def test_deprecated_io(self):
fh = StringIO()
npt.assert_warns(DeprecationWarning, self.ordination_results.to_file, fh)
fh.seek(0)
deserialized = npt.assert_warns(DeprecationWarning, OrdinationResults.from_file, fh)
assert_ordination_results_equal(deserialized, self.ordination_results)
self.assertTrue(type(deserialized) == OrdinationResults)
def test_deprecated_io(self):
fh = StringIO()
npt.assert_warns(UserWarning, self.ordination_results.to_file, fh)
fh.seek(0)
deserialized = npt.assert_warns(UserWarning,
OrdinationResults.from_file, fh)
assert_ordination_results_equal(deserialized, self.ordination_results)
self.assertTrue(type(deserialized) == OrdinationResults)
def test_io(self):
# Very basic check that read/write public API is present and appears to
# be functioning. Roundtrip from memory -> disk -> memory and ensure
# results match.
fh = StringIO()
self.ordination_results.write(fh)
fh.seek(0)
deserialized = OrdinationResults.read(fh)
assert_ordination_results_equal(deserialized, self.ordination_results)
self.assertTrue(type(deserialized) == OrdinationResults)
def test_roundtrip_read_write(self):
for fp in self.valid_fps:
# Read.
obj1 = _ordres_to_ordination_results(fp)
# Write.
fh = StringIO()
_ordination_results_to_ordres(obj1, fh)
fh.seek(0)
# Read.
obj2 = _ordres_to_ordination_results(fh)
fh.close()
assert_ordination_results_equal(obj1, obj2)
def test_roundtrip_read_write(self):
for fp in self.valid_fps:
# Read.
obj1 = _ordres_to_ordination_results(fp)
# Write.
fh = StringIO()
_ordination_results_to_ordres(obj1, fh)
fh.seek(0)
# Read.
obj2 = _ordres_to_ordination_results(fh)
fh.close()
assert_ordination_results_equal(obj1, obj2)
def test_read_valid_files(self):
for fp, obj in zip(self.valid_fps, self.ordination_results_objs):
obs = _ordres_to_ordination_results(fp)
assert_ordination_results_equal(obs, obj)
def test_assert_ordination_results_equal(self):
minimal1 = OrdinationResults([1, 2])
# a minimal set of results should be equal to itself
assert_ordination_results_equal(minimal1, minimal1)
# type mismatch
with npt.assert_raises(AssertionError):
assert_ordination_results_equal(minimal1, 'foo')
# numeric values should be checked that they're almost equal
almost_minimal1 = OrdinationResults([1.0000001, 1.9999999])
assert_ordination_results_equal(minimal1, almost_minimal1)
# species_ids missing in one, present in the other
almost_minimal1.species_ids = ['abc', 'def']
with npt.assert_raises(AssertionError):
assert_ordination_results_equal(minimal1, almost_minimal1)
almost_minimal1.species_ids = None
# site_ids missing in one, present in the other
almost_minimal1.site_ids = ['abc', 'def']
with npt.assert_raises(AssertionError):
assert_ordination_results_equal(minimal1, almost_minimal1)
almost_minimal1.site_ids = None
# test each of the optional numeric attributes
for attr in ('species', 'site', 'biplot', 'site_constraints',
'proportion_explained'):
# missing optional numeric attribute in one, present in the other
setattr(almost_minimal1, attr, [[1, 2], [3, 4]])
with npt.assert_raises(AssertionError):
assert_ordination_results_equal(minimal1, almost_minimal1)
setattr(almost_minimal1, attr, None)
# optional numeric attributes present in both, but not almost equal
setattr(minimal1, attr, [[1, 2], [3, 4]])
setattr(almost_minimal1, attr, [[1, 2], [3.00002, 4]])
with npt.assert_raises(AssertionError):
assert_ordination_results_equal(minimal1, almost_minimal1)
setattr(minimal1, attr, None)
setattr(almost_minimal1, attr, None)
# optional numeric attributes present in both, and almost equal
setattr(minimal1, attr, [[1, 2], [3, 4]])
setattr(almost_minimal1, attr, [[1, 2], [3.00000002, 4]])
assert_ordination_results_equal(minimal1, almost_minimal1)
setattr(minimal1, attr, None)
setattr(almost_minimal1, attr, None)
def test_assert_ordination_results_equal(self):
minimal1 = OrdinationResults([1, 2])
# a minimal set of results should be equal to itself
assert_ordination_results_equal(minimal1, minimal1)
# type mismatch
with npt.assert_raises(AssertionError):
assert_ordination_results_equal(minimal1, 'foo')
# numeric values should be checked that they're almost equal
almost_minimal1 = OrdinationResults([1.0000001, 1.9999999])
assert_ordination_results_equal(minimal1, almost_minimal1)
# species_ids missing in one, present in the other
almost_minimal1.species_ids = ['abc', 'def']
with npt.assert_raises(AssertionError):
assert_ordination_results_equal(minimal1, almost_minimal1)
almost_minimal1.species_ids = None
# site_ids missing in one, present in the other
almost_minimal1.site_ids = ['abc', 'def']
with npt.assert_raises(AssertionError):
assert_ordination_results_equal(minimal1, almost_minimal1)
almost_minimal1.site_ids = None
# test each of the optional numeric attributes
for attr in ('species', 'site', 'biplot', 'site_constraints',
'proportion_explained'):
# missing optional numeric attribute in one, present in the other
setattr(almost_minimal1, attr, [[1, 2], [3, 4]])
with npt.assert_raises(AssertionError):
assert_ordination_results_equal(minimal1, almost_minimal1)
setattr(almost_minimal1, attr, None)
# optional numeric attributes present in both, but not almost equal
setattr(minimal1, attr, [[1, 2], [3, 4]])
setattr(almost_minimal1, attr, [[1, 2], [3.00002, 4]])
with npt.assert_raises(AssertionError):
assert_ordination_results_equal(minimal1, almost_minimal1)
setattr(minimal1, attr, None)
setattr(almost_minimal1, attr, None)
# optional numeric attributes present in both, and almost equal
setattr(minimal1, attr, [[1, 2], [3, 4]])
setattr(almost_minimal1, attr, [[1, 2], [3.00000002, 4]])
assert_ordination_results_equal(minimal1, almost_minimal1)
setattr(minimal1, attr, None)
setattr(almost_minimal1, attr, None)
def test_read_valid_files(self):
for fp, obj in zip(self.valid_fps, self.ordination_results_objs):
obs = _ordres_to_ordination_results(fp)
assert_ordination_results_equal(obs, obj)
