#
# 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 pytest
-
-
-@pytest.fixture()
-def cleandir():
- """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
- """
- oldpath = os.getcwd()
- newpath = tempfile.mkdtemp()
- os.chdir(newpath)
- yield newpath
- os.chdir(oldpath)
- # TODO: Allow override to prevent removal of the temporary directory
- shutil.rmtree(newpath)
+pytest_plugins = ('gmxapi.testsupport',)
@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.
- command = shutil.which('gmx')
- 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('gmx', path=gmxbindir)
- else:
- message = "Tests need 'gmx' command line tool, but could not find it on the path."
- raise RuntimeError(message)
- 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):
- """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:
# # Ref https://setuptools.readthedocs.io/en/latest/setuptools.html#including-data-files
# from gmx.data import tprfilename
- tempdir = tempfile.mkdtemp()
-
- testdir = os.path.dirname(__file__)
- with open(os.path.join(testdir, 'testdata.json'), 'r') as fh:
- testdata = json.load(fh)
-
- # TODO: (#2756) Don't rely on so many automagical behaviors (as described in comments below)
-
- structurefile = os.path.join(tempdir, 'structure.gro')
- # We let `gmx solvate` use the default solvent. Otherwise, we would do
- # gro_input = testdata['solvent_structure']
- # with open(structurefile, 'w') as fh:
- # fh.write('\n'.join(gro_input))
- # fh.write('\n')
-
- topfile = os.path.join(tempdir, 'topology.top')
- top_input = testdata['solvent_topology']
- # `gmx solvate` will append a line to the provided file with the molecule count,
- # so we strip the last line from the input topology.
- with open(topfile, 'w') as fh:
- fh.write('\n'.join(top_input[:-1]))
- fh.write('\n')
-
- solvate = gmx.commandline_operation(gmxcli,
- arguments=['solvate', '-box', '5', '5', '5'],
- # We use the default solvent instead of specifying one.
- # input_files={'-cs': structurefile},
- output_files={'-p': topfile,
- '-o': structurefile,
- }
- )
- if solvate.output.returncode.result() != 0:
- logging.debug(solvate.output.erroroutput.result())
- raise RuntimeError('solvate failed in spc_water_box testing fixture.')
-
- mdp_input = [('integrator', 'md'),
- ('cutoff-scheme', 'Verlet'),
- ('nsteps', 2),
- ('nstxout', 1),
- ('nstvout', 1),
- ('nstfout', 1),
- ('tcoupl', 'v-rescale'),
- ('tc-grps', 'System'),
- ('tau-t', 1),
- ('ref-t', 298)]
- mdp_input = '\n'.join([' = '.join([str(item) for item in kvpair]) for kvpair in mdp_input])
- mdpfile = os.path.join(tempdir, 'md.mdp')
- with open(mdpfile, 'w') as fh:
- fh.write(mdp_input)
- fh.write('\n')
- tprfile = os.path.join(tempdir, 'topol.tpr')
- # We don't use mdout_mdp, but if we don't specify it to grompp,
- # it will be created in the current working directory.
- mdout_mdp = os.path.join(tempdir, 'mdout.mdp')
-
- grompp = gmx.commandline_operation(gmxcli, 'grompp',
- input_files={
- '-f': mdpfile,
- '-p': solvate.output.file['-p'],
- '-c': solvate.output.file['-o'],
- '-po': mdout_mdp,
- },
- output_files={'-o': tprfile})
- tprfilename = grompp.output.file['-o'].result()
- if grompp.output.returncode.result() != 0:
- logging.debug(grompp.output.erroroutput.result())
- raise RuntimeError('grompp failed in spc_water_box testing fixture.')
-
- # TODO: more inspection of grompp errors...
- assert os.path.exists(tprfilename)
- yield tprfilename
-
- # Clean up.
- # Note: these lines are not executed (and tempdir is not removed) if there
- # are exceptions before `yield`
- # TODO: Allow override to prevent removal of the temporary directory
- shutil.rmtree(tempdir)
+ with _cleandir(remove_tempdir) as tempdir:
+
+ testdir = os.path.dirname(__file__)
+ with open(os.path.join(testdir, 'testdata.json'), 'r') as fh:
+ testdata = json.load(fh)
+
+ # TODO: (#2756) Don't rely on so many automagical behaviors (as described in comments below)
+
+ structurefile = os.path.join(tempdir, 'structure.gro')
+ # We let `gmx solvate` use the default solvent. Otherwise, we would do
+ # gro_input = testdata['solvent_structure']
+ # with open(structurefile, 'w') as fh:
+ # fh.write('\n'.join(gro_input))
+ # fh.write('\n')
+
+ topfile = os.path.join(tempdir, 'topology.top')
+ top_input = testdata['solvent_topology']
+ # `gmx solvate` will append a line to the provided file with the molecule count,
+ # so we strip the last line from the input topology.
+ with open(topfile, 'w') as fh:
+ fh.write('\n'.join(top_input[:-1]))
+ fh.write('\n')
+
+ assert os.path.exists(topfile)
+ solvate = gmx.commandline_operation(gmxcli,
+ arguments=['solvate', '-box', '5', '5', '5'],
+ # We use the default solvent instead of specifying one.
+ # input_files={'-cs': structurefile},
+ output_files={'-p': topfile,
+ '-o': structurefile,
+ }
+ )
+ assert os.path.exists(topfile)
+
+ if solvate.output.returncode.result() != 0:
+ 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.
+ mdp_input = [('integrator', 'md'),
+ ('dt', dt),
+ ('cutoff-scheme', 'Verlet'),
+ ('nsteps', 2),
+ ('nstxout', 1),
+ ('nstvout', 1),
+ ('nstfout', 1),
+ ('tcoupl', 'v-rescale'),
+ ('tc-grps', 'System'),
+ ('tau-t', 1),
+ ('ref-t', 298)]
+ mdp_input = '\n'.join([' = '.join([str(item) for item in kvpair]) for kvpair in mdp_input])
+ mdpfile = os.path.join(tempdir, 'md.mdp')
+ with open(mdpfile, 'w') as fh:
+ fh.write(mdp_input)
+ fh.write('\n')
+ tprfile = os.path.join(tempdir, 'topol.tpr')
+ # We don't use mdout_mdp, but if we don't specify it to grompp,
+ # it will be created in the current working directory.
+ mdout_mdp = os.path.join(tempdir, 'mdout.mdp')
+
+ grompp = gmx.commandline_operation(gmxcli, 'grompp',
+ input_files={
+ '-f': mdpfile,
+ '-p': solvate.output.file['-p'],
+ '-c': solvate.output.file['-o'],
+ '-po': mdout_mdp,
+ },
+ output_files={'-o': tprfile})
+ tprfilename = grompp.output.file['-o'].result()
+ if grompp.output.returncode.result() != 0:
+ 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)
+ 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