# -*- coding: utf-8 -*-
"""
Created on Fri Jun 10 21:00:21 2016

@author: MaxBohnet
"""

import tempfile
import numpy as np
import pytest
import xarray as xr

from cythonarrays.tests.example_python import Example
import pyximport; pyximport.install()
from .example_cython import (_Example)


@pytest.fixture(scope='class')
def km_ij(request):
    """
    travel times
    """
    array = np.array([[1, 4, 5],
                      [2, 1, 7],
                      [5, 7, 2]])
    return array


@pytest.fixture(scope='class')
def jobs(request):
    """
    jobs
    """
    jobs = np.array([100, 200, 300])
    return jobs


@pytest.fixture(scope='class')
def params_groups(request):
    """
    different values for saving categories
    """
    return np.array([-0.2, -0.1])


@pytest.fixture(scope='class')
def persons_gi(request):
    """
    different values for home zone
    """
    arr = np.array([[100, 0, 200],
                    [0, 250, 50]])
    return arr


@pytest.fixture(scope='class')
def example(km_ij, jobs, params_groups, persons_gi):
    """
    different values for home zone
    """
    groups, zones = persons_gi.shape
    example = Example(groups, zones)
    example.set_array('km_ij', km_ij)
    example.set_array('jobs_j', jobs)
    example.set_array('param_g', params_groups)
    example.set_array('persons_gi', persons_gi)
    return example


@pytest.fixture()
def tempfile_h5():
    return tempfile.mktemp(suffix='h5')


class Test01_ExampleCDefClass:
    """Test the Example CDefClass"""

    def test_01_test_init_array(self, persons_gi):
        """Test the Example CDefClass creation"""
        groups, zones = persons_gi.shape
        example = Example(groups, zones)

        # set correct shape
        values = np.arange(zones)
        example.set_array('jobs_j', np.arange((zones)))
        np.testing.assert_array_equal(example.jobs_j, values)
        np.testing.assert_array_equal(example._jobs_j, values)

        # init the array with a default value
        example.init_array('jobs_j', default=0)
        np.testing.assert_array_equal(example.jobs_j, np.zeros(zones))

        # init the array with the other default value
        example.init_array('jobs_j', default=2)
        np.testing.assert_array_equal(example.jobs_j,
                                      np.full(zones, 2, dtype='d'))

        # new default value will be stored
        example.reset_array('jobs_j')
        np.testing.assert_array_equal(example.jobs_j,
                                      np.full(zones, 2, dtype='d'))

        # set new shape, keep old default value
        example.init_array('jobs_j', shape='groups')
        np.testing.assert_array_equal(example.jobs_j,
                                      np.full(groups, 2, dtype='d'))

    def test_02_test_shape(self, persons_gi):
        """
        Test if the shapes of array are controlled correctly
        """
        groups, zones = persons_gi.shape
        example = Example(groups, zones)

        # jobs_j should have the shape (zones)

        # correct shape
        arr = np.ones((zones))
        example.jobs_j = arr

        # try to set values with the wrong shape
        arr = np.ones((groups))
        message = """
Arrays are not equal
jobs_j: shape target: [3], actual: (2,)
(mismatch 100.0%)
 x: array([2])
 y: array([3])
        """
        with pytest.raises(AssertionError,
                           message=message):
            example.jobs_j = arr

        # change zones and try again
        example.destinations = groups
        # now the array fits to the shape defined
        example.jobs_j = arr

    def test_03_test_dimensions(self, persons_gi):
        """Test the dimensions"""
        groups, zones = persons_gi.shape
        example = Example(groups, zones)

        # try to set shape with the wrong number of dimensions
        msg = "builtins.ValueError: 1 Dimensions required, shape ['groups', 'zones'] has 2 dimensions"
        with pytest.raises(ValueError,
                           message=msg):
            example.init_array('jobs_j', shape='groups, zones')

        # access a non-initialized array
        target = np.empty((0, 0))
        actual = example.not_initialized_ij
        np.testing.assert_array_equal(actual, target)

        # set arbitrary values to non-initialized 2D-Array
        a = np.array([2, 3, 4], dtype='i4')
        # with less dimensions than required ...
        example.not_initialized_ij = a
        b = example.not_initialized_ij
        # another dimension is added
        assert b.ndim == 2
        assert b.shape == (1, 3)
        print(example.not_initialized_ij)

        # change value in cython-memoryview
        example._not_initialized_ij[0, 1] = 99
        target = np.array([[2, 99, 4]], dtype='i4')
        # the value will be changed in the numpy-view of the array
        np.testing.assert_array_equal(example.not_initialized_ij, target)
        # as this is a view on the input-data, it will be changed there, too
        np.testing.assert_array_equal(a[1], 99)

        # the right number of dimensions should be fine
        c = np.array([[0, 1],
                      [2, 3]], dtype='i4')
        example.not_initialized_ij = c
        d = example.not_initialized_ij
        np.testing.assert_array_equal(c, d)

        # too many dimensions will raise an error
        e = np.array([[[0, 1],
                       [2, 3]],
                      [[4, 5],
                       [6, 7]]], dtype='i4')
        with pytest.raises(AssertionError,
                           message="not_initialized_ij: ndim target: 2, actual: 3"):
            example.not_initialized_ij = e

        # when the dimensions can be reduced to the target dimensions,
        # it should be fine
        f = np.array([[[0, 1],
                       [2, 3]]], dtype='i4')
        example.not_initialized_ij = f
        g = example.not_initialized_ij
        np.testing.assert_array_equal(g, f[0])

        # change value in cython-memoryview
        example._not_initialized_ij[1, 1] = 88
        target = np.array([[0, 1],
                           [2, 88]], dtype='i4')
        # the value will be changed in the numpy-view of the array
        np.testing.assert_array_equal(example.not_initialized_ij, target)
        # as this is a view on the input-data, it will be changed there, too
        np.testing.assert_array_equal(f[0, 1, 1], 88)

        # use more dimensions than required
        # reset the array first
        del example.not_initialized_ij
        print(example.not_initialized_ij)
        c = np.array([[[2, 3, 4]]], dtype='i4')
        example.not_initialized_ij = c
        b = example.not_initialized_ij
        # one dimension can be taken away
        assert b.ndim == 2
        assert b.shape == (1, 3)
        print(example.not_initialized_ij)

        # use the correct number of dimensions
        # reset the array first
        del example.not_initialized_ij
        print(example.not_initialized_ij)
        d = np.array([[2, 3, 4]], dtype='i4')
        example.not_initialized_ij = d
        b = example.not_initialized_ij
        # one dimension can be taken away
        assert b.ndim == 2
        assert b.shape == (1, 3)
        print(example.not_initialized_ij)

    def test_04_test_dtype(self, persons_gi):
        """Test the dimensions"""
        groups, zones = persons_gi.shape
        example = Example(groups, zones)

        # dtype of jobs_j: f8
        # dtype of not_initialized_ij: i4
        # dtype of n_threads: char

        # test if n_threads is really a signed char
        example.n_threads = 127
        assert example.n_threads == 127

        with pytest.raises(OverflowError,
                           message='value too large to convert to char'):
            example.n_threads = 128

        # test if jobs_j is really an array of double precision
        arr_i4 = np.array([2, 3, 4], dtype='i4')
        example.jobs_j = arr_i4
        assert example.jobs_j.dtype == np.dtype('f8')
        # because the array set to jobs_j is of different dtype,
        # it had to be converted to double. So no view is used,
        # but a copy of the data
        arr_i4[1] = -1
        # the data in jobs_j stays untouched
        assert example.jobs_j[1] == 3

        # test if not_initialized_ij is really an array of 32bit integer
        arr_i4 = np.array([[2, 3, 4], [5, 6, 7]], dtype='i4')
        example.not_initialized_ij = arr_i4
        assert example.not_initialized_ij.dtype == np.dtype('i4')
        # because the array set to not_initialized_ij is of the same dtype,
        # a view on the data could have been used
        arr_i4[1, 2] = -1
        # the data in not_initialized_ij changes
        assert example.not_initialized_ij[1, 2] == -1

    def test_10_test_model(self, example):
        """Test the Example CDefClass model"""
        res = example.calc_model()
        print(example.trips_ij)
        total_trips_target = example.persons_gi.sum()
        total_trips_actual = example.trips_ij.sum()
        np.testing.assert_almost_equal(total_trips_target, total_trips_actual)

    def test_11_dataset(self, example):
        """Test the creation of an xarrays Dataset linked to the Cythonclass"""
        example.zonenumbers_i = np.array([100, 200, 300])
        example.groupnames_g = np.array(['Female', 'Male'], dtype='O')
        example.create_ds()
        assert isinstance(example.ds, xr.Dataset)
        for attr, dtype in example.dtypes.items():
            data_array = example.ds[attr]
            # test if the shapes are correct
            if dtype.shape:
                np.testing.assert_array_equal(dtype.get_shape(example),
                                              data_array.shape,
                                              'shape not correct')
            else:
                # not initialized array
                assert not np.any(data_array.shape), 'shape not initialized'
            #test if the datatypes are correct
            assert np.dtype(dtype.dtype) == data_array.dtype,  'dtype not correct'
        print(example.ds)

    def test_20_save_and_read_ds(self, example, tempfile_h5):
        """Test that saving and re-reading the data works"""
        example.zonenumbers_i = np.array([100, 200, 300])
        example.groupnames_g = np.array(['Female', 'Male'], dtype='O')
        example.create_ds()
        example.save_dataset_to_netcdf(tempfile_h5)

        # read the data into new class
        new_example = Example.from_netcdf(tempfile_h5)
        # assert that the data match
        np.testing.assert_array_equal(example.jobs_j, new_example.jobs_j)
        np.testing.assert_array_equal(example.groupnames_g,
                                      new_example.groupnames_g)

        # assert, that the array are correctly linked to the Dataset
        new_example.calc_model()
        old_value = new_example.ds.trips_ij.sum()
        # calculate the model with 77 persons more
        new_example.persons_gi[1, 0] += 77
        new_example.calc_model()
        new_value = new_example.ds.trips_ij.sum()
        np.testing.assert_allclose(old_value + 77, new_value)

        print(new_example.ds)

    def test_21_assign_bool(self, example):
        """Test boolean array"""
        # the boolean arrays are initialized with 0 and 1
        np.testing.assert_array_equal(example.valid_g.astype(bool),
                                      ~example.invalid_g.astype(bool))
        example.valid_g = np.zeros((example.groups), dtype=bool)
        example.invalid_g = np.ones((example.groups), dtype=bool)
        np.testing.assert_array_equal(example.valid_g.astype(bool),
                                      ~example.invalid_g.astype(bool))
        print(example.valid_g)
        print(example.invalid_g)

    def test_30_test_init_array(self, persons_gi):
        """Test the Example CDefClass creation"""
        example = Example(groups=7, origins=5)

        example.init_array('param_g', 7)
        assert example.param_g.shape == (7, )

    def test_32_test_not_init_array(self):
        """Test the Example CDefClass creation"""
        example = Example(groups=7, origins=5,
                          init_arrays=False, threading=False)
        with pytest.raises(AttributeError):
            print(example.not_initialized_ij)

    def test_32_test_not_init_array(self):
        """Test the Example CDefClass creation"""
        example = Example(groups=7, origins=5,
                          init_arrays=False, threading=False)
        with pytest.raises(AttributeError):
            print(example.not_initialized_ij)

    def test_33_del_property(self):
        """Test the Example CDefClass creation"""
        example = Example(groups=7, origins=5)
        print(example.km_ij)
        # remove the shape
        example.dtypes['km_ij'].shape = None

        # reset to default (not defined)
        example.reset_array('km_ij')
        np.testing.assert_array_equal(example.km_ij, np.NAN)

        # reset to default (new value defined)
        example.dtypes['km_ij'].default = 11
        example.reset_array('km_ij')
        np.testing.assert_array_equal(example.km_ij, 11)

        # delete values
        del example.km_ij
        np.testing.assert_array_equal(example.km_ij.shape, (0, 0))

        # set new values
        new_array = np.arange(10).reshape(2, 5)
        example.set_array('km_ij', value=new_array, shape=(2, 5))
        np.testing.assert_array_equal(example.km_ij, new_array)

    def test_34_save_ds(self, tempfile_h5):
        """Test the Example CDefClass creation"""
        example = Example(groups=7, origins=5, )
        example.save_dataset_to_netcdf(tempfile_h5)


class Test04_Test_Instantiation:
    """Test the instantiation of the class"""
    
    def test041_test_instantiation(self):
        """not subclassing shoud rais a NotImplementedError"""
        with pytest.raises(NotImplementedError):
            example = _Example()

    def test042_test_nan(self, persons_gi):
        """Test nan"""
        groups, zones = persons_gi.shape
        example = Example(groups, zones)

        assert example.isnan_py(np.NAN)
        assert not example.isnan_py(np.NINF)
        assert not example.isnan_py(np.Inf)
        assert not example.isnan_py(0)
        assert not example.isnan_py(1)
        assert not example.isnan_py(-1)


if __name__ == '__main__':
    pytest.main()
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@pytest.fixture(scope='class')
def params_groups(request):
    """
    different values for saving categories
    """
    return np.array([-0.2, -0.1])


@pytest.fixture(scope='class')
def persons_gi(request):
    """
    different values for home zone
    """
    arr = np.array([[100, 0, 200], [0, 250, 50]])
    return arr


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@pytest.fixture()
def tempfile_h5():
    return tempfile.mktemp(suffix='h5')


class Test01_ExampleCDefClass:
    """Test the Example CDefClass"""

    def test_01_test_init_array(self, persons_gi):
        """Test the Example CDefClass creation"""
        groups, zones = persons_gi.shape
        example = Example(groups, zones)
        values = np.arange(zones)
        example.set_array('jobs_j', np.arange(zones))
        np.testing.assert_array_equal(example.jobs_j, values)
        np.testing.assert_array_equal(example._jobs_j, values)
        example.init_array('jobs_j', default=0)
        np.testing.assert_array_equal(example.jobs_j, np.zeros(zones))
        example.init_array('jobs_j', default=2)
        np.testing.assert_array_equal(example.jobs_j, np.full(zones, 2,
            dtype='d'))
        example.reset_array('jobs_j')
        np.testing.assert_array_equal(example.jobs_j, np.full(zones, 2,
            dtype='d'))
        example.init_array('jobs_j', shape='groups')
        np.testing.assert_array_equal(example.jobs_j, np.full(groups, 2,
            dtype='d'))

    def test_02_test_shape(self, persons_gi):
        """
        Test if the shapes of array are controlled correctly
        """
        groups, zones = persons_gi.shape
        example = Example(groups, zones)
        arr = np.ones(zones)
        example.jobs_j = arr
        arr = np.ones(groups)
        message = """
Arrays are not equal
jobs_j: shape target: [3], actual: (2,)
(mismatch 100.0%)
 x: array([2])
 y: array([3])
        """
        with pytest.raises(AssertionError, message=message):
            example.jobs_j = arr
        example.destinations = groups
        example.jobs_j = arr

    def test_03_test_dimensions(self, persons_gi):
        """Test the dimensions"""
        groups, zones = persons_gi.shape
        example = Example(groups, zones)
        msg = (
            "builtins.ValueError: 1 Dimensions required, shape ['groups', 'zones'] has 2 dimensions"
            )
        with pytest.raises(ValueError, message=msg):
            example.init_array('jobs_j', shape='groups, zones')
        target = np.empty((0, 0))
        actual = example.not_initialized_ij
        np.testing.assert_array_equal(actual, target)
        a = np.array([2, 3, 4], dtype='i4')
        example.not_initialized_ij = a
        b = example.not_initialized_ij
        assert b.ndim == 2
        assert b.shape == (1, 3)
        print(example.not_initialized_ij)
        example._not_initialized_ij[0, 1] = 99
        target = np.array([[2, 99, 4]], dtype='i4')
        np.testing.assert_array_equal(example.not_initialized_ij, target)
        np.testing.assert_array_equal(a[1], 99)
        c = np.array([[0, 1], [2, 3]], dtype='i4')
        example.not_initialized_ij = c
        d = example.not_initialized_ij
        np.testing.assert_array_equal(c, d)
        e = np.array([[[0, 1], [2, 3]], [[4, 5], [6, 7]]], dtype='i4')
        with pytest.raises(AssertionError, message=
            'not_initialized_ij: ndim target: 2, actual: 3'):
            example.not_initialized_ij = e
        f = np.array([[[0, 1], [2, 3]]], dtype='i4')
        example.not_initialized_ij = f
        g = example.not_initialized_ij
        np.testing.assert_array_equal(g, f[0])
        example._not_initialized_ij[1, 1] = 88
        target = np.array([[0, 1], [2, 88]], dtype='i4')
        np.testing.assert_array_equal(example.not_initialized_ij, target)
        np.testing.assert_array_equal(f[0, 1, 1], 88)
        del example.not_initialized_ij
        print(example.not_initialized_ij)
        c = np.array([[[2, 3, 4]]], dtype='i4')
        example.not_initialized_ij = c
        b = example.not_initialized_ij
        assert b.ndim == 2
        assert b.shape == (1, 3)
        print(example.not_initialized_ij)
        del example.not_initialized_ij
        print(example.not_initialized_ij)
        d = np.array([[2, 3, 4]], dtype='i4')
        example.not_initialized_ij = d
        b = example.not_initialized_ij
        assert b.ndim == 2
        assert b.shape == (1, 3)
        print(example.not_initialized_ij)

    def test_04_test_dtype(self, persons_gi):
        """Test the dimensions"""
        groups, zones = persons_gi.shape
        example = Example(groups, zones)
        example.n_threads = 127
        assert example.n_threads == 127
        with pytest.raises(OverflowError, message=
            'value too large to convert to char'):
            example.n_threads = 128
        arr_i4 = np.array([2, 3, 4], dtype='i4')
        example.jobs_j = arr_i4
        assert example.jobs_j.dtype == np.dtype('f8')
        arr_i4[1] = -1
        assert example.jobs_j[1] == 3
        arr_i4 = np.array([[2, 3, 4], [5, 6, 7]], dtype='i4')
        example.not_initialized_ij = arr_i4
        assert example.not_initialized_ij.dtype == np.dtype('i4')
        arr_i4[1, 2] = -1
        assert example.not_initialized_ij[1, 2] == -1

    def test_10_test_model(self, example):
        """Test the Example CDefClass model"""
        res = example.calc_model()
        print(example.trips_ij)
        total_trips_target = example.persons_gi.sum()
        total_trips_actual = example.trips_ij.sum()
        np.testing.assert_almost_equal(total_trips_target, total_trips_actual)

    def test_11_dataset(self, example):
        """Test the creation of an xarrays Dataset linked to the Cythonclass"""
        example.zonenumbers_i = np.array([100, 200, 300])
        example.groupnames_g = np.array(['Female', 'Male'], dtype='O')
        example.create_ds()
        assert isinstance(example.ds, xr.Dataset)
        for attr, dtype in example.dtypes.items():
            data_array = example.ds[attr]
            if dtype.shape:
                np.testing.assert_array_equal(dtype.get_shape(example),
                    data_array.shape, 'shape not correct')
            else:
                assert not np.any(data_array.shape), 'shape not initialized'
            assert np.dtype(dtype.dtype
                ) == data_array.dtype, 'dtype not correct'
        print(example.ds)

    def test_20_save_and_read_ds(self, example, tempfile_h5):
        """Test that saving and re-reading the data works"""
        example.zonenumbers_i = np.array([100, 200, 300])
        example.groupnames_g = np.array(['Female', 'Male'], dtype='O')
        example.create_ds()
        example.save_dataset_to_netcdf(tempfile_h5)
        new_example = Example.from_netcdf(tempfile_h5)
        np.testing.assert_array_equal(example.jobs_j, new_example.jobs_j)
        np.testing.assert_array_equal(example.groupnames_g, new_example.
            groupnames_g)
        new_example.calc_model()
        old_value = new_example.ds.trips_ij.sum()
        new_example.persons_gi[1, 0] += 77
        new_example.calc_model()
        new_value = new_example.ds.trips_ij.sum()
        np.testing.assert_allclose(old_value + 77, new_value)
        print(new_example.ds)

    def test_21_assign_bool(self, example):
        """Test boolean array"""
        np.testing.assert_array_equal(example.valid_g.astype(bool), ~
            example.invalid_g.astype(bool))
        example.valid_g = np.zeros(example.groups, dtype=bool)
        example.invalid_g = np.ones(example.groups, dtype=bool)
        np.testing.assert_array_equal(example.valid_g.astype(bool), ~
            example.invalid_g.astype(bool))
        print(example.valid_g)
        print(example.invalid_g)

    def test_30_test_init_array(self, persons_gi):
        """Test the Example CDefClass creation"""
        example = Example(groups=7, origins=5)
        example.init_array('param_g', 7)
        assert example.param_g.shape == (7,)

    def test_32_test_not_init_array(self):
        """Test the Example CDefClass creation"""
        example = Example(groups=7, origins=5, init_arrays=False, threading
            =False)
        with pytest.raises(AttributeError):
            print(example.not_initialized_ij)

    def test_32_test_not_init_array(self):
        """Test the Example CDefClass creation"""
        example = Example(groups=7, origins=5, init_arrays=False, threading
            =False)
        with pytest.raises(AttributeError):
            print(example.not_initialized_ij)

    def test_33_del_property(self):
        """Test the Example CDefClass creation"""
        example = Example(groups=7, origins=5)
        print(example.km_ij)
        example.dtypes['km_ij'].shape = None
        example.reset_array('km_ij')
        np.testing.assert_array_equal(example.km_ij, np.NAN)
        example.dtypes['km_ij'].default = 11
        example.reset_array('km_ij')
        np.testing.assert_array_equal(example.km_ij, 11)
        del example.km_ij
        np.testing.assert_array_equal(example.km_ij.shape, (0, 0))
        new_array = np.arange(10).reshape(2, 5)
        example.set_array('km_ij', value=new_array, shape=(2, 5))
        np.testing.assert_array_equal(example.km_ij, new_array)

    def test_34_save_ds(self, tempfile_h5):
        """Test the Example CDefClass creation"""
        example = Example(groups=7, origins=5)
        example.save_dataset_to_netcdf(tempfile_h5)


class Test04_Test_Instantiation:
    """Test the instantiation of the class"""

    def test041_test_instantiation(self):
        """not subclassing shoud rais a NotImplementedError"""
        with pytest.raises(NotImplementedError):
            example = _Example()

    def test042_test_nan(self, persons_gi):
        """Test nan"""
        groups, zones = persons_gi.shape
        example = Example(groups, zones)
        assert example.isnan_py(np.NAN)
        assert not example.isnan_py(np.NINF)
        assert not example.isnan_py(np.Inf)
        assert not example.isnan_py(0)
        assert not example.isnan_py(1)
        assert not example.isnan_py(-1)


<mask token>

<mask token>


@pytest.fixture(scope='class')
def km_ij(request):
    """
    travel times
    """
    array = np.array([[1, 4, 5], [2, 1, 7], [5, 7, 2]])
    return array


<mask token>


@pytest.fixture(scope='class')
def params_groups(request):
    """
    different values for saving categories
    """
    return np.array([-0.2, -0.1])


@pytest.fixture(scope='class')
def persons_gi(request):
    """
    different values for home zone
    """
    arr = np.array([[100, 0, 200], [0, 250, 50]])
    return arr


<mask token>


@pytest.fixture()
def tempfile_h5():
    return tempfile.mktemp(suffix='h5')


class Test01_ExampleCDefClass:
    """Test the Example CDefClass"""

    def test_01_test_init_array(self, persons_gi):
        """Test the Example CDefClass creation"""
        groups, zones = persons_gi.shape
        example = Example(groups, zones)
        values = np.arange(zones)
        example.set_array('jobs_j', np.arange(zones))
        np.testing.assert_array_equal(example.jobs_j, values)
        np.testing.assert_array_equal(example._jobs_j, values)
        example.init_array('jobs_j', default=0)
        np.testing.assert_array_equal(example.jobs_j, np.zeros(zones))
        example.init_array('jobs_j', default=2)
        np.testing.assert_array_equal(example.jobs_j, np.full(zones, 2,
            dtype='d'))
        example.reset_array('jobs_j')
        np.testing.assert_array_equal(example.jobs_j, np.full(zones, 2,
            dtype='d'))
        example.init_array('jobs_j', shape='groups')
        np.testing.assert_array_equal(example.jobs_j, np.full(groups, 2,
            dtype='d'))

    def test_02_test_shape(self, persons_gi):
        """
        Test if the shapes of array are controlled correctly
        """
        groups, zones = persons_gi.shape
        example = Example(groups, zones)
        arr = np.ones(zones)
        example.jobs_j = arr
        arr = np.ones(groups)
        message = """
Arrays are not equal
jobs_j: shape target: [3], actual: (2,)
(mismatch 100.0%)
 x: array([2])
 y: array([3])
        """
        with pytest.raises(AssertionError, message=message):
            example.jobs_j = arr
        example.destinations = groups
        example.jobs_j = arr

    def test_03_test_dimensions(self, persons_gi):
        """Test the dimensions"""
        groups, zones = persons_gi.shape
        example = Example(groups, zones)
        msg = (
            "builtins.ValueError: 1 Dimensions required, shape ['groups', 'zones'] has 2 dimensions"
            )
        with pytest.raises(ValueError, message=msg):
            example.init_array('jobs_j', shape='groups, zones')
        target = np.empty((0, 0))
        actual = example.not_initialized_ij
        np.testing.assert_array_equal(actual, target)
        a = np.array([2, 3, 4], dtype='i4')
        example.not_initialized_ij = a
        b = example.not_initialized_ij
        assert b.ndim == 2
        assert b.shape == (1, 3)
        print(example.not_initialized_ij)
        example._not_initialized_ij[0, 1] = 99
        target = np.array([[2, 99, 4]], dtype='i4')
        np.testing.assert_array_equal(example.not_initialized_ij, target)
        np.testing.assert_array_equal(a[1], 99)
        c = np.array([[0, 1], [2, 3]], dtype='i4')
        example.not_initialized_ij = c
        d = example.not_initialized_ij
        np.testing.assert_array_equal(c, d)
        e = np.array([[[0, 1], [2, 3]], [[4, 5], [6, 7]]], dtype='i4')
        with pytest.raises(AssertionError, message=
            'not_initialized_ij: ndim target: 2, actual: 3'):
            example.not_initialized_ij = e
        f = np.array([[[0, 1], [2, 3]]], dtype='i4')
        example.not_initialized_ij = f
        g = example.not_initialized_ij
        np.testing.assert_array_equal(g, f[0])
        example._not_initialized_ij[1, 1] = 88
        target = np.array([[0, 1], [2, 88]], dtype='i4')
        np.testing.assert_array_equal(example.not_initialized_ij, target)
        np.testing.assert_array_equal(f[0, 1, 1], 88)
        del example.not_initialized_ij
        print(example.not_initialized_ij)
        c = np.array([[[2, 3, 4]]], dtype='i4')
        example.not_initialized_ij = c
        b = example.not_initialized_ij
        assert b.ndim == 2
        assert b.shape == (1, 3)
        print(example.not_initialized_ij)
        del example.not_initialized_ij
        print(example.not_initialized_ij)
        d = np.array([[2, 3, 4]], dtype='i4')
        example.not_initialized_ij = d
        b = example.not_initialized_ij
        assert b.ndim == 2
        assert b.shape == (1, 3)
        print(example.not_initialized_ij)

    def test_04_test_dtype(self, persons_gi):
        """Test the dimensions"""
        groups, zones = persons_gi.shape
        example = Example(groups, zones)
        example.n_threads = 127
        assert example.n_threads == 127
        with pytest.raises(OverflowError, message=
            'value too large to convert to char'):
            example.n_threads = 128
        arr_i4 = np.array([2, 3, 4], dtype='i4')
        example.jobs_j = arr_i4
        assert example.jobs_j.dtype == np.dtype('f8')
        arr_i4[1] = -1
        assert example.jobs_j[1] == 3
        arr_i4 = np.array([[2, 3, 4], [5, 6, 7]], dtype='i4')
        example.not_initialized_ij = arr_i4
        assert example.not_initialized_ij.dtype == np.dtype('i4')
        arr_i4[1, 2] = -1
        assert example.not_initialized_ij[1, 2] == -1

    def test_10_test_model(self, example):
        """Test the Example CDefClass model"""
        res = example.calc_model()
        print(example.trips_ij)
        total_trips_target = example.persons_gi.sum()
        total_trips_actual = example.trips_ij.sum()
        np.testing.assert_almost_equal(total_trips_target, total_trips_actual)

    def test_11_dataset(self, example):
        """Test the creation of an xarrays Dataset linked to the Cythonclass"""
        example.zonenumbers_i = np.array([100, 200, 300])
        example.groupnames_g = np.array(['Female', 'Male'], dtype='O')
        example.create_ds()
        assert isinstance(example.ds, xr.Dataset)
        for attr, dtype in example.dtypes.items():
            data_array = example.ds[attr]
            if dtype.shape:
                np.testing.assert_array_equal(dtype.get_shape(example),
                    data_array.shape, 'shape not correct')
            else:
                assert not np.any(data_array.shape), 'shape not initialized'
            assert np.dtype(dtype.dtype
                ) == data_array.dtype, 'dtype not correct'
        print(example.ds)

    def test_20_save_and_read_ds(self, example, tempfile_h5):
        """Test that saving and re-reading the data works"""
        example.zonenumbers_i = np.array([100, 200, 300])
        example.groupnames_g = np.array(['Female', 'Male'], dtype='O')
        example.create_ds()
        example.save_dataset_to_netcdf(tempfile_h5)
        new_example = Example.from_netcdf(tempfile_h5)
        np.testing.assert_array_equal(example.jobs_j, new_example.jobs_j)
        np.testing.assert_array_equal(example.groupnames_g, new_example.
            groupnames_g)
        new_example.calc_model()
        old_value = new_example.ds.trips_ij.sum()
        new_example.persons_gi[1, 0] += 77
        new_example.calc_model()
        new_value = new_example.ds.trips_ij.sum()
        np.testing.assert_allclose(old_value + 77, new_value)
        print(new_example.ds)

    def test_21_assign_bool(self, example):
        """Test boolean array"""
        np.testing.assert_array_equal(example.valid_g.astype(bool), ~
            example.invalid_g.astype(bool))
        example.valid_g = np.zeros(example.groups, dtype=bool)
        example.invalid_g = np.ones(example.groups, dtype=bool)
        np.testing.assert_array_equal(example.valid_g.astype(bool), ~
            example.invalid_g.astype(bool))
        print(example.valid_g)
        print(example.invalid_g)

    def test_30_test_init_array(self, persons_gi):
        """Test the Example CDefClass creation"""
        example = Example(groups=7, origins=5)
        example.init_array('param_g', 7)
        assert example.param_g.shape == (7,)

    def test_32_test_not_init_array(self):
        """Test the Example CDefClass creation"""
        example = Example(groups=7, origins=5, init_arrays=False, threading
            =False)
        with pytest.raises(AttributeError):
            print(example.not_initialized_ij)

    def test_32_test_not_init_array(self):
        """Test the Example CDefClass creation"""
        example = Example(groups=7, origins=5, init_arrays=False, threading
            =False)
        with pytest.raises(AttributeError):
            print(example.not_initialized_ij)

    def test_33_del_property(self):
        """Test the Example CDefClass creation"""
        example = Example(groups=7, origins=5)
        print(example.km_ij)
        example.dtypes['km_ij'].shape = None
        example.reset_array('km_ij')
        np.testing.assert_array_equal(example.km_ij, np.NAN)
        example.dtypes['km_ij'].default = 11
        example.reset_array('km_ij')
        np.testing.assert_array_equal(example.km_ij, 11)
        del example.km_ij
        np.testing.assert_array_equal(example.km_ij.shape, (0, 0))
        new_array = np.arange(10).reshape(2, 5)
        example.set_array('km_ij', value=new_array, shape=(2, 5))
        np.testing.assert_array_equal(example.km_ij, new_array)

    def test_34_save_ds(self, tempfile_h5):
        """Test the Example CDefClass creation"""
        example = Example(groups=7, origins=5)
        example.save_dataset_to_netcdf(tempfile_h5)


class Test04_Test_Instantiation:
    """Test the instantiation of the class"""

    def test041_test_instantiation(self):
        """not subclassing shoud rais a NotImplementedError"""
        with pytest.raises(NotImplementedError):
            example = _Example()

    def test042_test_nan(self, persons_gi):
        """Test nan"""
        groups, zones = persons_gi.shape
        example = Example(groups, zones)
        assert example.isnan_py(np.NAN)
        assert not example.isnan_py(np.NINF)
        assert not example.isnan_py(np.Inf)
        assert not example.isnan_py(0)
        assert not example.isnan_py(1)
        assert not example.isnan_py(-1)


<mask token>

<mask token>


@pytest.fixture(scope='class')
def km_ij(request):
    """
    travel times
    """
    array = np.array([[1, 4, 5], [2, 1, 7], [5, 7, 2]])
    return array


@pytest.fixture(scope='class')
def jobs(request):
    """
    jobs
    """
    jobs = np.array([100, 200, 300])
    return jobs


@pytest.fixture(scope='class')
def params_groups(request):
    """
    different values for saving categories
    """
    return np.array([-0.2, -0.1])


@pytest.fixture(scope='class')
def persons_gi(request):
    """
    different values for home zone
    """
    arr = np.array([[100, 0, 200], [0, 250, 50]])
    return arr


<mask token>


@pytest.fixture()
def tempfile_h5():
    return tempfile.mktemp(suffix='h5')


class Test01_ExampleCDefClass:
    """Test the Example CDefClass"""

    def test_01_test_init_array(self, persons_gi):
        """Test the Example CDefClass creation"""
        groups, zones = persons_gi.shape
        example = Example(groups, zones)
        values = np.arange(zones)
        example.set_array('jobs_j', np.arange(zones))
        np.testing.assert_array_equal(example.jobs_j, values)
        np.testing.assert_array_equal(example._jobs_j, values)
        example.init_array('jobs_j', default=0)
        np.testing.assert_array_equal(example.jobs_j, np.zeros(zones))
        example.init_array('jobs_j', default=2)
        np.testing.assert_array_equal(example.jobs_j, np.full(zones, 2,
            dtype='d'))
        example.reset_array('jobs_j')
        np.testing.assert_array_equal(example.jobs_j, np.full(zones, 2,
            dtype='d'))
        example.init_array('jobs_j', shape='groups')
        np.testing.assert_array_equal(example.jobs_j, np.full(groups, 2,
            dtype='d'))

    def test_02_test_shape(self, persons_gi):
        """
        Test if the shapes of array are controlled correctly
        """
        groups, zones = persons_gi.shape
        example = Example(groups, zones)
        arr = np.ones(zones)
        example.jobs_j = arr
        arr = np.ones(groups)
        message = """
Arrays are not equal
jobs_j: shape target: [3], actual: (2,)
(mismatch 100.0%)
 x: array([2])
 y: array([3])
        """
        with pytest.raises(AssertionError, message=message):
            example.jobs_j = arr
        example.destinations = groups
        example.jobs_j = arr

    def test_03_test_dimensions(self, persons_gi):
        """Test the dimensions"""
        groups, zones = persons_gi.shape
        example = Example(groups, zones)
        msg = (
            "builtins.ValueError: 1 Dimensions required, shape ['groups', 'zones'] has 2 dimensions"
            )
        with pytest.raises(ValueError, message=msg):
            example.init_array('jobs_j', shape='groups, zones')
        target = np.empty((0, 0))
        actual = example.not_initialized_ij
        np.testing.assert_array_equal(actual, target)
        a = np.array([2, 3, 4], dtype='i4')
        example.not_initialized_ij = a
        b = example.not_initialized_ij
        assert b.ndim == 2
        assert b.shape == (1, 3)
        print(example.not_initialized_ij)
        example._not_initialized_ij[0, 1] = 99
        target = np.array([[2, 99, 4]], dtype='i4')
        np.testing.assert_array_equal(example.not_initialized_ij, target)
        np.testing.assert_array_equal(a[1], 99)
        c = np.array([[0, 1], [2, 3]], dtype='i4')
        example.not_initialized_ij = c
        d = example.not_initialized_ij
        np.testing.assert_array_equal(c, d)
        e = np.array([[[0, 1], [2, 3]], [[4, 5], [6, 7]]], dtype='i4')
        with pytest.raises(AssertionError, message=
            'not_initialized_ij: ndim target: 2, actual: 3'):
            example.not_initialized_ij = e
        f = np.array([[[0, 1], [2, 3]]], dtype='i4')
        example.not_initialized_ij = f
        g = example.not_initialized_ij
        np.testing.assert_array_equal(g, f[0])
        example._not_initialized_ij[1, 1] = 88
        target = np.array([[0, 1], [2, 88]], dtype='i4')
        np.testing.assert_array_equal(example.not_initialized_ij, target)
        np.testing.assert_array_equal(f[0, 1, 1], 88)
        del example.not_initialized_ij
        print(example.not_initialized_ij)
        c = np.array([[[2, 3, 4]]], dtype='i4')
        example.not_initialized_ij = c
        b = example.not_initialized_ij
        assert b.ndim == 2
        assert b.shape == (1, 3)
        print(example.not_initialized_ij)
        del example.not_initialized_ij
        print(example.not_initialized_ij)
        d = np.array([[2, 3, 4]], dtype='i4')
        example.not_initialized_ij = d
        b = example.not_initialized_ij
        assert b.ndim == 2
        assert b.shape == (1, 3)
        print(example.not_initialized_ij)

    def test_04_test_dtype(self, persons_gi):
        """Test the dimensions"""
        groups, zones = persons_gi.shape
        example = Example(groups, zones)
        example.n_threads = 127
        assert example.n_threads == 127
        with pytest.raises(OverflowError, message=
            'value too large to convert to char'):
            example.n_threads = 128
        arr_i4 = np.array([2, 3, 4], dtype='i4')
        example.jobs_j = arr_i4
        assert example.jobs_j.dtype == np.dtype('f8')
        arr_i4[1] = -1
        assert example.jobs_j[1] == 3
        arr_i4 = np.array([[2, 3, 4], [5, 6, 7]], dtype='i4')
        example.not_initialized_ij = arr_i4
        assert example.not_initialized_ij.dtype == np.dtype('i4')
        arr_i4[1, 2] = -1
        assert example.not_initialized_ij[1, 2] == -1

    def test_10_test_model(self, example):
        """Test the Example CDefClass model"""
        res = example.calc_model()
        print(example.trips_ij)
        total_trips_target = example.persons_gi.sum()
        total_trips_actual = example.trips_ij.sum()
        np.testing.assert_almost_equal(total_trips_target, total_trips_actual)

    def test_11_dataset(self, example):
        """Test the creation of an xarrays Dataset linked to the Cythonclass"""
        example.zonenumbers_i = np.array([100, 200, 300])
        example.groupnames_g = np.array(['Female', 'Male'], dtype='O')
        example.create_ds()
        assert isinstance(example.ds, xr.Dataset)
        for attr, dtype in example.dtypes.items():
            data_array = example.ds[attr]
            if dtype.shape:
                np.testing.assert_array_equal(dtype.get_shape(example),
                    data_array.shape, 'shape not correct')
            else:
                assert not np.any(data_array.shape), 'shape not initialized'
            assert np.dtype(dtype.dtype
                ) == data_array.dtype, 'dtype not correct'
        print(example.ds)

    def test_20_save_and_read_ds(self, example, tempfile_h5):
        """Test that saving and re-reading the data works"""
        example.zonenumbers_i = np.array([100, 200, 300])
        example.groupnames_g = np.array(['Female', 'Male'], dtype='O')
        example.create_ds()
        example.save_dataset_to_netcdf(tempfile_h5)
        new_example = Example.from_netcdf(tempfile_h5)
        np.testing.assert_array_equal(example.jobs_j, new_example.jobs_j)
        np.testing.assert_array_equal(example.groupnames_g, new_example.
            groupnames_g)
        new_example.calc_model()
        old_value = new_example.ds.trips_ij.sum()
        new_example.persons_gi[1, 0] += 77
        new_example.calc_model()
        new_value = new_example.ds.trips_ij.sum()
        np.testing.assert_allclose(old_value + 77, new_value)
        print(new_example.ds)

    def test_21_assign_bool(self, example):
        """Test boolean array"""
        np.testing.assert_array_equal(example.valid_g.astype(bool), ~
            example.invalid_g.astype(bool))
        example.valid_g = np.zeros(example.groups, dtype=bool)
        example.invalid_g = np.ones(example.groups, dtype=bool)
        np.testing.assert_array_equal(example.valid_g.astype(bool), ~
            example.invalid_g.astype(bool))
        print(example.valid_g)
        print(example.invalid_g)

    def test_30_test_init_array(self, persons_gi):
        """Test the Example CDefClass creation"""
        example = Example(groups=7, origins=5)
        example.init_array('param_g', 7)
        assert example.param_g.shape == (7,)

    def test_32_test_not_init_array(self):
        """Test the Example CDefClass creation"""
        example = Example(groups=7, origins=5, init_arrays=False, threading
            =False)
        with pytest.raises(AttributeError):
            print(example.not_initialized_ij)

    def test_32_test_not_init_array(self):
        """Test the Example CDefClass creation"""
        example = Example(groups=7, origins=5, init_arrays=False, threading
            =False)
        with pytest.raises(AttributeError):
            print(example.not_initialized_ij)

    def test_33_del_property(self):
        """Test the Example CDefClass creation"""
        example = Example(groups=7, origins=5)
        print(example.km_ij)
        example.dtypes['km_ij'].shape = None
        example.reset_array('km_ij')
        np.testing.assert_array_equal(example.km_ij, np.NAN)
        example.dtypes['km_ij'].default = 11
        example.reset_array('km_ij')
        np.testing.assert_array_equal(example.km_ij, 11)
        del example.km_ij
        np.testing.assert_array_equal(example.km_ij.shape, (0, 0))
        new_array = np.arange(10).reshape(2, 5)
        example.set_array('km_ij', value=new_array, shape=(2, 5))
        np.testing.assert_array_equal(example.km_ij, new_array)

    def test_34_save_ds(self, tempfile_h5):
        """Test the Example CDefClass creation"""
        example = Example(groups=7, origins=5)
        example.save_dataset_to_netcdf(tempfile_h5)


class Test04_Test_Instantiation:
    """Test the instantiation of the class"""

    def test041_test_instantiation(self):
        """not subclassing shoud rais a NotImplementedError"""
        with pytest.raises(NotImplementedError):
            example = _Example()

    def test042_test_nan(self, persons_gi):
        """Test nan"""
        groups, zones = persons_gi.shape
        example = Example(groups, zones)
        assert example.isnan_py(np.NAN)
        assert not example.isnan_py(np.NINF)
        assert not example.isnan_py(np.Inf)
        assert not example.isnan_py(0)
        assert not example.isnan_py(1)
        assert not example.isnan_py(-1)


<mask token>

<mask token>
pyximport.install()
<mask token>


@pytest.fixture(scope='class')
def km_ij(request):
    """
    travel times
    """
    array = np.array([[1, 4, 5], [2, 1, 7], [5, 7, 2]])
    return array


@pytest.fixture(scope='class')
def jobs(request):
    """
    jobs
    """
    jobs = np.array([100, 200, 300])
    return jobs


@pytest.fixture(scope='class')
def params_groups(request):
    """
    different values for saving categories
    """
    return np.array([-0.2, -0.1])


@pytest.fixture(scope='class')
def persons_gi(request):
    """
    different values for home zone
    """
    arr = np.array([[100, 0, 200], [0, 250, 50]])
    return arr


@pytest.fixture(scope='class')
def example(km_ij, jobs, params_groups, persons_gi):
    """
    different values for home zone
    """
    groups, zones = persons_gi.shape
    example = Example(groups, zones)
    example.set_array('km_ij', km_ij)
    example.set_array('jobs_j', jobs)
    example.set_array('param_g', params_groups)
    example.set_array('persons_gi', persons_gi)
    return example


@pytest.fixture()
def tempfile_h5():
    return tempfile.mktemp(suffix='h5')


class Test01_ExampleCDefClass:
    """Test the Example CDefClass"""

    def test_01_test_init_array(self, persons_gi):
        """Test the Example CDefClass creation"""
        groups, zones = persons_gi.shape
        example = Example(groups, zones)
        values = np.arange(zones)
        example.set_array('jobs_j', np.arange(zones))
        np.testing.assert_array_equal(example.jobs_j, values)
        np.testing.assert_array_equal(example._jobs_j, values)
        example.init_array('jobs_j', default=0)
        np.testing.assert_array_equal(example.jobs_j, np.zeros(zones))
        example.init_array('jobs_j', default=2)
        np.testing.assert_array_equal(example.jobs_j, np.full(zones, 2,
            dtype='d'))
        example.reset_array('jobs_j')
        np.testing.assert_array_equal(example.jobs_j, np.full(zones, 2,
            dtype='d'))
        example.init_array('jobs_j', shape='groups')
        np.testing.assert_array_equal(example.jobs_j, np.full(groups, 2,
            dtype='d'))

    def test_02_test_shape(self, persons_gi):
        """
        Test if the shapes of array are controlled correctly
        """
        groups, zones = persons_gi.shape
        example = Example(groups, zones)
        arr = np.ones(zones)
        example.jobs_j = arr
        arr = np.ones(groups)
        message = """
Arrays are not equal
jobs_j: shape target: [3], actual: (2,)
(mismatch 100.0%)
 x: array([2])
 y: array([3])
        """
        with pytest.raises(AssertionError, message=message):
            example.jobs_j = arr
        example.destinations = groups
        example.jobs_j = arr

    def test_03_test_dimensions(self, persons_gi):
        """Test the dimensions"""
        groups, zones = persons_gi.shape
        example = Example(groups, zones)
        msg = (
            "builtins.ValueError: 1 Dimensions required, shape ['groups', 'zones'] has 2 dimensions"
            )
        with pytest.raises(ValueError, message=msg):
            example.init_array('jobs_j', shape='groups, zones')
        target = np.empty((0, 0))
        actual = example.not_initialized_ij
        np.testing.assert_array_equal(actual, target)
        a = np.array([2, 3, 4], dtype='i4')
        example.not_initialized_ij = a
        b = example.not_initialized_ij
        assert b.ndim == 2
        assert b.shape == (1, 3)
        print(example.not_initialized_ij)
        example._not_initialized_ij[0, 1] = 99
        target = np.array([[2, 99, 4]], dtype='i4')
        np.testing.assert_array_equal(example.not_initialized_ij, target)
        np.testing.assert_array_equal(a[1], 99)
        c = np.array([[0, 1], [2, 3]], dtype='i4')
        example.not_initialized_ij = c
        d = example.not_initialized_ij
        np.testing.assert_array_equal(c, d)
        e = np.array([[[0, 1], [2, 3]], [[4, 5], [6, 7]]], dtype='i4')
        with pytest.raises(AssertionError, message=
            'not_initialized_ij: ndim target: 2, actual: 3'):
            example.not_initialized_ij = e
        f = np.array([[[0, 1], [2, 3]]], dtype='i4')
        example.not_initialized_ij = f
        g = example.not_initialized_ij
        np.testing.assert_array_equal(g, f[0])
        example._not_initialized_ij[1, 1] = 88
        target = np.array([[0, 1], [2, 88]], dtype='i4')
        np.testing.assert_array_equal(example.not_initialized_ij, target)
        np.testing.assert_array_equal(f[0, 1, 1], 88)
        del example.not_initialized_ij
        print(example.not_initialized_ij)
        c = np.array([[[2, 3, 4]]], dtype='i4')
        example.not_initialized_ij = c
        b = example.not_initialized_ij
        assert b.ndim == 2
        assert b.shape == (1, 3)
        print(example.not_initialized_ij)
        del example.not_initialized_ij
        print(example.not_initialized_ij)
        d = np.array([[2, 3, 4]], dtype='i4')
        example.not_initialized_ij = d
        b = example.not_initialized_ij
        assert b.ndim == 2
        assert b.shape == (1, 3)
        print(example.not_initialized_ij)

    def test_04_test_dtype(self, persons_gi):
        """Test the dimensions"""
        groups, zones = persons_gi.shape
        example = Example(groups, zones)
        example.n_threads = 127
        assert example.n_threads == 127
        with pytest.raises(OverflowError, message=
            'value too large to convert to char'):
            example.n_threads = 128
        arr_i4 = np.array([2, 3, 4], dtype='i4')
        example.jobs_j = arr_i4
        assert example.jobs_j.dtype == np.dtype('f8')
        arr_i4[1] = -1
        assert example.jobs_j[1] == 3
        arr_i4 = np.array([[2, 3, 4], [5, 6, 7]], dtype='i4')
        example.not_initialized_ij = arr_i4
        assert example.not_initialized_ij.dtype == np.dtype('i4')
        arr_i4[1, 2] = -1
        assert example.not_initialized_ij[1, 2] == -1

    def test_10_test_model(self, example):
        """Test the Example CDefClass model"""
        res = example.calc_model()
        print(example.trips_ij)
        total_trips_target = example.persons_gi.sum()
        total_trips_actual = example.trips_ij.sum()
        np.testing.assert_almost_equal(total_trips_target, total_trips_actual)

    def test_11_dataset(self, example):
        """Test the creation of an xarrays Dataset linked to the Cythonclass"""
        example.zonenumbers_i = np.array([100, 200, 300])
        example.groupnames_g = np.array(['Female', 'Male'], dtype='O')
        example.create_ds()
        assert isinstance(example.ds, xr.Dataset)
        for attr, dtype in example.dtypes.items():
            data_array = example.ds[attr]
            if dtype.shape:
                np.testing.assert_array_equal(dtype.get_shape(example),
                    data_array.shape, 'shape not correct')
            else:
                assert not np.any(data_array.shape), 'shape not initialized'
            assert np.dtype(dtype.dtype
                ) == data_array.dtype, 'dtype not correct'
        print(example.ds)

    def test_20_save_and_read_ds(self, example, tempfile_h5):
        """Test that saving and re-reading the data works"""
        example.zonenumbers_i = np.array([100, 200, 300])
        example.groupnames_g = np.array(['Female', 'Male'], dtype='O')
        example.create_ds()
        example.save_dataset_to_netcdf(tempfile_h5)
        new_example = Example.from_netcdf(tempfile_h5)
        np.testing.assert_array_equal(example.jobs_j, new_example.jobs_j)
        np.testing.assert_array_equal(example.groupnames_g, new_example.
            groupnames_g)
        new_example.calc_model()
        old_value = new_example.ds.trips_ij.sum()
        new_example.persons_gi[1, 0] += 77
        new_example.calc_model()
        new_value = new_example.ds.trips_ij.sum()
        np.testing.assert_allclose(old_value + 77, new_value)
        print(new_example.ds)

    def test_21_assign_bool(self, example):
        """Test boolean array"""
        np.testing.assert_array_equal(example.valid_g.astype(bool), ~
            example.invalid_g.astype(bool))
        example.valid_g = np.zeros(example.groups, dtype=bool)
        example.invalid_g = np.ones(example.groups, dtype=bool)
        np.testing.assert_array_equal(example.valid_g.astype(bool), ~
            example.invalid_g.astype(bool))
        print(example.valid_g)
        print(example.invalid_g)

    def test_30_test_init_array(self, persons_gi):
        """Test the Example CDefClass creation"""
        example = Example(groups=7, origins=5)
        example.init_array('param_g', 7)
        assert example.param_g.shape == (7,)

    def test_32_test_not_init_array(self):
        """Test the Example CDefClass creation"""
        example = Example(groups=7, origins=5, init_arrays=False, threading
            =False)
        with pytest.raises(AttributeError):
            print(example.not_initialized_ij)

    def test_32_test_not_init_array(self):
        """Test the Example CDefClass creation"""
        example = Example(groups=7, origins=5, init_arrays=False, threading
            =False)
        with pytest.raises(AttributeError):
            print(example.not_initialized_ij)

    def test_33_del_property(self):
        """Test the Example CDefClass creation"""
        example = Example(groups=7, origins=5)
        print(example.km_ij)
        example.dtypes['km_ij'].shape = None
        example.reset_array('km_ij')
        np.testing.assert_array_equal(example.km_ij, np.NAN)
        example.dtypes['km_ij'].default = 11
        example.reset_array('km_ij')
        np.testing.assert_array_equal(example.km_ij, 11)
        del example.km_ij
        np.testing.assert_array_equal(example.km_ij.shape, (0, 0))
        new_array = np.arange(10).reshape(2, 5)
        example.set_array('km_ij', value=new_array, shape=(2, 5))
        np.testing.assert_array_equal(example.km_ij, new_array)

    def test_34_save_ds(self, tempfile_h5):
        """Test the Example CDefClass creation"""
        example = Example(groups=7, origins=5)
        example.save_dataset_to_netcdf(tempfile_h5)


class Test04_Test_Instantiation:
    """Test the instantiation of the class"""

    def test041_test_instantiation(self):
        """not subclassing shoud rais a NotImplementedError"""
        with pytest.raises(NotImplementedError):
            example = _Example()

    def test042_test_nan(self, persons_gi):
        """Test nan"""
        groups, zones = persons_gi.shape
        example = Example(groups, zones)
        assert example.isnan_py(np.NAN)
        assert not example.isnan_py(np.NINF)
        assert not example.isnan_py(np.Inf)
        assert not example.isnan_py(0)
        assert not example.isnan_py(1)
        assert not example.isnan_py(-1)


if __name__ == '__main__':
    pytest.main()

# -*- coding: utf-8 -*-
"""
Created on Fri Jun 10 21:00:21 2016

@author: MaxBohnet
"""

import tempfile
import numpy as np
import pytest
import xarray as xr

from cythonarrays.tests.example_python import Example
import pyximport; pyximport.install()
from .example_cython import (_Example)


@pytest.fixture(scope='class')
def km_ij(request):
    """
    travel times
    """
    array = np.array([[1, 4, 5],
                      [2, 1, 7],
                      [5, 7, 2]])
    return array


@pytest.fixture(scope='class')
def jobs(request):
    """
    jobs
    """
    jobs = np.array([100, 200, 300])
    return jobs


@pytest.fixture(scope='class')
def params_groups(request):
    """
    different values for saving categories
    """
    return np.array([-0.2, -0.1])


@pytest.fixture(scope='class')
def persons_gi(request):
    """
    different values for home zone
    """
    arr = np.array([[100, 0, 200],
                    [0, 250, 50]])
    return arr


@pytest.fixture(scope='class')
def example(km_ij, jobs, params_groups, persons_gi):
    """
    different values for home zone
    """
    groups, zones = persons_gi.shape
    example = Example(groups, zones)
    example.set_array('km_ij', km_ij)
    example.set_array('jobs_j', jobs)
    example.set_array('param_g', params_groups)
    example.set_array('persons_gi', persons_gi)
    return example


@pytest.fixture()
def tempfile_h5():
    return tempfile.mktemp(suffix='h5')


class Test01_ExampleCDefClass:
    """Test the Example CDefClass"""

    def test_01_test_init_array(self, persons_gi):
        """Test the Example CDefClass creation"""
        groups, zones = persons_gi.shape
        example = Example(groups, zones)

        # set correct shape
        values = np.arange(zones)
        example.set_array('jobs_j', np.arange((zones)))
        np.testing.assert_array_equal(example.jobs_j, values)
        np.testing.assert_array_equal(example._jobs_j, values)

        # init the array with a default value
        example.init_array('jobs_j', default=0)
        np.testing.assert_array_equal(example.jobs_j, np.zeros(zones))

        # init the array with the other default value
        example.init_array('jobs_j', default=2)
        np.testing.assert_array_equal(example.jobs_j,
                                      np.full(zones, 2, dtype='d'))

        # new default value will be stored
        example.reset_array('jobs_j')
        np.testing.assert_array_equal(example.jobs_j,
                                      np.full(zones, 2, dtype='d'))

        # set new shape, keep old default value
        example.init_array('jobs_j', shape='groups')
        np.testing.assert_array_equal(example.jobs_j,
                                      np.full(groups, 2, dtype='d'))

    def test_02_test_shape(self, persons_gi):
        """
        Test if the shapes of array are controlled correctly
        """
        groups, zones = persons_gi.shape
        example = Example(groups, zones)

        # jobs_j should have the shape (zones)

        # correct shape
        arr = np.ones((zones))
        example.jobs_j = arr

        # try to set values with the wrong shape
        arr = np.ones((groups))
        message = """
Arrays are not equal
jobs_j: shape target: [3], actual: (2,)
(mismatch 100.0%)
 x: array([2])
 y: array([3])
        """
        with pytest.raises(AssertionError,
                           message=message):
            example.jobs_j = arr

        # change zones and try again
        example.destinations = groups
        # now the array fits to the shape defined
        example.jobs_j = arr

    def test_03_test_dimensions(self, persons_gi):
        """Test the dimensions"""
        groups, zones = persons_gi.shape
        example = Example(groups, zones)

        # try to set shape with the wrong number of dimensions
        msg = "builtins.ValueError: 1 Dimensions required, shape ['groups', 'zones'] has 2 dimensions"
        with pytest.raises(ValueError,
                           message=msg):
            example.init_array('jobs_j', shape='groups, zones')

        # access a non-initialized array
        target = np.empty((0, 0))
        actual = example.not_initialized_ij
        np.testing.assert_array_equal(actual, target)

        # set arbitrary values to non-initialized 2D-Array
        a = np.array([2, 3, 4], dtype='i4')
        # with less dimensions than required ...
        example.not_initialized_ij = a
        b = example.not_initialized_ij
        # another dimension is added
        assert b.ndim == 2
        assert b.shape == (1, 3)
        print(example.not_initialized_ij)

        # change value in cython-memoryview
        example._not_initialized_ij[0, 1] = 99
        target = np.array([[2, 99, 4]], dtype='i4')
        # the value will be changed in the numpy-view of the array
        np.testing.assert_array_equal(example.not_initialized_ij, target)
        # as this is a view on the input-data, it will be changed there, too
        np.testing.assert_array_equal(a[1], 99)

        # the right number of dimensions should be fine
        c = np.array([[0, 1],
                      [2, 3]], dtype='i4')
        example.not_initialized_ij = c
        d = example.not_initialized_ij
        np.testing.assert_array_equal(c, d)

        # too many dimensions will raise an error
        e = np.array([[[0, 1],
                       [2, 3]],
                      [[4, 5],
                       [6, 7]]], dtype='i4')
        with pytest.raises(AssertionError,
                           message="not_initialized_ij: ndim target: 2, actual: 3"):
            example.not_initialized_ij = e

        # when the dimensions can be reduced to the target dimensions,
        # it should be fine
        f = np.array([[[0, 1],
                       [2, 3]]], dtype='i4')
        example.not_initialized_ij = f
        g = example.not_initialized_ij
        np.testing.assert_array_equal(g, f[0])

        # change value in cython-memoryview
        example._not_initialized_ij[1, 1] = 88
        target = np.array([[0, 1],
                           [2, 88]], dtype='i4')
        # the value will be changed in the numpy-view of the array
        np.testing.assert_array_equal(example.not_initialized_ij, target)
        # as this is a view on the input-data, it will be changed there, too
        np.testing.assert_array_equal(f[0, 1, 1], 88)

        # use more dimensions than required
        # reset the array first
        del example.not_initialized_ij
        print(example.not_initialized_ij)
        c = np.array([[[2, 3, 4]]], dtype='i4')
        example.not_initialized_ij = c
        b = example.not_initialized_ij
        # one dimension can be taken away
        assert b.ndim == 2
        assert b.shape == (1, 3)
        print(example.not_initialized_ij)

        # use the correct number of dimensions
        # reset the array first
        del example.not_initialized_ij
        print(example.not_initialized_ij)
        d = np.array([[2, 3, 4]], dtype='i4')
        example.not_initialized_ij = d
        b = example.not_initialized_ij
        # one dimension can be taken away
        assert b.ndim == 2
        assert b.shape == (1, 3)
        print(example.not_initialized_ij)

    def test_04_test_dtype(self, persons_gi):
        """Test the dimensions"""
        groups, zones = persons_gi.shape
        example = Example(groups, zones)

        # dtype of jobs_j: f8
        # dtype of not_initialized_ij: i4
        # dtype of n_threads: char

        # test if n_threads is really a signed char
        example.n_threads = 127
        assert example.n_threads == 127

        with pytest.raises(OverflowError,
                           message='value too large to convert to char'):
            example.n_threads = 128

        # test if jobs_j is really an array of double precision
        arr_i4 = np.array([2, 3, 4], dtype='i4')
        example.jobs_j = arr_i4
        assert example.jobs_j.dtype == np.dtype('f8')
        # because the array set to jobs_j is of different dtype,
        # it had to be converted to double. So no view is used,
        # but a copy of the data
        arr_i4[1] = -1
        # the data in jobs_j stays untouched
        assert example.jobs_j[1] == 3

        # test if not_initialized_ij is really an array of 32bit integer
        arr_i4 = np.array([[2, 3, 4], [5, 6, 7]], dtype='i4')
        example.not_initialized_ij = arr_i4
        assert example.not_initialized_ij.dtype == np.dtype('i4')
        # because the array set to not_initialized_ij is of the same dtype,
        # a view on the data could have been used
        arr_i4[1, 2] = -1
        # the data in not_initialized_ij changes
        assert example.not_initialized_ij[1, 2] == -1

    def test_10_test_model(self, example):
        """Test the Example CDefClass model"""
        res = example.calc_model()
        print(example.trips_ij)
        total_trips_target = example.persons_gi.sum()
        total_trips_actual = example.trips_ij.sum()
        np.testing.assert_almost_equal(total_trips_target, total_trips_actual)

    def test_11_dataset(self, example):
        """Test the creation of an xarrays Dataset linked to the Cythonclass"""
        example.zonenumbers_i = np.array([100, 200, 300])
        example.groupnames_g = np.array(['Female', 'Male'], dtype='O')
        example.create_ds()
        assert isinstance(example.ds, xr.Dataset)
        for attr, dtype in example.dtypes.items():
            data_array = example.ds[attr]
            # test if the shapes are correct
            if dtype.shape:
                np.testing.assert_array_equal(dtype.get_shape(example),
                                              data_array.shape,
                                              'shape not correct')
            else:
                # not initialized array
                assert not np.any(data_array.shape), 'shape not initialized'
            #test if the datatypes are correct
            assert np.dtype(dtype.dtype) == data_array.dtype,  'dtype not correct'
        print(example.ds)

    def test_20_save_and_read_ds(self, example, tempfile_h5):
        """Test that saving and re-reading the data works"""
        example.zonenumbers_i = np.array([100, 200, 300])
        example.groupnames_g = np.array(['Female', 'Male'], dtype='O')
        example.create_ds()
        example.save_dataset_to_netcdf(tempfile_h5)

        # read the data into new class
        new_example = Example.from_netcdf(tempfile_h5)
        # assert that the data match
        np.testing.assert_array_equal(example.jobs_j, new_example.jobs_j)
        np.testing.assert_array_equal(example.groupnames_g,
                                      new_example.groupnames_g)

        # assert, that the array are correctly linked to the Dataset
        new_example.calc_model()
        old_value = new_example.ds.trips_ij.sum()
        # calculate the model with 77 persons more
        new_example.persons_gi[1, 0] += 77
        new_example.calc_model()
        new_value = new_example.ds.trips_ij.sum()
        np.testing.assert_allclose(old_value + 77, new_value)

        print(new_example.ds)

    def test_21_assign_bool(self, example):
        """Test boolean array"""
        # the boolean arrays are initialized with 0 and 1
        np.testing.assert_array_equal(example.valid_g.astype(bool),
                                      ~example.invalid_g.astype(bool))
        example.valid_g = np.zeros((example.groups), dtype=bool)
        example.invalid_g = np.ones((example.groups), dtype=bool)
        np.testing.assert_array_equal(example.valid_g.astype(bool),
                                      ~example.invalid_g.astype(bool))
        print(example.valid_g)
        print(example.invalid_g)

    def test_30_test_init_array(self, persons_gi):
        """Test the Example CDefClass creation"""
        example = Example(groups=7, origins=5)

        example.init_array('param_g', 7)
        assert example.param_g.shape == (7, )

    def test_32_test_not_init_array(self):
        """Test the Example CDefClass creation"""
        example = Example(groups=7, origins=5,
                          init_arrays=False, threading=False)
        with pytest.raises(AttributeError):
            print(example.not_initialized_ij)

    def test_32_test_not_init_array(self):
        """Test the Example CDefClass creation"""
        example = Example(groups=7, origins=5,
                          init_arrays=False, threading=False)
        with pytest.raises(AttributeError):
            print(example.not_initialized_ij)

    def test_33_del_property(self):
        """Test the Example CDefClass creation"""
        example = Example(groups=7, origins=5)
        print(example.km_ij)
        # remove the shape
        example.dtypes['km_ij'].shape = None

        # reset to default (not defined)
        example.reset_array('km_ij')
        np.testing.assert_array_equal(example.km_ij, np.NAN)

        # reset to default (new value defined)
        example.dtypes['km_ij'].default = 11
        example.reset_array('km_ij')
        np.testing.assert_array_equal(example.km_ij, 11)

        # delete values
        del example.km_ij
        np.testing.assert_array_equal(example.km_ij.shape, (0, 0))

        # set new values
        new_array = np.arange(10).reshape(2, 5)
        example.set_array('km_ij', value=new_array, shape=(2, 5))
        np.testing.assert_array_equal(example.km_ij, new_array)

    def test_34_save_ds(self, tempfile_h5):
        """Test the Example CDefClass creation"""
        example = Example(groups=7, origins=5, )
        example.save_dataset_to_netcdf(tempfile_h5)


class Test04_Test_Instantiation:
    """Test the instantiation of the class"""
    
    def test041_test_instantiation(self):
        """not subclassing shoud rais a NotImplementedError"""
        with pytest.raises(NotImplementedError):
            example = _Example()

    def test042_test_nan(self, persons_gi):
        """Test nan"""
        groups, zones = persons_gi.shape
        example = Example(groups, zones)

        assert example.isnan_py(np.NAN)
        assert not example.isnan_py(np.NINF)
        assert not example.isnan_py(np.Inf)
        assert not example.isnan_py(0)
        assert not example.isnan_py(1)
        assert not example.isnan_py(-1)


if __name__ == '__main__':
    pytest.main()