MNT: update vendored docs files (nipreps#834)

* MNT: update vendored docs files

Copied from numpydoc 1.7.0.

* MNT: Ignore vendored files in CI spellchecking

Author: DimitriPapadopoulos

Diff for: .codespellrc

@@ -1,5 +1,5 @@
 [codespell]
-skip = .git,*.pdf,*.svg,viz-report.html
+skip = .git,*.pdf,*.svg,numpydoc.py,viz-report.html
 # objekt - used in the code purposefully different from object
 # nd - import scipy.ndimage as nd
 ignore-words-list = objekt,nd

Diff for: docs/sphinxext/docscrape.py

@@ -1,6 +1,7 @@
 """Extract reference documentation from the NumPy source tree.
 
 """
+
 import inspect
 import textwrap
 import re
@@ -11,12 +12,7 @@
 import copy
 import sys
 
-
-# TODO: Remove try-except when support for Python 3.7 is dropped
-try:
-    from functools import cached_property
-except ImportError:  # cached_property added in Python 3.8
-    cached_property = property
+from functools import cached_property
 
 
 def strip_blank_lines(l):
@@ -408,7 +404,7 @@ def _parse(self):
             msg = "Docstring contains a Receives section but not Yields."
             raise ValueError(msg)
 
-        for (section, content) in sections:
+        for section, content in sections:
             if not section.startswith(".."):
                 section = (s.capitalize() for s in section.split(" "))
                 section = " ".join(section)
@@ -631,7 +627,6 @@ def __init__(self, obj, doc=None, config=None):
 
 
 class ClassDoc(NumpyDocString):
-
     extra_public_methods = ["__call__"]
 
     def __init__(self, cls, doc=None, modulename="", func_doc=FunctionDoc, config=None):
@@ -711,6 +706,7 @@ def properties(self):
             for name, func in inspect.getmembers(self._cls)
             if (
                 not name.startswith("_")
+                and not self._should_skip_member(name, self._cls)
                 and (
                     func is None
                     or isinstance(func, (property, cached_property))
@@ -720,6 +716,19 @@ def properties(self):
             )
         ]
 
+    @staticmethod
+    def _should_skip_member(name, klass):
+        if (
+            # Namedtuples should skip everything in their ._fields as the
+            # docstrings for each of the members is: "Alias for field number X"
+            issubclass(klass, tuple)
+            and hasattr(klass, "_asdict")
+            and hasattr(klass, "_fields")
+            and name in klass._fields
+        ):
+            return True
+        return False
+
     def _is_show_member(self, name):
         if self.show_inherited_members:
             return True  # show all class members
@@ -728,7 +737,15 @@ def _is_show_member(self, name):
         return True
 
 
-def get_doc_object(obj, what=None, doc=None, config=None):
+def get_doc_object(
+    obj,
+    what=None,
+    doc=None,
+    config=None,
+    class_doc=ClassDoc,
+    func_doc=FunctionDoc,
+    obj_doc=ObjDoc,
+):
     if what is None:
         if inspect.isclass(obj):
             what = "class"
@@ -742,10 +759,10 @@ def get_doc_object(obj, what=None, doc=None, config=None):
         config = {}
 
     if what == "class":
-        return ClassDoc(obj, func_doc=FunctionDoc, doc=doc, config=config)
+        return class_doc(obj, func_doc=func_doc, doc=doc, config=config)
     elif what in ("function", "method"):
-        return FunctionDoc(obj, doc=doc, config=config)
+        return func_doc(obj, doc=doc, config=config)
     else:
         if doc is None:
             doc = pydoc.getdoc(obj)
-        return ObjDoc(obj, doc, config=config)
+        return obj_doc(obj, doc, config=config)

Diff for: docs/sphinxext/docscrape_sphinx.py

@@ -11,6 +11,7 @@
 from sphinx.jinja2glue import BuiltinTemplateLoader
 
 from .docscrape import NumpyDocString, FunctionDoc, ClassDoc, ObjDoc
+from .docscrape import get_doc_object as get_doc_object_orig
 from .xref import make_xref
 
 
@@ -372,9 +373,11 @@ def __str__(self, indent=0, func_role="obj"):
             "notes": self._str_section("Notes"),
             "references": self._str_references(),
             "examples": self._str_examples(),
-            "attributes": self._str_param_list("Attributes", fake_autosummary=True)
-            if self.attributes_as_param_list
-            else self._str_member_list("Attributes"),
+            "attributes": (
+                self._str_param_list("Attributes", fake_autosummary=True)
+                if self.attributes_as_param_list
+                else self._str_member_list("Attributes")
+            ),
             "methods": self._str_member_list("Methods"),
         }
         ns = {k: "\n".join(v) for k, v in ns.items()}
@@ -407,20 +410,10 @@ def __init__(self, obj, doc=None, config=None):
         ObjDoc.__init__(self, obj, doc=doc, config=config)
 
 
-# TODO: refactor to use docscrape.get_doc_object
 def get_doc_object(obj, what=None, doc=None, config=None, builder=None):
-    if what is None:
-        if inspect.isclass(obj):
-            what = "class"
-        elif inspect.ismodule(obj):
-            what = "module"
-        elif isinstance(obj, Callable):
-            what = "function"
-        else:
-            what = "object"
-
     if config is None:
         config = {}
+
     template_dirs = [os.path.join(os.path.dirname(__file__), "templates")]
     if builder is not None:
         template_loader = BuiltinTemplateLoader()
@@ -430,11 +423,12 @@ def get_doc_object(obj, what=None, doc=None, config=None, builder=None):
     template_env = SandboxedEnvironment(loader=template_loader)
     config["template"] = template_env.get_template("numpydoc_docstring.rst")
 
-    if what == "class":
-        return SphinxClassDoc(obj, func_doc=SphinxFunctionDoc, doc=doc, config=config)
-    elif what in ("function", "method"):
-        return SphinxFunctionDoc(obj, doc=doc, config=config)
-    else:
-        if doc is None:
-            doc = pydoc.getdoc(obj)
-        return SphinxObjDoc(obj, doc, config=config)
+    return get_doc_object_orig(
+        obj,
+        what=what,
+        doc=doc,
+        config=config,
+        class_doc=SphinxClassDoc,
+        func_doc=SphinxFunctionDoc,
+        obj_doc=SphinxObjDoc,
+    )

Diff for: docs/sphinxext/numpydoc.py

@@ -16,6 +16,7 @@
 .. [1] https://github.com/numpy/numpydoc
 
 """
+
 from copy import deepcopy
 import re
 import pydoc
@@ -24,17 +25,17 @@
 import hashlib
 import itertools
 
-from docutils.nodes import citation, Text, section, comment, reference
+from docutils.nodes import citation, Text, section, comment, reference, inline
 import sphinx
 from sphinx.addnodes import pending_xref, desc_content
 from sphinx.util import logging
 from sphinx.errors import ExtensionError
 
-if sphinx.__version__ < "4.2":
-    raise RuntimeError("Sphinx 4.2 or newer is required")
+if sphinx.__version__ < "5":
+    raise RuntimeError("Sphinx 5 or newer is required")
 
 from .docscrape_sphinx import get_doc_object
-from .validate import validate, ERROR_MSGS
+from .validate import validate, ERROR_MSGS, get_validation_checks
 from .xref import DEFAULT_LINKS
 from . import __version__
 
@@ -149,6 +150,10 @@ def clean_backrefs(app, doc, docname):
     for ref in _traverse_or_findall(doc, reference, descend=True):
         for id_ in ref["ids"]:
             known_ref_ids.add(id_)
+    # some extensions produce backrefs to inline elements
+    for ref in _traverse_or_findall(doc, inline, descend=True):
+        for id_ in ref["ids"]:
+            known_ref_ids.add(id_)
     for citation_node in _traverse_or_findall(doc, citation, descend=True):
         # remove backrefs to non-existent refs
         citation_node["backrefs"] = [
@@ -207,7 +212,19 @@ def mangle_docstrings(app, what, name, obj, options, lines):
                 # TODO: Currently, all validation checks are run and only those
                 # selected via config are reported. It would be more efficient to
                 # only run the selected checks.
-                errors = validate(doc)["errors"]
+                report = validate(doc)
+                errors = [
+                    err
+                    for err in report["errors"]
+                    if not (
+                        (
+                            overrides := app.config.numpydoc_validation_overrides.get(
+                                err[0]
+                            )
+                        )
+                        and re.search(overrides, report["docstring"])
+                    )
+                ]
                 if {err[0] for err in errors} & app.config.numpydoc_validation_checks:
                     msg = (
                         f"[numpydoc] Validation warnings while processing "
@@ -285,6 +302,7 @@ def setup(app, get_doc_object_=get_doc_object):
     app.add_config_value("numpydoc_xref_ignore", set(), True)
     app.add_config_value("numpydoc_validation_checks", set(), True)
     app.add_config_value("numpydoc_validation_exclude", set(), False)
+    app.add_config_value("numpydoc_validation_overrides", dict(), False)
 
     # Extra mangling domains
     app.add_domain(NumpyPythonDomain)
@@ -310,17 +328,9 @@ def update_config(app, config=None):
 
     # Processing to determine whether numpydoc_validation_checks is treated
     # as a blocklist or allowlist
-    valid_error_codes = set(ERROR_MSGS.keys())
-    if "all" in config.numpydoc_validation_checks:
-        block = deepcopy(config.numpydoc_validation_checks)
-        config.numpydoc_validation_checks = valid_error_codes - block
-    # Ensure that the validation check set contains only valid error codes
-    invalid_error_codes = config.numpydoc_validation_checks - valid_error_codes
-    if invalid_error_codes:
-        raise ValueError(
-            f"Unrecognized validation code(s) in numpydoc_validation_checks "
-            f"config value: {invalid_error_codes}"
-        )
+    config.numpydoc_validation_checks = get_validation_checks(
+        config.numpydoc_validation_checks
+    )
 
     # Generate the regexp for docstrings to ignore during validation
     if isinstance(config.numpydoc_validation_exclude, str):
@@ -335,6 +345,11 @@ def update_config(app, config=None):
         )
         config.numpydoc_validation_excluder = exclude_expr
 
+    for check, patterns in config.numpydoc_validation_overrides.items():
+        config.numpydoc_validation_overrides[check] = re.compile(
+            r"|".join(exp for exp in patterns)
+        )
+
 
 # ------------------------------------------------------------------------------
 # Docstring-mangling domains