Coverage for src/bioimageio/core/commands.py: 77%

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.spec import ( 

10 InvalidDescr, 

11 ResourceDescr, 

12 save_bioimageio_package, 

13 save_bioimageio_package_as_folder, 

14) 

15from bioimageio.spec._internal.types import FormatVersionPlaceholder 

16 

17from ._resource_tests import test_description 

18 

19# unfortunately this does not work with py3.9 and pydantic 2.11 

20# from bioimageio.core.common import SupportedWeightsFormat 

21# WeightFormatArgAll = Literal[SupportedWeightsFormat, "all"] 

22# WeightFormatArgAny = Literal[SupportedWeightsFormat, "any"] 

23# so we write out the literal explicitly 

24WeightFormatArgAll = Literal[ 

25 "keras_hdf5", 

26 "onnx", 

27 "pytorch_state_dict", 

28 "tensorflow_saved_model_bundle", 

29 "torchscript", 

30 "all", 

31] 

32WeightFormatArgAny = Literal[ 

33 "keras_hdf5", 

34 "onnx", 

35 "pytorch_state_dict", 

36 "tensorflow_saved_model_bundle", 

37 "torchscript", 

38 "any", 

39] 

40 

41 

42def test( 

43 descr: Union[ResourceDescr, InvalidDescr], 

44 *, 

45 weight_format: WeightFormatArgAll = "all", 

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

47 summary: Union[ 

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

49 ] = "display", 

50 runtime_env: Union[ 

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

52 ] = "currently-active", 

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

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

55) -> int: 

56 """Test a bioimageio resource. 

57 

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

59 """ 

60 if isinstance(descr, InvalidDescr): 

61 test_summary = descr.validation_summary 

62 else: 

63 test_summary = test_description( 

64 descr, 

65 format_version=format_version, 

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

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

68 runtime_env=runtime_env, 

69 determinism=determinism, 

70 ) 

71 

72 _ = test_summary.log(summary) 

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

74 

75 

76def validate_format( 

77 descr: Union[ResourceDescr, InvalidDescr], 

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

79): 

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

81 validate the meta data format of a bioimageio resource 

82 

83 Args: 

84 descr: a bioimageio resource description 

85 """ 

86 _ = descr.validation_summary.save(summary) 

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

88 

89 

90# TODO: absorb into `save_bioimageio_package` 

91def package( 

92 descr: ResourceDescr, 

93 path: Path, 

94 *, 

95 weight_format: WeightFormatArgAll = "all", 

96): 

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

98 

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

100 package as an unzipped folder instead. 

101 

102 Args: 

103 descr: a bioimageio resource description 

104 path: output path 

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

106 """ 

107 if isinstance(descr, InvalidDescr): 

108 logged = descr.validation_summary.save() 

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

110 if logged: 

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

112 

113 raise ValueError(msg) 

114 

115 if weight_format == "all": 

116 weights_priority_order = None 

117 else: 

118 weights_priority_order = (weight_format,) 

119 

120 if path.suffix == ".zip": 

121 _ = save_bioimageio_package( 

122 descr, 

123 output_path=path, 

124 weights_priority_order=weights_priority_order, 

125 ) 

126 else: 

127 _ = save_bioimageio_package_as_folder( 

128 descr, 

129 output_path=path, 

130 weights_priority_order=weights_priority_order, 

131 ) 

132 return 0