ENH: Enable validation during sphinx-build process (#302)

* WIP: Move get_doc_obj to docscrape

* WIP: mv _obj property to NumpyDocString

* Proof-of-concept: Docstring attrs covered by refactor.

Running the test suite on this patch demonstrates that refactoring
the boundary between NumpyDocString and SphinxDocString provides the
necessary info to (potentially) do away with the validate.Docstring
class.

* NOTE TO SELF: get_doc_object in docscrape_sphinx

* Docstring -> Validator.

* Activate validation during sphinx-build.

Add a conf option to turn on/off.

TODO: test

* Replace logger.warn with warning.

logger.warn is apparently deprecated

* DOC: Add numpydoc_validate to conf docs.

* Add mechanism for validation check selection.

Adds a config option with a set to allow users to select
which validation checks are used. Default is an empty set,
which means none of the validation checks raise warnings
during the build process.

Add documentation for new option and activate in the doc build.

* TST: modify how MockApp sets builder app.

* TST: Add test of validation warnings.

* Specify some sensible validation defaults.

* Add docstring name to validation warnings.

* Add all keyword to validation_check configuration.

More flexibility in configuring which validation checks to run during
sphinx build. If 'all' is present, treat the rest of the set as a
blocklist, else an allowlist.

* Fix failing test.

* Make validation error mapping easier to read.

* Add check for invalid error codes in configuration.

plus test.

* Add feature to exclude patterns from docstring validation.

Modify updated config name to avoid sphinx warning.

Add documentation for exclusion config value.

* Be explicit about regex syntax for exclude config val

Co-authored-by: Eric Larson <larson.eric.d@gmail.com>

* Rm redundant numpydoc_validate config param.

Co-authored-by: Eric Larson <larson.eric.d@gmail.com>

Author: rossbar

doc/conf.py

@@ -84,6 +84,8 @@
 version = re.sub(r'(\.dev\d+).*?$', r'\1', version)
 numpydoc_xref_param_type = True
 numpydoc_xref_ignore = {'optional', 'type_without_description', 'BadException'}
+# Run docstring validation as part of build process
+numpydoc_validation_checks = {"all", "GL01", "SA04", "RT03"}
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

doc/install.rst

@@ -96,6 +96,42 @@ numpydoc_xref_ignore : set or ``"all"``
   desired cross reference mappings in ``numpydoc_xref_aliases`` and setting
   ``numpydoc_xref_ignore="all"`` is more convenient than explicitly listing
   terms to ignore in a set.
+numpydoc_validation_checks : set
+    The set of validation checks to report during the sphinx build process.
+    The default is an empty set, so docstring validation is not run by
+    default.
+    If ``"all"`` is in the set, then the results of all of the
+    :ref:`built-in validation checks <validation_checks>` are reported.
+    If the set includes ``"all"`` and additional error codes, then all
+    validation checks *except* the listed error codes will be run.
+    If the set contains *only* individual error codes, then only those checks
+    will be run.
+    For example::
+
+        # Report warnings for all validation checks
+        numpydoc_validation_checks = {"all"}
+
+        # Report warnings for all checks *except* for GL01, GL02, and GL05
+        numpydoc_validation_checks = {"all", "GL01", "GL02", "GL05"}
+
+        # Only report warnings for the SA01 and EX01 checks
+        numpydoc_validation_checks = {"SA01", "EX01"}
+numpydoc_validation_exclude : set
+    A container of strings using :py:mod:`re` syntax specifying patterns to
+    ignore for docstring validation.
+    For example, to skip docstring validation for all objects in
+    ``mypkg.mymodule``::
+
+        numpydoc_validation_exclude = {"mypkg.mymodule."}
+
+    If you wanted to also skip getter methods of ``MyClass``::
+
+        numpydoc_validation_exclude = {r"mypkg\.mymodule\.", r"MyClass\.get$"}
+
+    The default is an empty set meaning no objects are excluded from docstring
+    validation.
+    Only has an effect when docstring validation is activated, i.e.
+    ``numpydoc_validation_checks`` is not an empty set.
 numpydoc_edit_link : bool
   .. deprecated:: 0.7.0
 

doc/validation.rst

@@ -15,3 +15,21 @@ For an exhaustive validation of the formatting of the docstring, use the
 ``--validate`` parameter. This will report the errors detected, such as
 incorrect capitalization, wrong order of the sections, and many other
 issues.
+
+.. _validation_checks:
+
+Built-in Validation Checks
+--------------------------
+
+The ``numpydoc.validation`` module provides a mapping with all of the checks
+that are run as part of the validation procedure.
+The mapping is of the form: ``error_code : <explanation>`` where ``error_code``
+provides a shorthand for the check being run, and ``<explanation>`` provides
+a more detailed message. For example::
+
+    "EX01" : "No examples section found"
+
+The full mapping of validation checks is given below.
+
+.. literalinclude:: ../numpydoc/validate.py
+   :lines: 36-90

numpydoc/__main__.py

@@ -6,13 +6,13 @@
 import ast
 
 from .docscrape_sphinx import get_doc_object
-from .validate import validate, Docstring
+from .validate import validate, Validator
 
 
 def render_object(import_path, config=None):
     """Test numpydoc docstring generation for a given object"""
-    # TODO: Move Docstring._load_obj to a better place than validate
-    print(get_doc_object(Docstring(import_path).obj,
+    # TODO: Move Validator._load_obj to a better place than validate
+    print(get_doc_object(Validator._load_obj(import_path),
                          config=dict(config or [])))
     return 0
 

numpydoc/docscrape.py

@@ -411,8 +411,16 @@ def _parse(self):
             else:
                 self[section] = content
 
+    @property
+    def _obj(self):
+        if hasattr(self, '_cls'):
+            return self._cls
+        elif hasattr(self, '_f'):
+            return self._f
+        return None
+
     def _error_location(self, msg, error=True):
-        if hasattr(self, '_obj') and self._obj is not None:
+        if self._obj is not None:
             # we know where the docs came from:
             try:
                 filename = inspect.getsourcefile(self._obj)
@@ -581,6 +589,12 @@ def __str__(self):
         return out
 
 
+class ObjDoc(NumpyDocString):
+    def __init__(self, obj, doc=None, config={}):
+        self._f = obj
+        NumpyDocString.__init__(self, doc, config=config)
+
+
 class ClassDoc(NumpyDocString):
 
     extra_public_methods = ['__call__']
@@ -663,3 +677,24 @@ def _is_show_member(self, name):
         if name not in self._cls.__dict__:
             return False  # class member is inherited, we do not show it
         return True
+
+
+def get_doc_object(obj, what=None, doc=None, config={}):
+    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 what == 'class':
+        return ClassDoc(obj, func_doc=FunctionDoc, doc=doc, config=config)
+    elif what in ('function', 'method'):
+        return FunctionDoc(obj, doc=doc, config=config)
+    else:
+        if doc is None:
+            doc = pydoc.getdoc(obj)
+        return ObjDoc(obj, doc, config=config)

numpydoc/docscrape_sphinx.py

@@ -10,7 +10,7 @@
 import sphinx
 from sphinx.jinja2glue import BuiltinTemplateLoader
 
-from .docscrape import NumpyDocString, FunctionDoc, ClassDoc
+from .docscrape import NumpyDocString, FunctionDoc, ClassDoc, ObjDoc
 from .xref import make_xref
 
 
@@ -229,14 +229,6 @@ def _str_param_list(self, name, fake_autosummary=False):
 
         return out
 
-    @property
-    def _obj(self):
-        if hasattr(self, '_cls'):
-            return self._cls
-        elif hasattr(self, '_f'):
-            return self._f
-        return None
-
     def _str_member_list(self, name):
         """
         Generate a member listing, autosummary:: table where possible,
@@ -411,13 +403,13 @@ def __init__(self, obj, doc=None, func_doc=None, config={}):
         ClassDoc.__init__(self, obj, doc=doc, func_doc=None, config=config)
 
 
-class SphinxObjDoc(SphinxDocString):
+class SphinxObjDoc(SphinxDocString, ObjDoc):
     def __init__(self, obj, doc=None, config={}):
-        self._f = obj
         self.load_config(config)
-        SphinxDocString.__init__(self, doc, config=config)
+        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={}, builder=None):
     if what is None:
         if inspect.isclass(obj):

numpydoc/numpydoc.py

@@ -34,6 +34,7 @@
     raise RuntimeError("Sphinx 1.6.5 or newer is required")
 
 from .docscrape_sphinx import get_doc_object
+from .validate import validate, ERROR_MSGS
 from .xref import DEFAULT_LINKS
 from . import __version__
 
@@ -173,6 +174,28 @@ def mangle_docstrings(app, what, name, obj, options, lines):
             logger.error('[numpydoc] While processing docstring for %r', name)
             raise
 
+        if app.config.numpydoc_validation_checks:
+            # If the user has supplied patterns to ignore via the
+            # numpydoc_validation_exclude config option, skip validation for
+            # any objs whose name matches any of the patterns
+            excluder = app.config.numpydoc_validation_excluder
+            exclude_from_validation = excluder.search(name) if excluder else False
+            if not exclude_from_validation:
+                # 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"]
+                if {err[0] for err in errors} & app.config.numpydoc_validation_checks:
+                    msg = (
+                        f"[numpydoc] Validation warnings while processing "
+                        f"docstring for {name!r}:\n"
+                    )
+                    for err in errors:
+                        if err[0] in app.config.numpydoc_validation_checks:
+                            msg += f"  {err[0]}: {err[1]}\n"
+                    logger.warning(msg)
+
+
     if (app.config.numpydoc_edit_link and hasattr(obj, '__name__') and
             obj.__name__):
         if hasattr(obj, '__module__'):
@@ -254,6 +277,8 @@ def setup(app, get_doc_object_=get_doc_object):
     app.add_config_value('numpydoc_xref_param_type', False, True)
     app.add_config_value('numpydoc_xref_aliases', dict(), True)
     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)
 
     # Extra mangling domains
     app.add_domain(NumpyPythonDomain)
@@ -278,6 +303,33 @@ def update_config(app, config=None):
             numpydoc_xref_aliases_complete[key] = value
     config.numpydoc_xref_aliases_complete = numpydoc_xref_aliases_complete
 
+    # 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}"
+        )
+
+    # Generate the regexp for docstrings to ignore during validation
+    if isinstance(config.numpydoc_validation_exclude, str):
+        raise ValueError(
+            f"numpydoc_validation_exclude must be a container of strings, "
+            f"e.g. [{config.numpydoc_validation_exclude!r}]."
+        )
+    config.numpydoc_validation_excluder = None
+    if config.numpydoc_validation_exclude:
+        exclude_expr = re.compile(
+            r"|".join(exp for exp in config.numpydoc_validation_exclude)
+        )
+        config.numpydoc_validation_excluder = exclude_expr
+
 
 # ------------------------------------------------------------------------------
 # Docstring-mangling domains

numpydoc/tests/test_docscrape.py

@@ -1497,6 +1497,9 @@ class Config():
         def __init__(self, a, b):
             self.numpydoc_xref_aliases = a
             self.numpydoc_xref_aliases_complete = b
+            # numpydoc.update_config fails if this config option not present
+            self.numpydoc_validation_checks = set()
+            self.numpydoc_validation_exclude = set()
 
     xref_aliases_complete = deepcopy(DEFAULT_LINKS)
     for key in xref_aliases: