803 lines
27 KiB
Python
803 lines
27 KiB
Python
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from tempfile import mkdtemp
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import os
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import io
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import shutil
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import textwrap
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import numpy as np
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from numpy import array, transpose, pi
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from numpy.testing import (assert_equal, assert_allclose,
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assert_array_equal, assert_array_almost_equal)
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import pytest
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from pytest import raises as assert_raises
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import scipy.sparse
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import scipy.io._mmio
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import scipy.io._fast_matrix_market as fmm
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parametrize_args = [('integer', 'int'),
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('unsigned-integer', 'uint')]
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# Run the entire test suite on both _mmio and _fast_matrix_market implementations
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@pytest.fixture(scope='module', params=(scipy.io._mmio, fmm), autouse=True)
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def implementations(request):
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global mminfo
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global mmread
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global mmwrite
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mminfo = request.param.mminfo
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mmread = request.param.mmread
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mmwrite = request.param.mmwrite
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class TestMMIOArray:
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def setup_method(self):
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self.tmpdir = mkdtemp()
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self.fn = os.path.join(self.tmpdir, 'testfile.mtx')
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def teardown_method(self):
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shutil.rmtree(self.tmpdir)
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def check(self, a, info):
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mmwrite(self.fn, a)
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assert_equal(mminfo(self.fn), info)
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b = mmread(self.fn)
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assert_array_almost_equal(a, b)
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def check_exact(self, a, info):
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mmwrite(self.fn, a)
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assert_equal(mminfo(self.fn), info)
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b = mmread(self.fn)
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assert_equal(a, b)
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@pytest.mark.parametrize('typeval, dtype', parametrize_args)
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def test_simple_integer(self, typeval, dtype):
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self.check_exact(array([[1, 2], [3, 4]], dtype=dtype),
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(2, 2, 4, 'array', typeval, 'general'))
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@pytest.mark.parametrize('typeval, dtype', parametrize_args)
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def test_32bit_integer(self, typeval, dtype):
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a = array([[2**31-1, 2**31-2], [2**31-3, 2**31-4]], dtype=dtype)
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self.check_exact(a, (2, 2, 4, 'array', typeval, 'general'))
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def test_64bit_integer(self):
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a = array([[2**31, 2**32], [2**63-2, 2**63-1]], dtype=np.int64)
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if (np.intp(0).itemsize < 8) and mmwrite == scipy.io._mmio.mmwrite:
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assert_raises(OverflowError, mmwrite, self.fn, a)
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else:
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self.check_exact(a, (2, 2, 4, 'array', 'integer', 'general'))
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def test_64bit_unsigned_integer(self):
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a = array([[2**31, 2**32], [2**64-2, 2**64-1]], dtype=np.uint64)
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self.check_exact(a, (2, 2, 4, 'array', 'unsigned-integer', 'general'))
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@pytest.mark.parametrize('typeval, dtype', parametrize_args)
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def test_simple_upper_triangle_integer(self, typeval, dtype):
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self.check_exact(array([[0, 1], [0, 0]], dtype=dtype),
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(2, 2, 4, 'array', typeval, 'general'))
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@pytest.mark.parametrize('typeval, dtype', parametrize_args)
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def test_simple_lower_triangle_integer(self, typeval, dtype):
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self.check_exact(array([[0, 0], [1, 0]], dtype=dtype),
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(2, 2, 4, 'array', typeval, 'general'))
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@pytest.mark.parametrize('typeval, dtype', parametrize_args)
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def test_simple_rectangular_integer(self, typeval, dtype):
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self.check_exact(array([[1, 2, 3], [4, 5, 6]], dtype=dtype),
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(2, 3, 6, 'array', typeval, 'general'))
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def test_simple_rectangular_float(self):
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self.check([[1, 2], [3.5, 4], [5, 6]],
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(3, 2, 6, 'array', 'real', 'general'))
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def test_simple_float(self):
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self.check([[1, 2], [3, 4.0]],
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(2, 2, 4, 'array', 'real', 'general'))
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def test_simple_complex(self):
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self.check([[1, 2], [3, 4j]],
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(2, 2, 4, 'array', 'complex', 'general'))
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@pytest.mark.parametrize('typeval, dtype', parametrize_args)
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def test_simple_symmetric_integer(self, typeval, dtype):
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self.check_exact(array([[1, 2], [2, 4]], dtype=dtype),
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(2, 2, 4, 'array', typeval, 'symmetric'))
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def test_simple_skew_symmetric_integer(self):
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self.check_exact([[0, 2], [-2, 0]],
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(2, 2, 4, 'array', 'integer', 'skew-symmetric'))
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def test_simple_skew_symmetric_float(self):
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self.check(array([[0, 2], [-2.0, 0.0]], 'f'),
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(2, 2, 4, 'array', 'real', 'skew-symmetric'))
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def test_simple_hermitian_complex(self):
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self.check([[1, 2+3j], [2-3j, 4]],
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(2, 2, 4, 'array', 'complex', 'hermitian'))
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def test_random_symmetric_float(self):
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sz = (20, 20)
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a = np.random.random(sz)
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a = a + transpose(a)
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self.check(a, (20, 20, 400, 'array', 'real', 'symmetric'))
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def test_random_rectangular_float(self):
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sz = (20, 15)
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a = np.random.random(sz)
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self.check(a, (20, 15, 300, 'array', 'real', 'general'))
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def test_bad_number_of_array_header_fields(self):
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s = """\
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%%MatrixMarket matrix array real general
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3 3 999
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1.0
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2.0
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3.0
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4.0
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5.0
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6.0
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7.0
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8.0
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9.0
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"""
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text = textwrap.dedent(s).encode('ascii')
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with pytest.raises(ValueError, match='not of length 2'):
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scipy.io.mmread(io.BytesIO(text))
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def test_gh13634_non_skew_symmetric_int(self):
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self.check_exact(array([[1, 2], [-2, 99]], dtype=np.int32),
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(2, 2, 4, 'array', 'integer', 'general'))
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def test_gh13634_non_skew_symmetric_float(self):
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self.check(array([[1, 2], [-2, 99.]], dtype=np.float32),
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(2, 2, 4, 'array', 'real', 'general'))
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class TestMMIOSparseCSR(TestMMIOArray):
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def setup_method(self):
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self.tmpdir = mkdtemp()
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self.fn = os.path.join(self.tmpdir, 'testfile.mtx')
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def teardown_method(self):
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shutil.rmtree(self.tmpdir)
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def check(self, a, info):
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mmwrite(self.fn, a)
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assert_equal(mminfo(self.fn), info)
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b = mmread(self.fn)
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assert_array_almost_equal(a.toarray(), b.toarray())
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def check_exact(self, a, info):
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mmwrite(self.fn, a)
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assert_equal(mminfo(self.fn), info)
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b = mmread(self.fn)
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assert_equal(a.toarray(), b.toarray())
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@pytest.mark.parametrize('typeval, dtype', parametrize_args)
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def test_simple_integer(self, typeval, dtype):
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self.check_exact(scipy.sparse.csr_matrix([[1, 2], [3, 4]], dtype=dtype),
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(2, 2, 4, 'coordinate', typeval, 'general'))
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def test_32bit_integer(self):
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a = scipy.sparse.csr_matrix(array([[2**31-1, -2**31+2],
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[2**31-3, 2**31-4]],
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dtype=np.int32))
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self.check_exact(a, (2, 2, 4, 'coordinate', 'integer', 'general'))
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def test_64bit_integer(self):
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a = scipy.sparse.csr_matrix(array([[2**32+1, 2**32+1],
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[-2**63+2, 2**63-2]],
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dtype=np.int64))
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if (np.intp(0).itemsize < 8) and mmwrite == scipy.io._mmio.mmwrite:
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assert_raises(OverflowError, mmwrite, self.fn, a)
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else:
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self.check_exact(a, (2, 2, 4, 'coordinate', 'integer', 'general'))
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def test_32bit_unsigned_integer(self):
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a = scipy.sparse.csr_matrix(array([[2**31-1, 2**31-2],
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[2**31-3, 2**31-4]],
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dtype=np.uint32))
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self.check_exact(a, (2, 2, 4, 'coordinate', 'unsigned-integer', 'general'))
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def test_64bit_unsigned_integer(self):
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a = scipy.sparse.csr_matrix(array([[2**32+1, 2**32+1],
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[2**64-2, 2**64-1]],
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dtype=np.uint64))
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self.check_exact(a, (2, 2, 4, 'coordinate', 'unsigned-integer', 'general'))
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@pytest.mark.parametrize('typeval, dtype', parametrize_args)
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def test_simple_upper_triangle_integer(self, typeval, dtype):
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self.check_exact(scipy.sparse.csr_matrix([[0, 1], [0, 0]], dtype=dtype),
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(2, 2, 1, 'coordinate', typeval, 'general'))
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@pytest.mark.parametrize('typeval, dtype', parametrize_args)
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def test_simple_lower_triangle_integer(self, typeval, dtype):
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self.check_exact(scipy.sparse.csr_matrix([[0, 0], [1, 0]], dtype=dtype),
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(2, 2, 1, 'coordinate', typeval, 'general'))
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@pytest.mark.parametrize('typeval, dtype', parametrize_args)
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def test_simple_rectangular_integer(self, typeval, dtype):
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self.check_exact(scipy.sparse.csr_matrix([[1, 2, 3], [4, 5, 6]], dtype=dtype),
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(2, 3, 6, 'coordinate', typeval, 'general'))
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def test_simple_rectangular_float(self):
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self.check(scipy.sparse.csr_matrix([[1, 2], [3.5, 4], [5, 6]]),
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(3, 2, 6, 'coordinate', 'real', 'general'))
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def test_simple_float(self):
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self.check(scipy.sparse.csr_matrix([[1, 2], [3, 4.0]]),
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(2, 2, 4, 'coordinate', 'real', 'general'))
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def test_simple_complex(self):
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self.check(scipy.sparse.csr_matrix([[1, 2], [3, 4j]]),
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(2, 2, 4, 'coordinate', 'complex', 'general'))
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@pytest.mark.parametrize('typeval, dtype', parametrize_args)
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def test_simple_symmetric_integer(self, typeval, dtype):
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self.check_exact(scipy.sparse.csr_matrix([[1, 2], [2, 4]], dtype=dtype),
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(2, 2, 3, 'coordinate', typeval, 'symmetric'))
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def test_simple_skew_symmetric_integer(self):
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self.check_exact(scipy.sparse.csr_matrix([[0, 2], [-2, 0]]),
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(2, 2, 1, 'coordinate', 'integer', 'skew-symmetric'))
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def test_simple_skew_symmetric_float(self):
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self.check(scipy.sparse.csr_matrix(array([[0, 2], [-2.0, 0]], 'f')),
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(2, 2, 1, 'coordinate', 'real', 'skew-symmetric'))
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def test_simple_hermitian_complex(self):
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self.check(scipy.sparse.csr_matrix([[1, 2+3j], [2-3j, 4]]),
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(2, 2, 3, 'coordinate', 'complex', 'hermitian'))
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def test_random_symmetric_float(self):
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sz = (20, 20)
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a = np.random.random(sz)
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a = a + transpose(a)
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a = scipy.sparse.csr_matrix(a)
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self.check(a, (20, 20, 210, 'coordinate', 'real', 'symmetric'))
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def test_random_rectangular_float(self):
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sz = (20, 15)
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a = np.random.random(sz)
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a = scipy.sparse.csr_matrix(a)
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self.check(a, (20, 15, 300, 'coordinate', 'real', 'general'))
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def test_simple_pattern(self):
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a = scipy.sparse.csr_matrix([[0, 1.5], [3.0, 2.5]])
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p = np.zeros_like(a.toarray())
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p[a.toarray() > 0] = 1
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info = (2, 2, 3, 'coordinate', 'pattern', 'general')
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mmwrite(self.fn, a, field='pattern')
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assert_equal(mminfo(self.fn), info)
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b = mmread(self.fn)
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assert_array_almost_equal(p, b.toarray())
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def test_gh13634_non_skew_symmetric_int(self):
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a = scipy.sparse.csr_matrix([[1, 2], [-2, 99]], dtype=np.int32)
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self.check_exact(a, (2, 2, 4, 'coordinate', 'integer', 'general'))
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def test_gh13634_non_skew_symmetric_float(self):
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a = scipy.sparse.csr_matrix([[1, 2], [-2, 99.]], dtype=np.float32)
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self.check(a, (2, 2, 4, 'coordinate', 'real', 'general'))
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_32bit_integer_dense_example = '''\
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%%MatrixMarket matrix array integer general
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2 2
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2147483647
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2147483646
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2147483647
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2147483646
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'''
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_32bit_integer_sparse_example = '''\
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%%MatrixMarket matrix coordinate integer symmetric
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2 2 2
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1 1 2147483647
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2 2 2147483646
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'''
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_64bit_integer_dense_example = '''\
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%%MatrixMarket matrix array integer general
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2 2
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2147483648
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-9223372036854775806
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-2147483648
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9223372036854775807
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'''
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_64bit_integer_sparse_general_example = '''\
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%%MatrixMarket matrix coordinate integer general
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2 2 3
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1 1 2147483648
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1 2 9223372036854775807
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2 2 9223372036854775807
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'''
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_64bit_integer_sparse_symmetric_example = '''\
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%%MatrixMarket matrix coordinate integer symmetric
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2 2 3
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1 1 2147483648
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1 2 -9223372036854775807
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2 2 9223372036854775807
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'''
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||
|
|
_64bit_integer_sparse_skew_example = '''\
|
||
|
|
%%MatrixMarket matrix coordinate integer skew-symmetric
|
||
|
|
2 2 3
|
||
|
|
1 1 2147483648
|
||
|
|
1 2 -9223372036854775807
|
||
|
|
2 2 9223372036854775807
|
||
|
|
'''
|
||
|
|
|
||
|
|
_over64bit_integer_dense_example = '''\
|
||
|
|
%%MatrixMarket matrix array integer general
|
||
|
|
2 2
|
||
|
|
2147483648
|
||
|
|
9223372036854775807
|
||
|
|
2147483648
|
||
|
|
9223372036854775808
|
||
|
|
'''
|
||
|
|
|
||
|
|
_over64bit_integer_sparse_example = '''\
|
||
|
|
%%MatrixMarket matrix coordinate integer symmetric
|
||
|
|
2 2 2
|
||
|
|
1 1 2147483648
|
||
|
|
2 2 19223372036854775808
|
||
|
|
'''
|
||
|
|
|
||
|
|
|
||
|
|
class TestMMIOReadLargeIntegers:
|
||
|
|
def setup_method(self):
|
||
|
|
self.tmpdir = mkdtemp()
|
||
|
|
self.fn = os.path.join(self.tmpdir, 'testfile.mtx')
|
||
|
|
|
||
|
|
def teardown_method(self):
|
||
|
|
shutil.rmtree(self.tmpdir)
|
||
|
|
|
||
|
|
def check_read(self, example, a, info, dense, over32, over64):
|
||
|
|
with open(self.fn, 'w') as f:
|
||
|
|
f.write(example)
|
||
|
|
assert_equal(mminfo(self.fn), info)
|
||
|
|
if ((over32 and (np.intp(0).itemsize < 8) and mmwrite == scipy.io._mmio.mmwrite)
|
||
|
|
or over64):
|
||
|
|
assert_raises(OverflowError, mmread, self.fn)
|
||
|
|
else:
|
||
|
|
b = mmread(self.fn)
|
||
|
|
if not dense:
|
||
|
|
b = b.toarray()
|
||
|
|
assert_equal(a, b)
|
||
|
|
|
||
|
|
def test_read_32bit_integer_dense(self):
|
||
|
|
a = array([[2**31-1, 2**31-1],
|
||
|
|
[2**31-2, 2**31-2]], dtype=np.int64)
|
||
|
|
self.check_read(_32bit_integer_dense_example,
|
||
|
|
a,
|
||
|
|
(2, 2, 4, 'array', 'integer', 'general'),
|
||
|
|
dense=True,
|
||
|
|
over32=False,
|
||
|
|
over64=False)
|
||
|
|
|
||
|
|
def test_read_32bit_integer_sparse(self):
|
||
|
|
a = array([[2**31-1, 0],
|
||
|
|
[0, 2**31-2]], dtype=np.int64)
|
||
|
|
self.check_read(_32bit_integer_sparse_example,
|
||
|
|
a,
|
||
|
|
(2, 2, 2, 'coordinate', 'integer', 'symmetric'),
|
||
|
|
dense=False,
|
||
|
|
over32=False,
|
||
|
|
over64=False)
|
||
|
|
|
||
|
|
def test_read_64bit_integer_dense(self):
|
||
|
|
a = array([[2**31, -2**31],
|
||
|
|
[-2**63+2, 2**63-1]], dtype=np.int64)
|
||
|
|
self.check_read(_64bit_integer_dense_example,
|
||
|
|
a,
|
||
|
|
(2, 2, 4, 'array', 'integer', 'general'),
|
||
|
|
dense=True,
|
||
|
|
over32=True,
|
||
|
|
over64=False)
|
||
|
|
|
||
|
|
def test_read_64bit_integer_sparse_general(self):
|
||
|
|
a = array([[2**31, 2**63-1],
|
||
|
|
[0, 2**63-1]], dtype=np.int64)
|
||
|
|
self.check_read(_64bit_integer_sparse_general_example,
|
||
|
|
a,
|
||
|
|
(2, 2, 3, 'coordinate', 'integer', 'general'),
|
||
|
|
dense=False,
|
||
|
|
over32=True,
|
||
|
|
over64=False)
|
||
|
|
|
||
|
|
def test_read_64bit_integer_sparse_symmetric(self):
|
||
|
|
a = array([[2**31, -2**63+1],
|
||
|
|
[-2**63+1, 2**63-1]], dtype=np.int64)
|
||
|
|
self.check_read(_64bit_integer_sparse_symmetric_example,
|
||
|
|
a,
|
||
|
|
(2, 2, 3, 'coordinate', 'integer', 'symmetric'),
|
||
|
|
dense=False,
|
||
|
|
over32=True,
|
||
|
|
over64=False)
|
||
|
|
|
||
|
|
def test_read_64bit_integer_sparse_skew(self):
|
||
|
|
a = array([[2**31, -2**63+1],
|
||
|
|
[2**63-1, 2**63-1]], dtype=np.int64)
|
||
|
|
self.check_read(_64bit_integer_sparse_skew_example,
|
||
|
|
a,
|
||
|
|
(2, 2, 3, 'coordinate', 'integer', 'skew-symmetric'),
|
||
|
|
dense=False,
|
||
|
|
over32=True,
|
||
|
|
over64=False)
|
||
|
|
|
||
|
|
def test_read_over64bit_integer_dense(self):
|
||
|
|
self.check_read(_over64bit_integer_dense_example,
|
||
|
|
None,
|
||
|
|
(2, 2, 4, 'array', 'integer', 'general'),
|
||
|
|
dense=True,
|
||
|
|
over32=True,
|
||
|
|
over64=True)
|
||
|
|
|
||
|
|
def test_read_over64bit_integer_sparse(self):
|
||
|
|
self.check_read(_over64bit_integer_sparse_example,
|
||
|
|
None,
|
||
|
|
(2, 2, 2, 'coordinate', 'integer', 'symmetric'),
|
||
|
|
dense=False,
|
||
|
|
over32=True,
|
||
|
|
over64=True)
|
||
|
|
|
||
|
|
|
||
|
|
_general_example = '''\
|
||
|
|
%%MatrixMarket matrix coordinate real general
|
||
|
|
%=================================================================================
|
||
|
|
%
|
||
|
|
% This ASCII file represents a sparse MxN matrix with L
|
||
|
|
% nonzeros in the following Matrix Market format:
|
||
|
|
%
|
||
|
|
% +----------------------------------------------+
|
||
|
|
% |%%MatrixMarket matrix coordinate real general | <--- header line
|
||
|
|
% |% | <--+
|
||
|
|
% |% comments | |-- 0 or more comment lines
|
||
|
|
% |% | <--+
|
||
|
|
% | M N L | <--- rows, columns, entries
|
||
|
|
% | I1 J1 A(I1, J1) | <--+
|
||
|
|
% | I2 J2 A(I2, J2) | |
|
||
|
|
% | I3 J3 A(I3, J3) | |-- L lines
|
||
|
|
% | . . . | |
|
||
|
|
% | IL JL A(IL, JL) | <--+
|
||
|
|
% +----------------------------------------------+
|
||
|
|
%
|
||
|
|
% Indices are 1-based, i.e. A(1,1) is the first element.
|
||
|
|
%
|
||
|
|
%=================================================================================
|
||
|
|
5 5 8
|
||
|
|
1 1 1.000e+00
|
||
|
|
2 2 1.050e+01
|
||
|
|
3 3 1.500e-02
|
||
|
|
1 4 6.000e+00
|
||
|
|
4 2 2.505e+02
|
||
|
|
4 4 -2.800e+02
|
||
|
|
4 5 3.332e+01
|
||
|
|
5 5 1.200e+01
|
||
|
|
'''
|
||
|
|
|
||
|
|
_hermitian_example = '''\
|
||
|
|
%%MatrixMarket matrix coordinate complex hermitian
|
||
|
|
5 5 7
|
||
|
|
1 1 1.0 0
|
||
|
|
2 2 10.5 0
|
||
|
|
4 2 250.5 22.22
|
||
|
|
3 3 1.5e-2 0
|
||
|
|
4 4 -2.8e2 0
|
||
|
|
5 5 12. 0
|
||
|
|
5 4 0 33.32
|
||
|
|
'''
|
||
|
|
|
||
|
|
_skew_example = '''\
|
||
|
|
%%MatrixMarket matrix coordinate real skew-symmetric
|
||
|
|
5 5 7
|
||
|
|
1 1 1.0
|
||
|
|
2 2 10.5
|
||
|
|
4 2 250.5
|
||
|
|
3 3 1.5e-2
|
||
|
|
4 4 -2.8e2
|
||
|
|
5 5 12.
|
||
|
|
5 4 0
|
||
|
|
'''
|
||
|
|
|
||
|
|
_symmetric_example = '''\
|
||
|
|
%%MatrixMarket matrix coordinate real symmetric
|
||
|
|
5 5 7
|
||
|
|
1 1 1.0
|
||
|
|
2 2 10.5
|
||
|
|
4 2 250.5
|
||
|
|
3 3 1.5e-2
|
||
|
|
4 4 -2.8e2
|
||
|
|
5 5 12.
|
||
|
|
5 4 8
|
||
|
|
'''
|
||
|
|
|
||
|
|
_symmetric_pattern_example = '''\
|
||
|
|
%%MatrixMarket matrix coordinate pattern symmetric
|
||
|
|
5 5 7
|
||
|
|
1 1
|
||
|
|
2 2
|
||
|
|
4 2
|
||
|
|
3 3
|
||
|
|
4 4
|
||
|
|
5 5
|
||
|
|
5 4
|
||
|
|
'''
|
||
|
|
|
||
|
|
# example (without comment lines) from Figure 1 in
|
||
|
|
# https://math.nist.gov/MatrixMarket/reports/MMformat.ps
|
||
|
|
_empty_lines_example = '''\
|
||
|
|
%%MatrixMarket MATRIX Coordinate Real General
|
||
|
|
|
||
|
|
5 5 8
|
||
|
|
|
||
|
|
1 1 1.0
|
||
|
|
2 2 10.5
|
||
|
|
3 3 1.5e-2
|
||
|
|
4 4 -2.8E2
|
||
|
|
5 5 12.
|
||
|
|
1 4 6
|
||
|
|
4 2 250.5
|
||
|
|
4 5 33.32
|
||
|
|
|
||
|
|
'''
|
||
|
|
|
||
|
|
|
||
|
|
class TestMMIOCoordinate:
|
||
|
|
def setup_method(self):
|
||
|
|
self.tmpdir = mkdtemp()
|
||
|
|
self.fn = os.path.join(self.tmpdir, 'testfile.mtx')
|
||
|
|
|
||
|
|
def teardown_method(self):
|
||
|
|
shutil.rmtree(self.tmpdir)
|
||
|
|
|
||
|
|
def check_read(self, example, a, info):
|
||
|
|
f = open(self.fn, 'w')
|
||
|
|
f.write(example)
|
||
|
|
f.close()
|
||
|
|
assert_equal(mminfo(self.fn), info)
|
||
|
|
b = mmread(self.fn).toarray()
|
||
|
|
assert_array_almost_equal(a, b)
|
||
|
|
|
||
|
|
def test_read_general(self):
|
||
|
|
a = [[1, 0, 0, 6, 0],
|
||
|
|
[0, 10.5, 0, 0, 0],
|
||
|
|
[0, 0, .015, 0, 0],
|
||
|
|
[0, 250.5, 0, -280, 33.32],
|
||
|
|
[0, 0, 0, 0, 12]]
|
||
|
|
self.check_read(_general_example, a,
|
||
|
|
(5, 5, 8, 'coordinate', 'real', 'general'))
|
||
|
|
|
||
|
|
def test_read_hermitian(self):
|
||
|
|
a = [[1, 0, 0, 0, 0],
|
||
|
|
[0, 10.5, 0, 250.5 - 22.22j, 0],
|
||
|
|
[0, 0, .015, 0, 0],
|
||
|
|
[0, 250.5 + 22.22j, 0, -280, -33.32j],
|
||
|
|
[0, 0, 0, 33.32j, 12]]
|
||
|
|
self.check_read(_hermitian_example, a,
|
||
|
|
(5, 5, 7, 'coordinate', 'complex', 'hermitian'))
|
||
|
|
|
||
|
|
def test_read_skew(self):
|
||
|
|
a = [[1, 0, 0, 0, 0],
|
||
|
|
[0, 10.5, 0, -250.5, 0],
|
||
|
|
[0, 0, .015, 0, 0],
|
||
|
|
[0, 250.5, 0, -280, 0],
|
||
|
|
[0, 0, 0, 0, 12]]
|
||
|
|
self.check_read(_skew_example, a,
|
||
|
|
(5, 5, 7, 'coordinate', 'real', 'skew-symmetric'))
|
||
|
|
|
||
|
|
def test_read_symmetric(self):
|
||
|
|
a = [[1, 0, 0, 0, 0],
|
||
|
|
[0, 10.5, 0, 250.5, 0],
|
||
|
|
[0, 0, .015, 0, 0],
|
||
|
|
[0, 250.5, 0, -280, 8],
|
||
|
|
[0, 0, 0, 8, 12]]
|
||
|
|
self.check_read(_symmetric_example, a,
|
||
|
|
(5, 5, 7, 'coordinate', 'real', 'symmetric'))
|
||
|
|
|
||
|
|
def test_read_symmetric_pattern(self):
|
||
|
|
a = [[1, 0, 0, 0, 0],
|
||
|
|
[0, 1, 0, 1, 0],
|
||
|
|
[0, 0, 1, 0, 0],
|
||
|
|
[0, 1, 0, 1, 1],
|
||
|
|
[0, 0, 0, 1, 1]]
|
||
|
|
self.check_read(_symmetric_pattern_example, a,
|
||
|
|
(5, 5, 7, 'coordinate', 'pattern', 'symmetric'))
|
||
|
|
|
||
|
|
def test_read_empty_lines(self):
|
||
|
|
a = [[1, 0, 0, 6, 0],
|
||
|
|
[0, 10.5, 0, 0, 0],
|
||
|
|
[0, 0, .015, 0, 0],
|
||
|
|
[0, 250.5, 0, -280, 33.32],
|
||
|
|
[0, 0, 0, 0, 12]]
|
||
|
|
self.check_read(_empty_lines_example, a,
|
||
|
|
(5, 5, 8, 'coordinate', 'real', 'general'))
|
||
|
|
|
||
|
|
def test_empty_write_read(self):
|
||
|
|
# https://github.com/scipy/scipy/issues/1410 (Trac #883)
|
||
|
|
|
||
|
|
b = scipy.sparse.coo_matrix((10, 10))
|
||
|
|
mmwrite(self.fn, b)
|
||
|
|
|
||
|
|
assert_equal(mminfo(self.fn),
|
||
|
|
(10, 10, 0, 'coordinate', 'real', 'symmetric'))
|
||
|
|
a = b.toarray()
|
||
|
|
b = mmread(self.fn).toarray()
|
||
|
|
assert_array_almost_equal(a, b)
|
||
|
|
|
||
|
|
def test_bzip2_py3(self):
|
||
|
|
# test if fix for #2152 works
|
||
|
|
try:
|
||
|
|
# bz2 module isn't always built when building Python.
|
||
|
|
import bz2
|
||
|
|
except ImportError:
|
||
|
|
return
|
||
|
|
I = array([0, 0, 1, 2, 3, 3, 3, 4])
|
||
|
|
J = array([0, 3, 1, 2, 1, 3, 4, 4])
|
||
|
|
V = array([1.0, 6.0, 10.5, 0.015, 250.5, -280.0, 33.32, 12.0])
|
||
|
|
|
||
|
|
b = scipy.sparse.coo_matrix((V, (I, J)), shape=(5, 5))
|
||
|
|
|
||
|
|
mmwrite(self.fn, b)
|
||
|
|
|
||
|
|
fn_bzip2 = "%s.bz2" % self.fn
|
||
|
|
with open(self.fn, 'rb') as f_in:
|
||
|
|
f_out = bz2.BZ2File(fn_bzip2, 'wb')
|
||
|
|
f_out.write(f_in.read())
|
||
|
|
f_out.close()
|
||
|
|
|
||
|
|
a = mmread(fn_bzip2).toarray()
|
||
|
|
assert_array_almost_equal(a, b.toarray())
|
||
|
|
|
||
|
|
def test_gzip_py3(self):
|
||
|
|
# test if fix for #2152 works
|
||
|
|
try:
|
||
|
|
# gzip module can be missing from Python installation
|
||
|
|
import gzip
|
||
|
|
except ImportError:
|
||
|
|
return
|
||
|
|
I = array([0, 0, 1, 2, 3, 3, 3, 4])
|
||
|
|
J = array([0, 3, 1, 2, 1, 3, 4, 4])
|
||
|
|
V = array([1.0, 6.0, 10.5, 0.015, 250.5, -280.0, 33.32, 12.0])
|
||
|
|
|
||
|
|
b = scipy.sparse.coo_matrix((V, (I, J)), shape=(5, 5))
|
||
|
|
|
||
|
|
mmwrite(self.fn, b)
|
||
|
|
|
||
|
|
fn_gzip = "%s.gz" % self.fn
|
||
|
|
with open(self.fn, 'rb') as f_in:
|
||
|
|
f_out = gzip.open(fn_gzip, 'wb')
|
||
|
|
f_out.write(f_in.read())
|
||
|
|
f_out.close()
|
||
|
|
|
||
|
|
a = mmread(fn_gzip).toarray()
|
||
|
|
assert_array_almost_equal(a, b.toarray())
|
||
|
|
|
||
|
|
def test_real_write_read(self):
|
||
|
|
I = array([0, 0, 1, 2, 3, 3, 3, 4])
|
||
|
|
J = array([0, 3, 1, 2, 1, 3, 4, 4])
|
||
|
|
V = array([1.0, 6.0, 10.5, 0.015, 250.5, -280.0, 33.32, 12.0])
|
||
|
|
|
||
|
|
b = scipy.sparse.coo_matrix((V, (I, J)), shape=(5, 5))
|
||
|
|
|
||
|
|
mmwrite(self.fn, b)
|
||
|
|
|
||
|
|
assert_equal(mminfo(self.fn),
|
||
|
|
(5, 5, 8, 'coordinate', 'real', 'general'))
|
||
|
|
a = b.toarray()
|
||
|
|
b = mmread(self.fn).toarray()
|
||
|
|
assert_array_almost_equal(a, b)
|
||
|
|
|
||
|
|
def test_complex_write_read(self):
|
||
|
|
I = array([0, 0, 1, 2, 3, 3, 3, 4])
|
||
|
|
J = array([0, 3, 1, 2, 1, 3, 4, 4])
|
||
|
|
V = array([1.0 + 3j, 6.0 + 2j, 10.50 + 0.9j, 0.015 + -4.4j,
|
||
|
|
250.5 + 0j, -280.0 + 5j, 33.32 + 6.4j, 12.00 + 0.8j])
|
||
|
|
|
||
|
|
b = scipy.sparse.coo_matrix((V, (I, J)), shape=(5, 5))
|
||
|
|
|
||
|
|
mmwrite(self.fn, b)
|
||
|
|
|
||
|
|
assert_equal(mminfo(self.fn),
|
||
|
|
(5, 5, 8, 'coordinate', 'complex', 'general'))
|
||
|
|
a = b.toarray()
|
||
|
|
b = mmread(self.fn).toarray()
|
||
|
|
assert_array_almost_equal(a, b)
|
||
|
|
|
||
|
|
def test_sparse_formats(self, tmp_path):
|
||
|
|
# Note: `tmp_path` is a pytest fixture, it handles cleanup
|
||
|
|
tmpdir = tmp_path / 'sparse_formats'
|
||
|
|
tmpdir.mkdir()
|
||
|
|
|
||
|
|
mats = []
|
||
|
|
I = array([0, 0, 1, 2, 3, 3, 3, 4])
|
||
|
|
J = array([0, 3, 1, 2, 1, 3, 4, 4])
|
||
|
|
|
||
|
|
V = array([1.0, 6.0, 10.5, 0.015, 250.5, -280.0, 33.32, 12.0])
|
||
|
|
mats.append(scipy.sparse.coo_matrix((V, (I, J)), shape=(5, 5)))
|
||
|
|
|
||
|
|
V = array([1.0 + 3j, 6.0 + 2j, 10.50 + 0.9j, 0.015 + -4.4j,
|
||
|
|
250.5 + 0j, -280.0 + 5j, 33.32 + 6.4j, 12.00 + 0.8j])
|
||
|
|
mats.append(scipy.sparse.coo_matrix((V, (I, J)), shape=(5, 5)))
|
||
|
|
|
||
|
|
for mat in mats:
|
||
|
|
expected = mat.toarray()
|
||
|
|
for fmt in ['csr', 'csc', 'coo']:
|
||
|
|
fname = tmpdir / (fmt + '.mtx')
|
||
|
|
mmwrite(fname, mat.asformat(fmt))
|
||
|
|
result = mmread(fname).toarray()
|
||
|
|
assert_array_almost_equal(result, expected)
|
||
|
|
|
||
|
|
def test_precision(self):
|
||
|
|
test_values = [pi] + [10**(i) for i in range(0, -10, -1)]
|
||
|
|
test_precisions = range(1, 10)
|
||
|
|
for value in test_values:
|
||
|
|
for precision in test_precisions:
|
||
|
|
# construct sparse matrix with test value at last main diagonal
|
||
|
|
n = 10**precision + 1
|
||
|
|
A = scipy.sparse.dok_matrix((n, n))
|
||
|
|
A[n-1, n-1] = value
|
||
|
|
# write matrix with test precision and read again
|
||
|
|
mmwrite(self.fn, A, precision=precision)
|
||
|
|
A = scipy.io.mmread(self.fn)
|
||
|
|
# check for right entries in matrix
|
||
|
|
assert_array_equal(A.row, [n-1])
|
||
|
|
assert_array_equal(A.col, [n-1])
|
||
|
|
assert_allclose(A.data, [float('%%.%dg' % precision % value)])
|
||
|
|
|
||
|
|
def test_bad_number_of_coordinate_header_fields(self):
|
||
|
|
s = """\
|
||
|
|
%%MatrixMarket matrix coordinate real general
|
||
|
|
5 5 8 999
|
||
|
|
1 1 1.000e+00
|
||
|
|
2 2 1.050e+01
|
||
|
|
3 3 1.500e-02
|
||
|
|
1 4 6.000e+00
|
||
|
|
4 2 2.505e+02
|
||
|
|
4 4 -2.800e+02
|
||
|
|
4 5 3.332e+01
|
||
|
|
5 5 1.200e+01
|
||
|
|
"""
|
||
|
|
text = textwrap.dedent(s).encode('ascii')
|
||
|
|
with pytest.raises(ValueError, match='not of length 3'):
|
||
|
|
scipy.io.mmread(io.BytesIO(text))
|
||
|
|
|
||
|
|
|
||
|
|
def test_gh11389():
|
||
|
|
mmread(io.StringIO("%%MatrixMarket matrix coordinate complex symmetric\n"
|
||
|
|
" 1 1 1\n"
|
||
|
|
"1 1 -2.1846000000000e+02 0.0000000000000e+00"))
|
||
|
|
|
||
|
|
|
||
|
|
def test_gh18123(tmp_path):
|
||
|
|
lines = [" %%MatrixMarket matrix coordinate real general\n",
|
||
|
|
"5 5 3\n",
|
||
|
|
"2 3 1.0\n",
|
||
|
|
"3 4 2.0\n",
|
||
|
|
"3 5 3.0\n"]
|
||
|
|
test_file = tmp_path / "test.mtx"
|
||
|
|
with open(test_file, "w") as f:
|
||
|
|
f.writelines(lines)
|
||
|
|
mmread(test_file)
|
||
|
|
|
||
|
|
|
||
|
|
def test_threadpoolctl():
|
||
|
|
try:
|
||
|
|
import threadpoolctl
|
||
|
|
if not hasattr(threadpoolctl, "register"):
|
||
|
|
pytest.skip("threadpoolctl too old")
|
||
|
|
return
|
||
|
|
except ImportError:
|
||
|
|
pytest.skip("no threadpoolctl")
|
||
|
|
return
|
||
|
|
|
||
|
|
with threadpoolctl.threadpool_limits(limits=4):
|
||
|
|
assert_equal(fmm.PARALLELISM, 4)
|
||
|
|
|
||
|
|
with threadpoolctl.threadpool_limits(limits=2, user_api='scipy'):
|
||
|
|
assert_equal(fmm.PARALLELISM, 2)
|