def test_dict_to_string(self):
net_settings = NetworkSettings(NET_SETS)
output = utils.dict_objects_to_str(net_settings)
assert_is_instance(output, dict)
for k, v in output.items():
assert_is_instance(k, str)
assert_not_is_instance(v, ipaddress.IPv4Address)
def add_test_yaml_files(cls):
"""Add in dodgy yaml files in an extra nbextensions dir."""
cls.jupyter_dirs['dodgy'] = {
'nbexts': os.path.join(cls.jupyter_dirs['root'], 'dodgy', 'nbext')}
dodgy_nbext_dir_path = cls.jupyter_dirs['dodgy']['nbexts']
if not os.path.exists(dodgy_nbext_dir_path):
os.makedirs(dodgy_nbext_dir_path)
cls.config.NotebookApp.setdefault(
'extra_nbextensions_path', []).append(dodgy_nbext_dir_path)
# an invalid yaml file
yaml_path_invalid = os.path.join(
dodgy_nbext_dir_path, 'nbext_invalid_yaml.yaml')
with io.open(yaml_path_invalid, 'w') as f:
f.write('not valid yaml!: [')
# various test yaml files
test_yamls = {
# we use str() because otherwise python2 will write
# !!python/unicode in the yaml, and pyyaml SafeLoader will refuse
# to reconstruct the objects :( boo!
'not_an_nbext': [
str('valid yaml'), str("doesn't always"),
str('make for a valid nbext yaml, right?'), 3423509],
'missing_key': {str('Main'): True},
'invalid_type': {
str('Main'): str('main.js'),
str('Type'): str('blahblahblah')
},
'dummy': {
str('Main'): str('dummy.js'),
str('Type'): str('Jupyter Notebook Extension'),
str('Description'): str('This is a dumb dummy description'),
str('Compatibility'): str('4.x 5.x'),
},
}
for fname, yaml_obj in test_yamls.items():
if fname != 'dummy':
nt.assert_not_is_instance(
jupyter_nbextensions_configurator._process_nbextension_spec(yaml_obj), # noqa: E501
dict)
yaml_path = os.path.join(dodgy_nbext_dir_path, fname + '.yaml')
with io.open(yaml_path, 'w') as f:
yaml.dump(yaml_obj, f, default_flow_style=False)
# a yaml file which shadows an existing nbextension.
nbdir = os.path.join(
os.path.dirname(jupyter_nbextensions_configurator.__file__),
'static')
nbexts = (
jupyter_nbextensions_configurator.get_configurable_nbextensions(
[nbdir], as_dict=True))
src = random.choice(list(nbexts.values()))['yaml_path']
dst = os.path.join(
dodgy_nbext_dir_path, os.path.relpath(src, start=nbdir))
dst_dir = os.path.dirname(dst)
if not os.path.exists(dst_dir):
os.makedirs(dst_dir)
shutil.copy(src, dst)
def test_sequence_request2(self):
# Request using class name, no views
self.workbench.register(PulsesManagerManifest())
core = self.workbench.get_plugin(u'enaml.workbench.core')
com = u'hqc_meas.pulses.sequences_request'
kwargs = {'sequences': ['ConditionalSequence'],
'use_class_names': True, 'views': False}
sequences, miss = core.invoke_command(com, kwargs, self)
assert_equal(sequences.keys(), ['ConditionalSequence'])
assert_not_is_instance(sequences['ConditionalSequence'], tuple)
assert_equal(miss, [])
def test_context_request2(self):
# Request using class name, no views
self.workbench.register(PulsesManagerManifest())
core = self.workbench.get_plugin(u'enaml.workbench.core')
com = u'hqc_meas.pulses.contexts_request'
contexts, miss = core.invoke_command(com, {'contexts': ['AWGContext'],
'use_class_names': True,
'views': False},
self)
assert_equal(contexts.keys(), ['AWGContext'])
assert_not_is_instance(contexts['AWGContext'], tuple)
assert_equal(miss, [])
def test_slice(self):
data = ['A', 'C', 'B', 'F']
lbl = UniqueIndex(data)
# row slice
s = lbl[1:]
assert_is_instance(s, UniqueIndex)
# index
s = lbl[0]
assert_is_instance(s, str)
assert_not_is_instance(s, UniqueIndex)
def test_slice(self):
data = ['A', 'C', 'B', 'F']
lbl = UniqueIndex(data)
# row slice
s = lbl[1:]
assert_is_instance(s, UniqueIndex)
# index
s = lbl[0]
assert_is_instance(s, str)
assert_not_is_instance(s, UniqueIndex)
def test_slice_types(self):
g = GenotypeArray(diploid_genotype_data, dtype='i1')
# row slice
s = g[1:]
assert_is_instance(s, GenotypeArray)
# col slice
s = g[:, 1:]
assert_is_instance(s, GenotypeArray)
# row index
s = g[0]
assert_is_instance(s, np.ndarray)
assert_not_is_instance(s, GenotypeArray)
# col index
s = g[:, 0]
assert_is_instance(s, np.ndarray)
assert_not_is_instance(s, GenotypeArray)
# ploidy index
s = g[:, :, 0]
assert_is_instance(s, np.ndarray)
assert_not_is_instance(s, GenotypeArray)
# item
s = g[0, 0, 0]
assert_is_instance(s, np.int8)
assert_not_is_instance(s, GenotypeArray)
def test_slice(self):
data = [1, 4, 5, 5, 7, 12]
idx = SortedIndex(data, dtype='u4')
# row slice
s = idx[1:]
assert_is_instance(s, SortedIndex)
# index
s = idx[0]
assert_is_instance(s, np.uint32)
assert_not_is_instance(s, SortedIndex)
eq(data[0], s)
def test_slice_types(self):
ac = AlleleCountsArray(allele_counts_data, dtype='u1')
# row slice
s = ac[1:]
assert_is_instance(s, AlleleCountsArray)
# col slice
s = ac[:, 1:]
assert_is_instance(s, np.ndarray)
assert_not_is_instance(s, AlleleCountsArray)
# row index
s = ac[0]
assert_is_instance(s, np.ndarray)
assert_not_is_instance(s, AlleleCountsArray)
# col index
s = ac[:, 0]
assert_is_instance(s, np.ndarray)
assert_not_is_instance(s, AlleleCountsArray)
# item
s = ac[0, 0]
assert_is_instance(s, np.uint8)
assert_not_is_instance(s, AlleleCountsArray)
def test_slice_types(self):
ac = AlleleCountsArray(allele_counts_data, dtype='u1')
# row slice
s = ac[1:]
assert_is_instance(s, AlleleCountsArray)
# col slice
s = ac[:, 1:]
assert_is_instance(s, np.ndarray)
assert_not_is_instance(s, AlleleCountsArray)
# row index
s = ac[0]
assert_is_instance(s, np.ndarray)
assert_not_is_instance(s, AlleleCountsArray)
# col index
s = ac[:, 0]
assert_is_instance(s, np.ndarray)
assert_not_is_instance(s, AlleleCountsArray)
# item
s = ac[0, 0]
assert_is_instance(s, np.uint8)
assert_not_is_instance(s, AlleleCountsArray)
def test_slice(self):
data = [1, 4, 5, 5, 7, 12]
idx = SortedIndex(data, dtype='u4')
# row slice
s = idx[1:]
assert_is_instance(s, SortedIndex)
# index
s = idx[0]
assert_is_instance(s, np.uint32)
assert_not_is_instance(s, SortedIndex)
eq(data[0], s)
def test_slice_types(self):
g = GenotypeArray(diploid_genotype_data, dtype='i1')
# row slice
s = g[1:]
assert_is_instance(s, GenotypeArray)
# col slice
s = g[:, 1:]
assert_is_instance(s, GenotypeArray)
# row index
s = g[0]
assert_is_instance(s, np.ndarray)
assert_not_is_instance(s, GenotypeArray)
# col index
s = g[:, 0]
assert_is_instance(s, np.ndarray)
assert_not_is_instance(s, GenotypeArray)
# ploidy index
s = g[:, :, 0]
assert_is_instance(s, np.ndarray)
assert_not_is_instance(s, GenotypeArray)
# item
s = g[0, 0, 0]
assert_is_instance(s, np.int8)
assert_not_is_instance(s, GenotypeArray)
def test_get_item_types(self):
vt = VariantTable(variant_table_data, dtype=variant_table_dtype)
# row slice
s = vt[1:]
assert_is_instance(s, VariantTable)
# row index
s = vt[0]
assert_is_instance(s, np.record)
assert_not_is_instance(s, VariantTable)
# col access
s = vt['CHROM']
assert_is_instance(s, np.ndarray)
assert_not_is_instance(s, VariantTable)
s = vt[['CHROM', 'POS']]
assert_is_instance(s, VariantTable)
def test_get_item_types(self):
ft = FeatureTable(feature_table_data, dtype=feature_table_dtype)
# row slice
s = ft[1:]
assert_is_instance(s, FeatureTable)
# row index
s = ft[0]
assert_is_instance(s, np.record)
assert_not_is_instance(s, FeatureTable)
# col access
s = ft['seqid']
assert_is_instance(s, np.ndarray)
assert_not_is_instance(s, FeatureTable)
s = ft[['seqid', 'start', 'end']]
assert_is_instance(s, FeatureTable)
def test_get_item_types(self):
vt = VariantTable(variant_table_data, dtype=variant_table_dtype)
# row slice
s = vt[1:]
assert_is_instance(s, VariantTable)
# row index
s = vt[0]
assert_is_instance(s, np.record)
assert_not_is_instance(s, VariantTable)
# col access
s = vt['CHROM']
assert_is_instance(s, np.ndarray)
assert_not_is_instance(s, VariantTable)
s = vt[['CHROM', 'POS']]
assert_is_instance(s, VariantTable)
def test_get_item_types(self):
ft = FeatureTable(feature_table_data, dtype=feature_table_dtype)
# row slice
s = ft[1:]
assert_is_instance(s, FeatureTable)
# row index
s = ft[0]
assert_is_instance(s, np.record)
assert_not_is_instance(s, FeatureTable)
# col access
s = ft['seqid']
assert_is_instance(s, np.ndarray)
assert_not_is_instance(s, FeatureTable)
s = ft[['seqid', 'start', 'end']]
assert_is_instance(s, FeatureTable)
def test_slice_types(self):
h = HaplotypeArray(haplotype_data, dtype='i1')
# row slice
s = h[1:]
assert_is_instance(s, HaplotypeArray)
# col slice
s = h[:, 1:]
assert_is_instance(s, HaplotypeArray)
# row index
s = h[0]
assert_is_instance(s, np.ndarray)
assert_not_is_instance(s, HaplotypeArray)
# col index
s = h[:, 0]
assert_is_instance(s, np.ndarray)
assert_not_is_instance(s, HaplotypeArray)
# item
s = h[0, 0]
assert_is_instance(s, np.int8)
assert_not_is_instance(s, HaplotypeArray)
def test_slice_types(self):
h = HaplotypeArray(haplotype_data, dtype='i1')
# row slice
s = h[1:]
assert_is_instance(s, HaplotypeArray)
# col slice
s = h[:, 1:]
assert_is_instance(s, HaplotypeArray)
# row index
s = h[0]
assert_is_instance(s, np.ndarray)
assert_not_is_instance(s, HaplotypeArray)
# col index
s = h[:, 0]
assert_is_instance(s, np.ndarray)
assert_not_is_instance(s, HaplotypeArray)
# item
s = h[0, 0]
assert_is_instance(s, np.int8)
assert_not_is_instance(s, HaplotypeArray)
def test_meta_dict_order(self):
# In Py2 cannot depend on order of declaration mapping;
# (it is the unordered built-in dict).
# *Force* a mapping that will be "unordered"
# (with an ordered dict -- but NOT the one used by the metaclass).
default_dict = faraday.item.DeclarativeItemBase.__prepare__('Broken', (faraday.Item,))
tools.assert_not_is_instance(default_dict, OrderedDict)
uid_field = faraday.HashKeyField(data_type=faraday.NUMBER)
defn = [
('__module__', 'totes_mod'), # (fake)
('token', faraday.RangeKeyField()),
# wuh oh! --
('user', faraday.ItemLinkField(self.User, db_key=uid_field)),
('uid', uid_field),
]
attrs = OrderedDict(defn)
tools.eq_(attrs.items(), defn) # preserves (bad) order
# There should be no KeyError:
NotBroken = faraday.item.DeclarativeItemBase('Broken', (faraday.Item,), attrs)
tools.eq_(NotBroken._meta.links['user'].db_key, ('uid',))
def test_getitem(self):
gv = GenotypeVector(diploid_genotype_data[0])
# these should return the same type
gs = gv[:]
assert_is_instance(gs, GenotypeVector)
gs = gv[:, :]
assert_is_instance(gs, GenotypeVector)
gs = gv[...]
assert_is_instance(gs, GenotypeVector)
gs = gv[0:2]
assert_is_instance(gs, GenotypeVector)
gs = gv[0:2, :]
assert_is_instance(gs, GenotypeVector)
gs = gv[np.array([True, False, True], dtype=bool)]
assert_is_instance(gs, GenotypeVector)
gs = gv[[0, 2]]
assert_is_instance(gs, GenotypeVector)
# these should return plain array
gs = gv[:, 0]
assert_not_is_instance(gs, GenotypeVector)
gs = gv[np.newaxis, :2, 0] # change dimension semantics
assert_not_is_instance(gs, GenotypeVector)
def test_not_is_instance(self):
assert_not_is_instance(TestToolsBIT.mylist, tuple)
def add_test_yaml_files(cls):
"""Add in dodgy yaml files in an extra nbextensions dir."""
cls.jupyter_dirs['dodgy'] = {
'nbexts': os.path.join(cls.jupyter_dirs['root'], 'dodgy', 'nbext')
}
dodgy_nbext_dir_path = cls.jupyter_dirs['dodgy']['nbexts']
if not os.path.exists(dodgy_nbext_dir_path):
os.makedirs(dodgy_nbext_dir_path)
cls.config.NotebookApp.setdefault('extra_nbextensions_path',
[]).append(dodgy_nbext_dir_path)
# an invalid yaml file
yaml_path_invalid = os.path.join(dodgy_nbext_dir_path,
'nbext_invalid_yaml.yaml')
with io.open(yaml_path_invalid, 'w') as f:
f.write('not valid yaml!: [')
# various test yaml files
test_yamls = {
# we use str() because otherwise python2 will write
# !!python/unicode in the yaml, and pyyaml SafeLoader will refuse
# to reconstruct the objects :( boo!
'not_an_nbext': [
str('valid yaml'),
str("doesn't always"),
str('make for a valid nbext yaml, right?'), 3423509
],
'missing_key': {
str('Main'): True
},
'invalid_type': {
str('Main'): str('main.js'),
str('Type'): str('blahblahblah')
},
'dummy': {
str('Main'): str('dummy.js'),
str('Type'): str('Jupyter Notebook Extension'),
str('Description'): str('This is a dumb dummy description'),
str('Compatibility'): str('4.x 5.x'),
},
}
for fname, yaml_obj in test_yamls.items():
if fname != 'dummy':
nt.assert_not_is_instance(
jupyter_nbextensions_configurator.
_process_nbextension_spec(yaml_obj), # noqa: E501
dict)
yaml_path = os.path.join(dodgy_nbext_dir_path, fname + '.yaml')
with io.open(yaml_path, 'w') as f:
yaml.dump(yaml_obj, f, default_flow_style=False)
# a yaml file which shadows an existing nbextension.
nbdir = os.path.join(
os.path.dirname(jupyter_nbextensions_configurator.__file__),
'static')
nbexts = (
jupyter_nbextensions_configurator.get_configurable_nbextensions(
[nbdir], as_dict=True))
src = random.choice(list(nbexts.values()))['yaml_path']
dst = os.path.join(dodgy_nbext_dir_path,
os.path.relpath(src, start=nbdir))
dst_dir = os.path.dirname(dst)
if not os.path.exists(dst_dir):
os.makedirs(dst_dir)
shutil.copy(src, dst)
def _isinstance_invalid(self, text, error):
assert_not_is_instance(text, tree.identifier)
def test_payload():
payload = stats._payload(email)
n.assert_not_is_instance(payload, builtins.str)
for bomb in payload:
n.assert_is_instance(bomb, Message)