#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2019, by the GROMACS development team, led by
+# Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
import json
import logging
import os
-import shutil
-import tempfile
-import warnings
-from contextlib import contextmanager
import pytest
pytest_plugins = ('gmxapi.testsupport',)
-def pytest_addoption(parser):
- """Add a command-line user option for the pytest invocation."""
- parser.addoption(
- '--rm',
- action='store',
- default='always',
- choices=['always', 'never', 'success'],
- help='Remove temporary directories "always", "never", or on "success".'
- )
-
-
-@pytest.fixture(scope='session')
-def remove_tempdir(request):
- """pytest fixture to get access to the --rm CLI option."""
- return request.config.getoption('--rm')
-
-
-@contextmanager
-def scoped_chdir(dir):
- oldpath = os.getcwd()
- os.chdir(dir)
- try:
- yield dir
- # If the `with` block using scoped_chdir produces an exception, it will
- # be raised at this point in this function. We want the exception to
- # propagate out of the `with` block, but first we want to restore the
- # original working directory, so we skip `except` but provide a `finally`.
- finally:
- os.chdir(oldpath)
-
-
-@contextmanager
-def _cleandir(remove_tempdir):
- """Context manager for a clean temporary working directory.
-
- Arguments:
- remove_tempdir (str): whether to remove temporary directory "always",
- "never", or on "success"
-
- The context manager will issue a warning for each temporary directory that
- is not removed.
- """
-
- newpath = tempfile.mkdtemp()
-
- def remove():
- shutil.rmtree(newpath)
-
- def warn():
- warnings.warn('Temporary directory not removed: {}'.format(newpath))
-
- if remove_tempdir == 'always':
- callback = remove
- else:
- callback = warn
- try:
- with scoped_chdir(newpath):
- yield newpath
- # If we get to this line, the `with` block using _cleandir did not throw.
- # Clean up the temporary directory unless the user specified `--rm never`.
- # I.e. If the user specified `--rm success`, then we need to toggle from `warn` to `remove`.
- if remove_tempdir != 'never':
- callback = remove
- finally:
- callback()
-
-
-@pytest.fixture
-def cleandir(remove_tempdir):
- """Provide a clean temporary working directory for a test.
-
- Example usage:
-
- import os
- import pytest
-
- @pytest.mark.usefixtures("cleandir")
- def test_cwd_starts_empty():
- assert os.listdir(os.getcwd()) == []
- with open("myfile", "w") as f:
- f.write("hello")
-
- def test_cwd_also_starts_empty(cleandir):
- assert os.listdir(os.getcwd()) == []
- assert os.path.abspath(os.getcwd()) == os.path.abspath(cleandir)
- with open("myfile", "w") as f:
- f.write("hello")
-
- @pytest.mark.usefixtures("cleandir")
- class TestDirectoryInit(object):
- def test_cwd_starts_empty(self):
- assert os.listdir(os.getcwd()) == []
- with open("myfile", "w") as f:
- f.write("hello")
-
- def test_cwd_also_starts_empty(self):
- assert os.listdir(os.getcwd()) == []
- with open("myfile", "w") as f:
- f.write("hello")
-
- Ref: https://docs.pytest.org/en/latest/fixture.html#using-fixtures-from-classes-modules-or-projects
- """
- with _cleandir(remove_tempdir) as newdir:
- yield newdir
-
@pytest.fixture(scope='session')
-def gmxcli():
- # TODO: (#2896) Find a more canonical way to identify the GROMACS commandline wrapper binary.
- # We should be able to get the GMXRC contents and related hints from a gmxapi
- # package resource or from module attributes of a ``gromacs`` stub package.
- allowed_command_names = ['gmx', 'gmx_mpi']
- command = None
- for command_name in allowed_command_names:
- if command is not None:
- break
- command = shutil.which(command_name)
- if command is None:
- gmxbindir = os.getenv('GMXBIN')
- if gmxbindir is None:
- gromacsdir = os.getenv('GROMACS_DIR')
- if gromacsdir is not None and gromacsdir != '':
- gmxbindir = os.path.join(gromacsdir, 'bin')
- if gmxbindir is None:
- gmxapidir = os.getenv('gmxapi_DIR')
- if gmxapidir is not None and gmxapidir != '':
- gmxbindir = os.path.join(gmxapidir, 'bin')
- if gmxbindir is not None:
- gmxbindir = os.path.abspath(gmxbindir)
- command = shutil.which(command_name, path=gmxbindir)
- if command is None:
- message = "Tests need 'gmx' command line tool, but could not find it on the path."
- raise RuntimeError(message)
- try:
- assert os.access(command, os.X_OK)
- except Exception as E:
- raise RuntimeError('"{}" is not an executable gmx wrapper program'.format(command)) from E
- yield command
-
-
-@pytest.fixture(scope='class')
-def spc_water_box(gmxcli, remove_tempdir):
- """Provide a TPR input file for a simple simulation.
+def spc_water_box_collection(gmxcli, remove_tempdir):
+ """Provide a collection of simulation input items for a simple simulation.
Prepare the MD input in a freshly created working directory.
+ Solvate a 5nm cubic box with spc water. Return a dictionary of the artifacts produced.
"""
import gmxapi as gmx
+ # TODO: Remove this import when the the spc_water_box fixture is migrated to gmxapi.testsupport
+ from gmxapi.testsupport import _cleandir
# TODO: (#2896) Fetch MD input from package / library data.
# Example:
assert os.path.exists(topfile)
if solvate.output.returncode.result() != 0:
- logging.debug(solvate.output.erroroutput.result())
+ logging.debug(solvate.output.stderr.result())
raise RuntimeError('solvate failed in spc_water_box testing fixture.')
# Choose an exactly representable dt of 2^-9 ps (approximately 0.002)
- dt = 2.**-9.
+ dt = 2. ** -9.
mdp_input = [('integrator', 'md'),
('dt', dt),
('cutoff-scheme', 'Verlet'),
output_files={'-o': tprfile})
tprfilename = grompp.output.file['-o'].result()
if grompp.output.returncode.result() != 0:
- logging.debug(grompp.output.erroroutput.result())
+ logging.debug(grompp.output.stderr.result())
raise RuntimeError('grompp failed in spc_water_box testing fixture.')
# TODO: more inspection of grompp errors...
assert os.path.exists(tprfilename)
- yield tprfilename
+ collection = {
+ 'tpr_filename': tprfilename,
+ 'mdp_input_filename': mdpfile,
+ 'mdp_output_filename': mdout_mdp,
+ 'topology_filename': solvate.output.file['-p'].result(),
+ 'gro_filename': solvate.output.file['-o'].result(),
+ 'mdp_input_list': mdp_input
+ }
+ yield collection
+
+
+@pytest.fixture(scope='session')
+def spc_water_box(spc_water_box_collection):
+ """Provide a TPR input file for a simple simulation."""
+ yield spc_water_box_collection['tpr_filename']
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff