def test_canonical_base_filename(self):
options = build_parser(modules=self.all_modules).parse_args([])
expected = os.path.join("out", "foo.1_example")
res = main.canonical_base_filename("foo.1_example.gbk", "out", options)
assert res == expected
assert get_config().output_basename == os.path.basename(expected)
res = main.canonical_base_filename(
"/some/long/path/foo.1_example.gbff", "out", options)
assert res == expected
res = main.canonical_base_filename("foo.1_example.fa", "out", options)
assert res == expected
res = main.canonical_base_filename("foo.1_example.gbff.gz", "out",
options)
assert res == expected
options = build_parser(modules=self.all_modules).parse_args(
["--output-basename", "foo.1"])
expected = os.path.join("out", "foo.1")
res = main.canonical_base_filename("foo.1_example.gbk", "out", options)
assert res == expected
res = main.canonical_base_filename("foo.1_example.gbff", "out",
options)
assert res == expected
res = main.canonical_base_filename("foo.1_example.fa", "out", options)
assert res == expected
res = main.canonical_base_filename("foo.1_example.gbff.gz", "out",
options)
assert res == expected
def test_help(capsys):
args.build_parser(modules=get_all_modules()).print_help()
out, err = capsys.readouterr()
assert "--minimal" not in out
args.build_parser(modules=get_all_modules()).print_help(show_all=True)
out_all, err_all = capsys.readouterr()
assert err == err_all and not err
# make sure show_all does something
assert out != out_all
assert "--minimal" in out_all
def test_config_files(self):
# TODO change some values in the file generated and check they're kept
with TemporaryDirectory(change=True):
args.build_parser()
parser = args.build_parser(modules=get_all_modules())
default_options = parser.parse_args([])
parser.write_to_config_file("default_options.cfg")
parser = args.build_parser(modules=get_all_modules(), from_config_file=True)
from_file = parser.parse_args(["@default_options.cfg"])
assert vars(default_options) == vars(from_file)
def setUp(self):
self.all_modules = main.get_all_modules()
self.default_options = build_parser(modules=self.all_modules).parse_args([])
def get_simple_options(module, args):
modules = get_all_modules()
if module is not None:
modules = [module]
return build_parser(from_config_file=False,
modules=modules).parse_args(args)
def setUp(self):
self.core_parser = args.build_parser()
self.default_parser = args.build_parser(modules=[])
self.old_executable_mapping = dict(
executables._ALTERNATE_EXECUTABLE_NAMES)
executables._ALTERNATE_EXECUTABLE_NAMES.clear()
def setUp(self):
self.core_parser = args.build_parser()
modules = get_all_modules()
self.default_parser = args.build_parser(modules=modules)
def setUp(self):
self.core_parser = args.build_parser()
self.core_parser.error = raise_not_exit
modules = get_all_modules()
self.default_parser = args.build_parser(modules=modules)
def setUp(self):
self.parser = args.build_parser(modules=[core])
