Coverage for bioimageio/core/commands.py: 78%

1"""These functions are used in the bioimageio command line interface 

2defined in `bioimageio.core.cli`.""" 

3 

4from pathlib import Path 

5from typing import Optional, Sequence, Union 

6 

7from typing_extensions import Literal 

8 

9from bioimageio.core.common import SupportedWeightsFormat 

10from bioimageio.spec import ( 

11 InvalidDescr, 

12 ResourceDescr, 

13 save_bioimageio_package, 

14 save_bioimageio_package_as_folder, 

15) 

16from bioimageio.spec._internal.types import FormatVersionPlaceholder 

17 

18from ._resource_tests import test_description 

19 

20WeightFormatArgAll = Literal[SupportedWeightsFormat, "all"] 

21WeightFormatArgAny = Literal[SupportedWeightsFormat, "any"] 

22 

23 

24def test( 

25 descr: Union[ResourceDescr, InvalidDescr], 

26 *, 

27 weight_format: WeightFormatArgAll = "all", 

28 devices: Optional[Union[str, Sequence[str]]] = None, 

29 summary: Union[ 

30 Literal["display"], Path, Sequence[Union[Literal["display"], Path]] 

31 ] = "display", 

32 runtime_env: Union[ 

33 Literal["currently-active", "as-described"], Path 

34 ] = "currently-active", 

35 determinism: Literal["seed_only", "full"] = "seed_only", 

36 format_version: Union[FormatVersionPlaceholder, str] = "discover", 

37) -> int: 

38 """Test a bioimageio resource. 

39 

40 Arguments as described in `bioimageio.core.cli.TestCmd` 

41 """ 

42 if isinstance(descr, InvalidDescr): 

43 test_summary = descr.validation_summary 

44 else: 

45 test_summary = test_description( 

46 descr, 

47 format_version=format_version, 

48 weight_format=None if weight_format == "all" else weight_format, 

49 devices=[devices] if isinstance(devices, str) else devices, 

50 runtime_env=runtime_env, 

51 determinism=determinism, 

52 ) 

53 

54 _ = test_summary.log(summary) 

55 return 0 if test_summary.status == "passed" else 1 

56 

57 

58def validate_format( 

59 descr: Union[ResourceDescr, InvalidDescr], 

60 summary: Union[Path, Sequence[Path]] = (), 

61): 

62 """DEPRECATED; Access the existing `validation_summary` attribute instead. 

63 validate the meta data format of a bioimageio resource 

64 

65 Args: 

66 descr: a bioimageio resource description 

67 """ 

68 _ = descr.validation_summary.save(summary) 

69 return 0 if descr.validation_summary.status in ("valid-format", "passed") else 1 

70 

71 

72# TODO: absorb into `save_bioimageio_package` 

73def package( 

74 descr: ResourceDescr, 

75 path: Path, 

76 *, 

77 weight_format: WeightFormatArgAll = "all", 

78): 

79 """Save a resource's metadata with its associated files. 

80 

81 Note: If `path` does not have a `.zip` suffix this command will save the 

82 package as an unzipped folder instead. 

83 

84 Args: 

85 descr: a bioimageio resource description 

86 path: output path 

87 weight-format: include only this single weight-format (if not 'all'). 

88 """ 

89 if isinstance(descr, InvalidDescr): 

90 logged = descr.validation_summary.save() 

91 msg = f"Invalid {descr.type} description." 

92 if logged: 

93 msg += f" Details saved to {logged}." 

94 

95 raise ValueError(msg) 

96 

97 if weight_format == "all": 

98 weights_priority_order = None 

99 else: 

100 weights_priority_order = (weight_format,) 

101 

102 if path.suffix == ".zip": 

103 _ = save_bioimageio_package( 

104 descr, 

105 output_path=path, 

106 weights_priority_order=weights_priority_order, 

107 ) 

108 else: 

109 _ = save_bioimageio_package_as_folder( 

110 descr, 

111 output_path=path, 

112 weights_priority_order=weights_priority_order, 

113 ) 

114 return 0