avoid circular imports

Author: FynnBe

bioimageio/core/__init__.py

@@ -2,7 +2,6 @@
 .. include:: ../../README.md
 """
 
-from bioimageio.core.stat_measures import Stat
 from bioimageio.spec import (
     build_description,
     dump_description,
@@ -42,6 +41,7 @@
 from .prediction import predict, predict_many
 from .sample import Sample
 from .stat_calculators import compute_dataset_measures
+from .stat_measures import Stat
 from .tensor import Tensor
 from .utils import VERSION
 

bioimageio/core/_resource_tests.py

@@ -6,7 +6,6 @@
 import numpy as np
 from loguru import logger
 
-from bioimageio.core.sample import Sample
 from bioimageio.spec import (
     InvalidDescr,
     ResourceDescr,
@@ -28,6 +27,7 @@
 from ._prediction_pipeline import create_prediction_pipeline
 from .axis import AxisId, BatchSize
 from .digest_spec import get_test_inputs, get_test_outputs
+from .sample import Sample
 from .utils import VERSION
 
 

bioimageio/core/cli.py

@@ -44,40 +44,34 @@
 from tqdm import tqdm
 from typing_extensions import assert_never
 
-from bioimageio.core import (
-    MemberId,
-    Sample,
-    __version__,
-    create_prediction_pipeline,
-)
-from bioimageio.core.commands import (
+from bioimageio.spec import AnyModelDescr, InvalidDescr, load_description
+from bioimageio.spec._internal.types import NotEmpty
+from bioimageio.spec.dataset import DatasetDescr
+from bioimageio.spec.model import ModelDescr, v0_4, v0_5
+from bioimageio.spec.notebook import NotebookDescr
+from bioimageio.spec.utils import download, ensure_description_is_model
+
+from .commands import (
     WeightFormatArgAll,
     WeightFormatArgAny,
     package,
     test,
     validate_format,
 )
-from bioimageio.core.common import SampleId
-from bioimageio.core.digest_spec import get_member_ids, load_sample_for_model
-from bioimageio.core.io import load_dataset_stat, save_dataset_stat, save_sample
-from bioimageio.core.proc_setup import (
+from .common import MemberId, SampleId
+from .digest_spec import get_member_ids, load_sample_for_model
+from .io import load_dataset_stat, save_dataset_stat, save_sample
+from .prediction import create_prediction_pipeline
+from .proc_setup import (
     DatasetMeasure,
     Measure,
     MeasureValue,
     StatsCalculator,
     get_required_dataset_measures,
 )
-from bioimageio.core.stat_measures import Stat
-from bioimageio.spec import (
-    AnyModelDescr,
-    InvalidDescr,
-    load_description,
-)
-from bioimageio.spec._internal.types import NotEmpty
-from bioimageio.spec.dataset import DatasetDescr
-from bioimageio.spec.model import ModelDescr, v0_4, v0_5
-from bioimageio.spec.notebook import NotebookDescr
-from bioimageio.spec.utils import download, ensure_description_is_model
+from .sample import Sample
+from .stat_measures import Stat
+from .utils import VERSION
 
 yaml = YAML(typ="safe")
 
@@ -633,8 +627,8 @@ def run(self):
 Bioimageio.__doc__ += f"""
 
 library versions:
-  bioimageio.core {__version__}
-  bioimageio.spec {__version__}
+  bioimageio.core {VERSION}
+  bioimageio.spec {VERSION}
 
 spec format versions:
         model RDF {ModelDescr.implemented_format_version}

bioimageio/core/commands.py

@@ -3,11 +3,10 @@
 
 import sys
 from pathlib import Path
-from typing import List, Optional, Sequence, Union
+from typing import Optional, Sequence, Union
 
 from typing_extensions import Literal
 
-from bioimageio.core import test_description
 from bioimageio.spec import (
     InvalidDescr,
     ResourceDescr,
@@ -16,6 +15,8 @@
 )
 from bioimageio.spec.model.v0_5 import WeightsFormat
 
+from ._resource_tests import test_description
+
 WeightFormatArgAll = Literal[WeightsFormat, "all"]
 WeightFormatArgAny = Literal[WeightsFormat, "any"]
 

bioimageio/core/dataset.py

@@ -1,5 +1,5 @@
 from typing import Iterable
 
-from bioimageio.core.sample import Sample
+from .sample import Sample
 
 Dataset = Iterable[Sample]

bioimageio/core/digest_spec.py

@@ -23,9 +23,6 @@
 from numpy.typing import NDArray
 from typing_extensions import Unpack, assert_never
 
-from bioimageio.core.common import MemberId, PerMember, SampleId
-from bioimageio.core.io import load_tensor
-from bioimageio.core.sample import Sample
 from bioimageio.spec._internal.io import resolve_and_extract
 from bioimageio.spec._internal.io_utils import HashKwargs
 from bioimageio.spec.common import FileSource
@@ -41,6 +38,7 @@
 from .axis import AxisId, AxisInfo, AxisLike, PerAxis
 from .block_meta import split_multiple_shapes_into_blocks
 from .common import Halo, MemberId, PerMember, SampleId, TotalNumberOfBlocks
+from .io import load_tensor
 from .sample import (
     LinearSampleAxisTransform,
     Sample,

bioimageio/core/io.py

@@ -1,20 +1,18 @@
 import collections.abc
-from os import PathLike
 from pathlib import Path
 from typing import Any, Mapping, Optional, Sequence, Union
 
-import imageio
 from imageio.v3 import imread, imwrite
 from loguru import logger
 from numpy.typing import NDArray
 from pydantic import BaseModel, ConfigDict, TypeAdapter
 
-from bioimageio.core.common import PerMember
-from bioimageio.core.stat_measures import DatasetMeasure, MeasureValue
 from bioimageio.spec.utils import load_array, save_array
 
-from .axis import Axis, AxisLike
+from .axis import AxisLike
+from .common import PerMember
 from .sample import Sample
+from .stat_measures import DatasetMeasure, MeasureValue
 from .tensor import Tensor
 
 

bioimageio/core/prediction.py

@@ -16,15 +16,15 @@
 from numpy.typing import NDArray
 from tqdm import tqdm
 
-from bioimageio.core.axis import AxisId
-from bioimageio.core.io import save_sample
 from bioimageio.spec import load_description
 from bioimageio.spec.common import PermissiveFileSource
 from bioimageio.spec.model import v0_4, v0_5
 
 from ._prediction_pipeline import PredictionPipeline, create_prediction_pipeline
+from .axis import AxisId
 from .common import MemberId, PerMember
 from .digest_spec import create_sample_for_model
+from .io import save_sample
 from .sample import Sample
 from .tensor import Tensor
 

bioimageio/core/proc_ops.py

@@ -16,13 +16,13 @@
 import xarray as xr
 from typing_extensions import Self, assert_never
 
-from bioimageio.core.block import Block
-from bioimageio.core.sample import Sample, SampleBlock, SampleBlockWithOrigin
 from bioimageio.spec.model import v0_4, v0_5
 
 from ._op_base import BlockedOperator, Operator
 from .axis import AxisId, PerAxis
+from .block import Block
 from .common import DTypeStr, MemberId
+from .sample import Sample, SampleBlock, SampleBlockWithOrigin
 from .stat_calculators import StatsCalculator
 from .stat_measures import (
     DatasetMean,

bioimageio/core/proc_setup.py

@@ -11,14 +11,12 @@
 
 from typing_extensions import assert_never
 
-from bioimageio.core.common import MemberId
-from bioimageio.core.digest_spec import get_member_ids
 from bioimageio.spec.model import AnyModelDescr, v0_4, v0_5
 from bioimageio.spec.model.v0_5 import TensorId
 
+from .digest_spec import get_member_ids
 from .proc_ops import (
     AddKnownDatasetStats,
-    EnsureDtype,
     Processing,
     UpdateStats,
     get_proc_class,