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#!/usr/bin/env python3
"""
refguide_check.py [OPTIONS] [-- ARGS]
- Check for a NumPy submodule whether the objects in its __all__ dict
correspond to the objects included in the reference guide.
- Check docstring examples
- Check example blocks in RST files
Example of usage::
$ python refguide_check.py optimize
Note that this is a helper script to be able to check if things are missing;
the output of this script does need to be checked manually. In some cases
objects are left out of the refguide for a good reason (it's an alias of
another function, or deprecated, or ...)
Another use of this helper script is to check validity of code samples
in docstrings::
$ python tools/refguide_check.py --doctests ma
or in RST-based documentations::
$ python tools/refguide_check.py --rst doc/source
"""
import copy
import doctest
import inspect
import io
import os
import re
import shutil
import sys
import tempfile
import warnings
import docutils.core
from argparse import ArgumentParser
from contextlib import contextmanager, redirect_stderr
from doctest import NORMALIZE_WHITESPACE, ELLIPSIS, IGNORE_EXCEPTION_DETAIL
from docutils.parsers.rst import directives
import sphinx
import numpy as np
sys.path.insert(0, os.path.join(os.path.dirname(__file__), '..', 'doc', 'sphinxext'))
from numpydoc.docscrape_sphinx import get_doc_object
SKIPBLOCK = doctest.register_optionflag('SKIPBLOCK')
# Enable specific Sphinx directives
from sphinx.directives.other import SeeAlso, Only
directives.register_directive('seealso', SeeAlso)
directives.register_directive('only', Only)
BASE_MODULE = "numpy"
PUBLIC_SUBMODULES = [
'core',
'f2py',
'linalg',
'lib',
'lib.recfunctions',
'fft',
'ma',
'polynomial',
'matrixlib',
'random',
'testing',
]
# Docs for these modules are included in the parent module
OTHER_MODULE_DOCS = {
'fftpack.convolve': 'fftpack',
'io.wavfile': 'io',
'io.arff': 'io',
}
# these names are known to fail doctesting and we like to keep it that way
# e.g. sometimes pseudocode is acceptable etc
#
# Optionally, a subset of methods can be skipped by setting dict-values
# to a container of method-names
DOCTEST_SKIPDICT = {
# cases where NumPy docstrings import things from SciPy:
'numpy.lib.vectorize': None,
'numpy.random.standard_gamma': None,
'numpy.random.gamma': None,
'numpy.random.vonmises': None,
'numpy.random.power': None,
'numpy.random.zipf': None,
# cases where NumPy docstrings import things from other 3'rd party libs:
'numpy.core.from_dlpack': None,
# remote / local file IO with DataSource is problematic in doctest:
'numpy.lib.DataSource': None,
'numpy.lib.Repository': None,
}
if sys.version_info < (3, 9):
DOCTEST_SKIPDICT.update({
"numpy.core.ndarray": {"__class_getitem__"},
"numpy.core.dtype": {"__class_getitem__"},
"numpy.core.number": {"__class_getitem__"},
})
# Skip non-numpy RST files, historical release notes
# Any single-directory exact match will skip the directory and all subdirs.
# Any exact match (like 'doc/release') will scan subdirs but skip files in
# the matched directory.
# Any filename will skip that file
RST_SKIPLIST = [
'scipy-sphinx-theme',
'sphinxext',
'neps',
'changelog',
'doc/release',
'doc/source/release',
'doc/release/upcoming_changes',
'c-info.ufunc-tutorial.rst',
'c-info.python-as-glue.rst',
'f2py.getting-started.rst',
'f2py-examples.rst',
'arrays.nditer.cython.rst',
'how-to-verify-bug.rst',
# See PR 17222, these should be fixed
'basics.dispatch.rst',
'basics.subclassing.rst',
'basics.interoperability.rst',
'misc.rst',
'TESTS.rst'
]
# these names are not required to be present in ALL despite being in
# autosummary:: listing
REFGUIDE_ALL_SKIPLIST = [
r'scipy\.sparse\.linalg',
r'scipy\.spatial\.distance',
r'scipy\.linalg\.blas\.[sdczi].*',
r'scipy\.linalg\.lapack\.[sdczi].*',
]
# these names are not required to be in an autosummary:: listing
# despite being in ALL
REFGUIDE_AUTOSUMMARY_SKIPLIST = [
# NOTE: should NumPy have a better match between autosummary
# listings and __all__? For now, TR isn't convinced this is a
# priority -- focus on just getting docstrings executed / correct
r'numpy\.*',
]
# deprecated windows in scipy.signal namespace
for name in ('barthann', 'bartlett', 'blackmanharris', 'blackman', 'bohman',
'boxcar', 'chebwin', 'cosine', 'exponential', 'flattop',
'gaussian', 'general_gaussian', 'hamming', 'hann', 'hanning',
'kaiser', 'nuttall', 'parzen', 'slepian', 'triang', 'tukey'):
REFGUIDE_AUTOSUMMARY_SKIPLIST.append(r'scipy\.signal\.' + name)
HAVE_MATPLOTLIB = False
def short_path(path, cwd=None):
"""
Return relative or absolute path name, whichever is shortest.
Parameters
----------
path : str or None
cwd : str or None
Returns
-------
str
Relative path or absolute path based on current working directory
"""
if not isinstance(path, str):
return path
if cwd is None:
cwd = os.getcwd()
abspath = os.path.abspath(path)
relpath = os.path.relpath(path, cwd)
if len(abspath) <= len(relpath):
return abspath
return relpath
def find_names(module, names_dict):
"""
Finds the occurrences of function names, special directives like data
and functions and scipy constants in the docstrings of `module`. The
following patterns are searched for:
* 3 spaces followed by function name, and maybe some spaces, some
dashes, and an explanation; only function names listed in
refguide are formatted like this (mostly, there may be some false
positives
* special directives, such as data and function
* (scipy.constants only): quoted list
The `names_dict` is updated by reference and accessible in calling method
Parameters
----------
module : ModuleType
The module, whose docstrings is to be searched
names_dict : dict
Dictionary which contains module name as key and a set of found
function names and directives as value
Returns
-------
None
"""
patterns = [
r"^\s\s\s([a-z_0-9A-Z]+)(\s+-+.*)?$",
r"^\.\. (?:data|function)::\s*([a-z_0-9A-Z]+)\s*$"
]
if module.__name__ == 'scipy.constants':
patterns += ["^``([a-z_0-9A-Z]+)``"]
patterns = [re.compile(pattern) for pattern in patterns]
module_name = module.__name__
for line in module.__doc__.splitlines():
res = re.search(r"^\s*\.\. (?:currentmodule|module):: ([a-z0-9A-Z_.]+)\s*$", line)
if res:
module_name = res.group(1)
continue
for pattern in patterns:
res = re.match(pattern, line)
if res is not None:
name = res.group(1)
entry = '.'.join([module_name, name])
names_dict.setdefault(module_name, set()).add(name)
break
def get_all_dict(module):
"""
Return a copy of the __all__ dict with irrelevant items removed.
Parameters
----------
module : ModuleType
The module whose __all__ dict has to be processed
Returns
-------
deprecated : list
List of callable and deprecated sub modules
not_deprecated : list
List of non callable or non deprecated sub modules
others : list
List of remaining types of sub modules
"""
if hasattr(module, "__all__"):
all_dict = copy.deepcopy(module.__all__)
else:
all_dict = copy.deepcopy(dir(module))
all_dict = [name for name in all_dict
if not name.startswith("_")]
for name in ['absolute_import', 'division', 'print_function']:
try:
all_dict.remove(name)
except ValueError:
pass
if not all_dict:
# Must be a pure documentation module
all_dict.append('__doc__')
# Modules are almost always private; real submodules need a separate
# run of refguide_check.
all_dict = [name for name in all_dict
if not inspect.ismodule(getattr(module, name, None))]
deprecated = []
not_deprecated = []
for name in all_dict:
f = getattr(module, name, None)
if callable(f) and is_deprecated(f):
deprecated.append(name)
else:
not_deprecated.append(name)
others = set(dir(module)).difference(set(deprecated)).difference(set(not_deprecated))
return not_deprecated, deprecated, others
def compare(all_dict, others, names, module_name):
"""
Return sets of objects from all_dict.
Will return three sets:
{in module_name.__all__},
{in REFGUIDE*},
and {missing from others}
Parameters
----------
all_dict : list
List of non deprecated sub modules for module_name
others : list
List of sub modules for module_name
names : set
Set of function names or special directives present in
docstring of module_name
module_name : ModuleType
Returns
-------
only_all : set
only_ref : set
missing : set
"""
only_all = set()
for name in all_dict:
if name not in names:
for pat in REFGUIDE_AUTOSUMMARY_SKIPLIST:
if re.match(pat, module_name + '.' + name):
break
else:
only_all.add(name)
only_ref = set()
missing = set()
for name in names:
if name not in all_dict:
for pat in REFGUIDE_ALL_SKIPLIST:
if re.match(pat, module_name + '.' + name):
if name not in others:
missing.add(name)
break
else:
only_ref.add(name)
return only_all, only_ref, missing
def is_deprecated(f):
"""
Check if module `f` is deprecated
Parameters
----------
f : ModuleType
Returns
-------
bool
"""
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter("error")
try:
f(**{"not a kwarg":None})
except DeprecationWarning:
return True
except Exception:
pass
return False
def check_items(all_dict, names, deprecated, others, module_name, dots=True):
"""
Check that `all_dict` is consistent with the `names` in `module_name`
For instance, that there are no deprecated or extra objects.
Parameters
----------
all_dict : list
names : set
deprecated : list
others : list
module_name : ModuleType
dots : bool
Whether to print a dot for each check
Returns
-------
list
List of [(name, success_flag, output)...]
"""
num_all = len(all_dict)
num_ref = len(names)
output = ""
output += "Non-deprecated objects in __all__: %i\n" % num_all
output += "Objects in refguide: %i\n\n" % num_ref
only_all, only_ref, missing = compare(all_dict, others, names, module_name)
dep_in_ref = only_ref.intersection(deprecated)
only_ref = only_ref.difference(deprecated)
if len(dep_in_ref) > 0:
output += "Deprecated objects in refguide::\n\n"
for name in sorted(deprecated):
output += " " + name + "\n"
if len(only_all) == len(only_ref) == len(missing) == 0:
if dots:
output_dot('.')
return [(None, True, output)]
else:
if len(only_all) > 0:
output += "ERROR: objects in %s.__all__ but not in refguide::\n\n" % module_name
for name in sorted(only_all):
output += " " + name + "\n"
output += "\nThis issue can be fixed by adding these objects to\n"
output += "the function listing in __init__.py for this module\n"
if len(only_ref) > 0:
output += "ERROR: objects in refguide but not in %s.__all__::\n\n" % module_name
for name in sorted(only_ref):
output += " " + name + "\n"
output += "\nThis issue should likely be fixed by removing these objects\n"
output += "from the function listing in __init__.py for this module\n"
output += "or adding them to __all__.\n"
if len(missing) > 0:
output += "ERROR: missing objects::\n\n"
for name in sorted(missing):
output += " " + name + "\n"
if dots:
output_dot('F')
return [(None, False, output)]
def validate_rst_syntax(text, name, dots=True):
"""
Validates the doc string in a snippet of documentation
`text` from file `name`
Parameters
----------
text : str
Docstring text
name : str
File name for which the doc string is to be validated
dots : bool
Whether to print a dot symbol for each check
Returns
-------
(bool, str)
"""
if text is None:
if dots:
output_dot('E')
return False, "ERROR: %s: no documentation" % (name,)
ok_unknown_items = set([
'mod', 'doc', 'currentmodule', 'autosummary', 'data', 'attr',
'obj', 'versionadded', 'versionchanged', 'module', 'class',
'ref', 'func', 'toctree', 'moduleauthor', 'term', 'c:member',
'sectionauthor', 'codeauthor', 'eq', 'doi', 'DOI', 'arXiv', 'arxiv'
])
# Run through docutils
error_stream = io.StringIO()
def resolve(name, is_label=False):
return ("http://foo", name)
token = '<RST-VALIDATE-SYNTAX-CHECK>'
docutils.core.publish_doctree(
text, token,
settings_overrides = dict(halt_level=5,
traceback=True,
default_reference_context='title-reference',
default_role='emphasis',
link_base='',
resolve_name=resolve,
stylesheet_path='',
raw_enabled=0,
file_insertion_enabled=0,
warning_stream=error_stream))
# Print errors, disregarding unimportant ones
error_msg = error_stream.getvalue()
errors = error_msg.split(token)
success = True
output = ""
for error in errors:
lines = error.splitlines()
if not lines:
continue
m = re.match(r'.*Unknown (?:interpreted text role|directive type) "(.*)".*$', lines[0])
if m:
if m.group(1) in ok_unknown_items:
continue
m = re.match(r'.*Error in "math" directive:.*unknown option: "label"', " ".join(lines), re.S)
if m:
continue
output += name + lines[0] + "::\n " + "\n ".join(lines[1:]).rstrip() + "\n"
success = False
if not success:
output += " " + "-"*72 + "\n"
for lineno, line in enumerate(text.splitlines()):
output += " %-4d %s\n" % (lineno+1, line)
output += " " + "-"*72 + "\n\n"
if dots:
output_dot('.' if success else 'F')
return success, output
def output_dot(msg='.', stream=sys.stderr):
stream.write(msg)
stream.flush()
def check_rest(module, names, dots=True):
"""
Check reStructuredText formatting of docstrings
Parameters
----------
module : ModuleType
names : set
Returns
-------
result : list
List of [(module_name, success_flag, output),...]
"""
try:
skip_types = (dict, str, unicode, float, int)
except NameError:
# python 3
skip_types = (dict, str, float, int)
results = []
if module.__name__[6:] not in OTHER_MODULE_DOCS:
results += [(module.__name__,) +
validate_rst_syntax(inspect.getdoc(module),
module.__name__, dots=dots)]
for name in names:
full_name = module.__name__ + '.' + name
obj = getattr(module, name, None)
if obj is None:
results.append((full_name, False, "%s has no docstring" % (full_name,)))
continue
elif isinstance(obj, skip_types):
continue
if inspect.ismodule(obj):
text = inspect.getdoc(obj)
else:
try:
text = str(get_doc_object(obj))
except Exception:
import traceback
results.append((full_name, False,
"Error in docstring format!\n" +
traceback.format_exc()))
continue
m = re.search("([\x00-\x09\x0b-\x1f])", text)
if m:
msg = ("Docstring contains a non-printable character %r! "
"Maybe forgot r\"\"\"?" % (m.group(1),))
results.append((full_name, False, msg))
continue
try:
src_file = short_path(inspect.getsourcefile(obj))
except TypeError:
src_file = None
if src_file:
file_full_name = src_file + ':' + full_name
else:
file_full_name = full_name
results.append((full_name,) + validate_rst_syntax(text, file_full_name, dots=dots))
return results
### Doctest helpers ####
# the namespace to run examples in
DEFAULT_NAMESPACE = {'np': np}
# the namespace to do checks in
CHECK_NAMESPACE = {
'np': np,
'numpy': np,
'assert_allclose': np.testing.assert_allclose,
'assert_equal': np.testing.assert_equal,
# recognize numpy repr's
'array': np.array,
'matrix': np.matrix,
'int64': np.int64,
'uint64': np.uint64,
'int8': np.int8,
'int32': np.int32,
'float32': np.float32,
'float64': np.float64,
'dtype': np.dtype,
'nan': np.nan,
'NaN': np.nan,
'inf': np.inf,
'Inf': np.inf,
'StringIO': io.StringIO,
}
class DTRunner(doctest.DocTestRunner):
"""
The doctest runner
"""
DIVIDER = "\n"
def __init__(self, item_name, checker=None, verbose=None, optionflags=0):
self._item_name = item_name
doctest.DocTestRunner.__init__(self, checker=checker, verbose=verbose,
optionflags=optionflags)
def _report_item_name(self, out, new_line=False):
if self._item_name is not None:
if new_line:
out("\n")
self._item_name = None
def report_start(self, out, test, example):
self._checker._source = example.source
return doctest.DocTestRunner.report_start(self, out, test, example)
def report_success(self, out, test, example, got):
if self._verbose:
self._report_item_name(out, new_line=True)
return doctest.DocTestRunner.report_success(self, out, test, example, got)
def report_unexpected_exception(self, out, test, example, exc_info):
self._report_item_name(out)
return doctest.DocTestRunner.report_unexpected_exception(
self, out, test, example, exc_info)
def report_failure(self, out, test, example, got):
self._report_item_name(out)
return doctest.DocTestRunner.report_failure(self, out, test,
example, got)
class Checker(doctest.OutputChecker):
"""
Check the docstrings
"""
obj_pattern = re.compile('at 0x[0-9a-fA-F]+>')
vanilla = doctest.OutputChecker()
rndm_markers = {'# random', '# Random', '#random', '#Random', "# may vary",
"# uninitialized", "#uninitialized"}
stopwords = {'plt.', '.hist', '.show', '.ylim', '.subplot(',
'set_title', 'imshow', 'plt.show', '.axis(', '.plot(',
'.bar(', '.title', '.ylabel', '.xlabel', 'set_ylim', 'set_xlim',
'# reformatted', '.set_xlabel(', '.set_ylabel(', '.set_zlabel(',
'.set(xlim=', '.set(ylim=', '.set(xlabel=', '.set(ylabel='}
def __init__(self, parse_namedtuples=True, ns=None, atol=1e-8, rtol=1e-2):
self.parse_namedtuples = parse_namedtuples
self.atol, self.rtol = atol, rtol
if ns is None:
self.ns = CHECK_NAMESPACE
else:
self.ns = ns
def check_output(self, want, got, optionflags):
# cut it short if they are equal
if want == got:
return True
# skip stopwords in source
if any(word in self._source for word in self.stopwords):
return True
# skip random stuff
if any(word in want for word in self.rndm_markers):
return True
# skip function/object addresses
if self.obj_pattern.search(got):
return True
# ignore comments (e.g. signal.freqresp)
if want.lstrip().startswith("#"):
return True
# try the standard doctest
try:
if self.vanilla.check_output(want, got, optionflags):
return True
except Exception:
pass
# OK then, convert strings to objects
try:
a_want = eval(want, dict(self.ns))
a_got = eval(got, dict(self.ns))
except Exception:
# Maybe we're printing a numpy array? This produces invalid python
# code: `print(np.arange(3))` produces "[0 1 2]" w/o commas between
# values. So, reinsert commas and retry.
# TODO: handle (1) abberivation (`print(np.arange(10000))`), and
# (2) n-dim arrays with n > 1
s_want = want.strip()
s_got = got.strip()
cond = (s_want.startswith("[") and s_want.endswith("]") and
s_got.startswith("[") and s_got.endswith("]"))
if cond:
s_want = ", ".join(s_want[1:-1].split())
s_got = ", ".join(s_got[1:-1].split())
return self.check_output(s_want, s_got, optionflags)
if not self.parse_namedtuples:
return False
# suppose that "want" is a tuple, and "got" is smth like
# MoodResult(statistic=10, pvalue=0.1).
# Then convert the latter to the tuple (10, 0.1),
# and then compare the tuples.
try:
num = len(a_want)
regex = (r'[\w\d_]+\(' +
', '.join([r'[\w\d_]+=(.+)']*num) +
r'\)')
grp = re.findall(regex, got.replace('\n', ' '))
if len(grp) > 1: # no more than one for now
return False
# fold it back to a tuple
got_again = '(' + ', '.join(grp[0]) + ')'
return self.check_output(want, got_again, optionflags)
except Exception:
return False
# ... and defer to numpy
try:
return self._do_check(a_want, a_got)
except Exception:
# heterog tuple, eg (1, np.array([1., 2.]))
try:
return all(self._do_check(w, g) for w, g in zip(a_want, a_got))
except (TypeError, ValueError):
return False
def _do_check(self, want, got):
# This should be done exactly as written to correctly handle all of
# numpy-comparable objects, strings, and heterogeneous tuples
try:
if want == got:
return True
except Exception:
pass
return np.allclose(want, got, atol=self.atol, rtol=self.rtol)
def _run_doctests(tests, full_name, verbose, doctest_warnings):
"""
Run modified doctests for the set of `tests`.
Parameters
----------
tests : list
full_name : str
verbose : bool
doctest_warnings : bool
Returns
-------
tuple(bool, list)
Tuple of (success, output)
"""
flags = NORMALIZE_WHITESPACE | ELLIPSIS
runner = DTRunner(full_name, checker=Checker(), optionflags=flags,
verbose=verbose)
output = io.StringIO(newline='')
success = True
# Redirect stderr to the stdout or output
tmp_stderr = sys.stdout if doctest_warnings else output
@contextmanager
def temp_cwd():
cwd = os.getcwd()
tmpdir = tempfile.mkdtemp()
try:
os.chdir(tmpdir)
yield tmpdir
finally:
os.chdir(cwd)
shutil.rmtree(tmpdir)
# Run tests, trying to restore global state afterward
cwd = os.getcwd()
with np.errstate(), np.printoptions(), temp_cwd() as tmpdir, \
redirect_stderr(tmp_stderr):
# try to ensure random seed is NOT reproducible
np.random.seed(None)
ns = {}
for t in tests:
# We broke the tests up into chunks to try to avoid PSEUDOCODE
# This has the unfortunate side effect of restarting the global
# namespace for each test chunk, so variables will be "lost" after
# a chunk. Chain the globals to avoid this
t.globs.update(ns)
t.filename = short_path(t.filename, cwd)
# Process our options
if any([SKIPBLOCK in ex.options for ex in t.examples]):
continue
fails, successes = runner.run(t, out=output.write, clear_globs=False)
if fails > 0:
success = False
ns = t.globs
output.seek(0)
return success, output.read()
def check_doctests(module, verbose, ns=None,
dots=True, doctest_warnings=False):
"""
Check code in docstrings of the module's public symbols.
Parameters
----------
module : ModuleType
Name of module
verbose : bool
Should the result be verbose
ns : dict
Name space of module
dots : bool
doctest_warnings : bool
Returns
-------
results : list
List of [(item_name, success_flag, output), ...]
"""
if ns is None:
ns = dict(DEFAULT_NAMESPACE)
# Loop over non-deprecated items
results = []
for name in get_all_dict(module)[0]:
full_name = module.__name__ + '.' + name
if full_name in DOCTEST_SKIPDICT:
skip_methods = DOCTEST_SKIPDICT[full_name]
if skip_methods is None:
continue
else:
skip_methods = None
try:
obj = getattr(module, name)
except AttributeError:
import traceback
results.append((full_name, False,
"Missing item!\n" +
traceback.format_exc()))
continue
finder = doctest.DocTestFinder()
try:
tests = finder.find(obj, name, globs=dict(ns))
except Exception:
import traceback
results.append((full_name, False,
"Failed to get doctests!\n" +
traceback.format_exc()))
continue
if skip_methods is not None:
tests = [i for i in tests if
i.name.partition(".")[2] not in skip_methods]
success, output = _run_doctests(tests, full_name, verbose,
doctest_warnings)
if dots:
output_dot('.' if success else 'F')
results.append((full_name, success, output))
if HAVE_MATPLOTLIB:
import matplotlib.pyplot as plt
plt.close('all')
return results
def check_doctests_testfile(fname, verbose, ns=None,
dots=True, doctest_warnings=False):
"""
Check code in a text file.
Mimic `check_doctests` above, differing mostly in test discovery.
(which is borrowed from stdlib's doctest.testfile here,
https://github.com/python-git/python/blob/master/Lib/doctest.py)
Parameters
----------
fname : str
File name
verbose : bool
ns : dict
Name space
dots : bool
doctest_warnings : bool
Returns
-------
list
List of [(item_name, success_flag, output), ...]
Notes
-----
refguide can be signalled to skip testing code by adding
``#doctest: +SKIP`` to the end of the line. If the output varies or is
random, add ``# may vary`` or ``# random`` to the comment. for example
>>> plt.plot(...) # doctest: +SKIP
>>> random.randint(0,10)
5 # random
We also try to weed out pseudocode:
* We maintain a list of exceptions which signal pseudocode,
* We split the text file into "blocks" of code separated by empty lines
and/or intervening text.
* If a block contains a marker, the whole block is then assumed to be
pseudocode. It is then not being doctested.
The rationale is that typically, the text looks like this:
blah
<BLANKLINE>
>>> from numpy import some_module # pseudocode!
>>> func = some_module.some_function
>>> func(42) # still pseudocode
146
<BLANKLINE>
blah
<BLANKLINE>
>>> 2 + 3 # real code, doctest it
5
"""
if ns is None:
ns = CHECK_NAMESPACE
results = []
_, short_name = os.path.split(fname)
if short_name in DOCTEST_SKIPDICT:
return results
full_name = fname
with open(fname, encoding='utf-8') as f:
text = f.read()
PSEUDOCODE = set(['some_function', 'some_module', 'import example',
'ctypes.CDLL', # likely need compiling, skip it
'integrate.nquad(func,' # ctypes integrate tutotial
])
# split the text into "blocks" and try to detect and omit pseudocode blocks.
parser = doctest.DocTestParser()
good_parts = []
base_line_no = 0
for part in text.split('\n\n'):
try:
tests = parser.get_doctest(part, ns, fname, fname, base_line_no)
except ValueError as e:
if e.args[0].startswith('line '):
# fix line number since `parser.get_doctest` does not increment
# the reported line number by base_line_no in the error message
parts = e.args[0].split()
parts[1] = str(int(parts[1]) + base_line_no)
e.args = (' '.join(parts),) + e.args[1:]
raise
if any(word in ex.source for word in PSEUDOCODE
for ex in tests.examples):
# omit it
pass
else:
# `part` looks like a good code, let's doctest it
good_parts.append((part, base_line_no))
base_line_no += part.count('\n') + 2
# Reassemble the good bits and doctest them:
tests = []
for good_text, line_no in good_parts:
tests.append(parser.get_doctest(good_text, ns, fname, fname, line_no))
success, output = _run_doctests(tests, full_name, verbose,
doctest_warnings)
if dots:
output_dot('.' if success else 'F')
results.append((full_name, success, output))
if HAVE_MATPLOTLIB:
import matplotlib.pyplot as plt
plt.close('all')
return results
def iter_included_files(base_path, verbose=0, suffixes=('.rst',)):
"""
Generator function to walk `base_path` and its subdirectories, skipping
files or directories in RST_SKIPLIST, and yield each file with a suffix in
`suffixes`
Parameters
----------
base_path : str
Base path of the directory to be processed
verbose : int
suffixes : tuple
Yields
------
path
Path of the directory and its sub directories
"""
if os.path.exists(base_path) and os.path.isfile(base_path):
yield base_path
for dir_name, subdirs, files in os.walk(base_path, topdown=True):
if dir_name in RST_SKIPLIST:
if verbose > 0:
sys.stderr.write('skipping files in %s' % dir_name)
files = []
for p in RST_SKIPLIST:
if p in subdirs:
if verbose > 0:
sys.stderr.write('skipping %s and subdirs' % p)
subdirs.remove(p)
for f in files:
if (os.path.splitext(f)[1] in suffixes and
f not in RST_SKIPLIST):
yield os.path.join(dir_name, f)
def check_documentation(base_path, results, args, dots):
"""
Check examples in any *.rst located inside `base_path`.
Add the output to `results`.
See Also
--------
check_doctests_testfile
"""
for filename in iter_included_files(base_path, args.verbose):
if dots:
sys.stderr.write(filename + ' ')
sys.stderr.flush()
tut_results = check_doctests_testfile(
filename,
(args.verbose >= 2), dots=dots,
doctest_warnings=args.doctest_warnings)
# stub out a "module" which is needed when reporting the result
def scratch():
pass
scratch.__name__ = filename
results.append((scratch, tut_results))
if dots:
sys.stderr.write('\n')
sys.stderr.flush()
def init_matplotlib():
"""
Check feasibility of matplotlib initialization.
"""
global HAVE_MATPLOTLIB
try:
import matplotlib
matplotlib.use('Agg')
HAVE_MATPLOTLIB = True
except ImportError:
HAVE_MATPLOTLIB = False
def main(argv):
"""
Validates the docstrings of all the pre decided set of
modules for errors and docstring standards.
"""
parser = ArgumentParser(usage=__doc__.lstrip())
parser.add_argument("module_names", metavar="SUBMODULES", default=[],
nargs='*', help="Submodules to check (default: all public)")
parser.add_argument("--doctests", action="store_true",
help="Run also doctests on ")
parser.add_argument("-v", "--verbose", action="count", default=0)
parser.add_argument("--doctest-warnings", action="store_true",
help="Enforce warning checking for doctests")
parser.add_argument("--rst", nargs='?', const='doc', default=None,
help=("Run also examples from *rst files "
"discovered walking the directory(s) specified, "
"defaults to 'doc'"))
args = parser.parse_args(argv)
modules = []
names_dict = {}
if not args.module_names:
args.module_names = list(PUBLIC_SUBMODULES)
os.environ['SCIPY_PIL_IMAGE_VIEWER'] = 'true'
module_names = list(args.module_names)
for name in module_names:
if name in OTHER_MODULE_DOCS:
name = OTHER_MODULE_DOCS[name]
if name not in module_names:
module_names.append(name)
dots = True
success = True
results = []
errormsgs = []
if args.doctests or args.rst:
init_matplotlib()
for submodule_name in module_names:
prefix = BASE_MODULE + '.'
if not submodule_name.startswith(prefix):
module_name = prefix + submodule_name
else:
module_name = submodule_name
__import__(module_name)
module = sys.modules[module_name]
if submodule_name not in OTHER_MODULE_DOCS:
find_names(module, names_dict)
if submodule_name in args.module_names:
modules.append(module)
if args.doctests or not args.rst:
print("Running checks for %d modules:" % (len(modules),))
for module in modules:
if dots:
sys.stderr.write(module.__name__ + ' ')
sys.stderr.flush()
all_dict, deprecated, others = get_all_dict(module)
names = names_dict.get(module.__name__, set())
mod_results = []
mod_results += check_items(all_dict, names, deprecated, others,
module.__name__)
mod_results += check_rest(module, set(names).difference(deprecated),
dots=dots)
if args.doctests:
mod_results += check_doctests(module, (args.verbose >= 2), dots=dots,
doctest_warnings=args.doctest_warnings)
for v in mod_results:
assert isinstance(v, tuple), v
results.append((module, mod_results))
if dots:
sys.stderr.write('\n')
sys.stderr.flush()
if args.rst:
base_dir = os.path.join(os.path.abspath(os.path.dirname(__file__)), '..')
rst_path = os.path.relpath(os.path.join(base_dir, args.rst))
if os.path.exists(rst_path):
print('\nChecking files in %s:' % rst_path)
check_documentation(rst_path, results, args, dots)
else:
sys.stderr.write(f'\ninvalid --rst argument "{args.rst}"')
errormsgs.append('invalid directory argument to --rst')
if dots:
sys.stderr.write("\n")
sys.stderr.flush()
# Report results
for module, mod_results in results:
success = all(x[1] for x in mod_results)
if not success:
errormsgs.append(f'failed checking {module.__name__}')
if success and args.verbose == 0:
continue
print("")
print("=" * len(module.__name__))
print(module.__name__)
print("=" * len(module.__name__))
print("")
for name, success, output in mod_results:
if name is None:
if not success or args.verbose >= 1:
print(output.strip())
print("")
elif not success or (args.verbose >= 2 and output.strip()):
print(name)
print("-"*len(name))
print("")
print(output.strip())
print("")
if len(errormsgs) == 0:
print("\nOK: all checks passed!")
sys.exit(0)
else:
print('\nERROR: ', '\n '.join(errormsgs))
sys.exit(1)
if __name__ == '__main__':
main(argv=sys.argv[1:])
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