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"""
========
briandoc
========
Sphinx extension that handles docstrings in the Numpy standard format with some
brian-specific tweaks. [1]
It will:
- Convert Parameters etc. sections to field lists.
- Convert See Also section to a See also entry.
- Renumber references.
- Extract the signature from the docstring, if it can't be determined otherwise.
.. [1] https://github.com/numpy/numpy/blob/master/doc/HOWTO_DOCUMENT.rst.txt
"""
import inspect
import pydoc
import re
from docutils import nodes, statemachine
from docutils.parsers.rst import Directive, directives
from docutils.statemachine import ViewList
from sphinx.domains.c import CDomain
from sphinx.domains.python import PythonDomain, PyXRefRole
from sphinx.roles import XRefRole
from brian2.core.preferences import prefs
from .docscrape_sphinx import SphinxDocString, get_doc_object
class BrianPrefsDirective(Directive):
"""
A sphinx 'Directive' for automatically generated documentation of Brian preferences.
The directive takes an optional argument, the basename of the preferences
to document. In addition, you can specify a `nolinks` option which means
that no target links for the references are added. Do this if you document
preferences in more then one place.
Examples
--------
Document one category of preferences and generate links::
.. document_brian_prefs:: core
Document all preferences without generating links::
.. document_brian_prefs::
:nolinks:
"""
required_arguments = 0
optional_arguments = 1
final_argument_whitespace = True
option_spec = {"nolinks": directives.flag, "as_file": directives.flag}
has_content = False
def run(self):
# The section that should be documented
if len(self.arguments):
section = self.arguments[0]
else:
section = None
if "as_file" in self.options:
rawtext = prefs.as_file
return [nodes.literal_block(text=rawtext)]
else:
rawtext = prefs.get_documentation(section, "nolinks" not in self.options)
include_lines = statemachine.string2lines(rawtext, convert_whitespace=True)
self.state_machine.insert_input(include_lines, "Brian preferences")
return []
def brianobj_role(role, rawtext, text, lineno, inliner, options=None, content=None):
"""
A Sphinx role, used as a wrapper for the default `py:obj` role, allowing
us to use the simple backtick syntax for brian classes/functions without
having to qualify the package for classes/functions that are available after
a `from brian2 import *`, e.g `NeuronGroup`.
Also allows to directly link to preference names using the same syntax.
"""
if options is None:
options = {}
if content is None:
content = []
if text in prefs:
linktext = text.replace("_", "-").replace(".", "-")
text = f"{text} <brian-pref-{linktext}>"
# Use sphinx's cross-reference role
xref = XRefRole(warn_dangling=True)
return xref("std:ref", rawtext, text, lineno, inliner, options, content)
else:
if text and ("~" not in text):
try:
# A simple class or function name
if "." not in text:
module = __import__("brian2", fromlist=[str(text)])
imported = getattr(module, str(text), None)
if getattr(imported, "__module__", None):
text = f"~{imported.__module__}.{text}"
if inspect.isfunction(imported):
text += "()"
# Possibly a method/classmethod/attribute name
elif len(text.split(".")) == 2:
classname, attrname = text.split(".")
# Remove trailing parentheses (will be readded for display)
if attrname.endswith("()"):
attrname = attrname[:-2]
module = __import__("brian2", fromlist=[str(classname)])
imported = getattr(module, str(classname), None)
if hasattr(imported, "__module__"):
# Add trailing parentheses only for methods not for
# attributes
if inspect.ismethod(getattr(imported, str(attrname), None)):
parentheses = "()"
else:
parentheses = ""
text = (
f"{classname}.{attrname}{parentheses} "
f"<{imported.__module__}.{classname}.{attrname}>"
)
except ImportError:
pass
role = "py:obj"
py_role = PyXRefRole()
return py_role(role, rawtext, text, lineno, inliner, options, content)
def mangle_docstrings(app, what, name, obj, options, lines, reference_offset=None):
if reference_offset is None:
reference_offset = [0]
cfg = dict()
if what == "module":
# Strip top title
title_re = re.compile(r"^\s*[#*=]{4,}\n[a-z0-9 -]+\n[#*=]{4,}\s*", re.I | re.S)
lines[:] = title_re.sub("", "\n".join(lines)).split("\n")
exported_members = getattr(obj, "__all__", None)
if exported_members:
lines.append("*Exported members:* ")
exported_members = sorted(exported_members)
# do not print more than 25 members
lines.append(", ".join([f"`{member}`" for member in exported_members[:25]]))
if len(exported_members) > 25:
lines.append(f"... ({int(len(exported_members) - 25)} more members)")
lines.append("")
else:
doc = get_doc_object(obj, what, "\n".join(lines), name=name, config=cfg)
lines[:] = str(doc).split("\n")
# replace reference numbers so that there are no duplicates
references = []
for line in lines:
line = line.strip()
m = re.match(r"^.. \[([a-z0-9_.-])\]", line, re.I)
if m:
references.append(m.group(1))
# start renaming from the longest string, to avoid overwriting parts
references.sort(key=lambda x: -len(x))
if references:
for i in range(len(lines)):
for r in references:
if re.match(r"^\d+$", r):
new_r = f"R{int(reference_offset[0] + int(r))}"
else:
new_r = f"{r}{int(reference_offset[0])}"
lines[i] = lines[i].replace(f"[{r}]_", f"[{new_r}]_")
lines[i] = lines[i].replace(f".. [{r}]", f".. [{new_r}]")
reference_offset[0] += len(references)
def mangle_signature(app, what, name, obj, options, sig, retann):
# Do not try to inspect classes that don't define `__init__`
if inspect.isclass(obj) and (
not hasattr(obj, "__init__")
or "initializes x; see " in pydoc.getdoc(obj.__init__)
):
return "", ""
if not (callable(obj) or hasattr(obj, "__argspec_is_invalid_")):
return
if not hasattr(obj, "__doc__"):
return
doc = SphinxDocString(pydoc.getdoc(obj))
if doc["Signature"]:
sig = re.sub("^[^(]*", "", doc["Signature"])
return sig, ""
def setup(app, get_doc_object_=get_doc_object):
global get_doc_object
get_doc_object = get_doc_object_
app.connect("autodoc-process-docstring", mangle_docstrings)
app.connect("autodoc-process-signature", mangle_signature)
# Extra mangling domains
app.add_domain(NumpyPythonDomain)
app.add_domain(NumpyCDomain)
directives.register_directive("document_brian_prefs", BrianPrefsDirective)
# provide the brianobj role with a link to the Python domain
app.add_role("brianobj", brianobj_role)
# ------------------------------------------------------------------------------
# Docstring-mangling domains
# ------------------------------------------------------------------------------
class ManglingDomainBase:
directive_mangling_map = {}
def __init__(self, *a, **kw):
super().__init__(*a, **kw)
self.wrap_mangling_directives()
def wrap_mangling_directives(self):
for name, objtype in self.directive_mangling_map.items():
self.directives[name] = wrap_mangling_directive(
self.directives[name], objtype
)
class NumpyPythonDomain(ManglingDomainBase, PythonDomain):
name = "np"
directive_mangling_map = {
"function": "function",
"class": "class",
"exception": "class",
"method": "function",
"classmethod": "function",
"staticmethod": "function",
"attribute": "attribute",
}
class NumpyCDomain(ManglingDomainBase, CDomain):
name = "np-c"
directive_mangling_map = {
"function": "function",
"member": "attribute",
"macro": "function",
"type": "class",
"var": "object",
}
def wrap_mangling_directive(base_directive, objtype):
class directive(base_directive):
def run(self):
env = self.state.document.settings.env
name = None
if self.arguments:
m = re.match(r"^(.*\s+)?(.*?)(\(.*)?", self.arguments[0])
name = m.group(2).strip()
if not name:
name = self.arguments[0]
lines = list(self.content)
mangle_docstrings(env.app, objtype, name, None, None, lines)
self.content = ViewList(lines, self.content.parent)
return base_directive.run(self)
return directive
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