conf.py

import math
import os
from os.path import relpath, dirname
import re
import sys
import warnings
from datetime import date
from docutils import nodes
from docutils.parsers.rst import Directive

from intersphinx_registry import get_intersphinx_mapping
import matplotlib
import matplotlib.pyplot as plt
from numpydoc.docscrape_sphinx import SphinxDocString
from sphinx.util import inspect

import scipy
from scipy._lib._util import _rng_html_rewrite
# Workaround for sphinx-doc/sphinx#6573
# ua._Function should not be treated as an attribute
import scipy._lib.uarray as ua
from scipy.stats._distn_infrastructure import rv_generic
from scipy.stats._multivariate import multi_rv_generic


old_isdesc = inspect.isdescriptor
inspect.isdescriptor = (lambda obj: old_isdesc(obj)
                        and not isinstance(obj, ua._Function))

# Currently required to build scipy.fft docs
os.environ['_SCIPY_BUILDING_DOC'] = 'True'

# -----------------------------------------------------------------------------
# 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.

sys.path.insert(0, os.path.abspath(os.path.dirname(__file__)))

import numpydoc.docscrape as np_docscrape  # noqa: E402

extensions = [
    'sphinx.ext.autodoc',
    'sphinx.ext.autosummary',
    'sphinx.ext.coverage',
    'sphinx.ext.mathjax',
    'sphinx.ext.intersphinx',
    'numpydoc',
    'sphinx_copybutton',
    'sphinx_design',
    'scipyoptdoc',
    'doi_role',
    'matplotlib.sphinxext.plot_directive',
    'myst_nb',
    'jupyterlite_sphinx',
]


# Do some matplotlib config in case users have a matplotlibrc that will break
# things
matplotlib.use('agg')
plt.ioff()

# Add any paths that contain templates here, relative to this directory.
templates_path = ['_templates']

# The suffix of source filenames.
source_suffix = '.rst'

# The main toctree document.
master_doc = 'index'

# General substitutions.
project = 'SciPy'
copyright = f'2008-{date.today().year}, The SciPy community'

# The default replacements for |version| and |release|, also used in various
# other places throughout the built documents.
version = re.sub(r'\.dev.*$', r'.dev', scipy.__version__)
release = version

if os.environ.get('CIRCLE_JOB', False) and \
        os.environ.get('CIRCLE_BRANCH', '') != 'main':
    version = os.environ['CIRCLE_BRANCH']
    release = version

print(f"{project} (VERSION {version})")

# 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 documents that shouldn't be included in the build.
#unused_docs = []

# The reST default role (used for this markup: `text`) to use for all documents.
default_role = "autolink"

# List of directories, relative to source directories, that shouldn't be searched
# for source files.
exclude_dirs = []
exclude_patterns = [  # glob-style
    "**.ipynb",
]

# 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'

# Ensure all our internal links work
nitpicky = True
nitpick_ignore = [
    # This ignores errors for classes (OptimizeResults, sparse.dok_matrix)
    # which inherit methods from `dict`. missing references to builtins get
    # ignored by default (see https://github.com/sphinx-doc/sphinx/pull/7254),
    # but that fix doesn't work for inherited methods.
    ("py:class", "a shallow copy of D"),
    ("py:class", "a set-like object providing a view on D's keys"),
    ("py:class", "a set-like object providing a view on D's items"),
    ("py:class", "an object providing a view on D's values"),
    ("py:class", "None.  Remove all items from D."),
    ("py:class", "(k, v), remove and return some (key, value) pair as a"),
    ("py:class", "None.  Update D from dict/iterable E and F."),
    ("py:class", "v, remove specified key and return the corresponding value."),
]

# be strict about warnings in our examples, we should write clean code
# (exceptions permitted for pedagogical purposes below)
warnings.resetwarnings()
warnings.filterwarnings('error')
# allow these and show them
warnings.filterwarnings('default', module='sphinx')  # internal warnings
# global weird ones that can be safely ignored
for key in (
        r"OpenSSL\.rand is deprecated",  # OpenSSL package in linkcheck
        r"distutils Version",  # distutils
        ):
    warnings.filterwarnings(  # deal with other modules having bad imports
        'ignore', message=".*" + key, category=DeprecationWarning)
warnings.filterwarnings(  # matplotlib<->pyparsing issue
    'ignore', message="Exception creating Regex for oneOf.*",
    category=SyntaxWarning)
# warnings in examples (mostly) that we allow
# TODO: eventually these should be eliminated!
for key in (
        'invalid escape sequence',  # numpydoc 0.8 has some bad escape chars
        'The integral is probably divergent',  # stats.mielke example
        'underflow encountered in square',  # signal.filtfilt underflow
        'underflow encountered in multiply',  # scipy.spatial.HalfspaceIntersection
        'underflow encountered in nextafter',  # tuterial/interpolate.rst
        # stats.skewnorm, stats.norminvgauss, stats.gaussian_kde,
        # tutorial/stats.rst (twice):
        'underflow encountered in exp',
        ):
    warnings.filterwarnings(
        'once', message='.*' + key)
# docutils warnings when using notebooks (see gh-17322)
# these will hopefully be removed in the near future
for key in (
    r"The frontend.OptionParser class will be replaced",
    r"The frontend.Option class will be removed",
    ):
    warnings.filterwarnings('ignore', message=key, category=DeprecationWarning)
warnings.filterwarnings(
    'ignore',
    message=r'.*is obsoleted by Node.findall()',
    category=PendingDeprecationWarning,
)
warnings.filterwarnings(
    'ignore',
    message=r'There is no current event loop',
    category=DeprecationWarning,
)
# See https://github.com/sphinx-doc/sphinx/issues/12589
suppress_warnings = [
    'autosummary.import_cycle',
]

# -----------------------------------------------------------------------------
# HTML output
# -----------------------------------------------------------------------------

html_theme = 'pydata_sphinx_theme'

html_logo = '_static/logo.svg'
html_favicon = '_static/favicon.ico'

html_sidebars = {
    "index": ["search-button-field"],
    "**": ["search-button-field", "sidebar-nav-bs"]
}

html_theme_options = {
    "github_url": "https://github.com/scipy/scipy",
    "twitter_url": "https://twitter.com/SciPy_team",
    "header_links_before_dropdown": 6,
    "icon_links": [],
    "logo": {
        "text": "SciPy",
    },
    "navbar_start": ["navbar-logo"],
    "navbar_end": ["version-switcher", "theme-switcher", "navbar-icon-links"],
    "navbar_persistent": [],
    "switcher": {
        "json_url": "https://scipy.github.io/devdocs/_static/version_switcher.json",
        "version_match": version,
    },
    "show_version_warning_banner": True,
    "secondary_sidebar_items": ["page-toc"],
    # The service https://plausible.io is used to gather simple
    # and privacy-friendly analytics for the site. The dashboard can be accessed
    # at https://analytics.scientific-python.org/docs.scipy.org
    # The Scientific-Python community is hosting and managing the account.
    "analytics": {
        "plausible_analytics_domain": "docs.scipy.org",
        "plausible_analytics_url": "https://views.scientific-python.org/js/script.js",
    },
}

if 'dev' in version:
    html_theme_options["switcher"]["version_match"] = "development"
    html_theme_options["show_version_warning_banner"] = False

if 'versionwarning' in tags:  # noqa: F821
    # Specific to docs.scipy.org deployment.
    # See https://github.com/scipy/docs.scipy.org/blob/main/_static/versionwarning.js_t
    src = ('var script = document.createElement("script");\n'
           'script.type = "text/javascript";\n'
           'script.src = "/doc/_static/versionwarning.js";\n'
           'document.head.appendChild(script);')
    html_context = {
        'VERSIONCHECK_JS': src
    }
    html_js_files = ['versioncheck.js']

html_title = f"{project} v{version} Manual"
html_static_path = ['_static']
html_last_updated_fmt = '%b %d, %Y'

html_css_files = [
    "scipy.css",
    "try_examples.css",
]

# html_additional_pages = {
#     'index': 'indexcontent.html',
# }
html_additional_pages = {}
html_use_modindex = True
html_domain_indices = False
html_copy_source = False
html_file_suffix = '.html'

htmlhelp_basename = 'scipy'

mathjax_path = "scipy-mathjax/MathJax.js?config=scipy-mathjax"

# sphinx-copybutton configurations
copybutton_prompt_text = r">>> |\.\.\. |\$ |In \[\d*\]: | {2,5}\.{3,}: | {5,8}: "
copybutton_prompt_is_regexp = True

# -----------------------------------------------------------------------------
# Intersphinx configuration
# -----------------------------------------------------------------------------
intersphinx_mapping = get_intersphinx_mapping(
    packages={"python", "numpy", "neps", "matplotlib", "asv", "statsmodels", "mpmath"}
)

# -----------------------------------------------------------------------------
# Numpy extensions
# -----------------------------------------------------------------------------

# If we want to do a phantom import from an XML file for all autodocs
phantom_import_file = 'dump.xml'

# Generate plots for example sections
numpydoc_use_plots = True
np_docscrape.ClassDoc.extra_public_methods = [  # should match class.rst
    '__call__', '__mul__', '__getitem__', '__len__',
]

# -----------------------------------------------------------------------------
# Autosummary
# -----------------------------------------------------------------------------

autosummary_generate = True

# maps functions with a name same as a class name that is indistinguishable
# Ex: scipy.signal.czt and scipy.signal.CZT or scipy.odr.odr and scipy.odr.ODR
# Otherwise, the stubs are overwritten when the name is same for
# OS (like MacOS) which has a filesystem that ignores the case
# See https://github.com/sphinx-doc/sphinx/pull/7927
autosummary_filename_map = {
    "scipy.odr.odr": "odr-function",
    "scipy.signal.czt": "czt-function",
    "scipy.signal.ShortTimeFFT.t": "scipy.signal.ShortTimeFFT.t.lower",
}


# -----------------------------------------------------------------------------
# Autodoc
# -----------------------------------------------------------------------------

autodoc_default_options = {
    'inherited-members': None,
}
autodoc_typehints = 'none'


# -----------------------------------------------------------------------------
# Coverage checker
# -----------------------------------------------------------------------------
coverage_ignore_modules = r"""
    """.split()
coverage_ignore_functions = r"""
    test($|_) (some|all)true bitwise_not cumproduct pkgload
    generic\.
    """.split()
coverage_ignore_classes = r"""
    """.split()

coverage_c_path = []
coverage_c_regexes = {}
coverage_ignore_c_items = {}


#------------------------------------------------------------------------------
# Matplotlib plot_directive options
#------------------------------------------------------------------------------

plot_pre_code = """
import warnings
for key in (
        'interp2d` is deprecated',  # Deprecation of scipy.interpolate.interp2d
        'scipy.misc',  # scipy.misc deprecated in v1.10.0; use scipy.datasets
        '`kurtosistest` p-value may be',  # intentionally "bad" example in docstring
        ):
    warnings.filterwarnings(action='ignore', message='.*' + key + '.*')

import numpy as np
np.random.seed(123)
"""

plot_include_source = True
plot_formats = [('png', 96)]
plot_html_show_formats = False
plot_html_show_source_link = False

phi = (math.sqrt(5) + 1)/2

font_size = 13*72/96.0  # 13 px

plot_rcparams = {
    'font.size': font_size,
    'axes.titlesize': font_size,
    'axes.labelsize': font_size,
    'xtick.labelsize': font_size,
    'ytick.labelsize': font_size,
    'legend.fontsize': font_size,
    'figure.figsize': (3*phi, 3),
    'figure.subplot.bottom': 0.2,
    'figure.subplot.left': 0.2,
    'figure.subplot.right': 0.9,
    'figure.subplot.top': 0.85,
    'figure.subplot.wspace': 0.4,
    'text.usetex': False,
}

# -----------------------------------------------------------------------------
# Notebook tutorials with MyST-NB
# -----------------------------------------------------------------------------

nb_execution_mode = "auto"
# Ignore notebooks generated by jupyterlite-sphinx for interactive examples.
nb_execution_excludepatterns = ["_contents/*.ipynb"]
# Prevent creation of transition syntax when adding footnotes
# See https://github.com/executablebooks/MyST-Parser/issues/352
myst_footnote_transition = False
myst_enable_extensions = [
    "colon_fence",
    "dollarmath",
    "substitution",
]
nb_render_markdown_format = "myst"
render_markdown_format = "myst"
# Fix rendering of MathJax objects in Jupyter notebooks
myst_update_mathjax = False

#------------------------------------------------------------------------------
# Interactive examples with jupyterlite-sphinx
#------------------------------------------------------------------------------
global_enable_try_examples = True
try_examples_global_button_text = "Try it in your browser!"
try_examples_global_warning_text = (
    "SciPy's interactive examples with Jupyterlite are experimental and may"
    " not always work as expected. Execution of cells containing imports may"
    " result in large downloads (up to 60MB of content for the first import"
    " from SciPy). Load times when importing from SciPy may take roughly 10-20"
    " seconds. If you notice any problems, feel free to open an"
    " [issue](https://github.com/scipy/scipy/issues/new/choose)."
)

# -----------------------------------------------------------------------------
# Source code links
# -----------------------------------------------------------------------------

# Not the same as from sphinx.util import inspect and needed here
import inspect  # noqa: E402

for name in ['sphinx.ext.linkcode', 'linkcode', 'numpydoc.linkcode']:
    try:
        __import__(name)
        extensions.append(name)
        break
    except ImportError:
        pass
else:
    print("NOTE: linkcode extension not found -- no links to source generated")


def linkcode_resolve(domain, info):
    """
    Determine the URL corresponding to Python object
    """
    if domain != 'py':
        return None

    modname = info['module']
    fullname = info['fullname']

    submod = sys.modules.get(modname)
    if submod is None:
        return None

    obj = submod
    for part in fullname.split('.'):
        try:
            obj = getattr(obj, part)
        except Exception:
            return None

    # Use the original function object if it is wrapped.
    while hasattr(obj, "__wrapped__"):
        obj = obj.__wrapped__
    # SciPy's distributions are instances of *_gen. Point to this
    # class since it contains the implementation of all the methods.
    if isinstance(obj, (rv_generic, multi_rv_generic)):
        obj = obj.__class__
    try:
        fn = inspect.getsourcefile(obj)
    except Exception:
        fn = None
    if not fn:
        try:
            fn = inspect.getsourcefile(sys.modules[obj.__module__])
        except Exception:
            fn = None
    if not fn:
        return None

    try:
        source, lineno = inspect.getsourcelines(obj)
    except Exception:
        lineno = None

    if lineno:
        linespec = "#L%d-L%d" % (lineno, lineno + len(source) - 1)
    else:
        linespec = ""

    startdir = os.path.abspath(os.path.join(dirname(scipy.__file__), '..'))
    fn = relpath(fn, start=startdir).replace(os.path.sep, '/')

    if fn.startswith('scipy/'):
        m = re.match(r'^.*dev0\+([a-f0-9]+)$', scipy.__version__)
        base_url = "https://github.com/scipy/scipy/blob"
        if m:
            return f"{base_url}/{m.group(1)}/{fn}{linespec}"
        elif 'dev' in scipy.__version__:
            return f"{base_url}/main/{fn}{linespec}"
        else:
            return f"{base_url}/v{scipy.__version__}/{fn}{linespec}"
    else:
        return None


# Tell overwrite numpydoc's logic to render examples containing rng.
SphinxDocString._str_examples = _rng_html_rewrite(
    SphinxDocString._str_examples
)


class LegacyDirective(Directive):
    """
    Adapted from docutils/parsers/rst/directives/admonitions.py

    Uses a default text if the directive does not have contents. If it does,
    the default text is concatenated to the contents.

    """
    has_content = True
    node_class = nodes.admonition
    optional_arguments = 1

    def run(self):
        try:
            obj = self.arguments[0]
        except IndexError:
            # Argument is empty; use default text
            obj = "submodule"
        text = (f"This {obj} is considered legacy and will no longer receive "
                "updates. This could also mean it will be removed in future "
                "SciPy versions.")

        try:
            self.content[0] = text+" "+self.content[0]
        except IndexError:
            # Content is empty; use the default text
            source, lineno = self.state_machine.get_source_and_line(
                self.lineno
            )
            self.content.append(
                text,
                source=source,
                offset=lineno
            )
        text = '\n'.join(self.content)
        # Create the admonition node, to be populated by `nested_parse`
        admonition_node = self.node_class(rawsource=text)
        # Set custom title
        title_text = "Legacy"
        textnodes, _ = self.state.inline_text(title_text, self.lineno)
        title = nodes.title(title_text, '', *textnodes)
        # Set up admonition node
        admonition_node += title
        # Select custom class for CSS styling
        admonition_node['classes'] = ['admonition-legacy']
        # Parse the directive contents
        self.state.nested_parse(self.content, self.content_offset,
                                admonition_node)
        return [admonition_node]


def setup(app):
    app.add_directive("legacy", LegacyDirective)