def test_user_function_str(self):
u_function_1 = user_function(self.foo, "aligned", "aligned")
u_function_2 = user_function(self.bar, "aligned", "pairwise_distances")
self.assertEqual(
str(u_function_1),
"user_function(name='foo', module='test_composable')")
self.assertEqual(
str(u_function_2),
"user_function(name='bar', module='test_composable')")
def test_user_function_str(self):
u_function_1 = user_function(self.foo, "aligned", "aligned")
u_function_2 = user_function(self.bar, "aligned", "pairwise_distances")
self.assertEqual(
str(u_function_1),
"user_function(name='foo', module='test_composable')")
self.assertEqual(
str(u_function_2),
"user_function(name='bar', module='test_composable')")
# added into a composable func
loader = io_app.load_aligned()
proc = loader + u_function_1
got = str(proc)
self.assertTrue(got.startswith("load_aligned"))
def test_user_function_multiple(self):
"""user defined composable functions should not interfere with each other"""
from cogent3 import make_aligned_seqs
from cogent3.core.alignment import Alignment
u_function_1 = user_function(self.foo, "aligned", "aligned")
u_function_2 = user_function(self.bar, "aligned", "pairwise_distances")
aln_1 = make_aligned_seqs(data=[("a", "GCAAGCGTTTAT"), ("b", "GCTTTTGTCAAT")])
data = dict([("s1", "ACGTACGTA"), ("s2", "GTGTACGTA")])
aln_2 = Alignment(data=data, moltype="dna")
got_1 = u_function_1(aln_1)
got_2 = u_function_2(aln_2)
self.assertEqual(got_1.to_dict(), {"a": "GCAA", "b": "GCTT"})
self.assertEqual(got_2, {("s1", "s2"): 2.0, ("s2", "s1"): 2.0})
def test_user_function_custom_variables(self):
# not sure what this is meant to be testing
demo = user_function(_demo, ("aligned", "serialisable"),
("aligned", "serialisable"))
frame_start = 2
demo.frame_start = frame_start
self.assertTrue(demo(demo, 2))
def test_user_function_custom_variables(self):
demo = user_function(self._demo, ("aligned", "serialisable"),
("aligned", "serialisable"))
foo = demo
frame_start = 2
foo.frame_start = frame_start
foo(frame_start)
def test_user_function_with_args_kwargs(self):
"""correctly handles definition with args, kwargs"""
from math import log
def product(val, multiplier, take_log=False):
result = val * multiplier
if take_log:
result = log(result)
return result
# without defining any args, kwargs
ufunc = user_function(
product,
SERIALISABLE_TYPE,
SERIALISABLE_TYPE,
)
self.assertEqual(ufunc(2, 2), 4)
self.assertEqual(ufunc(2, 2, take_log=True), log(4))
# defining default arg2
ufunc = user_function(
product,
SERIALISABLE_TYPE,
SERIALISABLE_TYPE,
2,
)
self.assertEqual(ufunc(2), 4)
self.assertEqual(ufunc(2, take_log=True), log(4))
# defining default kwarg only
ufunc = user_function(product,
SERIALISABLE_TYPE,
SERIALISABLE_TYPE,
take_log=True)
self.assertEqual(ufunc(2, 2), log(4))
self.assertEqual(ufunc(2, 2, take_log=False), 4)
# defining default arg and kwarg
ufunc = user_function(product,
SERIALISABLE_TYPE,
SERIALISABLE_TYPE,
2,
take_log=True)
self.assertEqual(ufunc(2), log(4))
def test_user_function(self):
"""composable functions should be user definable"""
from cogent3 import make_aligned_seqs
u_function = user_function(self.foo, "aligned", "aligned")
aln = make_aligned_seqs(data=[("a", "GCAAGCGTTTAT"), ("b", "GCTTTTGTCAAT")])
got = u_function(aln)
self.assertEqual(got.to_dict(), {"a": "GCAA", "b": "GCTT"})
