pymatgen.util.testing — pymatgen 2020.7.3 documentation

# Source code for pymatgen.util.testing

    # coding: utf-8
    # Copyright (c) Pymatgen Development Team.
    # Distributed under the terms of the MIT License.

    """
    Common test support for pymatgen test scripts.

    This single module should provide all the common functionality for pymatgen
    tests in a single location, so that test scripts can just import it and work
    right away.
    """

    import unittest
    import tempfile
    import numpy.testing as nptu
    from io import open
    from pathlib import Path
    import json

    from monty.json import MontyDecoder
    from monty.serialization import loadfn
    from monty.json import MSONable
    from monty.dev import requires

    from pymatgen import SETTINGS, MPRester

    class PymatgenTest(unittest.TestCase):
        """
        Extends unittest.TestCase with functions (taken from numpy.testing.utils)
        that support the comparison of arrays.
        """
        _multiprocess_shared_ = True
        MODULE_DIR = Path(__file__).absolute().parent
        STRUCTURES_DIR = MODULE_DIR / "structures"
        TEST_FILES_DIR = MODULE_DIR / ".." / ".." / "test_files"
        """
        Dict for test structures to aid testing.
        """
        TEST_STRUCTURES = {}
        for fn in STRUCTURES_DIR.iterdir():
            TEST_STRUCTURES[fn.name.rsplit(".", 1)[0]] = loadfn(str(fn))

        @classmethod
        def get_structure(cls, name):
            """
            Get a structure from the template directories.

            :param name: Name of a structure.
            :return: Structure
            """
            return cls.TEST_STRUCTURES[name].copy()

        @classmethod
        @requires(SETTINGS.get("PMG_MAPI_KEY"), "PMG_MAPI_KEY needs to be set.")
        def get_mp_structure(cls, mpid):
            """
            Get a structure from MP.

            :param mpid: Materials Project id.
            :return: Structure
            """
            m = MPRester()
            return m.get_structure_by_material_id(mpid)

        @staticmethod
        def assertArrayAlmostEqual(actual, desired, decimal=7, err_msg='',
                                   verbose=True):
            """
            Tests if two arrays are almost equal to a tolerance. The CamelCase
            naming is so that it is consistent with standard unittest methods.
            """
            return nptu.assert_almost_equal(actual, desired, decimal, err_msg,
                                            verbose)

        @staticmethod
        def assertDictsAlmostEqual(actual, desired, decimal=7, err_msg='',
                                   verbose=True):
            """
            Tests if two arrays are almost equal to a tolerance. The CamelCase
            naming is so that it is consistent with standard unittest methods.
            """

            for k, v in actual.items():
                if k not in desired:
                    return False
                v2 = desired[k]
                if isinstance(v, dict):
                    pass_test = PymatgenTest.assertDictArraysAlmostEqual(
                        v, v2, decimal=decimal, err_msg=err_msg, verbose=verbose)
                    if not pass_test:
                        return False
                elif isinstance(v, (list, tuple)):
                    pass_test = nptu.assert_almost_equal(v, v2, decimal, err_msg,
                                                         verbose)
                    if not pass_test:
                        return False
                elif isinstance(v, (int, float)):
                    pass_test = PymatgenTest.assertAlmostEqual(v, v2)
                    if not pass_test:
                        return False
                else:
                    assert v == v2
            return True

        @staticmethod
        def assertArrayEqual(actual, desired, err_msg='', verbose=True):
            """
            Tests if two arrays are equal. The CamelCase naming is so that it is
             consistent with standard unittest methods.
            """
            return nptu.assert_equal(actual, desired, err_msg=err_msg,
                                     verbose=verbose)

        @staticmethod
        def assertStrContentEqual(actual, desired, err_msg='', verbose=True):
            """
            Tests if two strings are equal, ignoring things like trailing spaces,
            etc.
            """
            lines1 = actual.split("\n")
            lines2 = desired.split("\n")
            if len(lines1) != len(lines2):
                return False
            failed = []
            for l1, l2 in zip(lines1, lines2):
                if l1.strip() != l2.strip():
                    failed.append("%s != %s" % (l1, l2))
            return len(failed) == 0

        def serialize_with_pickle(self, objects, protocols=None, test_eq=True):
            """
            Test whether the object(s) can be serialized and deserialized with
            pickle. This method tries to serialize the objects with pickle and the
            protocols specified in input. Then it deserializes the pickle format
            and compares the two objects with the __eq__ operator if
            test_eq == True.

            Args:
                objects: Object or list of objects.
                protocols: List of pickle protocols to test. If protocols is None,
                    HIGHEST_PROTOCOL is tested.

            Returns:
                Nested list with the objects deserialized with the specified
                protocols.
            """
            # Use the python version so that we get the traceback in case of errors
            import pickle as pickle
            from pymatgen.util.serialization import pmg_pickle_load, \
                pmg_pickle_dump

            # Build a list even when we receive a single object.
            got_single_object = False
            if not isinstance(objects, (list, tuple)):
                got_single_object = True
                objects = [objects]

            if protocols is None:
                # protocols = set([0, 1, 2] + [pickle.HIGHEST_PROTOCOL])
                protocols = [pickle.HIGHEST_PROTOCOL]

            # This list will contains the object deserialized with the different
            # protocols.
            objects_by_protocol, errors = [], []

            for protocol in protocols:
                # Serialize and deserialize the object.
                mode = "wb"
                fd, tmpfile = tempfile.mkstemp(text="b" not in mode)

                try:
                    with open(tmpfile, mode) as fh:
                        pmg_pickle_dump(objects, fh, protocol=protocol)
                except Exception as exc:
                    errors.append("pickle.dump with protocol %s raised:\n%s" %
                                  (protocol, str(exc)))
                    continue

                try:
                    with open(tmpfile, "rb") as fh:
                        new_objects = pmg_pickle_load(fh)
                except Exception as exc:
                    errors.append("pickle.load with protocol %s raised:\n%s" %
                                  (protocol, str(exc)))
                    continue

                # Test for equality
                if test_eq:
                    for old_obj, new_obj in zip(objects, new_objects):
                        self.assertEqual(old_obj, new_obj)

                # Save the deserialized objects and test for equality.
                objects_by_protocol.append(new_objects)

            if errors:
                raise ValueError("\n".join(errors))

            # Return nested list so that client code can perform additional tests.
            if got_single_object:
                return [o[0] for o in objects_by_protocol]
            else:
                return objects_by_protocol

        def tmpfile_write(self, string):
            """
            Write string to a temporary file. Returns the name of the temporary
            file.
            """
            fd, tmpfile = tempfile.mkstemp(text=True)

            with open(tmpfile, "w") as fh:
                fh.write(string)

            return tmpfile

        def assertMSONable(self, obj, test_if_subclass=True):
            """
            Tests if obj is MSONable and tries to verify whether the contract is
            fulfilled.

            By default, the method tests whether obj is an instance of MSONable.
            This check can be deactivated by setting test_if_subclass to False.
            """
            if test_if_subclass:
                self.assertIsInstance(obj, MSONable)
            self.assertDictEqual(obj.as_dict(), obj.__class__.from_dict(
                obj.as_dict()).as_dict())
            json.loads(obj.to_json(), cls=MontyDecoder)