n"
)
output.write(
" ".join(
["=" * package_header_len, "=" * version_header_len, "=" * tags_header_len]
)
)
output.write("\n")
for package, (version, tags) in dependent_packages.items():
output.write(
f"{package:<{package_header_len}} {version:<{version_header_len}} {tags}\n"
)
output.write(
" ".join(
["=" * package_header_len, "=" * version_header_len, "=" * tags_header_len]
)
)
output.write("\n")
output = output.getvalue()
with (Path(".") / "min_dependency_table.rst").open("w") as f:
f.write(output)
def generate_min_dependency_substitutions(app):
"""Generate min dependency substitutions for docs."""
from sklearn._min_dependencies import dependent_packages
output = StringIO()
for package, (version, _) in dependent_packages.items():
package = package.capitalize()
output.write(f".. |{package}MinVersion| replace:: {version}")
output.write("\n")
output = output.getvalue()
with (Path(".") / "min_dependency_substitutions.rst").open("w") as f:
f.write(output)
# Config for sphinx_issues
# we use the issues path for PRs since the issues URL will forward
issues_github_path = "scikit-learn/scikit-learn"
def disable_plot_gallery_for_linkcheck(app):
if app.builder.name == "linkcheck":
sphinx_gallery_conf["plot_gallery"] = "False"
def setup(app):
# do not run the examples when using linkcheck by using a small priority
# (default priority is 500 and sphinx-gallery using builder-inited event too)
app.connect("builder-inited", disable_plot_gallery_for_linkcheck, priority=50)
app.connect("builder-inited", generate_min_dependency_table)
app.connect("builder-inited", generate_min_dependency_substitutions)
# to hide/show the prompt in code examples:
app.connect("build-finished", make_carousel_thumbs)
app.connect("build-finished", filter_search_index)
# The following is used by sphinx.ext.linkcode to provide links to github
linkcode_resolve = make_linkcode_resolve(
"sklearn",
(
"https://github.com/scikit-learn/"
"scikit-learn/blob/{revision}/"
"{package}/{path}#L{lineno}"
),
)
warnings.filterwarnings(
"ignore",
category=UserWarning,
message=(
"Matplotlib is currently using agg, which is a"
" non-GUI backend, so cannot show the figure."
),
)
if os.environ.get("SKLEARN_WARNINGS_AS_ERRORS", "0") != "0":
turn_warnings_into_errors()
# maps functions with a class name that is indistinguishable when case is
# ignore to another filename
autosummary_filename_map = {
"sklearn.cluster.dbscan": "dbscan-function",
"sklearn.covariance.oas": "oas-function",
"sklearn.decomposition.fastica": "fastica-function",
}
# Config for sphinxext.opengraph
ogp_site_url = "https://scikit-learn/stable/"
ogp_image = "https://scikit-learn.org/stable/_static/scikit-learn-logo-small.png"
ogp_use_first_image = True
ogp_site_name = "scikit-learn"
# Config for linkcheck that checks the documentation for broken links
# ignore all links in 'whats_new' to avoid doing many github requests and
# hitting the github rate threshold that makes linkcheck take a lot of time
linkcheck_exclude_documents = [r"whats_new/.*"]
# default timeout to make some sites links fail faster
linkcheck_timeout = 10
# Allow redirects from doi.org
linkcheck_allowed_redirects = {r"https://doi.org/.+": r".*"}
linkcheck_ignore = [
# ignore links to local html files e.g. in image directive :target: field
r"^..?/",
# ignore links to specific pdf pages because linkcheck does not handle them
# ('utf-8' codec can't decode byte error)
r"http://www.utstat.toronto.edu/~rsalakhu/sta4273/notes/Lecture2.pdf#page=.*",
(
"https://www.fordfoundation.org/media/2976/roads-and-bridges"
"-the-unseen-labor-behind-our-digital-infrastructure.pdf#page=.*"
),
# links falsely flagged as broken
(
"https://www.researchgate.net/publication/"
"233096619_A_Dendrite_Method_for_Cluster_Analysis"
),
(
"https://www.researchgate.net/publication/221114584_Random_Fourier"
"_Approximations_for_Skewed_Multiplicative_Histogram_Kernels"
),
(
"https://www.researchgate.net/publication/4974606_"
"Hedonic_housing_prices_and_the_demand_for_clean_air"
),
(
"https://www.researchgate.net/profile/Anh-Huy-Phan/publication/220241471_Fast_"
"Local_Algorithms_for_Large_Scale_Nonnegative_Matrix_and_Tensor_Factorizations"
),
"https://doi.org/10.13140/RG.2.2.35280.02565",
(
"https://www.microsoft.com/en-us/research/uploads/prod/2006/01/"
"Bishop-Pattern-Recognition-and-Machine-Learning-2006.pdf"
),
"https://www.microsoft.com/en-us/research/wp-content/uploads/2016/02/tr-99-87.pdf",
"https://microsoft.com/",
"https://www.jstor.org/stable/2984099",
"https://stat.uw.edu/sites/default/files/files/reports/2000/tr371.pdf",
# Broken links from testimonials
"http://www.bestofmedia.com",
"http://www.data-publica.com/",
"https://livelovely.com",
"https://www.mars.com/global",
"https://www.yhat.com",
# Ignore some dynamically created anchors. See
# https://github.com/sphinx-doc/sphinx/issues/9016 for more details about
# the github example
r"https://github.com/conda-forge/miniforge#miniforge",
r"https://github.com/joblib/threadpoolctl/"
"#setting-the-maximum-size-of-thread-pools",
r"https://stackoverflow.com/questions/5836335/"
"consistently-create-same-random-numpy-array/5837352#comment6712034_5837352",
]
# Use a browser-like user agent to avoid some "403 Client Error: Forbidden for
# url" errors. This is taken from the variable navigator.userAgent inside a
# browser console.
user_agent = (
"Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:100.0) Gecko/20100101 Firefox/100.0"
)
# Use Github token from environment variable to avoid Github rate limits when
# checking Github links
github_token = os.getenv("GITHUB_TOKEN")
if github_token is None:
linkcheck_request_headers = {}
else:
linkcheck_request_headers = {
"https://github.com/": {"Authorization": f"token {github_token}"},
}
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