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validate_docstrings.py
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validate_docstrings.py
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#!/usr/bin/env python
"""
Analyze docstrings to detect errors.
If no argument is provided, it does a quick check of docstrings and returns
a csv with all API functions and results of basic checks.
If a function or method is provided in the form "pandas.function",
"pandas.module.class.method", etc. a list of all errors in the docstring for
the specified function or method.
Usage::
$ ./validate_docstrings.py
$ ./validate_docstrings.py pandas.DataFrame.head
"""
import os
import sys
import json
import re
import functools
import collections
import argparse
import pydoc
import inspect
import importlib
import doctest
import tempfile
import flake8.main.application
try:
from io import StringIO
except ImportError:
from cStringIO import StringIO
# Template backend makes matplotlib to not plot anything. This is useful
# to avoid that plot windows are open from the doctests while running the
# script. Setting here before matplotlib is loaded.
# We don't warn for the number of open plots, as none is actually being opened
os.environ['MPLBACKEND'] = 'Template'
import matplotlib
matplotlib.rc('figure', max_open_warning=10000)
import numpy
BASE_PATH = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
sys.path.insert(0, os.path.join(BASE_PATH))
import pandas
from pandas.compat import signature
sys.path.insert(1, os.path.join(BASE_PATH, 'doc', 'sphinxext'))
from numpydoc.docscrape import NumpyDocString
from pandas.io.formats.printing import pprint_thing
PRIVATE_CLASSES = ['NDFrame', 'IndexOpsMixin']
DIRECTIVES = ['versionadded', 'versionchanged', 'deprecated']
ALLOWED_SECTIONS = ['Parameters', 'Returns', 'Yields', 'Raises', 'Warns',
'See Also', 'Notes', 'References', 'Examples']
ERROR_MSGS = {
'GL01': 'Docstring text (summary) should start in the line immediately '
'after the opening quotes (not in the same line, or leaving a '
'blank line in between)',
'GL02': 'Closing quotes should be placed in the line after the last text '
'in the docstring (do not close the quotes in the same line as '
'the text, or leave a blank line between the last text and the '
'quotes)',
'GL03': 'Use only one blank line to separate sections or paragraphs',
'GL04': 'Private classes ({mentioned_private_classes}) should not be '
'mentioned in public docstrings',
'GL05': 'Tabs found at the start of line "{line_with_tabs}", please use '
'whitespace only',
'GL06': 'Found unknown section "{section}". Allowed sections are: '
'{allowed_sections}',
'GL07': 'Wrong order of sections. "{wrong_section}" should be located '
'before "{goes_before}", the right order is: {sorted_sections}',
'SS01': 'No summary found (a short summary in a single line should be '
'present at the beginning of the docstring)',
'SS02': 'Summary does not start with a capital letter',
'SS03': 'Summary does not end with a period',
'SS04': 'Summary contains heading whitespaces',
'SS05': 'Summary must start with infinitive verb, not third person '
'(e.g. use "Generate" instead of "Generates")',
'SS06': 'Summary should fit in a single line',
'ES01': 'No extended summary found',
'PR01': 'Parameters {missing_params} not documented',
'PR02': 'Unknown parameters {unknown_params}',
'PR03': 'Wrong parameters order. Actual: {actual_params}. '
'Documented: {documented_params}',
'PR04': 'Parameter "{param_name}" has no type',
'PR05': 'Parameter "{param_name}" type should not finish with "."',
'PR06': 'Parameter "{param_name}" type should use "{right_type}" instead '
'of "{wrong_type}"',
'PR07': 'Parameter "{param_name}" has no description',
'PR08': 'Parameter "{param_name}" description should start with a '
'capital letter',
'PR09': 'Parameter "{param_name}" description should finish with "."',
'RT01': 'No Returns section found',
'YD01': 'No Yields section found',
'SA01': 'See Also section not found',
'SA02': 'Missing period at end of description for See Also '
'"{reference_name}" reference',
'SA03': 'Description should be capitalized for See Also '
'"{reference_name}" reference',
'SA04': 'Missing description for See Also "{reference_name}" reference',
'SA05': '{reference_name} in `See Also` section does not need `pandas` '
'prefix, use {right_reference} instead.',
'EX01': 'No examples section found',
'EX02': 'Examples do not pass tests:\n{doctest_log}',
'EX03': 'flake8 error: {error_code} {error_message}{times_happening}',
'EX04': 'Do not import {imported_library}, as it is imported '
'automatically for the examples (numpy as np, pandas as pd)',
}
def error(code, **kwargs):
"""
Return a tuple with the error code and the message with variables replaced.
This is syntactic sugar so instead of:
- `('EX02', ERROR_MSGS['EX02'].format(doctest_log=log))`
We can simply use:
- `error('EX02', doctest_log=log)`
Parameters
----------
code : str
Error code.
**kwargs
Values for the variables in the error messages
Returns
-------
code : str
Error code.
message : str
Error message with varaibles replaced.
"""
return (code, ERROR_MSGS[code].format(**kwargs))
def get_api_items(api_doc_fd):
"""
Yield information about all public API items.
Parse api.rst file from the documentation, and extract all the functions,
methods, classes, attributes... This should include all pandas public API.
Parameters
----------
api_doc_fd : file descriptor
A file descriptor of the API documentation page, containing the table
of contents with all the public API.
Yields
------
name : str
The name of the object (e.g. 'pandas.Series.str.upper).
func : function
The object itself. In most cases this will be a function or method,
but it can also be classes, properties, cython objects...
section : str
The name of the section in the API page where the object item is
located.
subsection : str
The name of the subsection in the API page where the object item is
located.
"""
previous_line = current_section = current_subsection = ''
position = None
for line in api_doc_fd:
line = line.strip()
if len(line) == len(previous_line):
if set(line) == set('-'):
current_section = previous_line
continue
if set(line) == set('~'):
current_subsection = previous_line
continue
if line.startswith('.. currentmodule::'):
current_module = line.replace('.. currentmodule::', '').strip()
continue
if line == '.. autosummary::':
position = 'autosummary'
continue
if position == 'autosummary':
if line == '':
position = 'items'
continue
if position == 'items':
if line == '':
position = None
continue
item = line.strip()
func = importlib.import_module(current_module)
for part in item.split('.'):
func = getattr(func, part)
yield ('.'.join([current_module, item]), func,
current_section, current_subsection)
previous_line = line
class Docstring(object):
def __init__(self, name):
self.name = name
obj = self._load_obj(name)
self.obj = obj
self.code_obj = self._to_original_callable(obj)
self.raw_doc = obj.__doc__ or ''
self.clean_doc = pydoc.getdoc(obj)
self.doc = NumpyDocString(self.clean_doc)
def __len__(self):
return len(self.raw_doc)
@staticmethod
def _load_obj(name):
"""
Import Python object from its name as string.
Parameters
----------
name : str
Object name to import (e.g. pandas.Series.str.upper)
Returns
-------
object
Python object that can be a class, method, function...
Examples
--------
>>> Docstring._load_obj('pandas.Series')
<class 'pandas.core.series.Series'>
"""
for maxsplit in range(1, name.count('.') + 1):
# TODO when py3 only replace by: module, *func_parts = ...
func_name_split = name.rsplit('.', maxsplit)
module = func_name_split[0]
func_parts = func_name_split[1:]
try:
obj = importlib.import_module(module)
except ImportError:
pass
else:
continue
if 'module' not in locals():
raise ImportError('No module can be imported '
'from "{}"'.format(name))
for part in func_parts:
obj = getattr(obj, part)
return obj
@staticmethod
def _to_original_callable(obj):
"""
Find the Python object that contains the source code of the object.
This is useful to find the place in the source code (file and line
number) where a docstring is defined. It does not currently work for
all cases, but it should help find some (properties...).
"""
while True:
if inspect.isfunction(obj) or inspect.isclass(obj):
f = inspect.getfile(obj)
if f.startswith('<') and f.endswith('>'):
return None
return obj
if inspect.ismethod(obj):
obj = obj.__func__
elif isinstance(obj, functools.partial):
obj = obj.func
elif isinstance(obj, property):
obj = obj.fget
else:
return None
@property
def type(self):
return type(self.obj).__name__
@property
def is_function_or_method(self):
# TODO(py27): remove ismethod
return (inspect.isfunction(self.obj)
or inspect.ismethod(self.obj))
@property
def source_file_name(self):
"""
File name where the object is implemented (e.g. pandas/core/frame.py).
"""
try:
fname = inspect.getsourcefile(self.code_obj)
except TypeError:
# In some cases the object is something complex like a cython
# object that can't be easily introspected. An it's better to
# return the source code file of the object as None, than crash
pass
else:
if fname:
fname = os.path.relpath(fname, BASE_PATH)
return fname
@property
def source_file_def_line(self):
"""
Number of line where the object is defined in its file.
"""
try:
return inspect.getsourcelines(self.code_obj)[-1]
except (OSError, TypeError):
# In some cases the object is something complex like a cython
# object that can't be easily introspected. An it's better to
# return the line number as None, than crash
pass
@property
def github_url(self):
url = 'https://github.com/pandas-dev/pandas/blob/master/'
url += '{}#L{}'.format(self.source_file_name,
self.source_file_def_line)
return url
@property
def start_blank_lines(self):
i = None
if self.raw_doc:
for i, row in enumerate(self.raw_doc.split('\n')):
if row.strip():
break
return i
@property
def end_blank_lines(self):
i = None
if self.raw_doc:
for i, row in enumerate(reversed(self.raw_doc.split('\n'))):
if row.strip():
break
return i
@property
def double_blank_lines(self):
prev = True
for row in self.raw_doc.split('\n'):
if not prev and not row.strip():
return True
prev = row.strip()
return False
@property
def section_titles(self):
sections = []
self.doc._doc.reset()
while not self.doc._doc.eof():
content = self.doc._read_to_next_section()
if (len(content) > 1
and len(content[0]) == len(content[1])
and set(content[1]) == {'-'}):
sections.append(content[0])
return sections
@property
def summary(self):
return ' '.join(self.doc['Summary'])
@property
def num_summary_lines(self):
return len(self.doc['Summary'])
@property
def extended_summary(self):
if not self.doc['Extended Summary'] and len(self.doc['Summary']) > 1:
return ' '.join(self.doc['Summary'])
return ' '.join(self.doc['Extended Summary'])
@property
def needs_summary(self):
return not (bool(self.summary) and bool(self.extended_summary))
@property
def doc_parameters(self):
return collections.OrderedDict((name, (type_, ''.join(desc)))
for name, type_, desc
in self.doc['Parameters'])
@property
def signature_parameters(self):
if inspect.isclass(self.obj):
if hasattr(self.obj, '_accessors') and (
self.name.split('.')[-1] in
self.obj._accessors):
# accessor classes have a signature but don't want to show this
return tuple()
try:
sig = signature(self.obj)
except (TypeError, ValueError):
# Some objects, mainly in C extensions do not support introspection
# of the signature
return tuple()
params = sig.args
if sig.varargs:
params.append("*" + sig.varargs)
if sig.keywords:
params.append("**" + sig.keywords)
params = tuple(params)
if params and params[0] in ('self', 'cls'):
return params[1:]
return params
@property
def parameter_mismatches(self):
errs = []
signature_params = self.signature_parameters
doc_params = tuple(self.doc_parameters)
missing = set(signature_params) - set(doc_params)
if missing:
errs.append(error('PR01', missing_params=pprint_thing(missing)))
extra = set(doc_params) - set(signature_params)
if extra:
errs.append(error('PR02', unknown_params=pprint_thing(extra)))
if (not missing and not extra and signature_params != doc_params
and not (not signature_params and not doc_params)):
errs.append(error('PR03',
actual_params=signature_params,
documented_params=doc_params))
return errs
@property
def correct_parameters(self):
return not bool(self.parameter_mismatches)
def parameter_type(self, param):
return self.doc_parameters[param][0]
def parameter_desc(self, param):
desc = self.doc_parameters[param][1]
# Find and strip out any sphinx directives
for directive in DIRECTIVES:
full_directive = '.. {}'.format(directive)
if full_directive in desc:
# Only retain any description before the directive
desc = desc[:desc.index(full_directive)]
return desc
@property
def see_also(self):
return collections.OrderedDict((name, ''.join(desc))
for name, desc, _
in self.doc['See Also'])
@property
def examples(self):
return self.doc['Examples']
@property
def returns(self):
return self.doc['Returns']
@property
def yields(self):
return self.doc['Yields']
@property
def method_source(self):
try:
return inspect.getsource(self.obj)
except TypeError:
return ''
@property
def first_line_ends_in_dot(self):
if self.doc:
return self.doc.split('\n')[0][-1] == '.'
@property
def deprecated(self):
pattern = re.compile('.. deprecated:: ')
return (self.name.startswith('pandas.Panel')
or bool(pattern.search(self.summary))
or bool(pattern.search(self.extended_summary)))
@property
def mentioned_private_classes(self):
return [klass for klass in PRIVATE_CLASSES if klass in self.raw_doc]
@property
def examples_errors(self):
flags = doctest.NORMALIZE_WHITESPACE | doctest.IGNORE_EXCEPTION_DETAIL
finder = doctest.DocTestFinder()
runner = doctest.DocTestRunner(optionflags=flags)
context = {'np': numpy, 'pd': pandas}
error_msgs = ''
for test in finder.find(self.raw_doc, self.name, globs=context):
f = StringIO()
runner.run(test, out=f.write)
error_msgs += f.getvalue()
return error_msgs
@property
def examples_source_code(self):
lines = doctest.DocTestParser().get_examples(self.raw_doc)
return [line.source for line in lines]
def validate_pep8(self):
if not self.examples:
return
# F401 is needed to not generate flake8 errors in examples
# that do not user numpy or pandas
content = ''.join(('import numpy as np # noqa: F401\n',
'import pandas as pd # noqa: F401\n',
*self.examples_source_code))
application = flake8.main.application.Application()
application.initialize(["--quiet"])
with tempfile.NamedTemporaryFile(mode='w') as file:
file.write(content)
file.flush()
application.run_checks([file.name])
# We need this to avoid flake8 printing the names of the files to
# the standard output
application.formatter.write = lambda line, source: None
application.report()
yield from application.guide.stats.statistics_for('')
def validate_one(func_name):
"""
Validate the docstring for the given func_name
Parameters
----------
func_name : function
Function whose docstring will be evaluated (e.g. pandas.read_csv).
Returns
-------
dict
A dictionary containing all the information obtained from validating
the docstring.
Notes
-----
The errors codes are defined as:
- First two characters: Section where the error happens:
* GL: Global (no section, like section ordering errors)
* SS: Short summary
* ES: Extended summary
* PR: Parameters
* RT: Returns
* YD: Yields
* RS: Raises
* WN: Warns
* SA: See Also
* NT: Notes
* RF: References
* EX: Examples
- Last two characters: Numeric error code inside the section
For example, EX02 is the second codified error in the Examples section
(which in this case is assigned to examples that do not pass the tests).
The error codes, their corresponding error messages, and the details on how
they are validated, are not documented more than in the source code of this
function.
"""
doc = Docstring(func_name)
errs = []
wrns = []
if doc.start_blank_lines != 1:
errs.append(error('GL01'))
if doc.end_blank_lines != 1:
errs.append(error('GL02'))
if doc.double_blank_lines:
errs.append(error('GL03'))
mentioned_errs = doc.mentioned_private_classes
if mentioned_errs:
errs.append(error('GL04',
mentioned_private_classes=', '.join(mentioned_errs)))
for line in doc.raw_doc.splitlines():
if re.match("^ *\t", line):
errs.append(error('GL05', line_with_tabs=line.lstrip()))
unseen_sections = list(ALLOWED_SECTIONS)
for section in doc.section_titles:
if section not in ALLOWED_SECTIONS:
errs.append(error('GL06',
section=section,
allowed_sections=', '.join(ALLOWED_SECTIONS)))
else:
if section in unseen_sections:
section_idx = unseen_sections.index(section)
unseen_sections = unseen_sections[section_idx + 1:]
else:
section_idx = ALLOWED_SECTIONS.index(section)
goes_before = ALLOWED_SECTIONS[section_idx + 1]
errs.append(error('GL07',
sorted_sections=' > '.join(ALLOWED_SECTIONS),
wrong_section=section,
goes_before=goes_before))
break
if not doc.summary:
errs.append(error('SS01'))
else:
if not doc.summary[0].isupper():
errs.append(error('SS02'))
if doc.summary[-1] != '.':
errs.append(error('SS03'))
if doc.summary != doc.summary.lstrip():
errs.append(error('SS04'))
elif (doc.is_function_or_method
and doc.summary.split(' ')[0][-1] == 's'):
errs.append(error('SS05'))
if doc.num_summary_lines > 1:
errs.append(error('SS06'))
if not doc.extended_summary:
wrns.append(('ES01', 'No extended summary found'))
# PR01: Parameters not documented
# PR02: Unknown parameters
# PR03: Wrong parameters order
errs += doc.parameter_mismatches
for param in doc.doc_parameters:
if not param.startswith("*"): # Check can ignore var / kwargs
if not doc.parameter_type(param):
errs.append(error('PR04', param_name=param))
else:
if doc.parameter_type(param)[-1] == '.':
errs.append(error('PR05', param_name=param))
common_type_errors = [('integer', 'int'),
('boolean', 'bool'),
('string', 'str')]
for wrong_type, right_type in common_type_errors:
if wrong_type in doc.parameter_type(param):
errs.append(error('PR06',
param_name=param,
right_type=right_type,
wrong_type=wrong_type))
if not doc.parameter_desc(param):
errs.append(error('PR07', param_name=param))
else:
if not doc.parameter_desc(param)[0].isupper():
errs.append(error('PR08', param_name=param))
if doc.parameter_desc(param)[-1] != '.':
errs.append(error('PR09', param_name=param))
if doc.is_function_or_method:
if not doc.returns and 'return' in doc.method_source:
errs.append(error('RT01'))
if not doc.yields and 'yield' in doc.method_source:
errs.append(error('YD01'))
if not doc.see_also:
wrns.append(error('SA01'))
else:
for rel_name, rel_desc in doc.see_also.items():
if rel_desc:
if not rel_desc.endswith('.'):
errs.append(error('SA02', reference_name=rel_name))
if not rel_desc[0].isupper():
errs.append(error('SA03', reference_name=rel_name))
else:
errs.append(error('SA04', reference_name=rel_name))
if rel_name.startswith('pandas.'):
errs.append(error('SA05',
reference_name=rel_name,
right_reference=rel_name[len('pandas.'):]))
examples_errs = ''
if not doc.examples:
wrns.append(error('EX01'))
else:
examples_errs = doc.examples_errors
if examples_errs:
errs.append(error('EX02', doctest_log=examples_errs))
for err in doc.validate_pep8():
errs.append(error('EX03',
error_code=err.error_code,
error_message=err.message,
times_happening=' ({} times)'.format(err.count)
if err.count > 1 else ''))
examples_source_code = ''.join(doc.examples_source_code)
for wrong_import in ('numpy', 'pandas'):
if 'import {}'.format(wrong_import) in examples_source_code:
errs.append(error('EX04', imported_library=wrong_import))
return {'type': doc.type,
'docstring': doc.clean_doc,
'deprecated': doc.deprecated,
'file': doc.source_file_name,
'file_line': doc.source_file_def_line,
'github_link': doc.github_url,
'errors': errs,
'warnings': wrns,
'examples_errors': examples_errs}
def validate_all(prefix):
"""
Execute the validation of all docstrings, and return a dict with the
results.
Parameters
----------
prefix : str or None
If provided, only the docstrings that start with this pattern will be
validated. If None, all docstrings will be validated.
Returns
-------
dict
A dictionary with an item for every function/method... containing
all the validation information.
"""
result = {}
seen = {}
# functions from the API docs
api_doc_fname = os.path.join(BASE_PATH, 'doc', 'source', 'api.rst')
with open(api_doc_fname) as f:
api_items = list(get_api_items(f))
for func_name, func_obj, section, subsection in api_items:
if prefix and not func_name.startswith(prefix):
continue
doc_info = validate_one(func_name)
result[func_name] = doc_info
shared_code_key = doc_info['file'], doc_info['file_line']
shared_code = seen.get(shared_code_key, '')
result[func_name].update({'in_api': True,
'section': section,
'subsection': subsection,
'shared_code_with': shared_code})
seen[shared_code_key] = func_name
# functions from introspecting Series, DataFrame and Panel
api_item_names = set(list(zip(*api_items))[0])
for class_ in (pandas.Series, pandas.DataFrame, pandas.Panel):
for member in inspect.getmembers(class_):
func_name = 'pandas.{}.{}'.format(class_.__name__, member[0])
if (not member[0].startswith('_')
and func_name not in api_item_names):
if prefix and not func_name.startswith(prefix):
continue
doc_info = validate_one(func_name)
result[func_name] = doc_info
result[func_name]['in_api'] = False
return result
def main(func_name, prefix, errors, output_format):
def header(title, width=80, char='#'):
full_line = char * width
side_len = (width - len(title) - 2) // 2
adj = '' if len(title) % 2 == 0 else ' '
title_line = '{side} {title}{adj} {side}'.format(side=char * side_len,
title=title,
adj=adj)
return '\n{full_line}\n{title_line}\n{full_line}\n\n'.format(
full_line=full_line, title_line=title_line)
exit_status = 0
if func_name is None:
result = validate_all(prefix)
if output_format == 'json':
output = json.dumps(result)
else:
if output_format == 'default':
output_format = '{text}\n'
elif output_format == 'azure':
output_format = ('##vso[task.logissue type=error;'
'sourcepath={path};'
'linenumber={row};'
'code={code};'
']{text}\n')
else:
raise ValueError('Unknown output_format "{}"'.format(
output_format))
output = ''
for name, res in result.items():
for err_code, err_desc in res['errors']:
# The script would be faster if instead of filtering the
# errors after validating them, it didn't validate them
# initially. But that would complicate the code too much
if errors and err_code not in errors:
continue
exit_status += 1
output += output_format.format(
name=name,
path=res['file'],
row=res['file_line'],
code=err_code,
text='{}: {}'.format(name, err_desc))
sys.stdout.write(output)
else:
result = validate_one(func_name)
sys.stderr.write(header('Docstring ({})'.format(func_name)))
sys.stderr.write('{}\n'.format(result['docstring']))
sys.stderr.write(header('Validation'))
if result['errors']:
sys.stderr.write('{} Errors found:\n'.format(
len(result['errors'])))
for err_code, err_desc in result['errors']:
# Failing examples are printed at the end
if err_code == 'EX02':
sys.stderr.write('\tExamples do not pass tests\n')
continue
sys.stderr.write('\t{}\n'.format(err_desc))
if result['warnings']:
sys.stderr.write('{} Warnings found:\n'.format(
len(result['warnings'])))
for wrn_code, wrn_desc in result['warnings']:
sys.stderr.write('\t{}\n'.format(wrn_desc))
if not result['errors']:
sys.stderr.write('Docstring for "{}" correct. :)\n'.format(
func_name))
if result['examples_errors']:
sys.stderr.write(header('Doctests'))
sys.stderr.write(result['examples_errors'])
return exit_status
if __name__ == '__main__':
format_opts = 'default', 'json', 'azure'
func_help = ('function or method to validate (e.g. pandas.DataFrame.head) '
'if not provided, all docstrings are validated and returned '
'as JSON')
argparser = argparse.ArgumentParser(
description='validate pandas docstrings')
argparser.add_argument('function',
nargs='?',
default=None,
help=func_help)
argparser.add_argument('--format', default='default', choices=format_opts,
help='format of the output when validating '
'multiple docstrings (ignored when validating one).'
'It can be {}'.format(str(format_opts)[1:-1]))
argparser.add_argument('--prefix', default=None, help='pattern for the '
'docstring names, in order to decide which ones '
'will be validated. A prefix "pandas.Series.str.'
'will make the script validate all the docstrings'
'of methods starting by this pattern. It is '
'ignored if parameter function is provided')
argparser.add_argument('--errors', default=None, help='comma separated '
'list of error codes to validate. By default it '
'validates all errors (ignored when validating '
'a single docstring)')
args = argparser.parse_args()
sys.exit(main(args.function, args.prefix,
args.errors.split(',') if args.errors else None,
args.format))