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())