Coverage for bioimageio/spec/conda_env.py: 72%

1import warnings 

2from typing import Any, List, Optional, Union 

3 

4from pydantic import BaseModel, Field, field_validator, model_validator 

5 

6 

7class PipDeps(BaseModel): 

8 """Pip dependencies to include in conda dependecies""" 

9 

10 pip: List[str] = Field(default_factory=list) 

11 

12 @field_validator("pip", mode="after") 

13 @classmethod 

14 def _remove_empty_and_sort(cls, value: List[str]) -> List[str]: 

15 return sorted((vs for v in value if (vs := v.strip()))) 

16 

17 def __lt__(self, other: Any): 

18 if isinstance(other, PipDeps): 

19 return len(self.pip) < len(other.pip) 

20 else: 

21 return False 

22 

23 def __gt__(self, other: Any): 

24 if isinstance(other, PipDeps): 

25 return len(self.pip) > len(other.pip) 

26 else: 

27 return False 

28 

29 

30class CondaEnv(BaseModel): 

31 """Represenation of the content of a conda environment.yaml file""" 

32 

33 name: Optional[str] = None 

34 channels: List[str] = Field(default_factory=list) 

35 dependencies: List[Union[str, PipDeps]] = Field(default_factory=list) 

36 

37 @field_validator("name", mode="after") 

38 def _ensure_valid_conda_env_name(cls, value: Optional[str]) -> Optional[str]: 

39 if value is None: 

40 return None 

41 

42 for illegal in ("/", " ", ":", "#"): 

43 value = value.replace(illegal, "") 

44 

45 return value or "empty" 

46 

47 @property 

48 def wo_name(self): 

49 return self.model_construct(**{k: v for k, v in self if k != "name"}) 

50 

51 def _get_version(self, package: str): 

52 """Helper to return any verison pin for **package** 

53 

54 TODO: improve: interprete version pin and return structured information. 

55 """ 

56 for d in self.dependencies: 

57 if isinstance(d, PipDeps): 

58 for p in d.pip: 

59 if p.startswith(package): 

60 return p[len(package) :] 

61 elif d.startswith(package): 

62 return d[len(package) :] 

63 

64 

65class BioimageioCondaEnv(CondaEnv): 

66 """A special `CondaEnv` that 

67 - automatically adds bioimageio specific dependencies 

68 - sorts dependencies 

69 """ 

70 

71 @model_validator(mode="after") 

72 def _normalize_bioimageio_conda_env(self): 

73 """update a conda env such that we have bioimageio.core and sorted dependencies""" 

74 for req_channel in ("conda-forge", "nodefaults"): 

75 if req_channel not in self.channels: 

76 self.channels.append(req_channel) 

77 

78 if "defaults" in self.channels: 

79 warnings.warn("removing 'defaults' from conda-channels") 

80 self.channels.remove("defaults") 

81 

82 if "pip" not in self.dependencies: 

83 self.dependencies.append("pip") 

84 

85 for dep in self.dependencies: 

86 if isinstance(dep, PipDeps): 

87 pip_section = dep 

88 pip_section.pip.sort() 

89 break 

90 else: 

91 pip_section = None 

92 

93 if ( 

94 pip_section is None 

95 or not any(pd.startswith("bioimageio.core") for pd in pip_section.pip) 

96 ) and not any( 

97 d.startswith("bioimageio.core") 

98 or d.startswith("conda-forge::bioimageio.core") 

99 for d in self.dependencies 

100 if not isinstance(d, PipDeps) 

101 ): 

102 self.dependencies.append("conda-forge::bioimageio.core") 

103 

104 self.dependencies.sort() 

105 return self