From f869c2b0a9c681d08cc0c5f533fb59136ad7dbef Mon Sep 17 00:00:00 2001
From: fynnbe <thefynnbe@gmail.com>
Date: Mon, 18 Mar 2024 10:47:19 +0100
Subject: [PATCH 01/36] add default insertion of ensure_dtype procs

---
 bioimageio/spec/model/v0_5.py | 66 ++++++++++++++++++++++++++++++++---
 1 file changed, 61 insertions(+), 5 deletions(-)

diff --git a/bioimageio/spec/model/v0_5.py b/bioimageio/spec/model/v0_5.py
index d5ea0fd32..c9292a8c1 100644
--- a/bioimageio/spec/model/v0_5.py
+++ b/bioimageio/spec/model/v0_5.py
@@ -656,7 +656,19 @@ class ClipDescr(ProcessingDescrBase):
 
 
 class EnsureDtypeKwargs(ProcessingKwargs):
-    dtype: str
+    dtype: Literal[
+        "float32",
+        "float64",
+        "uint8",
+        "int8",
+        "uint16",
+        "int16",
+        "uint32",
+        "int32",
+        "uint64",
+        "int64",
+        "bool",
+    ]
 
 
 class EnsureDtypeDescr(ProcessingDescrBase):
@@ -1063,7 +1075,14 @@ class InputTensorDescr(TensorDescrBase[InputAxis]):
     """indicates that this tensor may be `None`"""
 
     preprocessing: List[PreprocessingDescr] = Field(default_factory=list)
-    """Description of how this input should be preprocessed."""
+    """Description of how this input should be preprocessed.
+
+    notes:
+    - If preprocessing does not start with an 'ensure_dtype' entry, it is added
+      to ensure a tensor's input data type matches the tensor's data description.
+    - If preprocessing does not end with an 'ensure_dtype' or 'binarize' entry, it is added
+      to ensure preprocessing steps are not unintentionally chaning the data type.
+    """
 
     @model_validator(mode="after")
     def _validate_preprocessing_kwargs(self) -> Self:
@@ -1072,11 +1091,32 @@ def _validate_preprocessing_kwargs(self) -> Self:
             kwargs_axes: Union[Any, Sequence[Any]] = p.kwargs.get("axes", ())
             if not isinstance(kwargs_axes, collections.abc.Sequence):
                 raise ValueError(
-                    f"Expeted `axes` to be a sequence, but got {type(kwargs_axes)}"
+                    f"Expeted `preprocessing.i.kwargs.axes` to be a sequence, but got {type(kwargs_axes)}"
                 )
 
             if any(a not in axes_ids for a in kwargs_axes):
-                raise ValueError("`kwargs.axes` needs to be subset of axes ids")
+                raise ValueError(
+                    "`preprocessing.i.kwargs.axes` needs to be subset of axes ids"
+                )
+
+        if isinstance(self.data, (NominalOrOrdinalDataDescr, IntervalOrRatioDataDescr)):
+            dtype = self.data.type
+        else:
+            dtype = self.data[0].type
+
+        # ensure `preprocessing` begins with `EnsureDtypeDescr`
+        if not self.preprocessing or not isinstance(
+            self.preprocessing[0], EnsureDtypeDescr
+        ):
+            self.preprocessing.insert(
+                0, EnsureDtypeDescr(kwargs=EnsureDtypeKwargs(dtype=dtype))
+            )
+
+        # ensure `preprocessing` ends with `EnsureDtypeDescr` or `BinarizeDescr`
+        if not isinstance(self.preprocessing[-1], (EnsureDtypeDescr, BinarizeDescr)):
+            self.preprocessing.append(
+                EnsureDtypeDescr(kwargs=EnsureDtypeKwargs(dtype=dtype))
+            )
 
         return self
 
@@ -1342,7 +1382,11 @@ class OutputTensorDescr(TensorDescrBase[OutputAxis]):
     No duplicates are allowed across all inputs and outputs."""
 
     postprocessing: List[PostprocessingDescr] = Field(default_factory=list)
-    """Description of how this output should be postprocessed."""
+    """Description of how this output should be postprocessed.
+
+    note: `postprocessing` always ends with an 'ensure_dtype' operation.
+          If not given this is added to cast to this tensor's `data.type`.
+    """
 
     @model_validator(mode="after")
     def _validate_postprocessing_kwargs(self) -> Self:
@@ -1357,6 +1401,18 @@ def _validate_postprocessing_kwargs(self) -> Self:
             if any(a not in axes_ids for a in kwargs_axes):
                 raise ValueError("`kwargs.axes` needs to be subset of axes ids")
 
+        if isinstance(self.data, (NominalOrOrdinalDataDescr, IntervalOrRatioDataDescr)):
+            dtype = self.data.type
+        else:
+            dtype = self.data[0].type
+
+        # ensure `postprocessing` ends with `EnsureDtypeDescr` or `BinarizeDescr`
+        if not self.postprocessing or not isinstance(
+            self.postprocessing[-1], (EnsureDtypeDescr, BinarizeDescr)
+        ):
+            self.postprocessing.append(
+                EnsureDtypeDescr(kwargs=EnsureDtypeKwargs(dtype=dtype))
+            )
         return self
 
 

From ffdf91d0779299f466a3ef34ef28564c5be0ccd2 Mon Sep 17 00:00:00 2001
From: fynnbe <thefynnbe@gmail.com>
Date: Mon, 18 Mar 2024 10:51:23 +0100
Subject: [PATCH 02/36] bump patch version

---
 README.md               | 7 ++++++-
 bioimageio/spec/VERSION | 2 +-
 2 files changed, 7 insertions(+), 2 deletions(-)

diff --git a/README.md b/README.md
index 91f84382b..31fdf34a2 100644
--- a/README.md
+++ b/README.md
@@ -85,6 +85,10 @@ Made with [contrib.rocks](https://contrib.rocks).
 
 ### bioimageio.spec Python package
 
+#### bioimageio.spec 0.5.1
+
+* new patch version model 0.5.1
+
 #### bioimageio.spec 0.5.0post2
 
 * don't fail if CI env var is a string
@@ -228,10 +232,11 @@ Made with [contrib.rocks](https://contrib.rocks).
 
 ### Resource Description Format Versions
 
-#### model 0.5.1 (planned)
+#### model 0.5.1
 
 * Non-breaking changes
   * added optional `inputs.i.optional` field to indicate that a tensor may be `None`
+  * made data type assumptions in `preprocessing` and `postprocessing` explicit by adding `'ensure_dtype'` operations per default.
 
 #### generic 0.3.0 / application 0.3.0 / collection 0.3.0 / dataset 0.3.0 / notebook 0.3.0
 
diff --git a/bioimageio/spec/VERSION b/bioimageio/spec/VERSION
index 0439e3604..4d78bfd6b 100644
--- a/bioimageio/spec/VERSION
+++ b/bioimageio/spec/VERSION
@@ -1,3 +1,3 @@
 {
-    "version": "0.5.0post2"
+    "version": "0.5.1"
 }

From 55a0104a666f35f21be4e51f9e1fc25352f2566d Mon Sep 17 00:00:00 2001
From: fynnbe <thefynnbe@gmail.com>
Date: Mon, 18 Mar 2024 14:38:28 +0100
Subject: [PATCH 03/36] remove wasm32 specific code

cannot run on pyodide atm
---
 bioimageio/spec/_internal/io_utils.py | 7 -------
 1 file changed, 7 deletions(-)

diff --git a/bioimageio/spec/_internal/io_utils.py b/bioimageio/spec/_internal/io_utils.py
index e3fe54b32..51a63e54d 100644
--- a/bioimageio/spec/_internal/io_utils.py
+++ b/bioimageio/spec/_internal/io_utils.py
@@ -1,5 +1,4 @@
 import io
-import platform
 import warnings
 from contextlib import nullcontext
 from pathlib import Path
@@ -25,12 +24,6 @@
 from .io_basics import ALTERNATIVE_BIOIMAGEIO_YAML_NAMES, FileName
 from .types import FileSource, PermissiveFileSource
 
-if platform.machine() == "wasm32":
-    import pyodide_http  # type: ignore
-
-    pyodide_http.patch_all()
-
-
 yaml = YAML(typ="safe")
 
 

From 3974ba595920fc5302b69337cc363f7cf7e4c706 Mon Sep 17 00:00:00 2001
From: fynnbe <thefynnbe@gmail.com>
Date: Mon, 18 Mar 2024 14:41:31 +0100
Subject: [PATCH 04/36] reformat long line

---
 bioimageio/spec/summary.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/bioimageio/spec/summary.py b/bioimageio/spec/summary.py
index 869db03b9..65f623572 100644
--- a/bioimageio/spec/summary.py
+++ b/bioimageio/spec/summary.py
@@ -267,7 +267,10 @@ def format_loc(loc: Loc):
             if d.warnings:
                 details.append(["", "", ""])
 
-        return f"{indent}{self.status_icon} {self.name.strip('.')}: {self.status}\n{src}{env}\n{self._format_md_table(details)}"
+        return (
+            f"{indent}{self.status_icon} {self.name.strip('.')}: {self.status}\n"
+            + f"{src}{env}\n{self._format_md_table(details)}"
+        )
 
     @no_type_check
     def display(self) -> None:

From 80a40f3904f5b5b068eaf647093ce73d20eadd25 Mon Sep 17 00:00:00 2001
From: fynnbe <thefynnbe@gmail.com>
Date: Mon, 18 Mar 2024 15:04:32 +0100
Subject: [PATCH 05/36] get_tensor_sizes -> get_axis_sizes

---
 bioimageio/spec/model/v0_5.py | 22 ++++++----------------
 tests/test_model/test_v0_5.py |  8 ++++----
 2 files changed, 10 insertions(+), 20 deletions(-)

diff --git a/bioimageio/spec/model/v0_5.py b/bioimageio/spec/model/v0_5.py
index f90a68f97..8ce0aa85e 100644
--- a/bioimageio/spec/model/v0_5.py
+++ b/bioimageio/spec/model/v0_5.py
@@ -1831,13 +1831,6 @@ class _DataDepSize(NamedTuple):
     max: Optional[int]
 
 
-class _TensorSizes(NamedTuple):
-    predetermined: Dict[Tuple[TensorId, AxisId], int]
-    """size of axis (given `n` for `ParameterizedSize`)"""
-    data_dependent: Dict[Tuple[TensorId, AxisId], _DataDepSize]
-    """min,max size of data dependent axis"""
-
-
 class ModelDescr(GenericModelDescrBase, title="bioimage.io model specification"):
     """Specification of the fields used in a bioimage.io-compliant RDF to describe AI models with pretrained weights.
     These fields are typically stored in a YAML file which we call a model resource description file (model RDF).
@@ -2202,15 +2195,14 @@ def get_output_test_arrays(self) -> List[NDArray[Any]]:
         assert all(isinstance(d, np.ndarray) for d in data)
         return data
 
-    def get_tensor_sizes(
+    def get_axis_sizes(
         self, ns: Dict[Tuple[TensorId, AxisId], ParameterizedSize.N], batch_size: int
-    ) -> _TensorSizes:
+    ) -> Dict[Tuple[TensorId, AxisId], Union[int, _DataDepSize]]:
         all_axes = {
             t.id: {a.id: a for a in t.axes} for t in chain(self.inputs, self.outputs)
         }
 
-        predetermined: Dict[Tuple[TensorId, AxisId], int] = {}
-        data_dependent: Dict[Tuple[TensorId, AxisId], _DataDepSize] = {}
+        ret: Dict[Tuple[TensorId, AxisId], Union[int, _DataDepSize]] = {}
         for t_descr in chain(self.inputs, self.outputs):
             for a in t_descr.axes:
                 if isinstance(a, BatchAxis):
@@ -2247,16 +2239,14 @@ def get_tensor_sizes(
                         raise ValueError(
                             f"No size increment factor (n) for data dependent size axis {a.id} of tensor {t_descr.id} expected."
                         )
-                    data_dependent[t_descr.id, a.id] = _DataDepSize(
-                        a.size.min, a.size.max
-                    )
+                    ret[t_descr.id, a.id] = _DataDepSize(a.size.min, a.size.max)
                     continue
                 else:
                     assert_never(a.size)
 
-                predetermined[t_descr.id, a.id] = s
+                ret[t_descr.id, a.id] = s
 
-        return _TensorSizes(predetermined, data_dependent)
+        return ret
 
     @model_validator(mode="before")
     @classmethod
diff --git a/tests/test_model/test_v0_5.py b/tests/test_model/test_v0_5.py
index 616c6b9bc..dcf38a757 100644
--- a/tests/test_model/test_v0_5.py
+++ b/tests/test_model/test_v0_5.py
@@ -360,7 +360,7 @@ def test_output_fixed_shape_too_small(model_data: Dict[str, Any]):
     assert summary.status == "failed", summary.format()
 
 
-def test_get_tensor_sizes_raises_with_surplus_n(model_data: Dict[str, Any]):
+def test_get_axis_sizes_raises_with_surplus_n(model_data: Dict[str, Any]):
     with ValidationContext(perform_io_checks=False):
         model = ModelDescr(**model_data)
 
@@ -368,12 +368,12 @@ def test_get_tensor_sizes_raises_with_surplus_n(model_data: Dict[str, Any]):
     output_axis_id = AxisId("y")
 
     with pytest.raises(ValueError):
-        _ = model.get_tensor_sizes(
+        _ = model.get_axis_sizes(
             ns={(output_tensor_id, output_axis_id): 1}, batch_size=1
         )
 
 
-def test_get_tensor_sizes_raises_with_missing_n(model_data: Dict[str, Any]):
+def test_get_axis_sizes_raises_with_missing_n(model_data: Dict[str, Any]):
     model_data["outputs"][0]["axes"][2] = {
         "type": "space",
         "id": "x",
@@ -384,7 +384,7 @@ def test_get_tensor_sizes_raises_with_missing_n(model_data: Dict[str, Any]):
     with ValidationContext(perform_io_checks=False):
         model = ModelDescr(**model_data)
     with pytest.raises(ValueError):
-        _ = model.get_tensor_sizes(ns={}, batch_size=1)
+        _ = model.get_axis_sizes(ns={}, batch_size=1)
 
 
 def test_output_ref_shape_mismatch(model_data: Dict[str, Any]):

From b96190ab9cb087263df469e552197c3414724028 Mon Sep 17 00:00:00 2001
From: fynnbe <thefynnbe@gmail.com>
Date: Mon, 18 Mar 2024 15:45:16 +0100
Subject: [PATCH 06/36] split return of `get_axis_sizes` into input and output
 tensors

---
 bioimageio/spec/model/v0_5.py | 23 ++++++++++++++++++-----
 1 file changed, 18 insertions(+), 5 deletions(-)

diff --git a/bioimageio/spec/model/v0_5.py b/bioimageio/spec/model/v0_5.py
index 8ce0aa85e..5dfccca7e 100644
--- a/bioimageio/spec/model/v0_5.py
+++ b/bioimageio/spec/model/v0_5.py
@@ -1831,6 +1831,11 @@ class _DataDepSize(NamedTuple):
     max: Optional[int]
 
 
+class _AxisSizes(NamedTuple):
+    inputs: Dict[Tuple[TensorId, AxisId], int]
+    outputs: Dict[Tuple[TensorId, AxisId], Union[int, _DataDepSize]]
+
+
 class ModelDescr(GenericModelDescrBase, title="bioimage.io model specification"):
     """Specification of the fields used in a bioimage.io-compliant RDF to describe AI models with pretrained weights.
     These fields are typically stored in a YAML file which we call a model resource description file (model RDF).
@@ -2197,12 +2202,15 @@ def get_output_test_arrays(self) -> List[NDArray[Any]]:
 
     def get_axis_sizes(
         self, ns: Dict[Tuple[TensorId, AxisId], ParameterizedSize.N], batch_size: int
-    ) -> Dict[Tuple[TensorId, AxisId], Union[int, _DataDepSize]]:
+    ) -> _AxisSizes:
         all_axes = {
             t.id: {a.id: a for a in t.axes} for t in chain(self.inputs, self.outputs)
         }
 
-        ret: Dict[Tuple[TensorId, AxisId], Union[int, _DataDepSize]] = {}
+        inputs: Dict[Tuple[TensorId, AxisId], int] = {}
+        outputs: Dict[Tuple[TensorId, AxisId], Union[int, _DataDepSize]] = {}
+        input_ids = {d.id for d in self.inputs}
+        output_ids = {d.id for d in self.outputs}
         for t_descr in chain(self.inputs, self.outputs):
             for a in t_descr.axes:
                 if isinstance(a, BatchAxis):
@@ -2239,14 +2247,19 @@ def get_axis_sizes(
                         raise ValueError(
                             f"No size increment factor (n) for data dependent size axis {a.id} of tensor {t_descr.id} expected."
                         )
-                    ret[t_descr.id, a.id] = _DataDepSize(a.size.min, a.size.max)
+                    assert t_descr.id in output_ids
+                    outputs[t_descr.id, a.id] = _DataDepSize(a.size.min, a.size.max)
                     continue
                 else:
                     assert_never(a.size)
 
-                ret[t_descr.id, a.id] = s
+                if t_descr.id in input_ids:
+                    inputs[t_descr.id, a.id] = s
+                else:
+                    assert t_descr.id in output_ids
+                    outputs[t_descr.id, a.id] = s
 
-        return ret
+        return _AxisSizes(inputs=inputs, outputs=outputs)
 
     @model_validator(mode="before")
     @classmethod

From 0c944d98ecf7352568d8649589eb928e15db50f4 Mon Sep 17 00:00:00 2001
From: fynnbe <thefynnbe@gmail.com>
Date: Mon, 18 Mar 2024 20:13:04 +0100
Subject: [PATCH 07/36] add ensure_dtype in example to make roundtrip test pass

---
 .../models/unet2d_nuclei_broad/bioimageio.yaml              | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/example_descriptions/models/unet2d_nuclei_broad/bioimageio.yaml b/example_descriptions/models/unet2d_nuclei_broad/bioimageio.yaml
index 781358ec6..f7d2ccb8a 100644
--- a/example_descriptions/models/unet2d_nuclei_broad/bioimageio.yaml
+++ b/example_descriptions/models/unet2d_nuclei_broad/bioimageio.yaml
@@ -52,9 +52,15 @@ inputs:
       source: test_input.png
       sha256: 8771f558305dd89f4a85fe659e8ef5e116c94d64e668dc23b9282fda3fe9cce8
     preprocessing: # list of preprocessing steps
+      - id: ensure_dtype # this would be added by default as well
+        kwargs:
+          dtype: float32
       - id: zero_mean_unit_variance # name of preprocessing step
         kwargs:
           axes: [x, y]
+      - id: ensure_dtype # this would be added by default as well
+        kwargs:
+          dtype: float32
 
 outputs:
   - id: probability

From caefb30a684226df3aa8adb3ab87fe8f791db1ad Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Fynn=20Beuttenm=C3=BCller?= <thefynnbe@gmail.com>
Date: Tue, 19 Mar 2024 09:01:43 +0100
Subject: [PATCH 08/36] Update bioimageio/spec/model/v0_5.py

---
 bioimageio/spec/model/v0_5.py | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/bioimageio/spec/model/v0_5.py b/bioimageio/spec/model/v0_5.py
index 5dfccca7e..0d8f4a9ad 100644
--- a/bioimageio/spec/model/v0_5.py
+++ b/bioimageio/spec/model/v0_5.py
@@ -1119,9 +1119,10 @@ class InputTensorDescr(TensorDescrBase[InputAxis]):
 
     notes:
     - If preprocessing does not start with an 'ensure_dtype' entry, it is added
-      to ensure a tensor's input data type matches the tensor's data description.
-    - If preprocessing does not end with an 'ensure_dtype' or 'binarize' entry, it is added
-      to ensure preprocessing steps are not unintentionally chaning the data type.
+      to ensure an input tensor's data type matches the input tensor's data description.
+    - If preprocessing does not end with an 'ensure_dtype' or 'binarize' entry, an 
+      'ensure_dtype' step is added to ensure preprocessing steps are not unintentionally 
+      changing the data type.
     """
 
     @model_validator(mode="after")

From 557fc25235016aef6ea86c3e3de3a8341fe8e707 Mon Sep 17 00:00:00 2001
From: fynnbe <thefynnbe@gmail.com>
Date: Tue, 19 Mar 2024 10:23:49 +0100
Subject: [PATCH 09/36] add BinarizeAlongAxisKwargs

---
 bioimageio/spec/model/v0_5.py | 20 ++++++++++++++++----
 1 file changed, 16 insertions(+), 4 deletions(-)

diff --git a/bioimageio/spec/model/v0_5.py b/bioimageio/spec/model/v0_5.py
index c926bda77..287c09523 100644
--- a/bioimageio/spec/model/v0_5.py
+++ b/bioimageio/spec/model/v0_5.py
@@ -97,7 +97,6 @@
 from ..generic.v0_3 import RelativeFilePath as RelativeFilePath
 from .v0_4 import Author as _Author_v0_4
 from .v0_4 import BinarizeDescr as _BinarizeDescr_v0_4
-from .v0_4 import BinarizeKwargs as BinarizeKwargs
 from .v0_4 import CallableFromDepencency as CallableFromDepencency
 from .v0_4 import CallableFromDepencency as _CallableFromDepencency_v0_4
 from .v0_4 import CallableFromFile as _CallableFromFile_v0_4
@@ -681,13 +680,26 @@ class ProcessingDescrBase(NodeWithExplicitlySetFields, ABC):
     fields_to_set_explicitly: ClassVar[FrozenSet[LiteralString]] = frozenset({"id"})
 
 
+class BinarizeKwargs(ProcessingKwargs):
+    threshold: float
+    """The fixed threshold"""
+
+
+class BinarizeAlongAxisKwargs(ProcessingKwargs):
+    threshold: NotEmpty[List[float]]
+    """The fixed threshold values along `axis`"""
+
+    axis: Annotated[NonBatchAxisId, Field(examples=["channel"])]
+    """The `threshold` axis"""
+
+
 class BinarizeDescr(ProcessingDescrBase):
     """Binarize the tensor with a fixed threshold.
     Values above the threshold will be set to one, values below the threshold to zero.
     """
 
     id: Literal["binarize"] = "binarize"
-    kwargs: BinarizeKwargs
+    kwargs: Union[BinarizeKwargs, BinarizeAlongAxisKwargs]
 
 
 class ClipDescr(ProcessingDescrBase):
@@ -1122,8 +1134,8 @@ class InputTensorDescr(TensorDescrBase[InputAxis]):
     notes:
     - If preprocessing does not start with an 'ensure_dtype' entry, it is added
       to ensure an input tensor's data type matches the input tensor's data description.
-    - If preprocessing does not end with an 'ensure_dtype' or 'binarize' entry, an 
-      'ensure_dtype' step is added to ensure preprocessing steps are not unintentionally 
+    - If preprocessing does not end with an 'ensure_dtype' or 'binarize' entry, an
+      'ensure_dtype' step is added to ensure preprocessing steps are not unintentionally
       changing the data type.
     """
 

From 2b4661450b5381a41cf5b238a2a5e67c10b7072a Mon Sep 17 00:00:00 2001
From: fynnbe <thefynnbe@gmail.com>
Date: Tue, 19 Mar 2024 10:31:47 +0100
Subject: [PATCH 10/36] refactor ScaleLinearKwargs and
 FixedZeroMeanUnitVarianceKwargs

---
 bioimageio/spec/model/v0_5.py | 122 +++++++++++++++++++++-------------
 1 file changed, 74 insertions(+), 48 deletions(-)

diff --git a/bioimageio/spec/model/v0_5.py b/bioimageio/spec/model/v0_5.py
index 287c09523..61180c184 100644
--- a/bioimageio/spec/model/v0_5.py
+++ b/bioimageio/spec/model/v0_5.py
@@ -731,12 +731,26 @@ class EnsureDtypeDescr(ProcessingDescrBase):
 
 
 class ScaleLinearKwargs(ProcessingKwargs):
-    axis: Annotated[Optional[NonBatchAxisId], Field(examples=["channel"])] = (
-        None  # todo: validate existence of axis
-    )
-    """The axis of non-scalar gains/offsets.
-    Invalid for scalar gains/offsets.
-    """
+    gain: float = 1.0
+    """multiplicative factor"""
+
+    offset: float = 0.0
+    """additive term"""
+
+    @model_validator(mode="after")
+    def _validate(self) -> Self:
+        if self.gain == 1.0 and self.offset == 0.0:
+            raise ValueError(
+                "Redundant linear scaling not allowd. Set `gain` != 1.0 and/or `offset`"
+                + " != 0.0."
+            )
+
+        return self
+
+
+class ScaleLinearAlongAxisKwargs(ProcessingKwargs):
+    axis: Annotated[NonBatchAxisId, Field(examples=["channel"])]
+    """The axis of of gains/offsets values."""
 
     gain: Union[float, NotEmpty[List[float]]] = 1.0
     """multiplicative factor"""
@@ -745,16 +759,24 @@ class ScaleLinearKwargs(ProcessingKwargs):
     """additive term"""
 
     @model_validator(mode="after")
-    def either_gain_or_offset(self) -> Self:
-        if (
-            self.gain == 1.0
-            or isinstance(self.gain, list)
-            and all(g == 1.0 for g in self.gain)
-        ) and (
-            self.offset == 0.0
-            or isinstance(self.offset, list)
-            and all(off == 0.0 for off in self.offset)
-        ):
+    def _validate(self) -> Self:
+
+        if isinstance(self.gain, list):
+            if isinstance(self.offset, list):
+                if len(self.gain) != len(self.offset):
+                    raise ValueError(
+                        f"Size of `gain` ({len(self.gain)}) and `offset` ({len(self.offset)}) must match."
+                    )
+            else:
+                self.offset = [float(self.offset)] * len(self.gain)
+        elif isinstance(self.offset, list):
+            self.gain = [float(self.gain)] * len(self.offset)
+        else:
+            raise ValueError(
+                "Do not specify an `axis` for scalar gain and offset values."
+            )
+
+        if all(g == 1.0 for g in self.gain) and all(off == 0.0 for off in self.offset):
             raise ValueError(
                 "Redundant linear scaling not allowd. Set `gain` != 1.0 and/or `offset`"
                 + " != 0.0."
@@ -767,7 +789,7 @@ class ScaleLinearDescr(ProcessingDescrBase):
     """Fixed linear scaling."""
 
     id: Literal["scale_linear"] = "scale_linear"
-    kwargs: ScaleLinearKwargs
+    kwargs: Union[ScaleLinearKwargs, ScaleLinearAlongAxisKwargs]
 
 
 class SigmoidDescr(ProcessingDescrBase):
@@ -785,34 +807,34 @@ class FixedZeroMeanUnitVarianceKwargs(ProcessingKwargs):
     """Normalize with fixed, precomputed values for mean and variance.
     See `zero_mean_unit_variance` for data dependent normalization."""
 
-    mean: Annotated[
-        Union[float, NotEmpty[Tuple[float, ...]]],
-        Field(examples=[3.14, (1.1, -2.2, 3.3)]),
-    ]
-    """The mean value(s) to normalize with. Specify `axis` for a sequence of `mean` values"""
+    mean: float
+    """The mean value to normalize with."""
 
-    std: Annotated[
-        Union[
-            Annotated[float, Ge(1e-6)], NotEmpty[Tuple[Annotated[float, Ge(1e-6)], ...]]
-        ],
-        Field(examples=[1.05, (0.1, 0.2, 0.3)]),
-    ]
-    """The standard deviation value(s) to normalize with. Size must match `mean` values."""
+    std: Annotated[float, Ge(1e-6)]
+    """The standard deviation value to normalize with."""
 
-    axis: Annotated[Optional[NonBatchAxisId], Field(examples=["channel", "index"])] = (
-        None  # todo: validate existence of axis
-    )
-    """The axis of the mean/std values to normalize each entry along that dimension separately.
-    Invalid for scalar gains/offsets.
-    """
+
+class FixedZeroMeanUnitVarianceAlongAxisKwargs(ProcessingKwargs):
+    """Normalize with fixed, precomputed values for mean and variance.
+    See `zero_mean_unit_variance` for data dependent normalization."""
+
+    mean: NotEmpty[List[float]]
+    """The mean value(s) to normalize with."""
+
+    std: NotEmpty[List[Annotated[float, Ge(1e-6)]]]
+    """The standard deviation value(s) to normalize with.
+    Size must match `mean` values."""
+
+    axis: Annotated[NonBatchAxisId, Field(examples=["channel", "index"])]
+    """The axis of the mean/std values to normalize each entry along that dimension
+    separately."""
 
     @model_validator(mode="after")
-    def mean_and_std_match(self) -> Self:
-        mean_len = 1 if isinstance(self.mean, (float, int)) else len(self.mean)
-        std_len = 1 if isinstance(self.std, (float, int)) else len(self.std)
-        if mean_len != std_len:
+    def _mean_and_std_match(self) -> Self:
+        if len(self.mean) != len(self.std):
             raise ValueError(
-                "size of `mean` ({mean_len}) and `std` ({std_len}) must match."
+                f"Size of `mean` ({len(self.mean)}) and `std` ({len(self.std)})"
+                + " must match."
             )
 
         return self
@@ -822,7 +844,9 @@ class FixedZeroMeanUnitVarianceDescr(ProcessingDescrBase):
     """Subtract a given mean and divide by a given variance."""
 
     id: Literal["fixed_zero_mean_unit_variance"] = "fixed_zero_mean_unit_variance"
-    kwargs: FixedZeroMeanUnitVarianceKwargs
+    kwargs: Union[
+        FixedZeroMeanUnitVarianceKwargs, FixedZeroMeanUnitVarianceAlongAxisKwargs
+    ]
 
 
 class ZeroMeanUnitVarianceKwargs(ProcessingKwargs):
@@ -1335,11 +1359,15 @@ def _convert_proc(
         else:
             axis = _get_complement_v04_axis(tensor_axes, p.kwargs.axes)
 
-        return ScaleLinearDescr(
-            kwargs=ScaleLinearKwargs(
+        if axis is None:
+            assert not isinstance(p.kwargs.gain, list)
+            assert not isinstance(p.kwargs.offset, list)
+            kwargs = ScaleLinearKwargs(gain=p.kwargs.gain, offset=p.kwargs.offset)
+        else:
+            kwargs = ScaleLinearAlongAxisKwargs(
                 axis=axis, gain=p.kwargs.gain, offset=p.kwargs.offset
             )
-        )
+        return ScaleLinearDescr(kwargs=kwargs)
     elif isinstance(p, _ScaleMeanVarianceDescr_v0_4):
         return ScaleMeanVarianceDescr(
             kwargs=ScaleMeanVarianceKwargs(
@@ -1352,13 +1380,11 @@ def _convert_proc(
         if p.kwargs.mode == "fixed":
             mean = p.kwargs.mean
             assert mean is not None
-            if isinstance(mean, list):
-                mean = tuple(mean)
+            assert not isinstance(mean, list)
 
             std = p.kwargs.std
             assert std is not None
-            if isinstance(std, list):
-                std = tuple(std)
+            assert not isinstance(std, list)
 
             return FixedZeroMeanUnitVarianceDescr(
                 kwargs=FixedZeroMeanUnitVarianceKwargs(mean=mean, std=std)

From 1949ba546729b72dc3780da7471411da62596e57 Mon Sep 17 00:00:00 2001
From: fynnbe <thefynnbe@gmail.com>
Date: Tue, 19 Mar 2024 10:34:12 +0100
Subject: [PATCH 11/36] update changelog

---
 README.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/README.md b/README.md
index 6367300af..b9a8797da 100644
--- a/README.md
+++ b/README.md
@@ -238,6 +238,7 @@ Made with [contrib.rocks](https://contrib.rocks).
   * added `DataDependentSize` for `outputs.i.size` to specify an output shape that is not known before inference is run.
   * added optional `inputs.i.optional` field to indicate that a tensor may be `None`
   * made data type assumptions in `preprocessing` and `postprocessing` explicit by adding `'ensure_dtype'` operations per default.
+  * allow to specify multiple thresholds (along an `axis`) in a 'binarize' processing step
 
 #### generic 0.3.0 / application 0.3.0 / collection 0.3.0 / dataset 0.3.0 / notebook 0.3.0
 

From d1dc684515be29059bfc0e4f43626fc3aca9dbd4 Mon Sep 17 00:00:00 2001
From: fynnbe <thefynnbe@gmail.com>
Date: Tue, 19 Mar 2024 11:00:28 +0100
Subject: [PATCH 12/36] check bioimageio_cache_path env var

---
 README.md                              | 4 ++++
 bioimageio/spec/__init__.py            | 1 +
 bioimageio/spec/_internal/_settings.py | 5 +++++
 bioimageio/spec/_internal/io.py        | 1 +
 tests/test_bioimageio_collection.py    | 5 ++++-
 5 files changed, 15 insertions(+), 1 deletion(-)

diff --git a/README.md b/README.md
index 6367300af..ca02f7422 100644
--- a/README.md
+++ b/README.md
@@ -71,6 +71,10 @@ or
 pip install -U bioimageio.core
 ```
 
+## 🏞 Environment variables
+
+TODO: link to settings in dev docs
+
 ## 🤝 How to contribute
 
 ## ♥ Contributors
diff --git a/bioimageio/spec/__init__.py b/bioimageio/spec/__init__.py
index 1ff71e56b..ba476e780 100644
--- a/bioimageio/spec/__init__.py
+++ b/bioimageio/spec/__init__.py
@@ -13,6 +13,7 @@
 from ._description import build_description as build_description
 from ._description import dump_description as dump_description
 from ._description import validate_format as validate_format
+from ._internal import settings as settings
 from ._internal.common_nodes import InvalidDescr as InvalidDescr
 from ._internal.constants import VERSION
 from ._internal.validation_context import ValidationContext as ValidationContext
diff --git a/bioimageio/spec/_internal/_settings.py b/bioimageio/spec/_internal/_settings.py
index 78ac500d4..8f80335aa 100644
--- a/bioimageio/spec/_internal/_settings.py
+++ b/bioimageio/spec/_internal/_settings.py
@@ -1,5 +1,7 @@
+from pathlib import Path
 from typing import Optional, Union
 
+import pooch
 from pydantic import Field
 from pydantic_settings import BaseSettings, SettingsConfigDict
 from typing_extensions import Annotated
@@ -33,6 +35,9 @@ class Settings(BaseSettings, extra="ignore"):
     user_agent: Optional[str] = None
     """user agent for http requests"""
 
+    cache_path: Path = pooch.os_cache("bioimageio")
+    """bioimageio cache location"""
+
     @property
     def github_auth(self):
         if self.github_username is None or self.github_token is None:
diff --git a/bioimageio/spec/_internal/io.py b/bioimageio/spec/_internal/io.py
index fc66e9fe0..4ebfec80f 100644
--- a/bioimageio/spec/_internal/io.py
+++ b/bioimageio/spec/_internal/io.py
@@ -533,6 +533,7 @@ def download(
             known_hash=_get_known_hash(kwargs),
             downloader=downloader,
             fname=fname,
+            path=settings.cache_path,
         )
         local_source = Path(_ls).absolute()
         root = strict_source.parent
diff --git a/tests/test_bioimageio_collection.py b/tests/test_bioimageio_collection.py
index 3baae018a..02364cbae 100644
--- a/tests/test_bioimageio_collection.py
+++ b/tests/test_bioimageio_collection.py
@@ -6,6 +6,7 @@
 import pooch
 import pytest
 
+from bioimageio.spec import settings
 from bioimageio.spec._description import DISCOVER, LATEST
 from bioimageio.spec._internal.types import FormatVersionPlaceholder
 from tests.utils import ParameterSet, check_bioimageio_yaml
@@ -227,7 +228,9 @@
 
 
 def yield_bioimageio_yaml_urls() -> Iterable[ParameterSet]:
-    collection_path: Any = pooch.retrieve(BASE_URL + "collection.json", None)
+    collection_path: Any = pooch.retrieve(
+        BASE_URL + "collection.json", None, path=settings.cache_path
+    )
     with Path(collection_path).open(encoding="utf-8") as f:
         collection_data = json.load(f)["collection"]
 

From 7c664864da929862bb7f9b2d9527f983293514c6 Mon Sep 17 00:00:00 2001
From: fynnbe <thefynnbe@gmail.com>
Date: Tue, 19 Mar 2024 11:13:27 +0100
Subject: [PATCH 13/36] restrict valid characters for resource ids

---
 bioimageio/spec/_internal/types.py | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/bioimageio/spec/_internal/types.py b/bioimageio/spec/_internal/types.py
index c62d04c5e..e81a4528b 100644
--- a/bioimageio/spec/_internal/types.py
+++ b/bioimageio/spec/_internal/types.py
@@ -1,5 +1,6 @@
 from __future__ import annotations
 
+import string
 from datetime import datetime
 from keyword import iskeyword
 from typing import Any, Sequence, TypeVar, Union
@@ -22,7 +23,7 @@
 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 .validator_annotations import AfterValidator, BeforeValidator, RestrictCharacters
 from .version_type import Version as Version
 
 S = TypeVar("S", bound=Sequence[Any])
@@ -117,8 +118,8 @@ class Datetime(
 
 _ResourceIdAnno = Annotated[
     NotEmpty[str],
-    annotated_types.LowerCase,
-    annotated_types.Predicate(lambda s: "\\" not in s and s[0] != "/" and s[-1] != "/"),
+    RestrictCharacters(string.ascii_lowercase + string.digits + "-/"),
+    annotated_types.Predicate(lambda s: not (s.startswith("/") or s.endswith("/"))),
 ]
 ResourceId = ValidatedString[_ResourceIdAnno]
 ApplicationId = ValidatedString[_ResourceIdAnno]

From b11afb634b54d11cd29521b899d885bd0c2858ed Mon Sep 17 00:00:00 2001
From: fynnbe <thefynnbe@gmail.com>
Date: Tue, 19 Mar 2024 11:22:42 +0100
Subject: [PATCH 14/36] fix conversion of fixed zero mean unit variance

---
 bioimageio/spec/model/v0_5.py | 29 ++++++++++++++++++++++-------
 1 file changed, 22 insertions(+), 7 deletions(-)

diff --git a/bioimageio/spec/model/v0_5.py b/bioimageio/spec/model/v0_5.py
index 61180c184..c4e53d0e1 100644
--- a/bioimageio/spec/model/v0_5.py
+++ b/bioimageio/spec/model/v0_5.py
@@ -1379,16 +1379,31 @@ def _convert_proc(
     elif isinstance(p, _ZeroMeanUnitVarianceDescr_v0_4):
         if p.kwargs.mode == "fixed":
             mean = p.kwargs.mean
-            assert mean is not None
-            assert not isinstance(mean, list)
-
             std = p.kwargs.std
+            assert mean is not None
             assert std is not None
-            assert not isinstance(std, list)
 
-            return FixedZeroMeanUnitVarianceDescr(
-                kwargs=FixedZeroMeanUnitVarianceKwargs(mean=mean, std=std)
-            )
+            axes = _axes_letters_to_ids(p.kwargs.axes)
+            axis = _get_complement_v04_axis(tensor_axes, p.kwargs.axes)
+
+            if axis is None:
+                assert not isinstance(mean, list)
+                assert not isinstance(std, list)
+                return FixedZeroMeanUnitVarianceDescr(
+                    kwargs=FixedZeroMeanUnitVarianceKwargs(mean=mean, std=std)
+                )
+            else:
+                if not isinstance(mean, list):
+                    mean = [float(mean)]
+                if not isinstance(std, list):
+                    std = [float(std)]
+
+                return FixedZeroMeanUnitVarianceDescr(
+                    kwargs=FixedZeroMeanUnitVarianceAlongAxisKwargs(
+                        axis=axis, mean=mean, std=std
+                    )
+                )
+
         else:
             axes = _axes_letters_to_ids(p.kwargs.axes) or []
             if p.kwargs.mode == "per_dataset":

From 12a983e0c22a38129f84034cee620b2686ed77c1 Mon Sep 17 00:00:00 2001
From: fynnbe <thefynnbe@gmail.com>
Date: Tue, 19 Mar 2024 11:39:43 +0100
Subject: [PATCH 15/36] fix _get_complement_v04_axis

---
 bioimageio/spec/model/v0_5.py | 8 +++-----
 1 file changed, 3 insertions(+), 5 deletions(-)

diff --git a/bioimageio/spec/model/v0_5.py b/bioimageio/spec/model/v0_5.py
index c4e53d0e1..c46c8a4c2 100644
--- a/bioimageio/spec/model/v0_5.py
+++ b/bioimageio/spec/model/v0_5.py
@@ -1330,13 +1330,12 @@ def _get_complement_v04_axis(
     if axes is None:
         return None
 
-    axes_str = str(axes)
-    all_axes = set(str(tensor_axes)) | {"b"}
-    complement_axes = [a for a in axes_str if a not in all_axes]
+    non_complement_axes = set(axes) | {"b"}
+    complement_axes = [a for a in tensor_axes if a not in non_complement_axes]
     if len(complement_axes) > 1:
         raise ValueError(
             f"Expected none or a single complement axis, but axes '{axes}' "
-            + f"for tensor dims '{all_axes}' leave '{complement_axes}'."
+            + f"for tensor dims '{tensor_axes}' leave '{complement_axes}'."
         )
 
     return None if not complement_axes else AxisId(complement_axes[0])
@@ -1383,7 +1382,6 @@ def _convert_proc(
             assert mean is not None
             assert std is not None
 
-            axes = _axes_letters_to_ids(p.kwargs.axes)
             axis = _get_complement_v04_axis(tensor_axes, p.kwargs.axes)
 
             if axis is None:

From 1f210b0839b3670ec343ff0a00f994f6cc409d45 Mon Sep 17 00:00:00 2001
From: fynnbe <thefynnbe@gmail.com>
Date: Tue, 19 Mar 2024 11:56:36 +0100
Subject: [PATCH 16/36] add docstring

---
 bioimageio/spec/_internal/io.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/bioimageio/spec/_internal/io.py b/bioimageio/spec/_internal/io.py
index fc66e9fe0..4e52da679 100644
--- a/bioimageio/spec/_internal/io.py
+++ b/bioimageio/spec/_internal/io.py
@@ -502,6 +502,7 @@ def download(
     /,
     **kwargs: Unpack[HashKwargs],
 ) -> DownloadedFile:
+    """download `source` URL (or pass local file path)"""
     if isinstance(source, FileDescr):
         return source.download()
 

From 8c9b7fe8d8a3da6d7df22150f8edbaaa7a4ae8e9 Mon Sep 17 00:00:00 2001
From: fynnbe <thefynnbe@gmail.com>
Date: Tue, 19 Mar 2024 12:02:38 +0100
Subject: [PATCH 17/36] mark 10.5281/zenodo.7274275/8123818/rdf.yaml as invalid
 as latest

---
 bioimageio/spec/model/v0_5.py       | 6 +++---
 tests/test_bioimageio_collection.py | 1 +
 2 files changed, 4 insertions(+), 3 deletions(-)

diff --git a/bioimageio/spec/model/v0_5.py b/bioimageio/spec/model/v0_5.py
index c46c8a4c2..670ab39d3 100644
--- a/bioimageio/spec/model/v0_5.py
+++ b/bioimageio/spec/model/v0_5.py
@@ -1385,10 +1385,10 @@ def _convert_proc(
             axis = _get_complement_v04_axis(tensor_axes, p.kwargs.axes)
 
             if axis is None:
-                assert not isinstance(mean, list)
-                assert not isinstance(std, list)
                 return FixedZeroMeanUnitVarianceDescr(
-                    kwargs=FixedZeroMeanUnitVarianceKwargs(mean=mean, std=std)
+                    kwargs=FixedZeroMeanUnitVarianceKwargs(
+                        mean=mean, std=std  # pyright: ignore[reportArgumentType]
+                    )
                 )
             else:
                 if not isinstance(mean, list):
diff --git a/tests/test_bioimageio_collection.py b/tests/test_bioimageio_collection.py
index 3baae018a..c375ddca2 100644
--- a/tests/test_bioimageio_collection.py
+++ b/tests/test_bioimageio_collection.py
@@ -73,6 +73,7 @@
     "10.5281/zenodo.6559929/6559930/rdf.yaml",
     "10.5281/zenodo.6811491/6811492/rdf.yaml",
     "10.5281/zenodo.6865412/6919253/rdf.yaml",
+    "10.5281/zenodo.7274275/8123818/rdf.yaml",
     "10.5281/zenodo.7380171/7405349/rdf.yaml",
     "10.5281/zenodo.7614645/7642674/rdf.yaml",
     "10.5281/zenodo.8401064/8429203/rdf.yaml",

From 4c558fb16a7a885590fc49603f1f4e4422640068 Mon Sep 17 00:00:00 2001
From: fynnbe <thefynnbe@gmail.com>
Date: Tue, 19 Mar 2024 13:46:06 +0100
Subject: [PATCH 18/36] move resource id types to their respective submodules

---
 bioimageio/spec/_internal/types.py                | 15 +--------------
 .../spec/_internal/validator_annotations.py       |  6 +++++-
 bioimageio/spec/application/v0_2.py               |  6 ++++--
 bioimageio/spec/application/v0_3.py               |  6 ++++--
 bioimageio/spec/collection/v0_2.py                | 15 +++++----------
 bioimageio/spec/collection/v0_3.py                | 14 +++++---------
 bioimageio/spec/dataset/v0_2.py                   |  6 ++++--
 bioimageio/spec/dataset/v0_3.py                   |  5 ++++-
 bioimageio/spec/generic/v0_2.py                   | 14 ++++++++++++--
 bioimageio/spec/generic/v0_3.py                   | 11 ++++++++++-
 bioimageio/spec/model/v0_4.py                     |  7 ++++---
 bioimageio/spec/model/v0_5.py                     | 10 ++++++----
 bioimageio/spec/notebook/v0_2.py                  |  7 ++++---
 bioimageio/spec/notebook/v0_3.py                  |  6 ++++--
 tests/test_internal/test_types.py                 |  6 ------
 15 files changed, 72 insertions(+), 62 deletions(-)

diff --git a/bioimageio/spec/_internal/types.py b/bioimageio/spec/_internal/types.py
index e81a4528b..07dd8aadf 100644
--- a/bioimageio/spec/_internal/types.py
+++ b/bioimageio/spec/_internal/types.py
@@ -1,6 +1,5 @@
 from __future__ import annotations
 
-import string
 from datetime import datetime
 from keyword import iskeyword
 from typing import Any, Sequence, TypeVar, Union
@@ -23,7 +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, RestrictCharacters
+from .validator_annotations import AfterValidator, BeforeValidator
 from .version_type import Version as Version
 
 S = TypeVar("S", bound=Sequence[Any])
@@ -115,15 +114,3 @@ class Datetime(
         ),
     ]
 ]
-
-_ResourceIdAnno = Annotated[
-    NotEmpty[str],
-    RestrictCharacters(string.ascii_lowercase + string.digits + "-/"),
-    annotated_types.Predicate(lambda s: not (s.startswith("/") or s.endswith("/"))),
-]
-ResourceId = ValidatedString[_ResourceIdAnno]
-ApplicationId = ValidatedString[_ResourceIdAnno]
-CollectionId = ValidatedString[_ResourceIdAnno]
-DatasetId = ValidatedString[_ResourceIdAnno]
-ModelId = ValidatedString[_ResourceIdAnno]
-NotebookId = ValidatedString[_ResourceIdAnno]
diff --git a/bioimageio/spec/_internal/validator_annotations.py b/bioimageio/spec/_internal/validator_annotations.py
index 5dce96e2a..00e396524 100644
--- a/bioimageio/spec/_internal/validator_annotations.py
+++ b/bioimageio/spec/_internal/validator_annotations.py
@@ -45,9 +45,13 @@ def __get_pydantic_core_schema__(
     ) -> 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":
+        if schema["type"] != "str" and not (
+            schema["type"] == "function-after" and schema["schema"]["type"] == "str"
+        ):
             raise TypeError("RestrictCharacters can only be applied to strings")
+
         return no_info_after_validator_function(
             self.validate,
             schema,
diff --git a/bioimageio/spec/application/v0_2.py b/bioimageio/spec/application/v0_2.py
index 2a4b67afd..3e799437d 100644
--- a/bioimageio/spec/application/v0_2.py
+++ b/bioimageio/spec/application/v0_2.py
@@ -5,15 +5,15 @@
 
 from .._internal.common_nodes import Node
 from .._internal.io_basics import AbsoluteFilePath as AbsoluteFilePath
-from .._internal.types import ApplicationId as ApplicationId
 from .._internal.types import ImportantFileSource
 from .._internal.url import HttpUrl as HttpUrl
+from .._internal.validated_string import ValidatedString
 from ..generic.v0_2 import AttachmentsDescr as AttachmentsDescr
 from ..generic.v0_2 import Author as Author
 from ..generic.v0_2 import BadgeDescr as BadgeDescr
 from ..generic.v0_2 import CiteEntry as CiteEntry
 from ..generic.v0_2 import Doi as Doi
-from ..generic.v0_2 import GenericDescrBase
+from ..generic.v0_2 import GenericDescrBase, ResourceId_v0_2_Anno
 from ..generic.v0_2 import LinkedResource as LinkedResource
 from ..generic.v0_2 import Maintainer as Maintainer
 from ..generic.v0_2 import OrcidId as OrcidId
@@ -22,6 +22,8 @@
 from ..generic.v0_2 import Uploader as Uploader
 from ..generic.v0_2 import Version as Version
 
+ApplicationId = ValidatedString[ResourceId_v0_2_Anno]
+
 
 class ApplicationDescr(GenericDescrBase, title="bioimage.io application specification"):
     """Bioimage.io description of an application."""
diff --git a/bioimageio/spec/application/v0_3.py b/bioimageio/spec/application/v0_3.py
index 31ae5eb51..acc27830a 100644
--- a/bioimageio/spec/application/v0_3.py
+++ b/bioimageio/spec/application/v0_3.py
@@ -7,14 +7,14 @@
 from .._internal.io import FileDescr as FileDescr
 from .._internal.io import Sha256 as Sha256
 from .._internal.io_basics import AbsoluteFilePath as AbsoluteFilePath
-from .._internal.types import ApplicationId as ApplicationId
 from .._internal.types import ImportantFileSource
 from .._internal.url import HttpUrl as HttpUrl
+from .._internal.validated_string import ValidatedString
 from ..generic.v0_3 import Author as Author
 from ..generic.v0_3 import BadgeDescr as BadgeDescr
 from ..generic.v0_3 import CiteEntry as CiteEntry
 from ..generic.v0_3 import Doi as Doi
-from ..generic.v0_3 import GenericDescrBase
+from ..generic.v0_3 import GenericDescrBase, ResourceIdAnno
 from ..generic.v0_3 import LinkedResource as LinkedResource
 from ..generic.v0_3 import Maintainer as Maintainer
 from ..generic.v0_3 import OrcidId as OrcidId
@@ -23,6 +23,8 @@
 from ..generic.v0_3 import Uploader as Uploader
 from ..generic.v0_3 import Version as Version
 
+ApplicationId = ValidatedString[ResourceIdAnno]
+
 
 class ApplicationDescr(GenericDescrBase, title="bioimage.io application specification"):
     """Bioimage.io description of an application."""
diff --git a/bioimageio/spec/collection/v0_2.py b/bioimageio/spec/collection/v0_2.py
index 7994eb14f..763e699c3 100644
--- a/bioimageio/spec/collection/v0_2.py
+++ b/bioimageio/spec/collection/v0_2.py
@@ -15,13 +15,9 @@
 from .._internal.io import BioimageioYamlContent, YamlValue
 from .._internal.io_basics import AbsoluteFilePath as AbsoluteFilePath
 from .._internal.io_utils import open_bioimageio_yaml
-from .._internal.types import ApplicationId as ApplicationId
-from .._internal.types import CollectionId as CollectionId
-from .._internal.types import DatasetId as DatasetId
-from .._internal.types import ModelId as ModelId
-from .._internal.types import NotebookId as NotebookId
 from .._internal.types import NotEmpty
 from .._internal.url import HttpUrl as HttpUrl
+from .._internal.validated_string import ValidatedString
 from .._internal.validation_context import validation_context_var
 from .._internal.warning_levels import ALERT
 from ..application import ApplicationDescr_v0_2, ApplicationDescr_v0_3
@@ -32,17 +28,18 @@
 from ..generic.v0_2 import BadgeDescr as BadgeDescr
 from ..generic.v0_2 import CiteEntry as CiteEntry
 from ..generic.v0_2 import Doi as Doi
-from ..generic.v0_2 import FileSource, GenericDescrBase
+from ..generic.v0_2 import FileSource, GenericDescrBase, ResourceId_v0_2_Anno
 from ..generic.v0_2 import LinkedResource as LinkedResource
 from ..generic.v0_2 import Maintainer as Maintainer
 from ..generic.v0_2 import OrcidId as OrcidId
 from ..generic.v0_2 import RelativeFilePath as RelativeFilePath
-from ..generic.v0_2 import ResourceId as ResourceId
 from ..generic.v0_2 import Uploader as Uploader
 from ..generic.v0_2 import Version as Version
 from ..model import ModelDescr_v0_4, ModelDescr_v0_5
 from ..notebook import NotebookDescr_v0_2, NotebookDescr_v0_3
 
+CollectionId = ValidatedString[ResourceId_v0_2_Anno]
+
 EntryDescr = Union[
     ApplicationDescr_v0_2,
     DatasetDescr_v0_2,
@@ -113,9 +110,7 @@ class CollectionEntry(Node, extra="allow"):
     rdf_source: Optional[FileSource] = None
     """resource description file (RDF) source to load entry from"""
 
-    id: Optional[Union[ResourceId, DatasetId, ApplicationId, ModelId, NotebookId]] = (
-        None
-    )
+    id: Optional[ResourceId_v0_2_Anno] = None
     """Collection entry sub id overwriting `rdf_source.id`.
     The full collection entry's id is the collection's base id, followed by this sub id and separated by a slash '/'."""
 
diff --git a/bioimageio/spec/collection/v0_3.py b/bioimageio/spec/collection/v0_3.py
index d21fbdc58..9b77aecba 100644
--- a/bioimageio/spec/collection/v0_3.py
+++ b/bioimageio/spec/collection/v0_3.py
@@ -23,13 +23,9 @@
 from .._internal.io import YamlValue
 from .._internal.io_basics import AbsoluteFilePath as AbsoluteFilePath
 from .._internal.io_utils import open_bioimageio_yaml
-from .._internal.types import ApplicationId as ApplicationId
-from .._internal.types import CollectionId as CollectionId
-from .._internal.types import DatasetId as DatasetId
 from .._internal.types import FileSource, NotEmpty
-from .._internal.types import ModelId as ModelId
-from .._internal.types import NotebookId as NotebookId
 from .._internal.url import HttpUrl as HttpUrl
+from .._internal.validated_string import ValidatedString
 from .._internal.validation_context import (
     validation_context_var,
 )
@@ -43,6 +39,7 @@
 from ..generic.v0_3 import Doi as Doi
 from ..generic.v0_3 import (
     GenericDescrBase,
+    ResourceIdAnno,
     _author_conv,  # pyright: ignore[reportPrivateUsage]
     _maintainer_conv,  # pyright: ignore[reportPrivateUsage]
 )
@@ -50,13 +47,14 @@
 from ..generic.v0_3 import Maintainer as Maintainer
 from ..generic.v0_3 import OrcidId as OrcidId
 from ..generic.v0_3 import RelativeFilePath as RelativeFilePath
-from ..generic.v0_3 import ResourceId as ResourceId
 from ..generic.v0_3 import Uploader as Uploader
 from ..generic.v0_3 import Version as Version
 from ..model import ModelDescr_v0_4, ModelDescr_v0_5
 from ..notebook import NotebookDescr_v0_2, NotebookDescr_v0_3
 from .v0_2 import CollectionDescr as _CollectionDescr_v0_2
 
+CollectionId = ValidatedString[ResourceIdAnno]
+
 EntryDescr = Union[
     ApplicationDescr_v0_2,
     ApplicationDescr_v0_3,
@@ -131,9 +129,7 @@ class CollectionEntry(Node, extra="allow"):
     entry_source: Optional[FileSource] = None
     """an external source this entry description is based on"""
 
-    id: Optional[Union[ResourceId, DatasetId, ApplicationId, ModelId, NotebookId]] = (
-        None
-    )
+    id: Optional[ResourceIdAnno] = None
     """Collection entry sub id overwriting `rdf_source.id`.
     The full collection entry's id is the collection's base id, followed by this sub id and separated by a slash '/'."""
 
diff --git a/bioimageio/spec/dataset/v0_2.py b/bioimageio/spec/dataset/v0_2.py
index 4c4892846..4adb34535 100644
--- a/bioimageio/spec/dataset/v0_2.py
+++ b/bioimageio/spec/dataset/v0_2.py
@@ -2,14 +2,14 @@
 
 from .._internal.common_nodes import Node
 from .._internal.io_basics import AbsoluteFilePath as AbsoluteFilePath
-from .._internal.types import DatasetId as DatasetId
 from .._internal.url import HttpUrl as HttpUrl
+from .._internal.validated_string import ValidatedString
 from ..generic.v0_2 import AttachmentsDescr as AttachmentsDescr
 from ..generic.v0_2 import Author as Author
 from ..generic.v0_2 import BadgeDescr as BadgeDescr
 from ..generic.v0_2 import CiteEntry as CiteEntry
 from ..generic.v0_2 import Doi as Doi
-from ..generic.v0_2 import GenericDescrBase
+from ..generic.v0_2 import GenericDescrBase, ResourceId_v0_2_Anno
 from ..generic.v0_2 import LinkedResource as LinkedResource
 from ..generic.v0_2 import Maintainer as Maintainer
 from ..generic.v0_2 import OrcidId as OrcidId
@@ -18,6 +18,8 @@
 from ..generic.v0_2 import Uploader as Uploader
 from ..generic.v0_2 import Version as Version
 
+DatasetId = ValidatedString[ResourceId_v0_2_Anno]
+
 
 class DatasetDescr(GenericDescrBase, title="bioimage.io dataset specification"):
     """A bioimage.io dataset resource description file (dataset RDF) describes a dataset relevant to bioimage
diff --git a/bioimageio/spec/dataset/v0_3.py b/bioimageio/spec/dataset/v0_3.py
index b50738622..79922eaec 100644
--- a/bioimageio/spec/dataset/v0_3.py
+++ b/bioimageio/spec/dataset/v0_3.py
@@ -6,14 +6,15 @@
 from .._internal.io import FileDescr as FileDescr
 from .._internal.io import Sha256 as Sha256
 from .._internal.io_basics import AbsoluteFilePath as AbsoluteFilePath
-from .._internal.types import DatasetId as DatasetId
 from .._internal.url import HttpUrl as HttpUrl
+from .._internal.validated_string import ValidatedString
 from ..generic.v0_3 import Author as Author
 from ..generic.v0_3 import BadgeDescr as BadgeDescr
 from ..generic.v0_3 import CiteEntry as CiteEntry
 from ..generic.v0_3 import (
     DocumentationSource,
     GenericDescrBase,
+    ResourceIdAnno,
     _author_conv,  # pyright: ignore[reportPrivateUsage]
     _maintainer_conv,  # pyright: ignore[reportPrivateUsage]
 )
@@ -27,6 +28,8 @@
 from ..generic.v0_3 import Version as Version
 from .v0_2 import DatasetDescr as DatasetDescr02
 
+DatasetId = ValidatedString[ResourceIdAnno]
+
 
 class DatasetDescr(GenericDescrBase, title="bioimage.io dataset specification"):
     """A bioimage.io dataset resource description file (dataset RDF) describes a dataset relevant to bioimage
diff --git a/bioimageio/spec/generic/v0_2.py b/bioimageio/spec/generic/v0_2.py
index 9765c6a76..617dc0625 100644
--- a/bioimageio/spec/generic/v0_2.py
+++ b/bioimageio/spec/generic/v0_2.py
@@ -1,4 +1,5 @@
 import collections.abc
+import string
 from typing import (
     Any,
     Dict,
@@ -11,6 +12,7 @@
     Union,
 )
 
+import annotated_types
 from annotated_types import Len, LowerCase, MaxLen
 from pydantic import EmailStr, Field, ValidationInfo, field_validator, model_validator
 from typing_extensions import Annotated, Self, assert_never
@@ -35,12 +37,20 @@
 from .._internal.types import Doi as Doi
 from .._internal.types import OrcidId as OrcidId
 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.validated_string import ValidatedString
+from .._internal.validator_annotations import AfterValidator, RestrictCharacters
 from .._internal.version_type import Version as Version
 from ._v0_2_converter import convert_from_older_format as _convert_from_older_format
 
+ResourceId_v0_2_Anno = Annotated[
+    NotEmpty[str],
+    AfterValidator(lambda s: s.lower()),  # convert upper case on the fly
+    RestrictCharacters(string.ascii_lowercase + string.digits + "_-/"),
+    annotated_types.Predicate(lambda s: not (s.startswith("/") or s.endswith("/"))),
+]
+ResourceId = ValidatedString[ResourceId_v0_2_Anno]
+
 KNOWN_SPECIFIC_RESOURCE_TYPES = (
     "application",
     "collection",
diff --git a/bioimageio/spec/generic/v0_3.py b/bioimageio/spec/generic/v0_3.py
index 2ecc4b578..8eb75bace 100644
--- a/bioimageio/spec/generic/v0_3.py
+++ b/bioimageio/spec/generic/v0_3.py
@@ -4,11 +4,13 @@
 from functools import partial
 from typing import Any, Dict, List, Literal, Optional, Sequence, TypeVar, Union
 
+import annotated_types
 from annotated_types import Len, LowerCase, MaxLen, MinLen
 from pydantic import Field, ValidationInfo, field_validator, model_validator
 from typing_extensions import Annotated
 
 from bioimageio.spec._internal.field_validation import validate_gh_user
+from bioimageio.spec._internal.validated_string import ValidatedString
 
 from .._internal.common_nodes import (
     Converter,
@@ -36,7 +38,6 @@
     NotEmpty,
 )
 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,
@@ -62,6 +63,14 @@
     "notebook",
 )
 
+ResourceIdAnno = Annotated[
+    NotEmpty[str],
+    RestrictCharacters(string.ascii_lowercase + string.digits + "_-/"),
+    annotated_types.Predicate(lambda s: not (s.startswith("/") or s.endswith("/"))),
+]
+
+ResourceId = ValidatedString[ResourceIdAnno]
+
 
 def _validate_md_suffix(value: V_suffix) -> V_suffix:
     return validate_suffix(value, suffix=".md", case_sensitive=True)
diff --git a/bioimageio/spec/model/v0_4.py b/bioimageio/spec/model/v0_4.py
index efd83f1ef..92941fc2c 100644
--- a/bioimageio/spec/model/v0_4.py
+++ b/bioimageio/spec/model/v0_4.py
@@ -54,9 +54,7 @@
     LowerCaseIdentifierAnno,
 )
 from .._internal.types import LicenseId as LicenseId
-from .._internal.types import ModelId as ModelId
 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
@@ -68,15 +66,18 @@
 from ..generic.v0_2 import BadgeDescr as BadgeDescr
 from ..generic.v0_2 import CiteEntry as CiteEntry
 from ..generic.v0_2 import Doi as Doi
-from ..generic.v0_2 import GenericModelDescrBase
+from ..generic.v0_2 import GenericModelDescrBase, ResourceId_v0_2_Anno
 from ..generic.v0_2 import LinkedResource as LinkedResource
 from ..generic.v0_2 import Maintainer as Maintainer
 from ..generic.v0_2 import OrcidId as OrcidId
 from ..generic.v0_2 import RelativeFilePath as RelativeFilePath
 from ..generic.v0_2 import Uploader as Uploader
+from ..generic.v0_3 import ResourceId as ResourceId
 from ..utils import load_array
 from ._v0_4_converter import convert_from_older_format
 
+ModelId = ValidatedString[ResourceId_v0_2_Anno]
+
 AxesStr = Annotated[
     str, RestrictCharacters("bitczyx"), AfterValidator(validate_unique_entries)
 ]
diff --git a/bioimageio/spec/model/v0_5.py b/bioimageio/spec/model/v0_5.py
index c926bda77..bf7788416 100644
--- a/bioimageio/spec/model/v0_5.py
+++ b/bioimageio/spec/model/v0_5.py
@@ -51,6 +51,7 @@
 
 from bioimageio.spec._internal.validated_string import ValidatedString
 from bioimageio.spec._internal.validator_annotations import RestrictCharacters
+from bioimageio.spec.generic.v0_3 import ResourceIdAnno
 
 from .._internal.common_nodes import (
     Converter,
@@ -71,9 +72,7 @@
 from .._internal.types import Identifier as Identifier
 from .._internal.types import ImportantFileSource, LowerCaseIdentifierAnno, SiUnit
 from .._internal.types import LicenseId as LicenseId
-from .._internal.types import ModelId as ModelId
 from .._internal.types import NotEmpty as NotEmpty
-from .._internal.types import ResourceId as ResourceId
 from .._internal.url import HttpUrl as HttpUrl
 from .._internal.validation_context import validation_context_var
 from .._internal.version_type import Version as Version
@@ -1122,8 +1121,8 @@ class InputTensorDescr(TensorDescrBase[InputAxis]):
     notes:
     - If preprocessing does not start with an 'ensure_dtype' entry, it is added
       to ensure an input tensor's data type matches the input tensor's data description.
-    - If preprocessing does not end with an 'ensure_dtype' or 'binarize' entry, an 
-      'ensure_dtype' step is added to ensure preprocessing steps are not unintentionally 
+    - If preprocessing does not end with an 'ensure_dtype' or 'binarize' entry, an
+      'ensure_dtype' step is added to ensure preprocessing steps are not unintentionally
       changing the data type.
     """
 
@@ -1819,6 +1818,9 @@ def check_entries(self) -> Self:
         return self
 
 
+ModelId = ValidatedString[ResourceIdAnno]
+
+
 class LinkedModel(Node):
     """Reference to a bioimage.io model."""
 
diff --git a/bioimageio/spec/notebook/v0_2.py b/bioimageio/spec/notebook/v0_2.py
index 13bb578fa..21b564188 100644
--- a/bioimageio/spec/notebook/v0_2.py
+++ b/bioimageio/spec/notebook/v0_2.py
@@ -5,22 +5,23 @@
 from .._internal.common_nodes import Node
 from .._internal.io import WithSuffix
 from .._internal.io_basics import AbsoluteFilePath as AbsoluteFilePath
-from .._internal.types import NotebookId as NotebookId
 from .._internal.url import HttpUrl
+from .._internal.validated_string import ValidatedString
 from ..generic.v0_2 import AttachmentsDescr as AttachmentsDescr
 from ..generic.v0_2 import Author as Author
 from ..generic.v0_2 import BadgeDescr as BadgeDescr
 from ..generic.v0_2 import CiteEntry as CiteEntry
 from ..generic.v0_2 import Doi as Doi
-from ..generic.v0_2 import GenericDescrBase
+from ..generic.v0_2 import GenericDescrBase, ResourceId_v0_2_Anno
 from ..generic.v0_2 import LinkedResource as LinkedResource
 from ..generic.v0_2 import Maintainer as Maintainer
 from ..generic.v0_2 import OrcidId as OrcidId
 from ..generic.v0_2 import RelativeFilePath as RelativeFilePath
-from ..generic.v0_2 import ResourceId as ResourceId
 from ..generic.v0_2 import Uploader as Uploader
 from ..generic.v0_2 import Version as Version
 
+NotebookId = ValidatedString[ResourceId_v0_2_Anno]
+
 _WithNotebookSuffix = WithSuffix(".ipynb", case_sensitive=True)
 NotebookSource = Union[
     Annotated[HttpUrl, _WithNotebookSuffix],
diff --git a/bioimageio/spec/notebook/v0_3.py b/bioimageio/spec/notebook/v0_3.py
index 214c30eb6..86114a086 100644
--- a/bioimageio/spec/notebook/v0_3.py
+++ b/bioimageio/spec/notebook/v0_3.py
@@ -4,13 +4,13 @@
 from .._internal.io import FileDescr as FileDescr
 from .._internal.io import Sha256 as Sha256
 from .._internal.io_basics import AbsoluteFilePath as AbsoluteFilePath
-from .._internal.types import NotebookId as NotebookId
 from .._internal.url import HttpUrl as HttpUrl
+from .._internal.validated_string import ValidatedString
 from ..generic.v0_3 import Author as Author
 from ..generic.v0_3 import BadgeDescr as BadgeDescr
 from ..generic.v0_3 import CiteEntry as CiteEntry
 from ..generic.v0_3 import Doi as Doi
-from ..generic.v0_3 import GenericDescrBase
+from ..generic.v0_3 import GenericDescrBase, ResourceIdAnno
 from ..generic.v0_3 import LinkedResource as LinkedResource
 from ..generic.v0_3 import Maintainer as Maintainer
 from ..generic.v0_3 import OrcidId as OrcidId
@@ -20,6 +20,8 @@
 from ..generic.v0_3 import Version as Version
 from .v0_2 import NotebookSource as NotebookSource
 
+NotebookId = ValidatedString[ResourceIdAnno]
+
 
 class NotebookDescr(GenericDescrBase, title="bioimage.io notebook specification"):
     """Bioimage.io description of a Jupyter notebook."""
diff --git a/tests/test_internal/test_types.py b/tests/test_internal/test_types.py
index e5aebe962..b886d560b 100644
--- a/tests/test_internal/test_types.py
+++ b/tests/test_internal/test_types.py
@@ -13,9 +13,6 @@
 from tests.utils import check_type
 
 TYPE_ARGS = {
-    types.ApplicationId: "appdev/app",
-    types.CollectionId: "collectionid",
-    types.DatasetId: "dataset-id",
     types.Datetime: (2024, 2, 14),
     types.Datetime: datetime.now().isoformat(),
     types.DeprecatedLicenseId: "AGPL-1.0",
@@ -26,11 +23,8 @@
     types.LicenseId: "MIT",
     types.LowerCaseIdentifier: "id",
     types.LowerCaseIdentifierAnno: "id",
-    types.ModelId: "modelid",
-    types.NotebookId: "notebookid",
     types.OrcidId: "0000-0001-2345-6789",
     types.RelativeFilePath: Path(__file__).relative_to(Path().absolute()),
-    types.ResourceId: "resoruce-id",
     types.SiUnit: "kg",
     types.AbsoluteDirectory: str(Path(__file__).absolute().parent),
     types.AbsoluteFilePath: str(Path(__file__).absolute()),

From f699cb9b1aa71c91ff3c45e2bd4e1c0cadf924ad Mon Sep 17 00:00:00 2001
From: fynnbe <thefynnbe@gmail.com>
Date: Tue, 19 Mar 2024 13:55:45 +0100
Subject: [PATCH 19/36] fix test_specific_reexports_generics

---
 tests/test_specific_reexports_generics.py | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/tests/test_specific_reexports_generics.py b/tests/test_specific_reexports_generics.py
index 1a27ff103..4baa2e152 100644
--- a/tests/test_specific_reexports_generics.py
+++ b/tests/test_specific_reexports_generics.py
@@ -8,6 +8,7 @@
 IGNORE_MEMBERS = {
     "AfterValidator",
     "ALERT",
+    "annotated_types",
     "Annotated",
     "annotations",
     "Any",
@@ -47,8 +48,6 @@
     "partial",
     "Predicate",
     "requests",
-    "ResourceDescrBase",
-    "ResourceDescrType",
     "RestrictCharacters",
     "Self",
     "Sequence",
@@ -85,6 +84,9 @@ def get_members(m: ModuleType):
     "GenericDescrBase",
     "GenericModelDescrBase",
     "KNOWN_SPECIFIC_RESOURCE_TYPES",
+    "ResourceDescrBase",
+    "ResourceDescrType",
+    "ResourceId",
     "VALID_COVER_IMAGE_EXTENSIONS",
 }
 

From d4ec59110fed02fe9c9a7fa8e385e27c2d982516 Mon Sep 17 00:00:00 2001
From: fynnbe <thefynnbe@gmail.com>
Date: Tue, 19 Mar 2024 13:57:50 +0100
Subject: [PATCH 20/36] allow dots in ids

---
 bioimageio/spec/generic/v0_2.py | 2 +-
 bioimageio/spec/generic/v0_3.py | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/bioimageio/spec/generic/v0_2.py b/bioimageio/spec/generic/v0_2.py
index 617dc0625..36a3c75cb 100644
--- a/bioimageio/spec/generic/v0_2.py
+++ b/bioimageio/spec/generic/v0_2.py
@@ -46,7 +46,7 @@
 ResourceId_v0_2_Anno = Annotated[
     NotEmpty[str],
     AfterValidator(lambda s: s.lower()),  # convert upper case on the fly
-    RestrictCharacters(string.ascii_lowercase + string.digits + "_-/"),
+    RestrictCharacters(string.ascii_lowercase + string.digits + "_-/."),
     annotated_types.Predicate(lambda s: not (s.startswith("/") or s.endswith("/"))),
 ]
 ResourceId = ValidatedString[ResourceId_v0_2_Anno]
diff --git a/bioimageio/spec/generic/v0_3.py b/bioimageio/spec/generic/v0_3.py
index 8eb75bace..0a648ebdc 100644
--- a/bioimageio/spec/generic/v0_3.py
+++ b/bioimageio/spec/generic/v0_3.py
@@ -65,7 +65,7 @@
 
 ResourceIdAnno = Annotated[
     NotEmpty[str],
-    RestrictCharacters(string.ascii_lowercase + string.digits + "_-/"),
+    RestrictCharacters(string.ascii_lowercase + string.digits + "_-/."),
     annotated_types.Predicate(lambda s: not (s.startswith("/") or s.endswith("/"))),
 ]
 

From 42731805618689482b52df4201a399c2d418b926 Mon Sep 17 00:00:00 2001
From: fynnbe <thefynnbe@gmail.com>
Date: Tue, 19 Mar 2024 14:03:08 +0100
Subject: [PATCH 21/36] update git_repo urls in tests

---
 tests/test_model/test_v0_4.py |  2 +-
 tests/test_model/test_v0_5.py | 30 ++++++++++++++++++++++--------
 2 files changed, 23 insertions(+), 9 deletions(-)

diff --git a/tests/test_model/test_v0_4.py b/tests/test_model/test_v0_4.py
index 3e00ac3a0..acf5e7e40 100644
--- a/tests/test_model/test_v0_4.py
+++ b/tests/test_model/test_v0_4.py
@@ -307,7 +307,7 @@ def model_data():
         return ModelDescr(
             documentation=UNET2D_ROOT / "README.md",
             license="MIT",
-            git_repo="https://github.com/bioimage-io/python-bioimage-io",
+            git_repo="https://github.com/bioimage-io/core-bioimage-io-python",
             description="description",
             authors=[
                 Author(name="Author 1", affiliation="Affiliation 1"),
diff --git a/tests/test_model/test_v0_5.py b/tests/test_model/test_v0_5.py
index c472e2c08..eeded455d 100644
--- a/tests/test_model/test_v0_5.py
+++ b/tests/test_model/test_v0_5.py
@@ -211,7 +211,7 @@ def model_data():
         model = ModelDescr(
             documentation=UNET2D_ROOT / "README.md",
             license=LicenseId("MIT"),
-            git_repo=HttpUrl("https://github.com/bioimage-io/python-bioimage-io"),
+            git_repo=HttpUrl("https://github.com/bioimage-io/core-bioimage-io-python"),
             format_version="0.5.0",
             description="description",
             authors=[
@@ -340,7 +340,9 @@ def test_warn_long_name(model_data: Dict[str, Any]):
     model_data["name"] = (
         "veeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeery loooooooooooooooong name"
     )
-    summary = validate_format(model_data)
+    summary = validate_format(
+        model_data, context=ValidationContext(perform_io_checks=False)
+    )
 
     assert summary.status == "passed", summary.format()
     assert summary.details[1].warnings[0].loc == ("name",), summary.format()
@@ -349,13 +351,17 @@ def test_warn_long_name(model_data: Dict[str, Any]):
 
 def test_model_schema_raises_invalid_input_id(model_data: Dict[str, Any]):
     model_data["inputs"][0]["id"] = "invalid/id"
-    summary = validate_format(model_data)
+    summary = validate_format(
+        model_data, context=ValidationContext(perform_io_checks=False)
+    )
     assert summary.status == "failed", summary.format()
 
 
 def test_output_fixed_shape_too_small(model_data: Dict[str, Any]):
     model_data["outputs"][0]["halo"] = 999
-    summary = validate_format(model_data)
+    summary = validate_format(
+        model_data, context=ValidationContext(perform_io_checks=False)
+    )
     assert summary.status == "failed", summary.format()
 
 
@@ -393,7 +399,9 @@ def test_output_ref_shape_mismatch(model_data: Dict[str, Any]):
         "size": {"tensor_id": "input_1", "axis_id": "x"},
         "halo": 2,
     }
-    summary = validate_format(model_data)
+    summary = validate_format(
+        model_data, context=ValidationContext(perform_io_checks=False)
+    )
     assert summary.status == "passed", summary.format()
     # input_1.x -> input_1.z
     model_data["outputs"][0]["axes"][2] = {
@@ -429,7 +437,9 @@ def test_output_ref_shape_too_small(model_data: Dict[str, Any]):
 
 def test_model_has_parent_with_id(model_data: Dict[str, Any]):
     model_data["parent"] = dict(id="10.5281/zenodo.5764892", version_number=1)
-    summary = validate_format(model_data)
+    summary = validate_format(
+        model_data, context=ValidationContext(perform_io_checks=False)
+    )
     assert summary.status == "passed", summary.format()
 
 
@@ -450,11 +460,15 @@ def test_model_with_expanded_output(model_data: Dict[str, Any]):
 def test_model_rdf_is_valid_general_rdf(model_data: Dict[str, Any]):
     model_data["type"] = "model_as_generic"
     model_data["format_version"] = "0.3.0"
-    summary = validate_format(model_data)
+    summary = validate_format(
+        model_data, context=ValidationContext(perform_io_checks=False)
+    )
     assert summary.status == "passed", summary.format()
 
 
 def test_model_does_not_accept_unknown_fields(model_data: Dict[str, Any]):
     model_data["unknown_additional_field"] = "shouldn't be here"
-    summary = validate_format(model_data)
+    summary = validate_format(
+        model_data, context=ValidationContext(perform_io_checks=False)
+    )
     assert summary.status == "failed", summary.format()

From d777407d0466db353c1f91957b57c54686628bab Mon Sep 17 00:00:00 2001
From: fynnbe <thefynnbe@gmail.com>
Date: Tue, 19 Mar 2024 14:23:07 +0100
Subject: [PATCH 22/36] fix license unions

---
 bioimageio/spec/generic/v0_2.py        |  6 ++++--
 bioimageio/spec/generic/v0_3.py        |  4 +++-
 tests/test_internal/test_license_id.py | 18 +++++++++++++++++-
 3 files changed, 24 insertions(+), 4 deletions(-)

diff --git a/bioimageio/spec/generic/v0_2.py b/bioimageio/spec/generic/v0_2.py
index 9765c6a76..9405e797f 100644
--- a/bioimageio/spec/generic/v0_2.py
+++ b/bioimageio/spec/generic/v0_2.py
@@ -369,8 +369,10 @@ def _convert_from_older_format(
     The recommended documentation file name is `README.md`. An `.md` suffix is mandatory."""
 
     license: Annotated[
-        Optional[Union[LicenseId, DeprecatedLicenseId, str]],
-        Field(examples=["CC-BY-4.0", "MIT", "BSD-2-Clause"]),
+        Union[LicenseId, DeprecatedLicenseId, str, None],
+        Field(
+            union_mode="left_to_right", examples=["CC-BY-4.0", "MIT", "BSD-2-Clause"]
+        ),
     ] = None
     """A [SPDX license identifier](https://spdx.org/licenses/).
     We do not support custom license beyond the SPDX license list, if you need that please
diff --git a/bioimageio/spec/generic/v0_3.py b/bioimageio/spec/generic/v0_3.py
index 2ecc4b578..d8d443366 100644
--- a/bioimageio/spec/generic/v0_3.py
+++ b/bioimageio/spec/generic/v0_3.py
@@ -206,7 +206,9 @@ class GenericModelDescrBase(ResourceDescrBase):
     """citations"""
 
     license: Annotated[
-        Union[LicenseId, DeprecatedLicenseId],
+        Annotated[
+            Union[LicenseId, DeprecatedLicenseId], Field(union_mode="left_to_right")
+        ],
         warn(
             LicenseId,
             "{value} is deprecated, see https://spdx.org/licenses/{value}.html",
diff --git a/tests/test_internal/test_license_id.py b/tests/test_internal/test_license_id.py
index 57e1721b3..f851cb345 100644
--- a/tests/test_internal/test_license_id.py
+++ b/tests/test_internal/test_license_id.py
@@ -1,5 +1,7 @@
+from typing import Union
+
 import pytest
-from pydantic import ValidationError
+from pydantic import BaseModel, Field, ValidationError
 
 
 def test_license_id():
@@ -11,6 +13,20 @@ def test_license_id():
         _ = LicenseId("not_a_valid_license_id")  # pyright: ignore[reportArgumentType]
 
 
+def test_license_id_in_model():
+    """pydantic 2 now defaults to smart unions, which try to find the best match,
+    somehow `str` is considered a better match than a valid `LicneseId`, so we should
+    only use 'left_to_right' unions with `RootModel[str]`, e.g. `ValidatedString`"""
+    from bioimageio.spec._internal.license_id import LicenseId
+
+    class Model(BaseModel):
+        lid: Union[LicenseId, str] = Field(union_mode="left_to_right")
+
+    out = Model.model_validate({"lid": "CC-BY-4.0"}).lid
+    assert isinstance(out, LicenseId)
+    assert not isinstance(out, str)
+
+
 def test_deprecated_license_id():
     from bioimageio.spec._internal.license_id import DeprecatedLicenseId
 

From 6cb2cf7c14268da2783157f28ee9102b35451e46 Mon Sep 17 00:00:00 2001
From: fynnbe <thefynnbe@gmail.com>
Date: Tue, 19 Mar 2024 18:11:17 +0100
Subject: [PATCH 23/36] make ValidatedString inherite from str

---
 bioimageio/spec/_internal/io.py               | 13 +++--
 bioimageio/spec/_internal/license_id.py       | 19 ++-----
 bioimageio/spec/_internal/root_url.py         | 27 +++-------
 bioimageio/spec/_internal/types.py            | 53 +++++++++++++------
 bioimageio/spec/_internal/url.py              | 22 ++++----
 bioimageio/spec/_internal/validated_string.py | 28 +++++++---
 bioimageio/spec/application/v0_2.py           |  7 +--
 bioimageio/spec/application/v0_3.py           |  8 +--
 bioimageio/spec/collection/v0_2.py            | 11 ++--
 bioimageio/spec/collection/v0_3.py            | 10 ++--
 bioimageio/spec/dataset/v0_2.py               |  8 +--
 bioimageio/spec/dataset/v0_3.py               |  8 +--
 bioimageio/spec/generic/v0_2.py               | 29 +++++++---
 bioimageio/spec/generic/v0_3.py               | 18 ++++---
 bioimageio/spec/model/v0_4.py                 | 20 +++----
 bioimageio/spec/model/v0_5.py                 | 37 ++++++-------
 bioimageio/spec/notebook/v0_2.py              |  9 ++--
 bioimageio/spec/notebook/v0_3.py              |  7 +--
 tests/test_internal/test_license_id.py        |  6 +--
 tests/test_internal/test_validated_string.py  | 18 +++++++
 tests/test_specific_reexports_generics.py     |  3 +-
 21 files changed, 208 insertions(+), 153 deletions(-)
 create mode 100644 tests/test_internal/test_validated_string.py

diff --git a/bioimageio/spec/_internal/io.py b/bioimageio/spec/_internal/io.py
index fc66e9fe0..9689b468b 100644
--- a/bioimageio/spec/_internal/io.py
+++ b/bioimageio/spec/_internal/io.py
@@ -73,18 +73,17 @@
     SLOTS = {"slots": True}
 
 
-class Sha256(
-    ValidatedString[
+class Sha256(ValidatedString):
+    """SHA-256 hash value"""
+
+    root_model = RootModel[
         Annotated[
             str,
             StringConstraints(
                 strip_whitespace=True, to_lower=True, min_length=64, max_length=64
             ),
         ]
-    ],
-    frozen=True,
-):
-    """SHA-256 hash value"""
+    ]
 
 
 AbsolutePathT = TypeVar(
@@ -323,7 +322,7 @@ def _package(value: FileSource, info: SerializationInfo) -> Union[str, Path, Fil
         if isinstance(value, Path):
             unpackaged = value
         elif isinstance(value, HttpUrl):
-            unpackaged = value.root
+            unpackaged = value
         elif isinstance(value, RelativeFilePath):
             unpackaged = Path(value.path)
         elif isinstance(value, AnyUrl):
diff --git a/bioimageio/spec/_internal/license_id.py b/bioimageio/spec/_internal/license_id.py
index 0e3dff689..ece095492 100644
--- a/bioimageio/spec/_internal/license_id.py
+++ b/bioimageio/spec/_internal/license_id.py
@@ -1,4 +1,4 @@
-from typing import TypeVar
+from pydantic import RootModel
 
 from ._generated_spdx_license_literals import (
     DeprecatedLicenseId as DeprecatedLicenseIdLiteral,
@@ -6,19 +6,10 @@
 from ._generated_spdx_license_literals import LicenseId as LicenseIdLiteral
 from .validated_string import ValidatedString
 
-LicenceT = TypeVar("LicenceT", LicenseIdLiteral, DeprecatedLicenseIdLiteral)
 
+class LicenseId(ValidatedString):
+    root_model = RootModel[LicenseIdLiteral]
 
-class _LicenseId(ValidatedString[LicenceT], frozen=True):
-    def __repr__(self):
-        # don't include full literal in class repr
-        name, *_ = self.__class__.__name__.split("[")
-        return f'{name}("{self.root}")'
 
-
-class DeprecatedLicenseId(_LicenseId[DeprecatedLicenseIdLiteral], frozen=True):
-    pass
-
-
-class LicenseId(_LicenseId[LicenseIdLiteral], frozen=True):
-    pass
+class DeprecatedLicenseId(ValidatedString):
+    root_model = RootModel[DeprecatedLicenseIdLiteral]
diff --git a/bioimageio/spec/_internal/root_url.py b/bioimageio/spec/_internal/root_url.py
index 9f9537da9..ed2d0c86c 100644
--- a/bioimageio/spec/_internal/root_url.py
+++ b/bioimageio/spec/_internal/root_url.py
@@ -4,41 +4,28 @@
 from urllib.parse import urlsplit, urlunsplit
 
 import pydantic
-from pydantic import TypeAdapter
-from typing_extensions import Annotated
+from pydantic import RootModel
 
 from .validated_string import ValidatedString
-from .validator_annotations import AfterValidator
 
-_http_url_adapter = TypeAdapter(pydantic.HttpUrl)  # pyright: ignore[reportCallIssue]
 
-
-class RootHttpUrl(
-    ValidatedString[
-        Annotated[
-            str,
-            AfterValidator(lambda value: str(_http_url_adapter.validate_python(value))),
-        ]
-    ],
-    frozen=True,
-):
+class RootHttpUrl(ValidatedString):
     """A 'URL folder', possibly an invalid http URL"""
 
-    @property
-    def _url(self):
-        return pydantic.AnyUrl(str(self))
+    root_model = RootModel[pydantic.HttpUrl]
+    _validated: pydantic.HttpUrl
 
     @property
     def scheme(self) -> str:
-        return self._url.scheme
+        return self._validated.scheme
 
     @property
     def host(self) -> Optional[str]:
-        return self._url.host
+        return self._validated.host
 
     @property
     def path(self) -> Optional[str]:
-        return self._url.path
+        return self._validated.path
 
     @property
     def parent(self) -> RootHttpUrl:
diff --git a/bioimageio/spec/_internal/types.py b/bioimageio/spec/_internal/types.py
index 07dd8aadf..6547043cc 100644
--- a/bioimageio/spec/_internal/types.py
+++ b/bioimageio/spec/_internal/types.py
@@ -90,27 +90,48 @@ class Datetime(
     """
 
 
-Doi = ValidatedString[Annotated[str, StringConstraints(pattern=DOI_REGEX)]]
+class Doi(ValidatedString):
+    root_model = RootModel[Annotated[str, StringConstraints(pattern=DOI_REGEX)]]
+
+
 FormatVersionPlaceholder = Literal["latest", "discover"]
 IdentifierAnno = Annotated[
     NotEmpty[str],
     AfterValidator(_validate_identifier),
     AfterValidator(_validate_is_not_keyword),
 ]
-Identifier = ValidatedString[IdentifierAnno]
+
+
+class Identifier(ValidatedString):
+    root_model = RootModel[IdentifierAnno]
+
+
 LowerCaseIdentifierAnno = Annotated[IdentifierAnno, annotated_types.LowerCase]
-LowerCaseIdentifier = ValidatedString[LowerCaseIdentifierAnno]
-OrcidId = ValidatedString[Annotated[str, AfterValidator(_validate_orcid_id)]]
-SiUnit = ValidatedString[
-    Annotated[
-        str,
-        StringConstraints(min_length=1, pattern=SI_UNIT_REGEX),
-        BeforeValidator(
-            lambda s: (
-                s.replace("×", "·").replace("*", "·").replace(" ", "·")
-                if isinstance(s, str)
-                else s
-            )
-        ),
+
+
+class LowerCaseIdentifier(ValidatedString):
+    root_model = RootModel[LowerCaseIdentifierAnno]
+
+
+class OrcidId(ValidatedString):
+    """an ORCID identifier"""
+
+    root_model = RootModel[Annotated[str, AfterValidator(_validate_orcid_id)]]
+
+
+class SiUnit(ValidatedString):
+    """Si unit"""
+
+    root_model = RootModel[
+        Annotated[
+            str,
+            StringConstraints(min_length=1, pattern=SI_UNIT_REGEX),
+            BeforeValidator(
+                lambda s: (
+                    s.replace("×", "·").replace("*", "·").replace(" ", "·")
+                    if isinstance(s, str)
+                    else s
+                )
+            ),
+        ]
     ]
-]
diff --git a/bioimageio/spec/_internal/url.py b/bioimageio/spec/_internal/url.py
index 11728b78e..8ecb47b3c 100644
--- a/bioimageio/spec/_internal/url.py
+++ b/bioimageio/spec/_internal/url.py
@@ -1,13 +1,21 @@
+from typing import Union
+
+import pydantic
 import requests
 import requests.exceptions
-from pydantic import model_validator
+from pydantic import AfterValidator, RootModel
+from typing_extensions import Annotated
 
 from .field_warning import issue_warning
 from .root_url import RootHttpUrl
 from .validation_context import validation_context_var
 
 
-def check_url(url: str) -> None:
+def _validate_url(url: Union[str, pydantic.HttpUrl]) -> pydantic.AnyUrl:
+    url = str(url)
+    if not validation_context_var.get().perform_io_checks:
+        return pydantic.AnyUrl(url)
+
     if url.startswith("https://colab.research.google.com/github/"):
         # head request for colab returns "Value error, 405: Method Not Allowed"
         # therefore we check if the source notebook exists at github instead
@@ -88,12 +96,8 @@ def check_url(url: str) -> None:
             # TODO follow up forbidden head request with get
             # motivating example: 403: Forbidden https://elifesciences.org/articles/57613
 
+    return pydantic.AnyUrl(url)
 
-class HttpUrl(RootHttpUrl, frozen=True):
-    @model_validator(mode="after")
-    def _check_url(self):
-        if not validation_context_var.get().perform_io_checks:
-            return self
 
-        check_url(str(self))
-        return self
+class HttpUrl(RootHttpUrl):
+    root_model = RootModel[Annotated[pydantic.HttpUrl, AfterValidator(_validate_url)]]
diff --git a/bioimageio/spec/_internal/validated_string.py b/bioimageio/spec/_internal/validated_string.py
index f635c69c8..cb0666e43 100644
--- a/bioimageio/spec/_internal/validated_string.py
+++ b/bioimageio/spec/_internal/validated_string.py
@@ -1,10 +1,26 @@
-from typing import TypeVar
+from typing import Any, ClassVar, Type
 
-from pydantic import RootModel
+from pydantic import GetCoreSchemaHandler, RootModel
+from pydantic_core.core_schema import (
+    CoreSchema,
+    no_info_after_validator_function,
+)
 
-S = TypeVar("S", bound=str)
 
+class ValidatedString(str):
+    root_model: ClassVar[Type[RootModel[Any]]] = RootModel[str]
+    """the pydantic root model to validate the string"""
+    # TODO: should we use a TypeAdapter instead?
+    # TODO: with future py version:  RootModel[Any] -> RootModel[str | "literal string type"]
+    _validated: Any  # pyright: ignore[reportUninitializedInstanceVariable]  # initalized in __new__
 
-class ValidatedString(RootModel[S], frozen=True):
-    def __str__(self) -> str:
-        return self.root
+    def __new__(cls, object: object):
+        self = super().__new__(cls, object)
+        self._validated = cls.root_model.model_validate(self)
+        return self
+
+    @classmethod
+    def __get_pydantic_core_schema__(
+        cls, source_type: Any, handler: GetCoreSchemaHandler
+    ) -> CoreSchema:
+        return no_info_after_validator_function(cls, handler(str))
diff --git a/bioimageio/spec/application/v0_2.py b/bioimageio/spec/application/v0_2.py
index 3e799437d..a0e9348c8 100644
--- a/bioimageio/spec/application/v0_2.py
+++ b/bioimageio/spec/application/v0_2.py
@@ -7,13 +7,12 @@
 from .._internal.io_basics import AbsoluteFilePath as AbsoluteFilePath
 from .._internal.types import ImportantFileSource
 from .._internal.url import HttpUrl as HttpUrl
-from .._internal.validated_string import ValidatedString
 from ..generic.v0_2 import AttachmentsDescr as AttachmentsDescr
 from ..generic.v0_2 import Author as Author
 from ..generic.v0_2 import BadgeDescr as BadgeDescr
 from ..generic.v0_2 import CiteEntry as CiteEntry
 from ..generic.v0_2 import Doi as Doi
-from ..generic.v0_2 import GenericDescrBase, ResourceId_v0_2_Anno
+from ..generic.v0_2 import GenericDescrBase
 from ..generic.v0_2 import LinkedResource as LinkedResource
 from ..generic.v0_2 import Maintainer as Maintainer
 from ..generic.v0_2 import OrcidId as OrcidId
@@ -22,7 +21,9 @@
 from ..generic.v0_2 import Uploader as Uploader
 from ..generic.v0_2 import Version as Version
 
-ApplicationId = ValidatedString[ResourceId_v0_2_Anno]
+
+class ApplicationId(ResourceId):
+    pass
 
 
 class ApplicationDescr(GenericDescrBase, title="bioimage.io application specification"):
diff --git a/bioimageio/spec/application/v0_3.py b/bioimageio/spec/application/v0_3.py
index acc27830a..31c39b7b2 100644
--- a/bioimageio/spec/application/v0_3.py
+++ b/bioimageio/spec/application/v0_3.py
@@ -9,21 +9,21 @@
 from .._internal.io_basics import AbsoluteFilePath as AbsoluteFilePath
 from .._internal.types import ImportantFileSource
 from .._internal.url import HttpUrl as HttpUrl
-from .._internal.validated_string import ValidatedString
 from ..generic.v0_3 import Author as Author
 from ..generic.v0_3 import BadgeDescr as BadgeDescr
 from ..generic.v0_3 import CiteEntry as CiteEntry
 from ..generic.v0_3 import Doi as Doi
-from ..generic.v0_3 import GenericDescrBase, ResourceIdAnno
+from ..generic.v0_3 import GenericDescrBase, ResourceId
 from ..generic.v0_3 import LinkedResource as LinkedResource
 from ..generic.v0_3 import Maintainer as Maintainer
 from ..generic.v0_3 import OrcidId as OrcidId
 from ..generic.v0_3 import RelativeFilePath as RelativeFilePath
-from ..generic.v0_3 import ResourceId as ResourceId
 from ..generic.v0_3 import Uploader as Uploader
 from ..generic.v0_3 import Version as Version
 
-ApplicationId = ValidatedString[ResourceIdAnno]
+
+class ApplicationId(ResourceId):
+    pass
 
 
 class ApplicationDescr(GenericDescrBase, title="bioimage.io application specification"):
diff --git a/bioimageio/spec/collection/v0_2.py b/bioimageio/spec/collection/v0_2.py
index 763e699c3..3a4d10588 100644
--- a/bioimageio/spec/collection/v0_2.py
+++ b/bioimageio/spec/collection/v0_2.py
@@ -17,7 +17,6 @@
 from .._internal.io_utils import open_bioimageio_yaml
 from .._internal.types import NotEmpty
 from .._internal.url import HttpUrl as HttpUrl
-from .._internal.validated_string import ValidatedString
 from .._internal.validation_context import validation_context_var
 from .._internal.warning_levels import ALERT
 from ..application import ApplicationDescr_v0_2, ApplicationDescr_v0_3
@@ -28,17 +27,21 @@
 from ..generic.v0_2 import BadgeDescr as BadgeDescr
 from ..generic.v0_2 import CiteEntry as CiteEntry
 from ..generic.v0_2 import Doi as Doi
-from ..generic.v0_2 import FileSource, GenericDescrBase, ResourceId_v0_2_Anno
+from ..generic.v0_2 import FileSource, GenericDescrBase
 from ..generic.v0_2 import LinkedResource as LinkedResource
 from ..generic.v0_2 import Maintainer as Maintainer
 from ..generic.v0_2 import OrcidId as OrcidId
 from ..generic.v0_2 import RelativeFilePath as RelativeFilePath
+from ..generic.v0_2 import ResourceId as ResourceId
 from ..generic.v0_2 import Uploader as Uploader
 from ..generic.v0_2 import Version as Version
 from ..model import ModelDescr_v0_4, ModelDescr_v0_5
 from ..notebook import NotebookDescr_v0_2, NotebookDescr_v0_3
 
-CollectionId = ValidatedString[ResourceId_v0_2_Anno]
+
+class CollectionId(ResourceId):
+    pass
+
 
 EntryDescr = Union[
     ApplicationDescr_v0_2,
@@ -110,7 +113,7 @@ class CollectionEntry(Node, extra="allow"):
     rdf_source: Optional[FileSource] = None
     """resource description file (RDF) source to load entry from"""
 
-    id: Optional[ResourceId_v0_2_Anno] = None
+    id: Optional[ResourceId] = None
     """Collection entry sub id overwriting `rdf_source.id`.
     The full collection entry's id is the collection's base id, followed by this sub id and separated by a slash '/'."""
 
diff --git a/bioimageio/spec/collection/v0_3.py b/bioimageio/spec/collection/v0_3.py
index 9b77aecba..f011a9713 100644
--- a/bioimageio/spec/collection/v0_3.py
+++ b/bioimageio/spec/collection/v0_3.py
@@ -25,7 +25,6 @@
 from .._internal.io_utils import open_bioimageio_yaml
 from .._internal.types import FileSource, NotEmpty
 from .._internal.url import HttpUrl as HttpUrl
-from .._internal.validated_string import ValidatedString
 from .._internal.validation_context import (
     validation_context_var,
 )
@@ -39,7 +38,7 @@
 from ..generic.v0_3 import Doi as Doi
 from ..generic.v0_3 import (
     GenericDescrBase,
-    ResourceIdAnno,
+    ResourceId,
     _author_conv,  # pyright: ignore[reportPrivateUsage]
     _maintainer_conv,  # pyright: ignore[reportPrivateUsage]
 )
@@ -53,7 +52,10 @@
 from ..notebook import NotebookDescr_v0_2, NotebookDescr_v0_3
 from .v0_2 import CollectionDescr as _CollectionDescr_v0_2
 
-CollectionId = ValidatedString[ResourceIdAnno]
+
+class CollectionId(ResourceId):
+    pass
+
 
 EntryDescr = Union[
     ApplicationDescr_v0_2,
@@ -129,7 +131,7 @@ class CollectionEntry(Node, extra="allow"):
     entry_source: Optional[FileSource] = None
     """an external source this entry description is based on"""
 
-    id: Optional[ResourceIdAnno] = None
+    id: Optional[ResourceId] = None
     """Collection entry sub id overwriting `rdf_source.id`.
     The full collection entry's id is the collection's base id, followed by this sub id and separated by a slash '/'."""
 
diff --git a/bioimageio/spec/dataset/v0_2.py b/bioimageio/spec/dataset/v0_2.py
index 4adb34535..ca1a3ad73 100644
--- a/bioimageio/spec/dataset/v0_2.py
+++ b/bioimageio/spec/dataset/v0_2.py
@@ -3,22 +3,22 @@
 from .._internal.common_nodes import Node
 from .._internal.io_basics import AbsoluteFilePath as AbsoluteFilePath
 from .._internal.url import HttpUrl as HttpUrl
-from .._internal.validated_string import ValidatedString
 from ..generic.v0_2 import AttachmentsDescr as AttachmentsDescr
 from ..generic.v0_2 import Author as Author
 from ..generic.v0_2 import BadgeDescr as BadgeDescr
 from ..generic.v0_2 import CiteEntry as CiteEntry
 from ..generic.v0_2 import Doi as Doi
-from ..generic.v0_2 import GenericDescrBase, ResourceId_v0_2_Anno
+from ..generic.v0_2 import GenericDescrBase, ResourceId
 from ..generic.v0_2 import LinkedResource as LinkedResource
 from ..generic.v0_2 import Maintainer as Maintainer
 from ..generic.v0_2 import OrcidId as OrcidId
 from ..generic.v0_2 import RelativeFilePath as RelativeFilePath
-from ..generic.v0_2 import ResourceId as ResourceId
 from ..generic.v0_2 import Uploader as Uploader
 from ..generic.v0_2 import Version as Version
 
-DatasetId = ValidatedString[ResourceId_v0_2_Anno]
+
+class DatasetId(ResourceId):
+    pass
 
 
 class DatasetDescr(GenericDescrBase, title="bioimage.io dataset specification"):
diff --git a/bioimageio/spec/dataset/v0_3.py b/bioimageio/spec/dataset/v0_3.py
index 79922eaec..39c183a4e 100644
--- a/bioimageio/spec/dataset/v0_3.py
+++ b/bioimageio/spec/dataset/v0_3.py
@@ -7,14 +7,12 @@
 from .._internal.io import Sha256 as Sha256
 from .._internal.io_basics import AbsoluteFilePath as AbsoluteFilePath
 from .._internal.url import HttpUrl as HttpUrl
-from .._internal.validated_string import ValidatedString
 from ..generic.v0_3 import Author as Author
 from ..generic.v0_3 import BadgeDescr as BadgeDescr
 from ..generic.v0_3 import CiteEntry as CiteEntry
 from ..generic.v0_3 import (
     DocumentationSource,
     GenericDescrBase,
-    ResourceIdAnno,
     _author_conv,  # pyright: ignore[reportPrivateUsage]
     _maintainer_conv,  # pyright: ignore[reportPrivateUsage]
 )
@@ -28,7 +26,9 @@
 from ..generic.v0_3 import Version as Version
 from .v0_2 import DatasetDescr as DatasetDescr02
 
-DatasetId = ValidatedString[ResourceIdAnno]
+
+class DatasetId(ResourceId):
+    pass
 
 
 class DatasetDescr(GenericDescrBase, title="bioimage.io dataset specification"):
@@ -81,7 +81,7 @@ def _convert(cls, data: Dict[str, Any], /) -> Dict[str, Any]:
                     format_version="0.3.0",
                     git_repo=old.git_repo,  # pyright: ignore[reportArgumentType]
                     icon=old.icon,
-                    id=old.id,
+                    id=None if old.id is None else DatasetId(old.id),
                     license=old.license,  # type: ignore
                     links=old.links,
                     maintainers=[
diff --git a/bioimageio/spec/generic/v0_2.py b/bioimageio/spec/generic/v0_2.py
index 36a3c75cb..436899156 100644
--- a/bioimageio/spec/generic/v0_2.py
+++ b/bioimageio/spec/generic/v0_2.py
@@ -14,7 +14,14 @@
 
 import annotated_types
 from annotated_types import Len, LowerCase, MaxLen
-from pydantic import EmailStr, Field, ValidationInfo, field_validator, model_validator
+from pydantic import (
+    EmailStr,
+    Field,
+    RootModel,
+    ValidationInfo,
+    field_validator,
+    model_validator,
+)
 from typing_extensions import Annotated, Self, assert_never
 
 from .._internal.common_nodes import Node, ResourceDescrBase
@@ -43,13 +50,19 @@
 from .._internal.version_type import Version as Version
 from ._v0_2_converter import convert_from_older_format as _convert_from_older_format
 
-ResourceId_v0_2_Anno = Annotated[
-    NotEmpty[str],
-    AfterValidator(lambda s: s.lower()),  # convert upper case on the fly
-    RestrictCharacters(string.ascii_lowercase + string.digits + "_-/."),
-    annotated_types.Predicate(lambda s: not (s.startswith("/") or s.endswith("/"))),
-]
-ResourceId = ValidatedString[ResourceId_v0_2_Anno]
+
+class ResourceId(ValidatedString):
+    root_model = RootModel[
+        Annotated[
+            NotEmpty[str],
+            AfterValidator(str.lower),  # convert upper case on the fly
+            RestrictCharacters(string.ascii_lowercase + string.digits + "_-/."),
+            annotated_types.Predicate(
+                lambda s: not (s.startswith("/") or s.endswith("/"))
+            ),
+        ]
+    ]
+
 
 KNOWN_SPECIFIC_RESOURCE_TYPES = (
     "application",
diff --git a/bioimageio/spec/generic/v0_3.py b/bioimageio/spec/generic/v0_3.py
index 0a648ebdc..8eed0e542 100644
--- a/bioimageio/spec/generic/v0_3.py
+++ b/bioimageio/spec/generic/v0_3.py
@@ -6,7 +6,7 @@
 
 import annotated_types
 from annotated_types import Len, LowerCase, MaxLen, MinLen
-from pydantic import Field, ValidationInfo, field_validator, model_validator
+from pydantic import Field, RootModel, ValidationInfo, field_validator, model_validator
 from typing_extensions import Annotated
 
 from bioimageio.spec._internal.field_validation import validate_gh_user
@@ -63,13 +63,17 @@
     "notebook",
 )
 
-ResourceIdAnno = Annotated[
-    NotEmpty[str],
-    RestrictCharacters(string.ascii_lowercase + string.digits + "_-/."),
-    annotated_types.Predicate(lambda s: not (s.startswith("/") or s.endswith("/"))),
-]
 
-ResourceId = ValidatedString[ResourceIdAnno]
+class ResourceId(ValidatedString):
+    root_model = RootModel[
+        Annotated[
+            NotEmpty[str],
+            RestrictCharacters(string.ascii_lowercase + string.digits + "_-/."),
+            annotated_types.Predicate(
+                lambda s: not (s.startswith("/") or s.endswith("/"))
+            ),
+        ]
+    ]
 
 
 def _validate_md_suffix(value: V_suffix) -> V_suffix:
diff --git a/bioimageio/spec/model/v0_4.py b/bioimageio/spec/model/v0_4.py
index 92941fc2c..e1316ab68 100644
--- a/bioimageio/spec/model/v0_4.py
+++ b/bioimageio/spec/model/v0_4.py
@@ -27,8 +27,6 @@
 )
 from typing_extensions import Annotated, LiteralString, Self, assert_never
 
-from bioimageio.spec._internal.validated_string import ValidatedString
-
 from .._internal.common_nodes import (
     KwargsNode,
     Node,
@@ -49,10 +47,7 @@
 from .._internal.io_basics import AbsoluteFilePath as AbsoluteFilePath
 from .._internal.types import Datetime as Datetime
 from .._internal.types import Identifier as Identifier
-from .._internal.types import (
-    ImportantFileSource,
-    LowerCaseIdentifierAnno,
-)
+from .._internal.types import ImportantFileSource, LowerCaseIdentifier
 from .._internal.types import LicenseId as LicenseId
 from .._internal.types import NotEmpty as NotEmpty
 from .._internal.url import HttpUrl as HttpUrl
@@ -66,17 +61,20 @@
 from ..generic.v0_2 import BadgeDescr as BadgeDescr
 from ..generic.v0_2 import CiteEntry as CiteEntry
 from ..generic.v0_2 import Doi as Doi
-from ..generic.v0_2 import GenericModelDescrBase, ResourceId_v0_2_Anno
+from ..generic.v0_2 import GenericModelDescrBase
 from ..generic.v0_2 import LinkedResource as LinkedResource
 from ..generic.v0_2 import Maintainer as Maintainer
 from ..generic.v0_2 import OrcidId as OrcidId
 from ..generic.v0_2 import RelativeFilePath as RelativeFilePath
+from ..generic.v0_2 import ResourceId as ResourceId
 from ..generic.v0_2 import Uploader as Uploader
-from ..generic.v0_3 import ResourceId as ResourceId
 from ..utils import load_array
 from ._v0_4_converter import convert_from_older_format
 
-ModelId = ValidatedString[ResourceId_v0_2_Anno]
+
+class ModelId(ResourceId):
+    pass
+
 
 AxesStr = Annotated[
     str, RestrictCharacters("bitczyx"), AfterValidator(validate_unique_entries)
@@ -103,7 +101,9 @@
     "scale_range",
 ]
 
-TensorName = ValidatedString[LowerCaseIdentifierAnno]
+
+class TensorName(LowerCaseIdentifier):
+    pass
 
 
 class CallableFromDepencency(StringNode):
diff --git a/bioimageio/spec/model/v0_5.py b/bioimageio/spec/model/v0_5.py
index bf7788416..9d209c0a4 100644
--- a/bioimageio/spec/model/v0_5.py
+++ b/bioimageio/spec/model/v0_5.py
@@ -38,20 +38,15 @@
 from numpy.typing import NDArray
 from pydantic import (
     Field,
-    GetCoreSchemaHandler,
+    RootModel,
     ValidationInfo,
     field_validator,
     model_validator,
 )
-from pydantic_core.core_schema import (
-    CoreSchema,
-    no_info_after_validator_function,
-)
 from typing_extensions import Annotated, LiteralString, Self, assert_never
 
-from bioimageio.spec._internal.validated_string import ValidatedString
 from bioimageio.spec._internal.validator_annotations import RestrictCharacters
-from bioimageio.spec.generic.v0_3 import ResourceIdAnno
+from bioimageio.spec.generic.v0_3 import ResourceId as ResourceId
 
 from .._internal.common_nodes import (
     Converter,
@@ -70,7 +65,12 @@
 from .._internal.types import Datetime as Datetime
 from .._internal.types import DeprecatedLicenseId as DeprecatedLicenseId
 from .._internal.types import Identifier as Identifier
-from .._internal.types import ImportantFileSource, LowerCaseIdentifierAnno, SiUnit
+from .._internal.types import (
+    ImportantFileSource,
+    LowerCaseIdentifier,
+    LowerCaseIdentifierAnno,
+    SiUnit,
+)
 from .._internal.types import LicenseId as LicenseId
 from .._internal.types import NotEmpty as NotEmpty
 from .._internal.url import HttpUrl as HttpUrl
@@ -177,22 +177,14 @@
 ]
 
 AxisType = Literal["batch", "channel", "index", "time", "space"]
-TensorId = ValidatedString[Annotated[LowerCaseIdentifierAnno, MaxLen(32)]]
 
 
-class AxisId(str):
-    root_model = ValidatedString[Annotated[LowerCaseIdentifierAnno, MaxLen(16)]]
+class TensorId(LowerCaseIdentifier):
+    root_model = RootModel[Annotated[LowerCaseIdentifierAnno, MaxLen(32)]]
 
-    @classmethod
-    def __get_pydantic_core_schema__(
-        cls, source_type: Any, handler: GetCoreSchemaHandler
-    ) -> CoreSchema:
-        return no_info_after_validator_function(cls._validate, handler(str))
 
-    @classmethod
-    def _validate(cls, value: str):
-        valid = cls.root_model.model_validate(value)
-        return cls(valid.root)
+class AxisId(LowerCaseIdentifier):
+    root_model = RootModel[Annotated[LowerCaseIdentifierAnno, MaxLen(16)]]
 
 
 NonBatchAxisId = Annotated[AxisId, Predicate(lambda x: x != "batch")]
@@ -1818,7 +1810,8 @@ def check_entries(self) -> Self:
         return self
 
 
-ModelId = ValidatedString[ResourceIdAnno]
+class ModelId(ResourceId):
+    pass
 
 
 class LinkedModel(Node):
@@ -2349,7 +2342,7 @@ def conv_authors(auths: Optional[Sequence[_Author_v0_4]]):
             format_version="0.5.0",
             git_repo=src.git_repo,  # pyright: ignore[reportArgumentType]
             icon=src.icon,
-            id=src.id,
+            id=None if src.id is None else ModelId(src.id),
             id_emoji=src.id_emoji,
             license=src.license,  # type: ignore
             links=src.links,
diff --git a/bioimageio/spec/notebook/v0_2.py b/bioimageio/spec/notebook/v0_2.py
index 21b564188..9414c912d 100644
--- a/bioimageio/spec/notebook/v0_2.py
+++ b/bioimageio/spec/notebook/v0_2.py
@@ -6,21 +6,24 @@
 from .._internal.io import WithSuffix
 from .._internal.io_basics import AbsoluteFilePath as AbsoluteFilePath
 from .._internal.url import HttpUrl
-from .._internal.validated_string import ValidatedString
 from ..generic.v0_2 import AttachmentsDescr as AttachmentsDescr
 from ..generic.v0_2 import Author as Author
 from ..generic.v0_2 import BadgeDescr as BadgeDescr
 from ..generic.v0_2 import CiteEntry as CiteEntry
 from ..generic.v0_2 import Doi as Doi
-from ..generic.v0_2 import GenericDescrBase, ResourceId_v0_2_Anno
+from ..generic.v0_2 import GenericDescrBase
 from ..generic.v0_2 import LinkedResource as LinkedResource
 from ..generic.v0_2 import Maintainer as Maintainer
 from ..generic.v0_2 import OrcidId as OrcidId
 from ..generic.v0_2 import RelativeFilePath as RelativeFilePath
+from ..generic.v0_2 import ResourceId as ResourceId
 from ..generic.v0_2 import Uploader as Uploader
 from ..generic.v0_2 import Version as Version
 
-NotebookId = ValidatedString[ResourceId_v0_2_Anno]
+
+class NotebookId(ResourceId):
+    pass
+
 
 _WithNotebookSuffix = WithSuffix(".ipynb", case_sensitive=True)
 NotebookSource = Union[
diff --git a/bioimageio/spec/notebook/v0_3.py b/bioimageio/spec/notebook/v0_3.py
index 86114a086..020b70e63 100644
--- a/bioimageio/spec/notebook/v0_3.py
+++ b/bioimageio/spec/notebook/v0_3.py
@@ -5,12 +5,11 @@
 from .._internal.io import Sha256 as Sha256
 from .._internal.io_basics import AbsoluteFilePath as AbsoluteFilePath
 from .._internal.url import HttpUrl as HttpUrl
-from .._internal.validated_string import ValidatedString
 from ..generic.v0_3 import Author as Author
 from ..generic.v0_3 import BadgeDescr as BadgeDescr
 from ..generic.v0_3 import CiteEntry as CiteEntry
 from ..generic.v0_3 import Doi as Doi
-from ..generic.v0_3 import GenericDescrBase, ResourceIdAnno
+from ..generic.v0_3 import GenericDescrBase
 from ..generic.v0_3 import LinkedResource as LinkedResource
 from ..generic.v0_3 import Maintainer as Maintainer
 from ..generic.v0_3 import OrcidId as OrcidId
@@ -20,7 +19,9 @@
 from ..generic.v0_3 import Version as Version
 from .v0_2 import NotebookSource as NotebookSource
 
-NotebookId = ValidatedString[ResourceIdAnno]
+
+class NotebookId(ResourceId):
+    pass
 
 
 class NotebookDescr(GenericDescrBase, title="bioimage.io notebook specification"):
diff --git a/tests/test_internal/test_license_id.py b/tests/test_internal/test_license_id.py
index 57e1721b3..acbe4556e 100644
--- a/tests/test_internal/test_license_id.py
+++ b/tests/test_internal/test_license_id.py
@@ -8,7 +8,7 @@ def test_license_id():
     _ = LicenseId("MIT")
 
     with pytest.raises(ValidationError):
-        _ = LicenseId("not_a_valid_license_id")  # pyright: ignore[reportArgumentType]
+        _ = LicenseId("not_a_valid_license_id")
 
 
 def test_deprecated_license_id():
@@ -17,6 +17,4 @@ def test_deprecated_license_id():
     _ = DeprecatedLicenseId("AGPL-1.0")
 
     with pytest.raises(ValidationError):
-        _ = DeprecatedLicenseId(
-            "not_a_valid_license_id"  # pyright: ignore[reportArgumentType]
-        )
+        _ = DeprecatedLicenseId("not_a_valid_license_id")
diff --git a/tests/test_internal/test_validated_string.py b/tests/test_internal/test_validated_string.py
new file mode 100644
index 000000000..8be29eaee
--- /dev/null
+++ b/tests/test_internal/test_validated_string.py
@@ -0,0 +1,18 @@
+import annotated_types
+import pytest
+from pydantic import RootModel, ValidationError
+from typing_extensions import Annotated
+
+
+def test_valid_validated_string():
+    from bioimageio.spec._internal.validated_string import ValidatedString
+
+    class V(ValidatedString):
+        root_model = RootModel[Annotated[str, annotated_types.Predicate(str.islower)]]
+
+    out = V("abc")
+    assert isinstance(out, str)
+    assert out == "abc"
+
+    with pytest.raises(ValidationError):
+        _ = V("ABC")
diff --git a/tests/test_specific_reexports_generics.py b/tests/test_specific_reexports_generics.py
index 4baa2e152..ae9665d69 100644
--- a/tests/test_specific_reexports_generics.py
+++ b/tests/test_specific_reexports_generics.py
@@ -49,6 +49,7 @@
     "Predicate",
     "requests",
     "RestrictCharacters",
+    "RootModel",
     "Self",
     "Sequence",
     "settings",
@@ -63,6 +64,7 @@
     "v0_5",
     "validate_gh_user",
     "validate_suffix",
+    "ValidatedString",
     "validation_context_var",
     "ValidationInfo",
     "warn",
@@ -86,7 +88,6 @@ def get_members(m: ModuleType):
     "KNOWN_SPECIFIC_RESOURCE_TYPES",
     "ResourceDescrBase",
     "ResourceDescrType",
-    "ResourceId",
     "VALID_COVER_IMAGE_EXTENSIONS",
 }
 

From ea406292c774f0c872b0203db19e30f047fd1c26 Mon Sep 17 00:00:00 2001
From: fynnbe <thefynnbe@gmail.com>
Date: Wed, 20 Mar 2024 21:55:00 +0100
Subject: [PATCH 24/36] fix root_model annotations

---
 bioimageio/spec/_internal/io.py              |  3 ++-
 bioimageio/spec/_internal/license_id.py      |  6 ++++--
 bioimageio/spec/_internal/root_url.py        |  4 ++--
 bioimageio/spec/_internal/types.py           | 16 ++++++++++------
 bioimageio/spec/_internal/url.py             |  6 ++++--
 bioimageio/spec/generic/v0_2.py              |  4 +++-
 bioimageio/spec/generic/v0_3.py              | 15 +++++++++++++--
 bioimageio/spec/model/v0_5.py                |  8 ++++++--
 tests/test_internal/test_validated_string.py |  6 +++++-
 9 files changed, 49 insertions(+), 19 deletions(-)

diff --git a/bioimageio/spec/_internal/io.py b/bioimageio/spec/_internal/io.py
index 9689b468b..847c7c17c 100644
--- a/bioimageio/spec/_internal/io.py
+++ b/bioimageio/spec/_internal/io.py
@@ -10,6 +10,7 @@
 from pathlib import Path, PurePath
 from typing import (
     Any,
+    ClassVar,
     Dict,
     Generic,
     List,
@@ -76,7 +77,7 @@
 class Sha256(ValidatedString):
     """SHA-256 hash value"""
 
-    root_model = RootModel[
+    root_model: ClassVar[Type[RootModel[Any]]] = RootModel[
         Annotated[
             str,
             StringConstraints(
diff --git a/bioimageio/spec/_internal/license_id.py b/bioimageio/spec/_internal/license_id.py
index ece095492..cef093d17 100644
--- a/bioimageio/spec/_internal/license_id.py
+++ b/bioimageio/spec/_internal/license_id.py
@@ -1,3 +1,5 @@
+from typing import Any, ClassVar, Type
+
 from pydantic import RootModel
 
 from ._generated_spdx_license_literals import (
@@ -8,8 +10,8 @@
 
 
 class LicenseId(ValidatedString):
-    root_model = RootModel[LicenseIdLiteral]
+    root_model: ClassVar[Type[RootModel[Any]]] = RootModel[LicenseIdLiteral]
 
 
 class DeprecatedLicenseId(ValidatedString):
-    root_model = RootModel[DeprecatedLicenseIdLiteral]
+    root_model: ClassVar[Type[RootModel[Any]]] = RootModel[DeprecatedLicenseIdLiteral]
diff --git a/bioimageio/spec/_internal/root_url.py b/bioimageio/spec/_internal/root_url.py
index ed2d0c86c..c88e8ae97 100644
--- a/bioimageio/spec/_internal/root_url.py
+++ b/bioimageio/spec/_internal/root_url.py
@@ -1,6 +1,6 @@
 from __future__ import annotations
 
-from typing import Optional
+from typing import Any, ClassVar, Optional, Type
 from urllib.parse import urlsplit, urlunsplit
 
 import pydantic
@@ -12,7 +12,7 @@
 class RootHttpUrl(ValidatedString):
     """A 'URL folder', possibly an invalid http URL"""
 
-    root_model = RootModel[pydantic.HttpUrl]
+    root_model: ClassVar[Type[RootModel[Any]]] = RootModel[pydantic.HttpUrl]
     _validated: pydantic.HttpUrl
 
     @property
diff --git a/bioimageio/spec/_internal/types.py b/bioimageio/spec/_internal/types.py
index 6547043cc..1d8a930da 100644
--- a/bioimageio/spec/_internal/types.py
+++ b/bioimageio/spec/_internal/types.py
@@ -2,7 +2,7 @@
 
 from datetime import datetime
 from keyword import iskeyword
-from typing import Any, Sequence, TypeVar, Union
+from typing import Any, ClassVar, Sequence, Type, TypeVar, Union
 
 import annotated_types
 from dateutil.parser import isoparse
@@ -91,7 +91,9 @@ class Datetime(
 
 
 class Doi(ValidatedString):
-    root_model = RootModel[Annotated[str, StringConstraints(pattern=DOI_REGEX)]]
+    root_model: ClassVar[Type[RootModel[Any]]] = RootModel[
+        Annotated[str, StringConstraints(pattern=DOI_REGEX)]
+    ]
 
 
 FormatVersionPlaceholder = Literal["latest", "discover"]
@@ -103,26 +105,28 @@ class Doi(ValidatedString):
 
 
 class Identifier(ValidatedString):
-    root_model = RootModel[IdentifierAnno]
+    root_model: ClassVar[Type[RootModel[Any]]] = RootModel[IdentifierAnno]
 
 
 LowerCaseIdentifierAnno = Annotated[IdentifierAnno, annotated_types.LowerCase]
 
 
 class LowerCaseIdentifier(ValidatedString):
-    root_model = RootModel[LowerCaseIdentifierAnno]
+    root_model: ClassVar[Type[RootModel[Any]]] = RootModel[LowerCaseIdentifierAnno]
 
 
 class OrcidId(ValidatedString):
     """an ORCID identifier"""
 
-    root_model = RootModel[Annotated[str, AfterValidator(_validate_orcid_id)]]
+    root_model: ClassVar[Type[RootModel[Any]]] = RootModel[
+        Annotated[str, AfterValidator(_validate_orcid_id)]
+    ]
 
 
 class SiUnit(ValidatedString):
     """Si unit"""
 
-    root_model = RootModel[
+    root_model: ClassVar[Type[RootModel[Any]]] = RootModel[
         Annotated[
             str,
             StringConstraints(min_length=1, pattern=SI_UNIT_REGEX),
diff --git a/bioimageio/spec/_internal/url.py b/bioimageio/spec/_internal/url.py
index 8ecb47b3c..987d429ae 100644
--- a/bioimageio/spec/_internal/url.py
+++ b/bioimageio/spec/_internal/url.py
@@ -1,4 +1,4 @@
-from typing import Union
+from typing import Any, ClassVar, Type, Union
 
 import pydantic
 import requests
@@ -100,4 +100,6 @@ def _validate_url(url: Union[str, pydantic.HttpUrl]) -> pydantic.AnyUrl:
 
 
 class HttpUrl(RootHttpUrl):
-    root_model = RootModel[Annotated[pydantic.HttpUrl, AfterValidator(_validate_url)]]
+    root_model: ClassVar[Type[RootModel[Any]]] = RootModel[
+        Annotated[pydantic.HttpUrl, AfterValidator(_validate_url)]
+    ]
diff --git a/bioimageio/spec/generic/v0_2.py b/bioimageio/spec/generic/v0_2.py
index 436899156..b302d3bb0 100644
--- a/bioimageio/spec/generic/v0_2.py
+++ b/bioimageio/spec/generic/v0_2.py
@@ -2,12 +2,14 @@
 import string
 from typing import (
     Any,
+    ClassVar,
     Dict,
     List,
     Literal,
     Mapping,
     Optional,
     Sequence,
+    Type,
     TypeVar,
     Union,
 )
@@ -52,7 +54,7 @@
 
 
 class ResourceId(ValidatedString):
-    root_model = RootModel[
+    root_model: ClassVar[Type[RootModel[Any]]] = RootModel[
         Annotated[
             NotEmpty[str],
             AfterValidator(str.lower),  # convert upper case on the fly
diff --git a/bioimageio/spec/generic/v0_3.py b/bioimageio/spec/generic/v0_3.py
index 8eed0e542..58a9a6de0 100644
--- a/bioimageio/spec/generic/v0_3.py
+++ b/bioimageio/spec/generic/v0_3.py
@@ -2,7 +2,18 @@
 
 import string
 from functools import partial
-from typing import Any, Dict, List, Literal, Optional, Sequence, TypeVar, Union
+from typing import (
+    Any,
+    ClassVar,
+    Dict,
+    List,
+    Literal,
+    Optional,
+    Sequence,
+    Type,
+    TypeVar,
+    Union,
+)
 
 import annotated_types
 from annotated_types import Len, LowerCase, MaxLen, MinLen
@@ -65,7 +76,7 @@
 
 
 class ResourceId(ValidatedString):
-    root_model = RootModel[
+    root_model: ClassVar[Type[RootModel[Any]]] = RootModel[
         Annotated[
             NotEmpty[str],
             RestrictCharacters(string.ascii_lowercase + string.digits + "_-/."),
diff --git a/bioimageio/spec/model/v0_5.py b/bioimageio/spec/model/v0_5.py
index 9d209c0a4..6cf8d5950 100644
--- a/bioimageio/spec/model/v0_5.py
+++ b/bioimageio/spec/model/v0_5.py
@@ -180,11 +180,15 @@
 
 
 class TensorId(LowerCaseIdentifier):
-    root_model = RootModel[Annotated[LowerCaseIdentifierAnno, MaxLen(32)]]
+    root_model: ClassVar[Type[RootModel[Any]]] = RootModel[
+        Annotated[LowerCaseIdentifierAnno, MaxLen(32)]
+    ]
 
 
 class AxisId(LowerCaseIdentifier):
-    root_model = RootModel[Annotated[LowerCaseIdentifierAnno, MaxLen(16)]]
+    root_model: ClassVar[Type[RootModel[Any]]] = RootModel[
+        Annotated[LowerCaseIdentifierAnno, MaxLen(16)]
+    ]
 
 
 NonBatchAxisId = Annotated[AxisId, Predicate(lambda x: x != "batch")]
diff --git a/tests/test_internal/test_validated_string.py b/tests/test_internal/test_validated_string.py
index 8be29eaee..12f81fdb1 100644
--- a/tests/test_internal/test_validated_string.py
+++ b/tests/test_internal/test_validated_string.py
@@ -1,3 +1,5 @@
+from typing import Any, ClassVar, Type
+
 import annotated_types
 import pytest
 from pydantic import RootModel, ValidationError
@@ -8,7 +10,9 @@ def test_valid_validated_string():
     from bioimageio.spec._internal.validated_string import ValidatedString
 
     class V(ValidatedString):
-        root_model = RootModel[Annotated[str, annotated_types.Predicate(str.islower)]]
+        root_model: ClassVar[Type[RootModel[Any]]] = RootModel[
+            Annotated[str, annotated_types.Predicate(str.islower)]
+        ]
 
     out = V("abc")
     assert isinstance(out, str)

From 11b996afa730d65a3948b2f8d975d9451c661d40 Mon Sep 17 00:00:00 2001
From: fynnbe <thefynnbe@gmail.com>
Date: Thu, 21 Mar 2024 00:16:14 +0100
Subject: [PATCH 25/36] fix _ValidatedString.validated

---
 bioimageio/spec/_internal/validated_string.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/bioimageio/spec/_internal/validated_string.py b/bioimageio/spec/_internal/validated_string.py
index cb0666e43..519cd66ca 100644
--- a/bioimageio/spec/_internal/validated_string.py
+++ b/bioimageio/spec/_internal/validated_string.py
@@ -16,7 +16,7 @@ class ValidatedString(str):
 
     def __new__(cls, object: object):
         self = super().__new__(cls, object)
-        self._validated = cls.root_model.model_validate(self)
+        self._validated = cls.root_model.model_validate(str(self)).root
         return self
 
     @classmethod

From 33461525b3cec494a82d721a28370f27b48a56fb Mon Sep 17 00:00:00 2001
From: fynnbe <thefynnbe@gmail.com>
Date: Thu, 21 Mar 2024 00:47:30 +0100
Subject: [PATCH 26/36] fix test_specific_reexports_generics

---
 tests/test_specific_reexports_generics.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/tests/test_specific_reexports_generics.py b/tests/test_specific_reexports_generics.py
index ae9665d69..6eaf35a54 100644
--- a/tests/test_specific_reexports_generics.py
+++ b/tests/test_specific_reexports_generics.py
@@ -15,6 +15,7 @@
     "as_warning",
     "assert_never",
     "BioimageioYamlContent",
+    "ClassVar",
     "collections",
     "convert_from_older_format",
     "Converter",
@@ -55,6 +56,7 @@
     "settings",
     "string",
     "TAG_CATEGORIES",
+    "Type",
     "TypeVar",
     "Union",
     "V_suffix",

From 40f36a423aef0ce09b230e5a3cc3e7fe54298e1d Mon Sep 17 00:00:00 2001
From: fynnbe <thefynnbe@gmail.com>
Date: Thu, 21 Mar 2024 10:00:50 +0100
Subject: [PATCH 27/36] avoid pydantic warning

---
 tests/test_model/test_v0_4.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/tests/test_model/test_v0_4.py b/tests/test_model/test_v0_4.py
index acf5e7e40..590bda59a 100644
--- a/tests/test_model/test_v0_4.py
+++ b/tests/test_model/test_v0_4.py
@@ -329,7 +329,7 @@ def model_data():
                     description="Input 1",
                     data_type="float32",
                     axes="xyc",
-                    shape=(128, 128, 3),
+                    shape=[128, 128, 3],
                 ),
             ],
             outputs=[
@@ -338,7 +338,7 @@ def model_data():
                     description="Output 1",
                     data_type="float32",
                     axes="xyc",
-                    shape=(128, 128, 3),
+                    shape=[128, 128, 3],
                 ),
             ],
             name="Model",

From 830547c61afc5b9748633b3e4f69b24edb4fee8f Mon Sep 17 00:00:00 2001
From: fynnbe <thefynnbe@gmail.com>
Date: Thu, 21 Mar 2024 14:32:41 +0100
Subject: [PATCH 28/36] refactor internal bioimageio.yaml file name helpers

---
 bioimageio/spec/_internal/io.py         | 57 +++++++++++++++++++------
 bioimageio/spec/_internal/io_basics.py  |  4 +-
 bioimageio/spec/_internal/io_utils.py   | 35 ++-------------
 bioimageio/spec/_package.py             |  8 ++--
 bioimageio/spec/utils.py                |  2 +-
 tests/test_internal/test_file_source.py |  8 ++--
 tests/test_internal/test_types.py       |  8 +---
 7 files changed, 63 insertions(+), 59 deletions(-)

diff --git a/bioimageio/spec/_internal/io.py b/bioimageio/spec/_internal/io.py
index 847c7c17c..3c1726449 100644
--- a/bioimageio/spec/_internal/io.py
+++ b/bioimageio/spec/_internal/io.py
@@ -13,6 +13,7 @@
     ClassVar,
     Dict,
     Generic,
+    Iterable,
     List,
     Optional,
     Sequence,
@@ -23,6 +24,7 @@
     Union,
 )
 from urllib.parse import urlparse, urlsplit, urlunsplit
+from zipfile import ZipFile, is_zipfile
 
 import pooch
 import pydantic
@@ -53,6 +55,7 @@
 from .._internal._settings import settings
 from .._internal.io_basics import (
     ALL_BIOIMAGEIO_YAML_NAMES,
+    ALTERNATIVE_BIOIMAGEIO_YAML_NAMES,
     BIOIMAGEIO_YAML,
     AbsoluteDirectory,
     AbsoluteFilePath,
@@ -303,7 +306,7 @@ def validate(self, value: FileSource) -> FileSource:
 
 
 def wo_special_file_name(src: FileSource) -> FileSource:
-    if has_valid_rdf_name(src):
+    if has_valid_bioimageio_yaml_name(src):
         raise ValueError(
             f"'{src}' not allowed here as its filename is reserved to identify"
             + f" '{BIOIMAGEIO_YAML}' (or equivalent) files."
@@ -397,20 +400,50 @@ def _package(value: FileSource, info: SerializationInfo) -> Union[str, Path, Fil
 ]
 
 
-def has_valid_rdf_name(src: FileSource) -> bool:
-    return is_valid_rdf_name(extract_file_name(src))
+def has_valid_bioimageio_yaml_name(src: FileSource) -> bool:
+    return is_valid_bioimageio_yaml_name(extract_file_name(src))
 
 
-def is_valid_rdf_name(file_name: FileName) -> bool:
-    for special in ALL_BIOIMAGEIO_YAML_NAMES:
-        if file_name.endswith(special):
+def is_valid_bioimageio_yaml_name(file_name: FileName) -> bool:
+    for bioimageio_name in ALL_BIOIMAGEIO_YAML_NAMES:
+        if file_name == bioimageio_name or file_name.endswith("." + bioimageio_name):
             return True
 
     return False
 
 
-def ensure_has_valid_rdf_name(src: FileSource) -> FileSource:
-    if not has_valid_rdf_name(src):
+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 file_name in file_names:
+            if file_name == bioimageio_name or file_name.endswith(
+                "." + bioimageio_name
+            ):
+                return file_name
+
+    raise ValueError(
+        f"No {BIOIMAGEIO_YAML} found in {file_names}. (Looking for '{BIOIMAGEIO_YAML}'"
+        + " or or any of the alterntive file names:"
+        + f" {ALTERNATIVE_BIOIMAGEIO_YAML_NAMES}, or any file with an extension of"
+        + f"  those, e.g. 'anything.{BIOIMAGEIO_YAML}')."
+    )
+
+
+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_name(f.namelist())
+    else:
+        file_names = [p.name for p in path.glob("*")]
+
+    return identify_bioimageio_yaml_file_name(file_names)
+
+
+def ensure_has_valid_bioimageio_yaml_name(src: FileSource) -> FileSource:
+    if not has_valid_bioimageio_yaml_name(src):
         raise ValueError(
             f"'{src}' does not have a valid filename to identify"
             + f" '{BIOIMAGEIO_YAML}' (or equivalent) files."
@@ -419,8 +452,8 @@ def ensure_has_valid_rdf_name(src: FileSource) -> FileSource:
     return src
 
 
-def ensure_is_valid_rdf_name(file_name: FileName) -> FileName:
-    if not is_valid_rdf_name(file_name):
+def ensure_is_valid_bioimageio_yaml_name(file_name: FileName) -> FileName:
+    if not is_valid_bioimageio_yaml_name(file_name):
         raise ValueError(
             f"'{file_name}' is not a valid filename to identify"
             + f" '{BIOIMAGEIO_YAML}' (or equivalent) files."
@@ -448,14 +481,14 @@ def ensure_is_valid_rdf_name(file_name: FileName) -> FileName:
 class OpenedBioimageioYaml:
     content: BioimageioYamlContent
     original_root: Union[AbsoluteDirectory, RootHttpUrl]
-    original_file_name: str
+    original_file_name: FileName
 
 
 @dataclass
 class DownloadedFile:
     path: FilePath
     original_root: Union[AbsoluteDirectory, RootHttpUrl]
-    original_file_name: str
+    original_file_name: FileName
 
 
 class HashKwargs(TypedDict):
diff --git a/bioimageio/spec/_internal/io_basics.py b/bioimageio/spec/_internal/io_basics.py
index a2410298c..0c7c98169 100644
--- a/bioimageio/spec/_internal/io_basics.py
+++ b/bioimageio/spec/_internal/io_basics.py
@@ -8,6 +8,6 @@
 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")
+BIOIMAGEIO_YAML = "bioimageio.yaml"
+ALTERNATIVE_BIOIMAGEIO_YAML_NAMES = ("rdf.yaml", "model.yaml")
 ALL_BIOIMAGEIO_YAML_NAMES = (BIOIMAGEIO_YAML,) + ALTERNATIVE_BIOIMAGEIO_YAML_NAMES
diff --git a/bioimageio/spec/_internal/io_utils.py b/bioimageio/spec/_internal/io_utils.py
index 51a63e54d..1f85c4f48 100644
--- a/bioimageio/spec/_internal/io_utils.py
+++ b/bioimageio/spec/_internal/io_utils.py
@@ -2,7 +2,7 @@
 import warnings
 from contextlib import nullcontext
 from pathlib import Path
-from typing import IO, Any, Dict, Iterable, Mapping, Optional, TextIO, Union, cast
+from typing import IO, Any, Dict, Mapping, Optional, TextIO, Union, cast
 from zipfile import ZipFile, is_zipfile
 
 import numpy
@@ -11,8 +11,9 @@
 from ruyaml import YAML
 from typing_extensions import Unpack
 
+from bioimageio.spec._internal.io import find_bioimageio_yaml_file_name
+
 from .io import (
-    ALL_BIOIMAGEIO_YAML_NAMES,
     BIOIMAGEIO_YAML,
     BioimageioYamlContent,
     FileDescr,
@@ -21,7 +22,7 @@
     YamlValue,
     download,
 )
-from .io_basics import ALTERNATIVE_BIOIMAGEIO_YAML_NAMES, FileName
+from .io_basics import FileName
 from .types import FileSource, PermissiveFileSource
 
 yaml = YAML(typ="safe")
@@ -84,34 +85,6 @@ def open_bioimageio_yaml(
     return OpenedBioimageioYaml(content, root, downloaded.original_file_name)
 
 
-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:
-            if fname == bioimageio_name or fname.endswith(f".{bioimageio_name}"):
-                return fname
-
-    raise ValueError(
-        f"No {BIOIMAGEIO_YAML} found in {file_names}. (Looking for '{BIOIMAGEIO_YAML}'"
-        + " or or any of the alterntive file names:"
-        + f" {ALTERNATIVE_BIOIMAGEIO_YAML_NAMES}, or any file with an extension of"
-        + f"  those, e.g. 'anything.{BIOIMAGEIO_YAML}')."
-    )
-
-
-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_name(f.namelist())
-    else:
-        file_names = [p.name for p in path.glob("*")]
-
-    return identify_bioimageio_yaml_file_name(file_names)
-
-
 def unzip(
     zip_file: Union[FilePath, ZipFile],
     out_path: Optional[DirectoryPath] = None,
diff --git a/bioimageio/spec/_package.py b/bioimageio/spec/_package.py
index 910a8debf..c044a2b1f 100644
--- a/bioimageio/spec/_package.py
+++ b/bioimageio/spec/_package.py
@@ -1,7 +1,7 @@
 import collections.abc
-from io import BytesIO
 import re
 import shutil
+from io import BytesIO
 from pathlib import Path
 from tempfile import NamedTemporaryFile, mkdtemp
 from typing import IO, Dict, Literal, Optional, Sequence, Union, cast
@@ -16,7 +16,7 @@
     BioimageioYamlSource,
     YamlValue,
     download,
-    ensure_is_valid_rdf_name,
+    ensure_is_valid_bioimageio_yaml_name,
 )
 from ._internal.io_basics import BIOIMAGEIO_YAML, AbsoluteFilePath, FileName
 from ._internal.io_utils import open_bioimageio_yaml, write_yaml, write_zip
@@ -53,7 +53,9 @@ def get_resource_package_content(
         name=os_friendly_name, type=rd.type
     )
 
-    bioimageio_yaml_file_name = ensure_is_valid_rdf_name(bioimageio_yaml_file_name)
+    bioimageio_yaml_file_name = ensure_is_valid_bioimageio_yaml_name(
+        bioimageio_yaml_file_name
+    )
     content: Dict[FileName, Union[HttpUrl, AbsoluteFilePath]] = {}
     with PackagingContext(
         bioimageio_yaml_file_name=bioimageio_yaml_file_name, file_sources=content
diff --git a/bioimageio/spec/utils.py b/bioimageio/spec/utils.py
index 4cb57dd8a..d3ccbe855 100644
--- a/bioimageio/spec/utils.py
+++ b/bioimageio/spec/utils.py
@@ -1,5 +1,5 @@
 from ._internal.io import download as download
-from ._internal.io_utils import (
+from ._internal.io import (
     identify_bioimageio_yaml_file_name as identify_bioimageio_yaml_file_name,
 )
 from ._internal.io_utils import load_array as load_array
diff --git a/tests/test_internal/test_file_source.py b/tests/test_internal/test_file_source.py
index f82cb2b81..38eeaa2bc 100644
--- a/tests/test_internal/test_file_source.py
+++ b/tests/test_internal/test_file_source.py
@@ -15,13 +15,13 @@
     ],
 )
 def test_is_valid_rdf_name(name: FileName):
-    from bioimageio.spec._internal.io import is_valid_rdf_name
+    from bioimageio.spec._internal.io import is_valid_bioimageio_yaml_name
 
-    assert is_valid_rdf_name(name), name
+    assert is_valid_bioimageio_yaml_name(name), name
 
 
 @pytest.mark.parametrize("name", ["bioimageio.yml", "RDF.yaml", "smth.yaml"])
 def test_is_invalid_rdf_name(name: FileName):
-    from bioimageio.spec._internal.io import is_valid_rdf_name
+    from bioimageio.spec._internal.io import is_valid_bioimageio_yaml_name
 
-    assert not is_valid_rdf_name(name), name
+    assert not is_valid_bioimageio_yaml_name(name), name
diff --git a/tests/test_internal/test_types.py b/tests/test_internal/test_types.py
index b886d560b..73f0ab773 100644
--- a/tests/test_internal/test_types.py
+++ b/tests/test_internal/test_types.py
@@ -1,4 +1,3 @@
-import typing
 from datetime import datetime
 from pathlib import Path
 
@@ -70,7 +69,7 @@
     ],
 )
 def test_type_is_usable(name: str):
-    """check if a type can be instantiated or is a common Python type (e.g. Union or Literal)"""
+    """check if a type can be instantiated"""
     typ = getattr(types, name)
     if typ in TYPE_ARGS:
         args = TYPE_ARGS[typ]
@@ -80,10 +79,7 @@ def test_type_is_usable(name: str):
     elif isinstance(typ, str):
         pass  # ignore string constants
     else:
-        origin = typing.get_origin(typ)
-        assert origin in (dict, list, typing.Union, typing.Literal) or type(typ) in (
-            typing.TypeVar,
-        ), name
+        raise ValueError(f"No idea how to test {name} -> {typ}")
 
 
 @pytest.mark.parametrize("path", [Path(__file__), Path()])

From e4cd9762693fe5083042c3497a004198589598b8 Mon Sep 17 00:00:00 2001
From: fynnbe <thefynnbe@gmail.com>
Date: Thu, 21 Mar 2024 14:36:07 +0100
Subject: [PATCH 29/36] expose is_valid_bioimageio_yaml_name

---
 bioimageio/spec/utils.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/bioimageio/spec/utils.py b/bioimageio/spec/utils.py
index d3ccbe855..3f13bf38b 100644
--- a/bioimageio/spec/utils.py
+++ b/bioimageio/spec/utils.py
@@ -2,5 +2,6 @@
 from ._internal.io import (
     identify_bioimageio_yaml_file_name as identify_bioimageio_yaml_file_name,
 )
+from ._internal.io import is_valid_bioimageio_yaml_name as is_valid_bioimageio_yaml_name
 from ._internal.io_utils import load_array as load_array
 from ._internal.io_utils import save_array as save_array

From 7a52fe82a6c6d3129ebad708221c8f360eecf96a Mon Sep 17 00:00:00 2001
From: fynnbe <thefynnbe@gmail.com>
Date: Thu, 21 Mar 2024 14:56:59 +0100
Subject: [PATCH 30/36] include local badges in package

use InPackageIfLocalFileSource in badges.i.icon
---
 bioimageio/spec/_internal/io.py | 8 ++++++++
 bioimageio/spec/generic/v0_2.py | 5 +++--
 bioimageio/spec/generic/v0_3.py | 2 +-
 3 files changed, 12 insertions(+), 3 deletions(-)

diff --git a/bioimageio/spec/_internal/io.py b/bioimageio/spec/_internal/io.py
index 3c1726449..86890d0be 100644
--- a/bioimageio/spec/_internal/io.py
+++ b/bioimageio/spec/_internal/io.py
@@ -398,6 +398,14 @@ def _package(value: FileSource, info: SerializationInfo) -> Union[str, Path, Fil
     AfterValidator(wo_special_file_name),
     include_in_package_serializer,
 ]
+InPackageIfLocalFileSource = Union[
+    Annotated[
+        Union[FilePath, RelativeFilePath],
+        AfterValidator(wo_special_file_name),
+        include_in_package_serializer,
+    ],
+    Union[HttpUrl, pydantic.HttpUrl],
+]
 
 
 def has_valid_bioimageio_yaml_name(src: FileSource) -> bool:
diff --git a/bioimageio/spec/generic/v0_2.py b/bioimageio/spec/generic/v0_2.py
index b302d3bb0..9d09083f2 100644
--- a/bioimageio/spec/generic/v0_2.py
+++ b/bioimageio/spec/generic/v0_2.py
@@ -31,6 +31,7 @@
 from .._internal.field_warning import as_warning, issue_warning, warn
 from .._internal.io import (
     BioimageioYamlContent,
+    InPackageIfLocalFileSource,
     WithSuffix,
     YamlValue,
     include_in_package_serializer,
@@ -140,7 +141,7 @@ class BadgeDescr(Node, title="Custom badge"):
     """badge label to display on hover"""
 
     icon: Annotated[
-        Union[HttpUrl, None],
+        Optional[InPackageIfLocalFileSource],
         Field(examples=["https://colab.research.google.com/assets/colab-badge.svg"]),
     ] = None
     """badge icon"""
@@ -299,7 +300,7 @@ def _warn_empty_cite(cls, value: Any):
     """A URL to the Git repository where the resource is being developed."""
 
     icon: Union[
-        ImportantFileSource, Annotated[str, Len(min_length=1, max_length=2)], None
+        Annotated[str, Len(min_length=1, max_length=2)], ImportantFileSource, None
     ] = None
     """An icon for illustration"""
 
diff --git a/bioimageio/spec/generic/v0_3.py b/bioimageio/spec/generic/v0_3.py
index 58a9a6de0..47e2b5c8a 100644
--- a/bioimageio/spec/generic/v0_3.py
+++ b/bioimageio/spec/generic/v0_3.py
@@ -286,7 +286,7 @@ class GenericModelDescrBase(ResourceDescrBase):
     """A URL to the Git repository where the resource is being developed."""
 
     icon: Union[
-        ImportantFileSource, Annotated[str, Len(min_length=1, max_length=2)], None
+        Annotated[str, Len(min_length=1, max_length=2)], ImportantFileSource, None
     ] = None
     """An icon for illustration, e.g. on bioimage.io"""
 

From 879c33d88c86cca91ea691d10994f7c05cd44a54 Mon Sep 17 00:00:00 2001
From: fynnbe <thefynnbe@gmail.com>
Date: Thu, 21 Mar 2024 15:12:26 +0100
Subject: [PATCH 31/36] expose VALID_COVER_IMAGE_EXTENSIONS in subspecs

---
 bioimageio/spec/application/v0_2.py       | 1 +
 bioimageio/spec/application/v0_3.py       | 1 +
 bioimageio/spec/collection/v0_2.py        | 1 +
 bioimageio/spec/collection/v0_3.py        | 1 +
 bioimageio/spec/dataset/v0_2.py           | 1 +
 bioimageio/spec/dataset/v0_3.py           | 1 +
 bioimageio/spec/notebook/v0_2.py          | 1 +
 bioimageio/spec/notebook/v0_3.py          | 1 +
 tests/test_specific_reexports_generics.py | 2 +-
 9 files changed, 9 insertions(+), 1 deletion(-)

diff --git a/bioimageio/spec/application/v0_2.py b/bioimageio/spec/application/v0_2.py
index a0e9348c8..fae82093b 100644
--- a/bioimageio/spec/application/v0_2.py
+++ b/bioimageio/spec/application/v0_2.py
@@ -7,6 +7,7 @@
 from .._internal.io_basics import AbsoluteFilePath as AbsoluteFilePath
 from .._internal.types import ImportantFileSource
 from .._internal.url import HttpUrl as HttpUrl
+from ..generic.v0_2 import VALID_COVER_IMAGE_EXTENSIONS as VALID_COVER_IMAGE_EXTENSIONS
 from ..generic.v0_2 import AttachmentsDescr as AttachmentsDescr
 from ..generic.v0_2 import Author as Author
 from ..generic.v0_2 import BadgeDescr as BadgeDescr
diff --git a/bioimageio/spec/application/v0_3.py b/bioimageio/spec/application/v0_3.py
index 31c39b7b2..d6192e6be 100644
--- a/bioimageio/spec/application/v0_3.py
+++ b/bioimageio/spec/application/v0_3.py
@@ -9,6 +9,7 @@
 from .._internal.io_basics import AbsoluteFilePath as AbsoluteFilePath
 from .._internal.types import ImportantFileSource
 from .._internal.url import HttpUrl as HttpUrl
+from ..generic.v0_3 import VALID_COVER_IMAGE_EXTENSIONS as VALID_COVER_IMAGE_EXTENSIONS
 from ..generic.v0_3 import Author as Author
 from ..generic.v0_3 import BadgeDescr as BadgeDescr
 from ..generic.v0_3 import CiteEntry as CiteEntry
diff --git a/bioimageio/spec/collection/v0_2.py b/bioimageio/spec/collection/v0_2.py
index 3a4d10588..f2cbfb5f6 100644
--- a/bioimageio/spec/collection/v0_2.py
+++ b/bioimageio/spec/collection/v0_2.py
@@ -22,6 +22,7 @@
 from ..application import ApplicationDescr_v0_2, ApplicationDescr_v0_3
 from ..dataset import DatasetDescr_v0_2, DatasetDescr_v0_3
 from ..generic import GenericDescr_v0_2, GenericDescr_v0_3
+from ..generic.v0_2 import VALID_COVER_IMAGE_EXTENSIONS as VALID_COVER_IMAGE_EXTENSIONS
 from ..generic.v0_2 import AttachmentsDescr as AttachmentsDescr
 from ..generic.v0_2 import Author as Author
 from ..generic.v0_2 import BadgeDescr as BadgeDescr
diff --git a/bioimageio/spec/collection/v0_3.py b/bioimageio/spec/collection/v0_3.py
index f011a9713..a054c1943 100644
--- a/bioimageio/spec/collection/v0_3.py
+++ b/bioimageio/spec/collection/v0_3.py
@@ -32,6 +32,7 @@
 from ..application import ApplicationDescr_v0_2, ApplicationDescr_v0_3
 from ..dataset import DatasetDescr_v0_2, DatasetDescr_v0_3
 from ..generic import GenericDescr_v0_2, GenericDescr_v0_3
+from ..generic.v0_3 import VALID_COVER_IMAGE_EXTENSIONS as VALID_COVER_IMAGE_EXTENSIONS
 from ..generic.v0_3 import Author as Author
 from ..generic.v0_3 import BadgeDescr as BadgeDescr
 from ..generic.v0_3 import CiteEntry as CiteEntry
diff --git a/bioimageio/spec/dataset/v0_2.py b/bioimageio/spec/dataset/v0_2.py
index ca1a3ad73..13336ed59 100644
--- a/bioimageio/spec/dataset/v0_2.py
+++ b/bioimageio/spec/dataset/v0_2.py
@@ -3,6 +3,7 @@
 from .._internal.common_nodes import Node
 from .._internal.io_basics import AbsoluteFilePath as AbsoluteFilePath
 from .._internal.url import HttpUrl as HttpUrl
+from ..generic.v0_2 import VALID_COVER_IMAGE_EXTENSIONS as VALID_COVER_IMAGE_EXTENSIONS
 from ..generic.v0_2 import AttachmentsDescr as AttachmentsDescr
 from ..generic.v0_2 import Author as Author
 from ..generic.v0_2 import BadgeDescr as BadgeDescr
diff --git a/bioimageio/spec/dataset/v0_3.py b/bioimageio/spec/dataset/v0_3.py
index 39c183a4e..cd0fa13d3 100644
--- a/bioimageio/spec/dataset/v0_3.py
+++ b/bioimageio/spec/dataset/v0_3.py
@@ -7,6 +7,7 @@
 from .._internal.io import Sha256 as Sha256
 from .._internal.io_basics import AbsoluteFilePath as AbsoluteFilePath
 from .._internal.url import HttpUrl as HttpUrl
+from ..generic.v0_3 import VALID_COVER_IMAGE_EXTENSIONS as VALID_COVER_IMAGE_EXTENSIONS
 from ..generic.v0_3 import Author as Author
 from ..generic.v0_3 import BadgeDescr as BadgeDescr
 from ..generic.v0_3 import CiteEntry as CiteEntry
diff --git a/bioimageio/spec/notebook/v0_2.py b/bioimageio/spec/notebook/v0_2.py
index 9414c912d..a607a68cb 100644
--- a/bioimageio/spec/notebook/v0_2.py
+++ b/bioimageio/spec/notebook/v0_2.py
@@ -6,6 +6,7 @@
 from .._internal.io import WithSuffix
 from .._internal.io_basics import AbsoluteFilePath as AbsoluteFilePath
 from .._internal.url import HttpUrl
+from ..generic.v0_2 import VALID_COVER_IMAGE_EXTENSIONS as VALID_COVER_IMAGE_EXTENSIONS
 from ..generic.v0_2 import AttachmentsDescr as AttachmentsDescr
 from ..generic.v0_2 import Author as Author
 from ..generic.v0_2 import BadgeDescr as BadgeDescr
diff --git a/bioimageio/spec/notebook/v0_3.py b/bioimageio/spec/notebook/v0_3.py
index 020b70e63..ddefe1523 100644
--- a/bioimageio/spec/notebook/v0_3.py
+++ b/bioimageio/spec/notebook/v0_3.py
@@ -5,6 +5,7 @@
 from .._internal.io import Sha256 as Sha256
 from .._internal.io_basics import AbsoluteFilePath as AbsoluteFilePath
 from .._internal.url import HttpUrl as HttpUrl
+from ..generic.v0_3 import VALID_COVER_IMAGE_EXTENSIONS as VALID_COVER_IMAGE_EXTENSIONS
 from ..generic.v0_3 import Author as Author
 from ..generic.v0_3 import BadgeDescr as BadgeDescr
 from ..generic.v0_3 import CiteEntry as CiteEntry
diff --git a/tests/test_specific_reexports_generics.py b/tests/test_specific_reexports_generics.py
index 6eaf35a54..35086190b 100644
--- a/tests/test_specific_reexports_generics.py
+++ b/tests/test_specific_reexports_generics.py
@@ -32,6 +32,7 @@
     "ImportantFileSource",
     "include_in_package_serializer",
     "INFO",
+    "InPackageIfLocalFileSource",
     "issue_warning",
     "Len",
     "LicenseId",
@@ -90,7 +91,6 @@ def get_members(m: ModuleType):
     "KNOWN_SPECIFIC_RESOURCE_TYPES",
     "ResourceDescrBase",
     "ResourceDescrType",
-    "VALID_COVER_IMAGE_EXTENSIONS",
 }
 
 GENERIC_v0_2_MEMBERS = {

From 9690db3f7f33a29973b349c843a46e218a18452d Mon Sep 17 00:00:00 2001
From: fynnbe <thefynnbe@gmail.com>
Date: Thu, 21 Mar 2024 15:14:26 +0100
Subject: [PATCH 32/36] fix test_specific_reexports_generics

---
 tests/test_specific_reexports_generics.py | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/tests/test_specific_reexports_generics.py b/tests/test_specific_reexports_generics.py
index 35086190b..099c315c2 100644
--- a/tests/test_specific_reexports_generics.py
+++ b/tests/test_specific_reexports_generics.py
@@ -16,6 +16,7 @@
     "assert_never",
     "BioimageioYamlContent",
     "ClassVar",
+    "ClassVar",
     "collections",
     "convert_from_older_format",
     "Converter",
@@ -27,6 +28,7 @@
     "field_validator",
     "Field",
     "FileSource",
+    "FileSource",
     "Ge",
     "get_args",
     "ImportantFileSource",
@@ -48,10 +50,12 @@
     "NotEmpty",
     "Optional",
     "partial",
+    "PermissiveFileSource",
     "Predicate",
     "requests",
     "RestrictCharacters",
     "RootModel",
+    "S",
     "Self",
     "Sequence",
     "settings",

From d48430bd844d0f0bb8af264c79e0efa77405d38a Mon Sep 17 00:00:00 2001
From: fynnbe <thefynnbe@gmail.com>
Date: Thu, 21 Mar 2024 15:17:22 +0100
Subject: [PATCH 33/36] update license examples

(also debugging ci fails non-existing test_license_id_in_model)
---
 bioimageio/spec/generic/v0_2.py | 2 +-
 bioimageio/spec/generic/v0_3.py | 2 +-
 bioimageio/spec/model/v0_4.py   | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/bioimageio/spec/generic/v0_2.py b/bioimageio/spec/generic/v0_2.py
index 9d09083f2..a26e85a57 100644
--- a/bioimageio/spec/generic/v0_2.py
+++ b/bioimageio/spec/generic/v0_2.py
@@ -396,7 +396,7 @@ def _convert_from_older_format(
 
     license: Annotated[
         Optional[Union[LicenseId, DeprecatedLicenseId, str]],
-        Field(examples=["CC-BY-4.0", "MIT", "BSD-2-Clause"]),
+        Field(examples=["CC0-1.0", "MIT", "BSD-2-Clause"]),
     ] = None
     """A [SPDX license identifier](https://spdx.org/licenses/).
     We do not support custom license beyond the SPDX license list, if you need that please
diff --git a/bioimageio/spec/generic/v0_3.py b/bioimageio/spec/generic/v0_3.py
index 47e2b5c8a..1451dbdc8 100644
--- a/bioimageio/spec/generic/v0_3.py
+++ b/bioimageio/spec/generic/v0_3.py
@@ -235,7 +235,7 @@ class GenericModelDescrBase(ResourceDescrBase):
             LicenseId,
             "{value} is deprecated, see https://spdx.org/licenses/{value}.html",
         ),
-        Field(examples=["CC-BY-4.0", "MIT", "BSD-2-Clause"]),
+        Field(examples=["CC0-1.0", "MIT", "BSD-2-Clause"]),
     ]
     """A [SPDX license identifier](https://spdx.org/licenses/).
     We do not support custom license beyond the SPDX license list, if you need that please
diff --git a/bioimageio/spec/model/v0_4.py b/bioimageio/spec/model/v0_4.py
index e1316ab68..408c86759 100644
--- a/bioimageio/spec/model/v0_4.py
+++ b/bioimageio/spec/model/v0_4.py
@@ -900,7 +900,7 @@ class ModelDescr(GenericModelDescrBase, title="bioimage.io model specification")
     license: Annotated[
         Union[LicenseId, str],
         warn(LicenseId, "Unknown license id '{value}'."),
-        Field(examples=["CC-BY-4.0", "MIT", "BSD-2-Clause"]),
+        Field(examples=["CC0-1.0", "MIT", "BSD-2-Clause"]),
     ]
     """A [SPDX license identifier](https://spdx.org/licenses/).
     We do notsupport custom license beyond the SPDX license list, if you need that please

From eb4af738ef7a6b04c2855cd9e3eadbcbf3c1d296 Mon Sep 17 00:00:00 2001
From: fynnbe <thefynnbe@gmail.com>
Date: Thu, 21 Mar 2024 15:20:07 +0100
Subject: [PATCH 34/36] fix test_types

---
 tests/test_internal/test_types.py         | 5 +++++
 tests/test_specific_reexports_generics.py | 1 +
 2 files changed, 6 insertions(+)

diff --git a/tests/test_internal/test_types.py b/tests/test_internal/test_types.py
index 73f0ab773..fe18b3fbe 100644
--- a/tests/test_internal/test_types.py
+++ b/tests/test_internal/test_types.py
@@ -40,18 +40,23 @@
     "annotations",
     "Any",
     "BeforeValidator",
+    "ClassVar",
     "datetime",
     "field_validation",
+    "FileSource",
     "FormatVersionPlaceholder",  # a literal
     "ImportantFileSource",  # an annoated union
     "iskeyword",
     "isoparse",
     "Literal",
     "NotEmpty",
+    "PermissiveFileSource",
     "PlainSerializer",
     "RootModel",
+    "S",
     "Sequence",
     "StringConstraints",
+    "Type",
     "TypeVar",
     "typing",
     "Union",
diff --git a/tests/test_specific_reexports_generics.py b/tests/test_specific_reexports_generics.py
index 099c315c2..a40c2fc65 100644
--- a/tests/test_specific_reexports_generics.py
+++ b/tests/test_specific_reexports_generics.py
@@ -62,6 +62,7 @@
     "string",
     "TAG_CATEGORIES",
     "Type",
+    "Type",
     "TypeVar",
     "Union",
     "V_suffix",

From 7e6a6213e8f077ed357d8d21f47dd7a9218a329e Mon Sep 17 00:00:00 2001
From: fynnbe <thefynnbe@gmail.com>
Date: Thu, 21 Mar 2024 15:32:08 +0100
Subject: [PATCH 35/36] remove cyclic imports

---
 bioimageio/spec/_internal/field_validation.py | 8 ++++----
 bioimageio/spec/_internal/io_utils.py         | 3 +--
 bioimageio/spec/generic/v0_3.py               | 5 ++---
 bioimageio/spec/model/v0_4.py                 | 1 +
 bioimageio/spec/model/v0_5.py                 | 8 +++++---
 5 files changed, 13 insertions(+), 12 deletions(-)

diff --git a/bioimageio/spec/_internal/field_validation.py b/bioimageio/spec/_internal/field_validation.py
index 03956162a..b0298da90 100644
--- a/bioimageio/spec/_internal/field_validation.py
+++ b/bioimageio/spec/_internal/field_validation.py
@@ -12,10 +12,10 @@
 
 import requests
 
-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
+from ._settings import settings
+from .constants import KNOWN_GH_USERS, KNOWN_INVALID_GH_USERS
+from .field_warning import issue_warning
+from .validation_context import validation_context_var
 
 
 def is_valid_yaml_leaf_value(value: Any) -> bool:
diff --git a/bioimageio/spec/_internal/io_utils.py b/bioimageio/spec/_internal/io_utils.py
index 1f85c4f48..50afa5ecf 100644
--- a/bioimageio/spec/_internal/io_utils.py
+++ b/bioimageio/spec/_internal/io_utils.py
@@ -11,8 +11,6 @@
 from ruyaml import YAML
 from typing_extensions import Unpack
 
-from bioimageio.spec._internal.io import find_bioimageio_yaml_file_name
-
 from .io import (
     BIOIMAGEIO_YAML,
     BioimageioYamlContent,
@@ -21,6 +19,7 @@
     OpenedBioimageioYaml,
     YamlValue,
     download,
+    find_bioimageio_yaml_file_name,
 )
 from .io_basics import FileName
 from .types import FileSource, PermissiveFileSource
diff --git a/bioimageio/spec/generic/v0_3.py b/bioimageio/spec/generic/v0_3.py
index eeeb918b4..855701ace 100644
--- a/bioimageio/spec/generic/v0_3.py
+++ b/bioimageio/spec/generic/v0_3.py
@@ -20,9 +20,6 @@
 from pydantic import Field, RootModel, ValidationInfo, field_validator, model_validator
 from typing_extensions import Annotated
 
-from bioimageio.spec._internal.field_validation import validate_gh_user
-from bioimageio.spec._internal.validated_string import ValidatedString
-
 from .._internal.common_nodes import (
     Converter,
     Node,
@@ -31,6 +28,7 @@
 from .._internal.constants import (
     TAG_CATEGORIES,
 )
+from .._internal.field_validation import validate_gh_user
 from .._internal.field_warning import as_warning, warn
 from .._internal.io import (
     BioimageioYamlContent,
@@ -50,6 +48,7 @@
 )
 from .._internal.types import RelativeFilePath as RelativeFilePath
 from .._internal.url import HttpUrl as HttpUrl
+from .._internal.validated_string import ValidatedString
 from .._internal.validator_annotations import (
     AfterValidator,
     Predicate,
diff --git a/bioimageio/spec/model/v0_4.py b/bioimageio/spec/model/v0_4.py
index 408c86759..724e60f25 100644
--- a/bioimageio/spec/model/v0_4.py
+++ b/bioimageio/spec/model/v0_4.py
@@ -54,6 +54,7 @@
 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 VALID_COVER_IMAGE_EXTENSIONS as VALID_COVER_IMAGE_EXTENSIONS
 from ..dataset.v0_2 import DatasetDescr as DatasetDescr
 from ..dataset.v0_2 import LinkedDataset as LinkedDataset
 from ..generic.v0_2 import AttachmentsDescr as AttachmentsDescr
diff --git a/bioimageio/spec/model/v0_5.py b/bioimageio/spec/model/v0_5.py
index 51235dcc9..6171e3274 100644
--- a/bioimageio/spec/model/v0_5.py
+++ b/bioimageio/spec/model/v0_5.py
@@ -45,9 +45,6 @@
 )
 from typing_extensions import Annotated, LiteralString, Self, assert_never
 
-from bioimageio.spec._internal.validator_annotations import RestrictCharacters
-from bioimageio.spec.generic.v0_3 import ResourceId as ResourceId
-
 from .._internal.common_nodes import (
     Converter,
     InvalidDescr,
@@ -75,11 +72,15 @@
 from .._internal.types import NotEmpty as NotEmpty
 from .._internal.url import HttpUrl as HttpUrl
 from .._internal.validation_context import validation_context_var
+from .._internal.validator_annotations import RestrictCharacters
 from .._internal.version_type import Version as Version
 from .._internal.warning_levels import INFO
 from ..dataset.v0_3 import DatasetDescr as DatasetDescr
 from ..dataset.v0_3 import LinkedDataset as LinkedDataset
 from ..dataset.v0_3 import Uploader as Uploader
+from ..generic.v0_3 import (
+    VALID_COVER_IMAGE_EXTENSIONS as VALID_COVER_IMAGE_EXTENSIONS,
+)
 from ..generic.v0_3 import Author as Author
 from ..generic.v0_3 import BadgeDescr as BadgeDescr
 from ..generic.v0_3 import CiteEntry as CiteEntry
@@ -94,6 +95,7 @@
 from ..generic.v0_3 import Maintainer as Maintainer
 from ..generic.v0_3 import OrcidId as OrcidId
 from ..generic.v0_3 import RelativeFilePath as RelativeFilePath
+from ..generic.v0_3 import ResourceId as ResourceId
 from .v0_4 import Author as _Author_v0_4
 from .v0_4 import BinarizeDescr as _BinarizeDescr_v0_4
 from .v0_4 import CallableFromDepencency as CallableFromDepencency

From 1e299397ba5b22f74a5b3e20b7ad6a4136aa5c9f Mon Sep 17 00:00:00 2001
From: fynnbe <thefynnbe@gmail.com>
Date: Thu, 21 Mar 2024 15:32:55 +0100
Subject: [PATCH 36/36] fix test_license_id_in_model

---
 tests/test_internal/test_license_id.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/tests/test_internal/test_license_id.py b/tests/test_internal/test_license_id.py
index f917a237a..a3cee8b25 100644
--- a/tests/test_internal/test_license_id.py
+++ b/tests/test_internal/test_license_id.py
@@ -24,7 +24,6 @@ class Model(BaseModel):
 
     out = Model.model_validate({"lid": "CC-BY-4.0"}).lid
     assert isinstance(out, LicenseId)
-    assert not isinstance(out, str)
 
 
 def test_deprecated_license_id():