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# Copyright 2011-2016 by Peter Cock. All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
# This script looks for entries in the LaTeX source for the
# Biopython Tutorial which can be turned into Python doctests,
# e.g.
# %doctest
# \begin{verbatim}
# >>> from Bio.Alphabet import generic_dna
# >>> from Bio.Seq import Seq
# >>> len("ACGT")
# 4
# \end{verbatim}
# Code snippets can be extended using a similar syntax, which
# will create a single combined doctest:
# %cont-doctest
# \begin{verbatim}
# >>> Seq("ACGT") == Seq("ACGT", generic_dna)
# True
# \end{verbatim}
# The %doctest line also supports a relative working directory,
# and listing multiple Python dependencies as lib:XXX which will
# ensure "import XXX" works before using the test. e.g.
# %doctest examples lib:numpy lib:scipy
# Additionally after the path, special keyword 'internet' is
# used to flag online tests.
# Note if using lib:XXX or special value 'internet' you must
# include a relative path to the working directory, just use '.'
# for the default path, e.g.
# %doctest . lib:reportlab
# %doctest . internet
# TODO: Adding bin:XXX for checking binary XXX is on $PATH?
# See also "Writing doctests in the Tutorial" in the Tutorial
# itself.
# This future import will apply to all the doctests too:
from __future__ import print_function
from Bio._py3k import _universal_read_mode
import unittest
import doctest
import os
import sys
import warnings
from Bio import BiopythonExperimentalWarning, MissingExternalDependencyError
# This is the same mechanism used for --offline
# to skip tests requiring the network.
import requires_internet
online = True
except MissingExternalDependencyError:
online = False
if "--offline" in sys.argv:
# Allow manual override via "python --offline"
online = False
warnings.simplefilter('ignore', BiopythonExperimentalWarning)
if sys.version_info[0] >= 3:
from lib2to3 import refactor
from lib2to3.pgen2.tokenize import TokenError
fixers = refactor.get_fixers_from_package("lib2to3.fixes")
fixers.remove("lib2to3.fixes.fix_print") # Already using print function
rt = refactor.RefactoringTool(fixers)
assert rt.refactor_docstring(">>> print(2+2)\n4\n", "example1") == \
">>> print(2+2)\n4\n"
assert rt.refactor_docstring('>>> print("Two plus two is", 2+2)\n'
'Two plus two is 4\n', "example2") == \
'>>> print("Two plus two is", 2+2)\nTwo plus two is 4\n'
# Cache this to restore the cwd at the end of the tests
original_path = os.path.abspath(".")
if os.path.basename(sys.argv[0]) == "":
# sys.argv[0] will be (relative) path to - use this to allow, e.g.
# [base]$ python Tests/
# [Tests/]$ python
tutorial_base = os.path.abspath(os.path.join(os.path.dirname(sys.argv[0]), "../Doc/"))
tutorial = os.path.join(tutorial_base, "Tutorial.tex")
# Probably called via so current directory should (now) be Tests/
# but may have been changed by so can't infer from sys.argv[0] with e.g.
# [base]$ python Tests/ test_Tutorial
tutorial_base = os.path.abspath("../Doc/")
tutorial = os.path.join(tutorial_base, "Tutorial.tex")
if not os.path.isfile(tutorial):
from Bio import MissingExternalDependencyError
raise MissingExternalDependencyError("Could not find ../Doc/Tutorial.tex file")
# Build a list of all the Tutorial LaTeX files:
files = [tutorial]
for latex in os.listdir(os.path.join(tutorial_base, "Tutorial/")):
if latex.startswith("chapter_") and latex.endswith(".tex"):
files.append(os.path.join(tutorial_base, "Tutorial", latex))
def _extract(handle):
line = handle.readline()
if line != "\\begin{verbatim}\n":
raise ValueError("Any '%doctest' or '%cont-doctest' line should be followed by '\\begin{verbatim}'")
lines = []
while True:
line = handle.readline()
if not line:
if lines:
raise ValueError("Didn't find end of test starting: %r", lines[0])
raise ValueError("Didn't find end of test!")
elif line.startswith("\end{verbatim}"):
return lines
def extract_doctests(latex_filename):
"""Scan LaTeX file and pull out marked doctests as strings.
This is a generator, yielding one tuple per doctest.
base_name = os.path.splitext(os.path.basename(latex_filename))[0]
deps = ""
folder = ""
with open(latex_filename, _universal_read_mode) as handle:
line_number = 0
lines = []
name = None
while True:
line = handle.readline()
line_number += 1
if not line:
# End of file
elif line.startswith("%cont-doctest"):
x = _extract(handle)
line_number += len(x) + 2
elif line.startswith("%doctest"):
if lines:
if not lines[0].startswith(">>> "):
raise ValueError("Should start '>>> ' not %r" % lines[0])
yield name, "".join(lines), folder, deps
lines = []
deps = [x.strip() for x in line.split()[1:]]
if deps:
folder = deps[0]
deps = deps[1:]
folder = ""
name = "test_%s_line_%05i" % (base_name, line_number)
x = _extract(handle)
line_number += len(x) + 2
if lines:
if not lines[0].startswith(">>> "):
raise ValueError("Should start '>>> ' not %r" % lines[0])
yield name, "".join(lines), folder, deps
# yield "dummy", ">>> 2 + 2\n5\n"
class TutorialDocTestHolder(object):
"""Python doctests extracted from the Biopython Tutorial."""
def check_deps(dependencies):
"""Check 'lib:XXX' and 'internet' dependencies are met."""
missing = []
for dep in dependencies:
if dep == "internet":
if not online:
assert dep.startswith("lib:"), dep
lib = dep[4:]
tmp = __import__(lib)
del tmp
except ImportError:
return missing
# Create dummy methods on the object purely to hold doctests
missing_deps = set()
for latex in files:
# print("Extracting doctests from %s" % latex)
for name, example, folder, deps in extract_doctests(latex):
missing = check_deps(deps)
if missing:
if sys.version_info[0] >= 3:
example = ">>> from __future__ import print_function\n" + example
example = rt.refactor_docstring(example, name)
except TokenError:
raise ValueError("Problem with %s:\n%s" % (name, example))
def funct(n, d, f):
global tutorial_base
method = lambda x: None
if f:
p = os.path.join(tutorial_base, f)
method.__doc__ = "%s\n\n>>> import os\n>>> os.chdir(%r)\n%s\n" \
% (n, p, d)
method.__doc__ = "%s\n\n%s\n" % (n, d)
method._folder = f
return method
"doctest_%s" % name.replace(" ", "_"),
funct(name, example, folder))
del funct
# This is a TestCase class so it is found by
class TutorialTestCase(unittest.TestCase):
"""Python doctests extracted from the Biopython Tutorial."""
# Single method to be invoked by
def test_doctests(self):
"""Run tutorial doctests."""
# TODO: Remove IGNORE_EXCEPTION_DETAIL once drop Python 2 support
runner = doctest.DocTestRunner(optionflags=doctest.IGNORE_EXCEPTION_DETAIL)
failures = []
for test in doctest.DocTestFinder().find(TutorialDocTestHolder):
failed, success =
if failed:
name =
assert name.startswith("TutorialDocTestHolder.doctest_")
# raise ValueError("Tutorial doctest %s failed" %[30:])
if failures:
raise ValueError("%i Tutorial doctests failed: %s" %
(len(failures), ", ".join(failures)))
def tearDown(self):
global original_path
# This is to run the doctests if the script is called directly:
if __name__ == "__main__":
if missing_deps:
print("Skipping tests needing the following:")
for dep in sorted(missing_deps):
print(" - %s" % dep)
print("Running Tutorial doctests...")
tests = doctest.testmod()
if tests.failed:
raise RuntimeError("%i/%i tests failed" % tests)
print("Tests done")