1from pathlib import Path 

2 

3import pytest 

4# from py.xml import html 

5 

6from .bio import Alignment, Data, Sequence, Tree 

7from .main import main as main 

8 

9 

10def pytest_addoption(parser): 

11 parser.addoption("--sequence", "-S", action="store", default=None, help="sequence file") 

12 parser.addoption("--sequence-format", action="store", default='fasta', help="sequence file format") 

13 parser.addoption("--tree", "-T", action="store", default=None, help="tree file") 

14 parser.addoption("--tree-format", action="store", default='newick', help="tree file format") 

15 parser.addoption("--data", "-D", action="store", default=None, help="data file") 

16 parser.addoption("--data-format", action="store", default='csv', help="data file format") 

17 parser.addoption( 

18 "--apply-fixes", action="store_true", default=None, help="automatically apply fixes where possible" 

19 ) 

20 

21 

22def pytest_generate_tests(metafunc): 

23 sequence_path = metafunc.config.getoption("sequence") 

24 if 'alignment' in metafunc.fixturenames: 

25 if sequence_path is None: 

26 raise ValueError(f"{metafunc.function.__name__} requires an alignment file") 

27 fpth = Path(sequence_path) 

28 if not fpth.exists(): 

29 raise FileNotFoundError(f"Unable to locate requested alignment file ({fpth})! 😱") 

30 tree_path = metafunc.config.getoption("tree") 

31 if 'tree' in metafunc.fixturenames: 

32 if tree_path is None: 

33 raise ValueError(f"{metafunc.function.__name__} requires a tree file") 

34 fpth = Path(tree_path) 

35 if not fpth.exists(): 

36 raise FileNotFoundError(f"Unable to locate requested tree file ({fpth})! 😱") 

37 tree_format = metafunc.config.getoption("--tree-format") 

38 trees = Tree.parse(tree_path, tree_format) 

39 metafunc.parametrize("tree", trees, ids=lambda t: t.name) 

40 data_path = metafunc.config.getoption("data") 

41 if 'data' in metafunc.fixturenames: 

42 if data_path is None: 

43 raise ValueError(f"{metafunc.function.__name__} requires a data file") 

44 fpth = Path(data_path) 

45 if not fpth.exists(): 

46 raise FileNotFoundError(f"Unable to locate requested data file ({fpth})! 😱") 

47 if "sequence" in metafunc.fixturenames: 

48 if sequence_path is None: 

49 raise ValueError(f"{metafunc.function.__name__} requires a sequence file") 

50 fpth = Path(sequence_path) 

51 if not fpth.exists(): 

52 raise FileNotFoundError(f"Unable to locate requested sequence file ({fpth})! 😱") 

53 alignment_format = metafunc.config.getoption("--sequence-format") 

54 sequences = Sequence.parse(sequence_path, alignment_format) 

55 metafunc.parametrize("sequence", sequences, ids=lambda s: s.id) 

56 

57 

58@pytest.fixture(scope="session", name="alignment") 

59def _alignment_fixture(request): 

60 alignment_path = request.config.getoption("sequence") 

61 alignment_format = request.config.getoption("--sequence-format") 

62 alignment = Alignment.read(alignment_path, alignment_format) 

63 return alignment 

64 

65 

66@pytest.fixture(scope="session", name="data") 

67def _data_fixture(request): 

68 data_path = request.config.getoption("data") 

69 data_format = request.config.getoption("--data-format") 

70 data = Data.read(data_path, data_format) 

71 return data 

72 

73 

74def pytest_html_report_title(report): 

75 report.title = "report"