-
Notifications
You must be signed in to change notification settings - Fork 17
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Merge pull request #558 from bioimage-io/fix-win-line-endings
convert line endings to unix
- Loading branch information
Showing
18 changed files
with
1,195 additions
and
1,195 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,13 +1,13 @@ | ||
| from pathlib import Path | ||
|
|
||
| from annotated_types import Predicate | ||
| from pydantic import DirectoryPath, FilePath | ||
| from typing_extensions import Annotated | ||
|
|
||
| FileName = str | ||
| AbsoluteDirectory = Annotated[DirectoryPath, Predicate(Path.is_absolute)] | ||
| AbsoluteFilePath = Annotated[FilePath, Predicate(Path.is_absolute)] | ||
|
|
||
| BIOIMAGEIO_YAML = "rdf.yaml" | ||
| ALTERNATIVE_BIOIMAGEIO_YAML_NAMES = ("bioimageio.yaml", "model.yaml") | ||
| ALL_BIOIMAGEIO_YAML_NAMES = (BIOIMAGEIO_YAML,) + ALTERNATIVE_BIOIMAGEIO_YAML_NAMES | ||
| from pathlib import Path | ||
|
|
||
| from annotated_types import Predicate | ||
| from pydantic import DirectoryPath, FilePath | ||
| from typing_extensions import Annotated | ||
|
|
||
| FileName = str | ||
| AbsoluteDirectory = Annotated[DirectoryPath, Predicate(Path.is_absolute)] | ||
| AbsoluteFilePath = Annotated[FilePath, Predicate(Path.is_absolute)] | ||
|
|
||
| BIOIMAGEIO_YAML = "rdf.yaml" | ||
| ALTERNATIVE_BIOIMAGEIO_YAML_NAMES = ("bioimageio.yaml", "model.yaml") | ||
| ALL_BIOIMAGEIO_YAML_NAMES = (BIOIMAGEIO_YAML,) + ALTERNATIVE_BIOIMAGEIO_YAML_NAMES |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,52 +1,52 @@ | ||
| from __future__ import annotations | ||
|
|
||
| from contextvars import ContextVar, Token | ||
| from dataclasses import dataclass, field | ||
| from typing import Dict, List, Optional, Union | ||
|
|
||
| from .io_basics import AbsoluteFilePath, FileName | ||
| from .url import HttpUrl | ||
|
|
||
|
|
||
| @dataclass(frozen=True) | ||
| class PackagingContext: | ||
| _context_tokens: "List[Token[Optional[PackagingContext]]]" = field( | ||
| init=False, default_factory=list | ||
| ) | ||
|
|
||
| bioimageio_yaml_file_name: FileName | ||
|
|
||
| file_sources: Dict[FileName, Union[AbsoluteFilePath, HttpUrl]] = field( | ||
| default_factory=dict | ||
| ) | ||
| """File sources to include in the packaged resource""" | ||
|
|
||
| def replace( | ||
| self, | ||
| *, | ||
| bioimageio_yaml_file_name: Optional[FileName] = None, | ||
| file_sources: Optional[Dict[FileName, Union[AbsoluteFilePath, HttpUrl]]] = None, | ||
| ) -> "PackagingContext": | ||
| """return a modiefied copy""" | ||
| return PackagingContext( | ||
| bioimageio_yaml_file_name=( | ||
| self.bioimageio_yaml_file_name | ||
| if bioimageio_yaml_file_name is None | ||
| else bioimageio_yaml_file_name | ||
| ), | ||
| file_sources=( | ||
| dict(self.file_sources) if file_sources is None else file_sources | ||
| ), | ||
| ) | ||
|
|
||
| def __enter__(self): | ||
| self._context_tokens.append(packaging_context_var.set(self)) | ||
| return self | ||
|
|
||
| def __exit__(self, type, value, traceback): # type: ignore | ||
| packaging_context_var.reset(self._context_tokens.pop(-1)) | ||
|
|
||
|
|
||
| packaging_context_var: ContextVar[Optional[PackagingContext]] = ContextVar( | ||
| "packaging_context_var", default=None | ||
| ) | ||
| from __future__ import annotations | ||
|
|
||
| from contextvars import ContextVar, Token | ||
| from dataclasses import dataclass, field | ||
| from typing import Dict, List, Optional, Union | ||
|
|
||
| from .io_basics import AbsoluteFilePath, FileName | ||
| from .url import HttpUrl | ||
|
|
||
|
|
||
| @dataclass(frozen=True) | ||
| class PackagingContext: | ||
| _context_tokens: "List[Token[Optional[PackagingContext]]]" = field( | ||
| init=False, default_factory=list | ||
| ) | ||
|
|
||
| bioimageio_yaml_file_name: FileName | ||
|
|
||
| file_sources: Dict[FileName, Union[AbsoluteFilePath, HttpUrl]] = field( | ||
| default_factory=dict | ||
| ) | ||
| """File sources to include in the packaged resource""" | ||
|
|
||
| def replace( | ||
| self, | ||
| *, | ||
| bioimageio_yaml_file_name: Optional[FileName] = None, | ||
| file_sources: Optional[Dict[FileName, Union[AbsoluteFilePath, HttpUrl]]] = None, | ||
| ) -> "PackagingContext": | ||
| """return a modiefied copy""" | ||
| return PackagingContext( | ||
| bioimageio_yaml_file_name=( | ||
| self.bioimageio_yaml_file_name | ||
| if bioimageio_yaml_file_name is None | ||
| else bioimageio_yaml_file_name | ||
| ), | ||
| file_sources=( | ||
| dict(self.file_sources) if file_sources is None else file_sources | ||
| ), | ||
| ) | ||
|
|
||
| def __enter__(self): | ||
| self._context_tokens.append(packaging_context_var.set(self)) | ||
| return self | ||
|
|
||
| def __exit__(self, type, value, traceback): # type: ignore | ||
| packaging_context_var.reset(self._context_tokens.pop(-1)) | ||
|
|
||
|
|
||
| packaging_context_var: ContextVar[Optional[PackagingContext]] = ContextVar( | ||
| "packaging_context_var", default=None | ||
| ) |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,98 +1,98 @@ | ||
| from __future__ import annotations | ||
|
|
||
| from contextvars import ContextVar, Token | ||
| from dataclasses import dataclass, field | ||
| from pathlib import Path | ||
| from typing import List, Optional, Union | ||
| from urllib.parse import urlsplit, urlunsplit | ||
|
|
||
| from pydantic import DirectoryPath | ||
|
|
||
| from ._settings import settings | ||
| from .io_basics import AbsoluteDirectory, FileName | ||
| from .root_url import RootHttpUrl | ||
| from .warning_levels import WarningLevel | ||
|
|
||
|
|
||
| @dataclass(frozen=True) | ||
| class ValidationContext: | ||
| _context_tokens: "List[Token[ValidationContext]]" = field( | ||
| init=False, default_factory=list | ||
| ) | ||
|
|
||
| root: Union[RootHttpUrl, AbsoluteDirectory] = Path() | ||
| """url/directory serving as base to resolve any relative file paths""" | ||
|
|
||
| warning_level: WarningLevel = 50 | ||
| """raise warnings of severity `s` as validation errors if `s >= warning_level`""" | ||
|
|
||
| log_warnings: bool = settings.log_warnings | ||
| """if `True` log warnings that are not raised to the console""" | ||
|
|
||
| file_name: Optional[FileName] = None | ||
| """file name of the bioimageio Yaml file""" | ||
|
|
||
| perform_io_checks: bool = settings.perform_io_checks | ||
| """wether or not to perform validation that requires file io, | ||
| e.g. downloading a remote files. | ||
| Existence of local absolute file paths is still being checked.""" | ||
|
|
||
| def replace( | ||
| self, | ||
| root: Optional[Union[RootHttpUrl, DirectoryPath]] = None, | ||
| warning_level: Optional[WarningLevel] = None, | ||
| log_warnings: Optional[bool] = None, | ||
| file_name: Optional[str] = None, | ||
| perform_io_checks: Optional[bool] = None, | ||
| ) -> "ValidationContext": | ||
| return ValidationContext( | ||
| root=self.root if root is None else root, | ||
| warning_level=( | ||
| self.warning_level if warning_level is None else warning_level | ||
| ), | ||
| log_warnings=self.log_warnings if log_warnings is None else log_warnings, | ||
| file_name=self.file_name if file_name is None else file_name, | ||
| perform_io_checks=( | ||
| self.perform_io_checks | ||
| if perform_io_checks is None | ||
| else perform_io_checks | ||
| ), | ||
| ) | ||
|
|
||
| def __enter__(self): | ||
| self._context_tokens.append(validation_context_var.set(self)) | ||
| return self | ||
|
|
||
| def __exit__(self, type, value, traceback): # type: ignore | ||
| validation_context_var.reset(self._context_tokens.pop(-1)) | ||
|
|
||
| @property | ||
| def source_name(self) -> str: | ||
| if self.file_name is None: | ||
| return "in-memory" | ||
| else: | ||
| try: | ||
| if isinstance(self.root, Path): | ||
| source = (self.root / self.file_name).absolute() | ||
| else: | ||
| parsed = urlsplit(str(self.root)) | ||
| path = list(parsed.path.strip("/").split("/")) + [self.file_name] | ||
| source = urlunsplit( | ||
| ( | ||
| parsed.scheme, | ||
| parsed.netloc, | ||
| "/".join(path), | ||
| parsed.query, | ||
| parsed.fragment, | ||
| ) | ||
| ) | ||
| except ValueError: | ||
| return self.file_name | ||
| else: | ||
| return str(source) | ||
|
|
||
|
|
||
| validation_context_var: ContextVar[ValidationContext] = ContextVar( | ||
| "validation_context_var", default=ValidationContext() | ||
| ) | ||
| from __future__ import annotations | ||
|
|
||
| from contextvars import ContextVar, Token | ||
| from dataclasses import dataclass, field | ||
| from pathlib import Path | ||
| from typing import List, Optional, Union | ||
| from urllib.parse import urlsplit, urlunsplit | ||
|
|
||
| from pydantic import DirectoryPath | ||
|
|
||
| from ._settings import settings | ||
| from .io_basics import AbsoluteDirectory, FileName | ||
| from .root_url import RootHttpUrl | ||
| from .warning_levels import WarningLevel | ||
|
|
||
|
|
||
| @dataclass(frozen=True) | ||
| class ValidationContext: | ||
| _context_tokens: "List[Token[ValidationContext]]" = field( | ||
| init=False, default_factory=list | ||
| ) | ||
|
|
||
| root: Union[RootHttpUrl, AbsoluteDirectory] = Path() | ||
| """url/directory serving as base to resolve any relative file paths""" | ||
|
|
||
| warning_level: WarningLevel = 50 | ||
| """raise warnings of severity `s` as validation errors if `s >= warning_level`""" | ||
|
|
||
| log_warnings: bool = settings.log_warnings | ||
| """if `True` log warnings that are not raised to the console""" | ||
|
|
||
| file_name: Optional[FileName] = None | ||
| """file name of the bioimageio Yaml file""" | ||
|
|
||
| perform_io_checks: bool = settings.perform_io_checks | ||
| """wether or not to perform validation that requires file io, | ||
| e.g. downloading a remote files. | ||
| Existence of local absolute file paths is still being checked.""" | ||
|
|
||
| def replace( | ||
| self, | ||
| root: Optional[Union[RootHttpUrl, DirectoryPath]] = None, | ||
| warning_level: Optional[WarningLevel] = None, | ||
| log_warnings: Optional[bool] = None, | ||
| file_name: Optional[str] = None, | ||
| perform_io_checks: Optional[bool] = None, | ||
| ) -> "ValidationContext": | ||
| return ValidationContext( | ||
| root=self.root if root is None else root, | ||
| warning_level=( | ||
| self.warning_level if warning_level is None else warning_level | ||
| ), | ||
| log_warnings=self.log_warnings if log_warnings is None else log_warnings, | ||
| file_name=self.file_name if file_name is None else file_name, | ||
| perform_io_checks=( | ||
| self.perform_io_checks | ||
| if perform_io_checks is None | ||
| else perform_io_checks | ||
| ), | ||
| ) | ||
|
|
||
| def __enter__(self): | ||
| self._context_tokens.append(validation_context_var.set(self)) | ||
| return self | ||
|
|
||
| def __exit__(self, type, value, traceback): # type: ignore | ||
| validation_context_var.reset(self._context_tokens.pop(-1)) | ||
|
|
||
| @property | ||
| def source_name(self) -> str: | ||
| if self.file_name is None: | ||
| return "in-memory" | ||
| else: | ||
| try: | ||
| if isinstance(self.root, Path): | ||
| source = (self.root / self.file_name).absolute() | ||
| else: | ||
| parsed = urlsplit(str(self.root)) | ||
| path = list(parsed.path.strip("/").split("/")) + [self.file_name] | ||
| source = urlunsplit( | ||
| ( | ||
| parsed.scheme, | ||
| parsed.netloc, | ||
| "/".join(path), | ||
| parsed.query, | ||
| parsed.fragment, | ||
| ) | ||
| ) | ||
| except ValueError: | ||
| return self.file_name | ||
| else: | ||
| return str(source) | ||
|
|
||
|
|
||
| validation_context_var: ContextVar[ValidationContext] = ContextVar( | ||
| "validation_context_var", default=ValidationContext() | ||
| ) |
Oops, something went wrong.