def test_check_prereqs_missing_executables(self):
options = build_config(["--check-prereqs"], isolated=True, modules=get_all_modules())
update_config({"executables": Namespace()})
mock("antismash.config.get_config", returns=options)
assert hasattr(get_config(), "executables")
assert not get_config().executables.__dict__
with self.assertRaisesRegex(RuntimeError, "failing prereq"):
antismash.main.check_prerequisites(get_all_modules(), options)
def setUp(self):
options = build_config(self.get_args(), isolated=True, modules=get_all_modules())
self.old_config = get_config().__dict__
self.options = update_config(options)
assert clusterblast.check_prereqs(self.options) == []
assert clusterblast.check_options(self.options) == []
assert clusterblast.is_enabled(self.options)
def setUp(self):
self.format0_file = path.get_full_path(__file__, "data", "format0.dmnd")
self.format1_file = path.get_full_path(__file__, "data", "format1.dmnd")
self.empty = path.get_full_path(__file__, "data", "empty.dmnd")
options = build_config([], isolated=True, modules=get_all_modules())
self.old_config = get_config().__dict__
self.options = update_config(options)
def test_prepare_module_data(self):
self.default_options = build_config([], isolated=True, modules=get_all_modules())
# make sure there's some to start with
search = path.get_full_path(antismash.__file__, '**', "*.h3?")
existing_press_files = glob.glob(search, recursive=True)
assert existing_press_files
# then remove them all
for pressed in existing_press_files:
os.unlink(pressed)
current_press_files = glob.glob(search, recursive=True)
assert not current_press_files
# and make sure they're all regenerated properly
prepare_module_data()
current_press_files = glob.glob(search, recursive=True)
assert current_press_files == existing_press_files
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 plugins(self) -> List[AntismashModule]:
""" A list of all modules """
from antismash.main import get_all_modules
return get_all_modules()
def setUp(self):
options = build_config([], isolated=True, modules=get_all_modules())
self.old_config = get_config().__dict__
self.options = update_config(options)
def build_config(self, args):
self.default_options = build_config(args, isolated=True, modules=get_all_modules())
self.default_options.all_enabled_modules = []
self.default_options.output_dir = self.temp_dir.name
def setUp(self):
self.temp_dir = TemporaryDirectory()
self.config = build_config(self.get_args() + ["--out", self.temp_dir.name],
isolated=True, modules=get_all_modules())
def test_check_prereqs(self):
options = build_config(["--check-prereqs"], isolated=False, modules=get_all_modules())
assert run_antismash("", options) == 0
def setUp(self):
build_config([], isolated=True, modules=get_all_modules())
def setUp(self):
self.options = build_config(["--cc-mibig"], isolated=True, modules=get_all_modules())
