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conf.py
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conf.py
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# Configuration file for the Sphinx documentation app.
# This file only contains a selection of the most common options. For a full
# list see the documentation:
# https://www.sphinx-doc.org/en/master/usage/configuration.html
import inspect
import os
from os.path import relpath, dirname
import re
import sys
from pyxem import release_info
import pyxem
# 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.append("../")
# Project information
project = "pyxem"
copyright = release_info.copyright
author = release_info.author
version = release_info.version
release = release_info.version
# The name of an image file (relative to this directory) to place at the top
# of the sidebar.
html_logo = "_static/logo.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 = "_static/logo.ico"
master_doc = "index"
# Add any Sphinx extension module names here, as strings. They can be extensions
# coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
extensions = [
"sphinxcontrib.bibtex",
"sphinx_design",
"sphinx.ext.autodoc",
"sphinx.ext.autosummary",
"sphinx.ext.githubpages",
"sphinx.ext.graphviz",
"sphinx.ext.mathjax",
"sphinx.ext.inheritance_diagram",
"sphinx.ext.intersphinx",
"sphinx.ext.napoleon",
"sphinx.ext.linkcode",
"sphinx_codeautolink",
"sphinx_gallery.gen_gallery",
"sphinx_copybutton",
"nbsphinx",
]
# Create links to references within pyxem's documentation to these packages.
intersphinx_mapping = {
"dask": ("https://docs.dask.org/en/stable", None),
"diffpy.structure": ("https://www.diffpy.org/diffpy.structure", None),
"diffsims": ("https://diffsims.readthedocs.io/en/stable", None),
"hyperspy": ("https://hyperspy.org/hyperspy-doc/current", None),
"h5py": ("https://docs.h5py.org/en/stable", None),
"matplotlib": ("https://matplotlib.org/stable", None),
"numpy": ("https://numpy.org/doc/stable", None),
"orix": ("https://orix.readthedocs.io/en/stable", None),
"python": ("https://docs.python.org/3", None),
"scipy": ("https://docs.scipy.org/doc/scipy", None),
"skimage": ("https://scikit-image.org/docs/stable", None),
"sklearn": ("https://scikit-learn.org/stable", None),
"rosettasciio": ("https://hyperspy.org/rosettasciio/", None),
}
linkcheck_ignore = [
"https://doi.org/10.1002/smll.201904738", # 403 Client Error: Forbidden for url
"http://dx.doi.org/10.1088/0965-0393/23/8/083501", # 403 Client Error: Forbidden for url
"https://doi.org/10.1111/jmi.12065", # 403 Client Error: Forbidden for url
"https://doi.org/10.1111/j.0022-2720.2004.01293.x", # 403 Client Error: Forbidden for url
]
# Add any paths that contain templates here, relative to this directory.
templates_path = [
"_templates",
]
# List of patterns, relative to source directory, that match files and
# directories to ignore when looking for source files. This image also affects
# html_static_path and html_extra_path.
# The theme to use for HTML and HTML Help pages. See the documentation for a
# list of builtin themes.
html_theme = "pydata_sphinx_theme"
html_theme_options = {
"github_url": "https://github.com/pyxem/pyxem",
"header_links_before_dropdown": 7,
"navigation_with_keys": True,
"show_toc_level": 2,
"use_edit_page_button": True,
}
html_context = {
"github_user": "pyxem",
"github_repo": "pyxem",
"github_version": "main",
"doc_path": "doc",
}
# 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 = ["_static"]
# Syntax highlighting
pygments_style = "friendly"
napoleon_google_docstring = False
napoleon_use_param = False
napoleon_use_ivar = True
# Figure references
numfig = True
# nbsphinx configuration
# Taken from nbsphinx' own nbsphinx configuration file, with slight
# modification to point nbviewer and Binder to the GitHub master links
# when the documentation is launched from a pyxem version with
# "dev" in the version.
if "dev" in version:
release_version = "master"
else:
release_version = "v" + version
# This is processed by Jinja2 and inserted before each notebook
nbsphinx_prolog = (
r"""
{% set docname = 'doc/' + env.doc2path(env.docname, base=None) %}
.. raw:: html
<style>a:hover { text-decoration: underline; }</style>
<div class="admonition note">
This page was generated from
<a class="reference external" href="https://github.com/pyxem/pyxem-demos/blob/"""
+ f"{release_version}"
+ r"""/{{ docname|e }}">{{ docname|e }}</a>.
Interactive online version:
<span style="white-space: nowrap;"><a href="https://mybinder.org/v2/gh/pyxem/pyxem-demos/"""
+ f"{release_version}"
+ r"""?filepath={{ docname|e }}"><img alt="Binder badge" src="https://mybinder.org/badge_logo.svg" style="vertical-align:text-bottom"></a>.</span>
<script>
if (document.location.host) {
$(document.currentScript).replaceWith(
'<a class="reference external" ' +
'href="https://nbviewer.jupyter.org/url' +
(window.location.protocol == 'https:' ? 's/' : '/') +
window.location.host +
window.location.pathname.slice(0, -4) +
'ipynb">View in <em>nbviewer</em></a>.'
);
}
</script>
</div>
.. raw:: latex
\nbsphinxstartnotebook{\scriptsize\noindent\strut
\textcolor{gray}{The following section was generated from
\sphinxcode{\sphinxupquote{\strut {{ docname | escape_latex }}}} \dotfill}}
"""
)
# https://nbsphinx.readthedocs.io/en/0.8.0/never-execute.html
nbsphinx_execute = "never" # auto, always, never
nbsphinx_kernel_name = "python3"
nbsphinx_allow_errors = True
exclude_patterns = ["_build", "**.ipynb_checkpoints", "examples/*/*.ipynb"]
# sphinxcontrib-bibtex configuration
bibtex_bibfiles = ["bibliography.bib"]
# -- Sphinx-Gallery---------------
# https://sphinx-gallery.github.io
sphinx_gallery_conf = {
"backreferences_dir": "reference/generated",
"doc_module": ("pyxem",),
"examples_dirs": "../examples", # path to your example scripts
"gallery_dirs": "examples", # path to where to save gallery generated output
"filename_pattern": "^((?!sgskip).)*$", # pattern to define which will be executed
"ignore_pattern": "_sgskip.py", # pattern to define which will not be executed
"reference_url": {"pyxem": None},
"show_memory": True,
}
autodoc_default_options = {
"show-inheritance": True,
}
graphviz_output_format = "svg"
# -- Linkcode ----------------------------------
def linkcode_resolve(domain, info):
"""Determine the URL corresponding to Python object.
This is taken from SciPy's conf.py:
https://github.com/scipy/scipy/blob/master/doc/source/conf.py.
"""
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
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(pyxem.__file__), ".."))
fn = relpath(fn, start=startdir).replace(os.path.sep, "/")
if fn.startswith("pyxem/"):
m = re.match(r"^.*dev0\+([a-f0-9]+)$", pyxem.__version__)
pre_link = "https://github.com/pyxem/pyxem/blob/"
if m:
return pre_link + "%s/%s%s" % (m.group(1), fn, linespec)
elif "dev" in pyxem.__version__:
return pre_link + "master/%s%s" % (fn, linespec)
else:
return pre_link + "v%s/%s%s" % (pyxem.__version__, fn, linespec)
else:
return None
# sphinx.ext.autodoc
# ------------------
# https://www.sphinx-doc.org/en/master/usage/extensions/autodoc.html
autosummary_ignore_module_all = False
autosummary_imported_members = True
autodoc_typehints_format = "short"
autodoc_default_options = {
"show-inheritance": True,
}
autosummary_generate = True