Merge pull request #556 from bioimage-io/better_axis_id_repr

Make AxisId inherite from str to be usable with xarray.DataArray

bioimageio/spec/__init__.py

@@ -1,6 +1,6 @@
-# """
-# .. include:: ../../README.md
-# """
+"""
+.. include:: ../../README.md
+"""
 
 from . import application as application
 from . import collection as collection

bioimageio/spec/_description.py

@@ -1,3 +1,4 @@
+from pathlib import Path
 from types import MappingProxyType
 from typing import Any, Literal, Optional, TypeVar, Union
 
@@ -6,7 +7,7 @@
 
 from ._build_description import DISCOVER, build_description_impl, get_rd_class_impl
 from ._internal.common_nodes import InvalidDescr
-from ._internal.io import BioimageioYamlContent
+from ._internal.io import BioimageioYamlContent, BioimageioYamlSource
 from ._internal.types import FormatVersionPlaceholder
 from ._internal.validation_context import ValidationContext, validation_context_var
 from .application import AnyApplicationDescr, ApplicationDescr
@@ -157,8 +158,19 @@ def validate_format(
     format_version: Union[Literal["discover", "latest"], str] = DISCOVER,
     context: Optional[ValidationContext] = None,
 ) -> ValidationSummary:
+    """validate a bioimageio.yaml file (RDF)"""
     with context or validation_context_var.get():
         rd = build_description(data, format_version=format_version)
 
     assert rd.validation_summary is not None
     return rd.validation_summary
+
+
+def update_format(
+    source: BioimageioYamlSource,
+    *,
+    output_path: Optional[Path] = None,
+    target_format_version: Union[Literal["latest"], str] = LATEST,
+) -> BioimageioYamlContent:
+    """update a bioimageio.yaml file without validating it"""
+    raise NotImplementedError("Oh no! This feature is not yet implemented")

bioimageio/spec/_internal/field_validation.py

@@ -1,60 +1,22 @@
 from __future__ import annotations
 
 import collections.abc
-import dataclasses
-import sys
-from dataclasses import dataclass
 from datetime import date, datetime
 from typing import (
     Any,
-    Dict,
     Hashable,
     Mapping,
     Sequence,
-    Type,
     Union,
 )
 
-import annotated_types
 import requests
-from pydantic import GetCoreSchemaHandler, functional_validators
-from pydantic_core.core_schema import CoreSchema, no_info_after_validator_function
 
 from bioimageio.spec._internal._settings import settings
 from bioimageio.spec._internal.constants import KNOWN_GH_USERS, KNOWN_INVALID_GH_USERS
 from bioimageio.spec._internal.field_warning import issue_warning
 from bioimageio.spec._internal.validation_context import validation_context_var
 
-if sys.version_info < (3, 10):
-    SLOTS: Dict[str, bool] = {}
-    KW_ONLY: Dict[str, bool] = {}
-else:
-    SLOTS = {"slots": True}
-    KW_ONLY = {"kw_only": True}
-
-
-@dataclasses.dataclass(frozen=True, **SLOTS)
-class RestrictCharacters:
-    alphabet: str
-
-    def __get_pydantic_core_schema__(
-        self, source: Type[Any], handler: GetCoreSchemaHandler
-    ) -> CoreSchema:
-        if not self.alphabet:
-            raise ValueError("Alphabet may not be empty")
-        schema = handler(source)  # get the CoreSchema from the type / inner constraints
-        if schema["type"] != "str":
-            raise TypeError("RestrictCharacters can only be applied to strings")
-        return no_info_after_validator_function(
-            self.validate,
-            schema,
-        )
-
-    def validate(self, value: str) -> str:
-        if any(c not in self.alphabet for c in value):
-            raise ValueError(f"{value!r} is not restricted to {self.alphabet!r}")
-        return value
-
 
 def is_valid_yaml_leaf_value(value: Any) -> bool:
     return value is None or isinstance(value, (bool, date, datetime, int, float, str))
@@ -97,27 +59,6 @@ def validate_unique_entries(seq: Sequence[Hashable]):
     return seq
 
 
-# TODO: make sure we use this one everywhere and not the vanilla pydantic one
-@dataclass(frozen=True, **SLOTS)
-class AfterValidator(functional_validators.AfterValidator):
-    def __str__(self):
-        return f"AfterValidator({self.func.__name__})"
-
-
-# TODO: make sure we use this one everywhere and not the vanilla pydantic one
-@dataclass(frozen=True, **SLOTS)
-class BeforeValidator(functional_validators.BeforeValidator):
-    def __str__(self):
-        return f"BeforeValidator({self.func.__name__})"
-
-
-# TODO: make sure we use this one everywhere and not the vanilla pydantic one
-@dataclass(frozen=True, **SLOTS)
-class Predicate(annotated_types.Predicate):
-    def __str__(self):
-        return f"Predicate({self.func.__name__})"
-
-
 def validate_gh_user(username: str, hotfix_known_errorenous_names: bool = True) -> str:
     if hotfix_known_errorenous_names:
         if username == "Constantin Pape":

bioimageio/spec/_internal/io.py

@@ -26,7 +26,6 @@
 import pooch
 import pydantic
 from pydantic import (
-    AfterValidator,
     AnyUrl,
     DirectoryPath,
     FilePath,
@@ -66,6 +65,7 @@
 from .._internal.validation_context import (
     validation_context_var,
 )
+from .validator_annotations import AfterValidator
 
 if sys.version_info < (3, 10):
     SLOTS: Dict[str, bool] = {}

bioimageio/spec/_internal/io_utils.py

@@ -84,14 +84,14 @@ def open_bioimageio_yaml(
 
     if local_source.is_dir():
         root = local_source
-        local_source = local_source / find_description_file_name(local_source)
+        local_source = local_source / find_bioimageio_yaml_file_name(local_source)
 
     content = _sanitize_bioimageio_yaml(read_yaml(local_source))
 
     return OpenedBioimageioYaml(content, root, downloaded.original_file_name)
 
 
-def identify_bioimageio_yaml_file(file_names: Iterable[FileName]) -> FileName:
+def identify_bioimageio_yaml_file_name(file_names: Iterable[FileName]) -> FileName:
     file_names = sorted(file_names)
     for bioimageio_name in ALL_BIOIMAGEIO_YAML_NAMES:
         for fname in file_names:
@@ -106,17 +106,17 @@ def identify_bioimageio_yaml_file(file_names: Iterable[FileName]) -> FileName:
     )
 
 
-def find_description_file_name(path: Path) -> FileName:
+def find_bioimageio_yaml_file_name(path: Path) -> FileName:
     if path.is_file():
         if not is_zipfile(path):
             return path.name
 
         with ZipFile(path, "r") as f:
-            file_names = identify_bioimageio_yaml_file(f.namelist())
+            file_names = identify_bioimageio_yaml_file_name(f.namelist())
     else:
         file_names = [p.name for p in path.glob("*")]
 
-    return identify_bioimageio_yaml_file(file_names)
+    return identify_bioimageio_yaml_file_name(file_names)
 
 
 def unzip(

bioimageio/spec/_internal/root_url.py

@@ -4,10 +4,11 @@
 from urllib.parse import urlsplit, urlunsplit
 
 import pydantic
-from pydantic import AfterValidator, TypeAdapter
+from pydantic import TypeAdapter
 from typing_extensions import Annotated
 
 from .validated_string import ValidatedString
+from .validator_annotations import AfterValidator
 
 _http_url_adapter = TypeAdapter(pydantic.HttpUrl)  # pyright: ignore[reportCallIssue]
 

bioimageio/spec/_internal/types.py

@@ -10,7 +10,6 @@
 from typing_extensions import Annotated, Literal
 
 from .constants import DOI_REGEX, SI_UNIT_REGEX
-from .field_validation import AfterValidator, BeforeValidator
 from .io import FileSource as FileSource
 from .io import ImportantFileSource as ImportantFileSource
 from .io import PermissiveFileSource as PermissiveFileSource
@@ -23,6 +22,7 @@
 from .license_id import LicenseId as LicenseId
 from .url import HttpUrl as HttpUrl
 from .validated_string import ValidatedString
+from .validator_annotations import AfterValidator, BeforeValidator
 from .version_type import Version as Version
 
 S = TypeVar("S", bound=Sequence[Any])

bioimageio/spec/_internal/validator_annotations.py

@@ -0,0 +1,59 @@
+import sys
+from dataclasses import dataclass
+from typing import Any, Dict, Type
+
+import annotated_types
+from pydantic import GetCoreSchemaHandler, functional_validators
+from pydantic_core import CoreSchema
+from pydantic_core.core_schema import no_info_after_validator_function
+
+if sys.version_info < (3, 10):
+    SLOTS: Dict[str, bool] = {}
+    KW_ONLY: Dict[str, bool] = {}
+else:
+    SLOTS = {"slots": True}
+    KW_ONLY = {"kw_only": True}
+
+
+# TODO: make sure we use this one everywhere and not the vanilla pydantic one
+@dataclass(frozen=True, **SLOTS)
+class AfterValidator(functional_validators.AfterValidator):
+    def __str__(self):
+        return f"AfterValidator({self.func.__name__})"
+
+
+# TODO: make sure we use this one everywhere and not the vanilla pydantic one
+@dataclass(frozen=True, **SLOTS)
+class BeforeValidator(functional_validators.BeforeValidator):
+    def __str__(self):
+        return f"BeforeValidator({self.func.__name__})"
+
+
+# TODO: make sure we use this one everywhere and not the vanilla pydantic one
+@dataclass(frozen=True, **SLOTS)
+class Predicate(annotated_types.Predicate):
+    def __str__(self):
+        return f"Predicate({self.func.__name__})"
+
+
+@dataclass(frozen=True, **SLOTS)
+class RestrictCharacters:
+    alphabet: str
+
+    def __get_pydantic_core_schema__(
+        self, source: Type[Any], handler: GetCoreSchemaHandler
+    ) -> CoreSchema:
+        if not self.alphabet:
+            raise ValueError("Alphabet may not be empty")
+        schema = handler(source)  # get the CoreSchema from the type / inner constraints
+        if schema["type"] != "str":
+            raise TypeError("RestrictCharacters can only be applied to strings")
+        return no_info_after_validator_function(
+            self.validate,
+            schema,
+        )
+
+    def validate(self, value: str) -> str:
+        if any(c not in self.alphabet for c in value):
+            raise ValueError(f"{value!r} is not restricted to {self.alphabet!r}")
+        return value

bioimageio/spec/common.py

@@ -7,6 +7,9 @@
 from ._internal.io import Sha256 as Sha256
 from ._internal.io import YamlValue as YamlValue
 from ._internal.io_basics import FileName as FileName
+from ._internal.io_utils import (
+    identify_bioimageio_yaml_file_name as identify_bioimageio_yaml_file_name,
+)
 from ._internal.root_url import RootHttpUrl as RootHttpUrl
 from ._internal.types import FileSource as FileSource
 from ._internal.types import PermissiveFileSource as PermissiveFileSource

bioimageio/spec/generic/v0_2.py

@@ -17,9 +17,6 @@
 
 from .._internal.common_nodes import Node, ResourceDescrBase
 from .._internal.constants import TAG_CATEGORIES
-from .._internal.field_validation import (
-    AfterValidator as _AfterValidator,
-)
 from .._internal.field_warning import as_warning, issue_warning, warn
 from .._internal.io import (
     BioimageioYamlContent,
@@ -40,6 +37,7 @@
 from .._internal.types import RelativeFilePath as RelativeFilePath
 from .._internal.types import ResourceId as ResourceId
 from .._internal.url import HttpUrl as HttpUrl
+from .._internal.validator_annotations import AfterValidator
 from .._internal.version_type import Version as Version
 from ._v0_2_converter import convert_from_older_format as _convert_from_older_format
 
@@ -81,7 +79,7 @@ def _remove_slashes(s: str):
 class Uploader(Node):
     email: EmailStr
     """Email"""
-    name: Optional[Annotated[str, _AfterValidator(_remove_slashes)]] = None
+    name: Optional[Annotated[str, AfterValidator(_remove_slashes)]] = None
     """name"""
 
 
@@ -101,12 +99,12 @@ class _Person(Node):
 
 
 class Author(_Person):
-    name: Annotated[str, _AfterValidator(_remove_slashes)]
+    name: Annotated[str, AfterValidator(_remove_slashes)]
     github_user: Optional[str] = None  # TODO: validate github_user
 
 
 class Maintainer(_Person):
-    name: Optional[Annotated[str, _AfterValidator(_remove_slashes)]] = None
+    name: Optional[Annotated[str, AfterValidator(_remove_slashes)]] = None
     github_user: str
 
 

bioimageio/spec/generic/v0_3.py

@@ -17,7 +17,6 @@
 from .._internal.constants import (
     TAG_CATEGORIES,
 )
-from .._internal.field_validation import AfterValidator, Predicate
 from .._internal.field_warning import as_warning, warn
 from .._internal.io import (
     BioimageioYamlContent,
@@ -38,6 +37,7 @@
 from .._internal.types import RelativeFilePath as RelativeFilePath
 from .._internal.types import ResourceId as ResourceId
 from .._internal.url import HttpUrl as HttpUrl
+from .._internal.validator_annotations import AfterValidator, Predicate
 from .._internal.version_type import Version as Version
 from .._internal.warning_levels import ALERT
 from ._v0_3_converter import convert_from_older_format

bioimageio/spec/model/v0_4.py

@@ -36,11 +36,7 @@
     StringNode,
 )
 from .._internal.constants import SHA256_HINT
-from .._internal.field_validation import (
-    AfterValidator,
-    RestrictCharacters,
-    validate_unique_entries,
-)
+from .._internal.field_validation import validate_unique_entries
 from .._internal.field_warning import issue_warning, warn
 from .._internal.io import (
     BioimageioYamlContent,
@@ -62,6 +58,7 @@
 from .._internal.types import NotEmpty as NotEmpty
 from .._internal.types import ResourceId as ResourceId
 from .._internal.url import HttpUrl as HttpUrl
+from .._internal.validator_annotations import AfterValidator, RestrictCharacters
 from .._internal.version_type import Version as Version
 from .._internal.warning_levels import ALERT, INFO
 from ..dataset.v0_2 import DatasetDescr as DatasetDescr