add docstinrgs and annotations

Author: FynnBe

bioimageio/core/_settings.py

@@ -10,11 +10,12 @@
 
 
 class Settings(SpecSettings):
-    """environment variables"""
+    """environment variables for bioimageio.spec and bioimageio.core"""
 
     keras_backend: Annotated[
         Literal["torch", "tensorflow", "jax"], Field(alias="KERAS_BACKEND")
     ] = "torch"
 
 
 settings = Settings()
+"""parsed environment variables for bioimageio.spec and bioimageio.core"""

bioimageio/core/digest_spec.py

@@ -190,8 +190,8 @@ class IO_SampleBlockMeta(NamedTuple):
 
 
 def get_input_halo(model: v0_5.ModelDescr, output_halo: PerMember[PerAxis[Halo]]):
-    """returns which halo input tensors need to be divided into blocks with such that
-    `output_halo` can be cropped from their outputs without intorducing gaps."""
+    """returns which halo input tensors need to be divided into blocks with, such that
+    `output_halo` can be cropped from their outputs without introducing gaps."""
     input_halo: Dict[MemberId, Dict[AxisId, Halo]] = {}
     outputs = {t.id: t for t in model.outputs}
     all_tensors = {**{t.id: t for t in model.inputs}, **outputs}
@@ -221,8 +221,10 @@ def get_input_halo(model: v0_5.ModelDescr, output_halo: PerMember[PerAxis[Halo]]
     return input_halo
 
 
-def get_block_transform(model: v0_5.ModelDescr):
-    """returns how a model's output tensor shapes relate to its input shapes"""
+def get_block_transform(
+    model: v0_5.ModelDescr,
+) -> PerMember[PerAxis[Union[LinearSampleAxisTransform, int]]]:
+    """returns how a model's output tensor shapes relates to its input shapes"""
     ret: Dict[MemberId, Dict[AxisId, Union[LinearSampleAxisTransform, int]]] = {}
     batch_axis_trf = None
     for ipt in model.inputs:

bioimageio/core/sample.py

@@ -293,8 +293,10 @@ def get_transformed_meta(
 
 @dataclass
 class SampleBlockWithOrigin(SampleBlock):
+    """A `SampleBlock` with a reference (`origin`) to the whole `Sample`"""
+
     origin: Sample
-    """the sample this sample black was taken from"""
+    """the sample this sample block was taken from"""
 
 
 class _ConsolidatedMemberBlocks:
@@ -330,7 +332,7 @@ def sample_block_generator(
     *,
     origin: Sample,
     pad_mode: PadMode,
-):
+) -> Iterable[SampleBlockWithOrigin]:
     for member_blocks in blocks:
         cons = _ConsolidatedMemberBlocks(member_blocks)
         yield SampleBlockWithOrigin(