def test_bedtools_window_sm():
"""
These two flags have almost the same name, and almost the same description
"""
flags = [
Flag(
synonyms=["-sm"],
description=
"Only report hits in B that overlap A on the _same_ strand.",
args=EmptyFlagArg(),
),
Flag(
synonyms=["-sm"],
description=
"Only report hits in B that overlap A on the _opposite_ strand.",
args=EmptyFlagArg(),
),
Flag(
synonyms=["-c"],
description=
"For each entry in A, report the number of overlaps with B.",
args=EmptyFlagArg(),
),
]
args = WrapperGenerator().choose_variable_names(flags)
assert len(set([arg.name for arg in args])) == 3
def test_snake_short(snake_gen):
flag = Flag(synonyms=["-t"],
description="number of threads [1]",
args=EmptyFlagArg())
names = snake_gen.choose_variable_names([flag], length=2)
assert "number" in names[0].name
assert "threads" in names[0].name
def test_snake_long(snake_gen):
flag = Flag(
synonyms=["-g", "--genomepaths", "--genomefolders"],
description="number of threads [1]",
args=EmptyFlagArg(),
)
names = snake_gen.choose_variable_names([flag], length=2)
assert names[0].name == "genome_folders"
def test_same_description():
"""
Normally we ignore one-character flag names, and instead try to read their descriptions for a more informative name.
However, if the descriptions are identical to each other, we have to fall back to the description
"""
flags = [
Flag(
synonyms=["-a"],
description="Makes the program do a certain thing",
args=EmptyFlagArg(),
),
Flag(
synonyms=["-b"],
description="Makes the program do a certain thing",
args=EmptyFlagArg(),
),
]
names = WrapperGenerator().choose_variable_names(flags)
assert names[0].name == "a"
assert names[1].name == "b"
def test_name_to_words_symbol(gen):
"""
Check that we can get an argument name even if the argument's flag is a symbol
"""
arg = Flag(
synonyms=["-@"],
description="Number of additional threads to use",
args=EmptyFlagArg(),
)
name = gen.choose_variable_names([arg])[0].name
assert name == "at"
def test_name_to_words(gen):
"""
Check that we can get an argument name even if the argument's flag is a symbol
"""
arg = Flag(
synonyms=["--genomepaths"],
description="",
args=EmptyFlagArg(),
)
name = gen.choose_variable_names([arg])[0].name
assert "genome" in name
assert "paths" in name
def test_camel_short(camel_gen):
flag = Flag(synonyms=["-t"],
description="number of threads [1]",
args=EmptyFlagArg())
names = camel_gen.choose_variable_names([flag], length=3)
assert names[0].name == "numberOfThreads"
@pytest.mark.parametrize(
"flag,typ",
[
[
Flag(
description=
"Filename to output the counts to instead of stdout.",
synonyms=["-c", "--counts_output"],
args=SimpleFlagArg("OUTPUT_FILENAME"),
),
CliFile(output=True),
],
pytest.param(
Flag(
description=
"redirect output to specified file\ndefault: undefined",
synonyms=["-o"],
args=EmptyFlagArg(),
),
CliFile(output=True),
marks=pytest.mark.xfail(
reason=
"Because the help doesn't indicate an argument, we can't know that this is an output file"
),
),
],
)
def test_flag_type_inference(flag: CliArgument, typ: CliType):
inferred_type = flag.get_type()
assert inferred_type == typ
def visit_short_flag_list(s, loc, toks):
return [
Flag.from_synonyms(
[FlagSynonym(name="-" + flag, argtype=EmptyFlagArg())],
description=None) for flag in toks[1:]
]