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# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8
#
# MDAnalysis --- https://www.mdanalysis.org
# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#
# Released under the GNU Public Licence, v2 or any higher version
#
# Please cite your use of MDAnalysis in published work:
#
# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler,
# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein.
# MDAnalysis: A Python package for the rapid analysis of molecular dynamics
# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th
# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy.
# doi: 10.25080/majora-629e541a-00e
#
# N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein.
# MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations.
# J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787
#
"""
Test the user facing API is as we expect...
"""
import importlib
import os
from pathlib import PurePath
import pytest
from numpy.testing import assert_equal
import MDAnalysis as mda
mda_dirname = os.path.dirname(mda.__file__)
def test_Universe():
assert mda.Universe is mda.core.universe.Universe
def test_fetch_mmtf():
assert mda.fetch_mmtf is mda.coordinates.MMTF.fetch_mmtf
def test_Writer():
assert mda.Writer is mda.coordinates.core.writer
def test_AtomGroup():
assert mda.AtomGroup is mda.core.groups.AtomGroup
def test_ResidueGroup():
assert mda.ResidueGroup is mda.core.groups.ResidueGroup
def test_SegmentGroup():
assert mda.SegmentGroup is mda.core.groups.SegmentGroup
def init_files():
"""A generator yielding all MDAnalysis __init__ files."""
os.chdir(mda_dirname)
for root, dirs, files in os.walk("."):
if "__init__.py" in files:
submodule = ".".join(PurePath(root).parts)
submodule = "."*(len(submodule) > 0) + submodule
yield submodule
@pytest.mark.parametrize('submodule', init_files())
def test_all_import(submodule):
module = importlib.import_module("MDAnalysis" + submodule)
module_path = os.path.join(mda_dirname, *submodule.split("."))
if hasattr(module, "__all__"):
missing = [name for name in module.__all__
if name not in module.__dict__.keys()
and name not in [os.path.splitext(f)[0] for
f in os.listdir(module_path)]]
assert_equal(missing, [], err_msg="{}".format(submodule) +
" has errors in __all__ list: " +
"missing = {}".format(missing))
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