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# Copyright 2010 by Eric Talevich. All rights reserved.
# Copyright 2012 by Wibowo Arindrarto. All rights reserved.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Common utility functions for various Bio submodules."""
import os
def find_test_dir(start_dir=None):
"""Find the absolute path of Biopython's Tests directory.
Arguments:
start_dir -- Initial directory to begin lookup (default to current dir)
If the directory is not found up the filesystem's root directory, an
exception will be raised.
"""
if not start_dir:
# no callbacks in function signatures!
# defaults to the current directory
# (using __file__ would give the installed Biopython)
start_dir = "."
target = os.path.abspath(start_dir)
while True:
if os.path.isdir(os.path.join(target, "Bio")) and os.path.isdir(
os.path.join(target, "Tests")
):
# Good, we're in the Biopython root now
return os.path.abspath(os.path.join(target, "Tests"))
# Recurse up the tree
# TODO - Test this on Windows
new, tmp = os.path.split(target)
if target == new:
# Reached root
break
target = new
raise ValueError(
"Not within Biopython source tree: %r" % os.path.abspath(start_dir)
)
def run_doctest(target_dir=None, *args, **kwargs):
"""Run doctest for the importing module."""
import doctest
# default doctest options
default_kwargs = {"optionflags": doctest.ELLIPSIS}
kwargs.update(default_kwargs)
cur_dir = os.path.abspath(os.curdir)
print("Running doctests...")
try:
os.chdir(find_test_dir(target_dir))
doctest.testmod(*args, **kwargs)
finally:
# and revert back to initial directory
os.chdir(cur_dir)
print("Done")
if __name__ == "__main__":
run_doctest()
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