Coverage for src/bioimageio/spec/_internal/_settings.py: 95%

1from __future__ import annotations 

2 

3import os 

4from functools import cached_property 

5from pathlib import Path 

6from typing import Any 

7 

8import platformdirs 

9from genericache import DiskCache 

10from genericache.digest import UrlDigest 

11from pydantic import Field, field_validator 

12from pydantic_settings import BaseSettings, SettingsConfigDict 

13from typing_extensions import Annotated 

14 

15from .root_url import RootHttpUrl 

16 

17 

18class Settings( 

19 BaseSettings, extra="ignore", allow_inf_nan=False, validate_assignment=True 

20): 

21 """environment variables for bioimageio.spec""" 

22 

23 model_config = SettingsConfigDict( 

24 env_prefix="BIOIMAGEIO_", env_file=".env", env_file_encoding="utf-8" 

25 ) 

26 

27 allow_pickle: bool = False 

28 """Sets the `allow_pickle` argument for `numpy.load()`""" 

29 

30 cache_path: Path = Path(platformdirs.user_cache_dir("bioimageio")) 

31 """bioimageio cache location""" 

32 

33 def __setattr__(self, name: str, value: Any): 

34 super().__setattr__(name, value) 

35 # if cache_path is being changed, we need to reset the disk_cache so that it gets re-created with the new path when accessed next time 

36 if ( 

37 name == "cache_path" 

38 and "disk_cache" in self.__dict__ 

39 and self.disk_cache.dir_path != value 

40 ): 

41 del self.disk_cache 

42 

43 @field_validator("cache_path", mode="after") 

44 @classmethod 

45 def _expand_user(cls, value: Path): 

46 return Path(os.path.expanduser(str(value))) 

47 

48 CI: Annotated[bool | str, Field(alias="CI")] = False 

49 """Wether or not the execution happens in a continuous integration (CI) environment.""" 

50 

51 collection_http_pattern: str = ( 

52 "https://hypha.aicell.io/bioimage-io/artifacts/{bioimageio_id}/files/rdf.yaml" 

53 ) 

54 """A pattern to map bioimageio IDs to bioimageio.yaml URLs. 

55 Notes: 

56 - '{bioimageio_id}' is replaced with user query, 

57 e.g. "affable-shark" when calling `load_description("affable-shark")`. 

58 - This method takes precedence over resolving via `id_map`. 

59 - If this endpoints fails, we fall back to `id_map`. 

60 """ 

61 

62 github_username: str | None = None 

63 """GitHub username for API requests""" 

64 

65 github_token: str | None = None 

66 """GitHub token for API requests""" 

67 

68 http_timeout: float = 10.0 

69 """Timeout in seconds for http requests.""" 

70 

71 huggingface_http_pattern: str = ( 

72 "https://huggingface.co/{repo_id}/resolve/{branch}/package/bioimageio.yaml" 

73 ) 

74 """A pattern to map huggingface repo IDs to bioimageio.yaml URLs. 

75 Notes: 

76 - Used for loading source strings of the form "huggingface/{user_or_org}/{resource_id}[/{version}]" 

77 - example use: `load_description("huggingface/fynnbe/ambitious-sloth/1.3")` 

78 - A given version {version} is mapped to a branch name "v{version}", e.g. "v1.3". 

79 - If no version is provided the "main" branch is used. 

80 - This method takes precedence over resolving via `id_map`. 

81 - If this endpoints fails, we fall back to `id_map`. 

82 """ 

83 

84 hypha_upload: str = ( 

85 "https://hypha.aicell.io/public/services/artifact-manager/create" 

86 ) 

87 """URL to the upload endpoint for bioimageio resources.""" 

88 

89 hypha_upload_token: str | None = None 

90 """Hypha API token to use for uploads. 

91 

92 By setting this token you agree to our terms of service at https://bioimage.io/#/toc. 

93 

94 How to obtain a token: 

95 1. Login to https://bioimage.io 

96 2. Generate a new token at https://bioimage.io/#/api?tab=hypha-rpc 

97 """ 

98 

99 id_map: str = ( 

100 "https://uk1s3.embassy.ebi.ac.uk/public-datasets/bioimage.io/id_map.json" 

101 ) 

102 """URL to bioimageio id_map.json to resolve resource IDs.""" 

103 

104 id_map_draft: str = ( 

105 "https://uk1s3.embassy.ebi.ac.uk/public-datasets/bioimage.io/id_map_draft.json" 

106 ) 

107 """URL to bioimageio id_map_draft.json to resolve draft IDs ending with '/draft'.""" 

108 

109 log_warnings: bool = True 

110 """Log validation warnings to console.""" 

111 

112 perform_io_checks: bool = True 

113 """Wether or not to perform validation that requires file io, 

114 e.g. downloading a remote files. 

115 

116 Existence of any local absolute file paths is still being checked.""" 

117 

118 resolve_draft: bool = True 

119 """Flag to resolve draft resource versions following the pattern 

120 <resource id>/draft. 

121 

122 Note that anyone may stage a new draft and that such a draft version 

123 may not have been reviewed yet. 

124 Set this flag to False to avoid this potential security risk 

125 and disallow loading draft versions.""" 

126 

127 user_agent: str | None = None 

128 """user agent for http requests""" 

129 

130 @cached_property 

131 def disk_cache(self): 

132 cache = DiskCache[RootHttpUrl].create( 

133 url_type=RootHttpUrl, 

134 cache_dir=self.cache_path, 

135 url_hasher=UrlDigest.from_str, 

136 ) 

137 return cache 

138 

139 @property 

140 def github_auth(self): 

141 if self.github_username is None or self.github_token is None: 

142 return None 

143 else: 

144 return (self.github_username, self.github_token) 

145 

146 

147settings = Settings() 

148"""parsed environment variables for bioimageio.spec"""