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"""Configuration and fixtures for pytest."""

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.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') from E
    yield command


@pytest.fixture(scope='class')
def spc216(gmxcli):
    """Provide a TPR input file for a simple simulation.

    Prepare the MD input in a freshly created working directory.
    """
    import gmxapi as gmx

    # TODO: (#2896) Fetch MD input from package / library data.
    # Example:
    #     import pkg_resources
    #     # Note: importing pkg_resources means setuptools is required for running this test.
    #     # Get or build TPR file from data bundled via setup(package_data=...)
    #     # 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,
                                                      }
                                        )
    assert solvate.output.returncode.result() == 0

    mdp_input = [('integrator', 'md'),
                 ('cutoff-scheme', 'Verlet'),
                 ('nsteps', 1000),
                 ('nstxout', 100),
                 ('nstvout', 100),
                 ('nstfout', 100),
                 ('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('\n'.join(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 spc216 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)
