def test_flags(capsys, hf):
contributors = list()
contributors.append(br.Contributor("Bud", "Suite", "D", commits=10, github="buddysuite"))
contributors.append(br.Contributor("Sweet", "Water", commits=5, github="sweetwater"))
version = br.Version("BudddySuite", "3", "5", contributors, release_date={"day": 13, "month": 7, "year": 2016})
parser = argparse.ArgumentParser(prog="SeqBuddy.py", add_help=False)
pos_dict = ("sequence", "Supply file path(s) or raw sequence. If piping sequences "
"into SeqBuddy this argument can be left blank.")
flag_dict = {"annotate": {"flag": "ano",
"nargs": "*",
"metavar": "args",
"help": "Add a feature (annotation) to selected sequences. "
"Args: <name>, <location (start1-end1,start2-end2...)>, [strand (+|-)], "
"[qualifier (foo=bar) [qualifier]], [regex_pattern [regex_[pattern]]}"},
"ave_seq_length": {"flag": "asl",
"action": "append",
"nargs": "?",
"metavar": "'clean'",
"help": "Calculate average sequence length. Specify 'clean' to remove gaps etc "
"first"}}
mod_dict = {"alpha": {"flag": "a",
"action": "store",
"help": "If you want the file read with a specific alphabet"},
"in_format": {"flag": "f",
"action": "store",
"help": "If SeqBuddy can't guess the file format, try specifying it directly"}}
br.flags(parser, _positional=pos_dict, _flags=flag_dict, _modifiers=mod_dict, version=version)
parser.print_help()
out, err = capsys.readouterr()
assert hf.string2hash(out) == "9ea2d4ac842b1712687034ea0abf497b"
def test_contributor():
contributor = br.Contributor("Bud", "Suite", "D", commits=10, github="buddysuite")
assert contributor.name() == "Bud D Suite"
assert str(contributor) == "Bud Suite, buddysuite"
contributor = br.Contributor("Bud", "Suite")
assert contributor.name() == "Bud Suite"
assert str(contributor) == "Bud Suite"
def test_version():
contributors = list()
contributors.append(br.Contributor("Bud", "Suite", "D", commits=10, github="buddysuite"))
contributors.append(br.Contributor("Sweet", "Water", commits=5, github="sweetwater"))
version = br.Version("BudddySuite", "3", "5", contributors, release_date={"day": 13, "month": 7, "year": 2016})
assert version.short() == "3.5"
assert version.contributors_string() == "Bud D Suite buddysuite\nSweet Water sweetwater"
version_string = re.sub("[\n| ]", "", str(version))
assert version_string == "BudddySuite3.5(2016-07-13)PublicDomainNoticeThisisfreesoftware;seethesourcefordetailed" \
"copyingconditions.ThereisNOwarranty;notevenforMERCHANTABILITYorFITNESSFORAPARTICULAR" \
"PURPOSE.Questions/comments/concernscanbedirectedtoSteveBond,[email protected]" \
"Contributors:BudDSuitebuddysuiteSweetWatersweetwater"