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])