Merge pull request #657 from bioimage-io/cleanup

Cleanup

bioimageio/spec/_internal/docs_utils.py → scripts/docs_utils.py

@@ -10,13 +10,14 @@ def get_ref_url(
 ) -> str:
     """get github url with line range fragment to reference implementation from non-raw github file url
 
-    example:
-    >>> get_ref_url(
-    ...     "class",
-    ...     "Binarize",
-    ...     "https://github.com/bioimage-io/core-bioimage-io-python/blob/main/bioimageio/core/prediction_pipeline/_processing.py"
-    ... )
-    'https://github.com/bioimage-io/core-bioimage-io-python/blob/main/bioimageio/core/prediction_pipeline/_processing.py#L120-L127'
+    Example:
+        >>> get_ref_url(
+        ...     "class",
+        ...     "Binarize",
+        ...     "https://github.com/bioimage-io/core-bioimage-io-python/blob/main/bioimageio/core/prediction_pipeline/_processing.py"
+        ... )
+        'https://github.com/bioimage-io/core-bioimage-io-python/blob/main/bioimageio/core/prediction_pipeline/_processing.py#L120-L127'
+
     """
     # hotfix to handle requests not available in pyodide, see
     # https://github.com/bioimage-io/bioimage.io/issues/216#issuecomment-1012422194

tests/test_package.py

@@ -1,7 +1,6 @@
 import io
 import shutil
 from pathlib import Path
-from tempfile import TemporaryDirectory
 
 from deepdiff import DeepDiff
 
@@ -54,34 +53,31 @@ def test_save_bioimageio_package_to_stream_default(unet2d_path: Path):
     assert isinstance(stream, io.BytesIO)
 
 
-def test_save_bioimageio_package_as_folder(unet2d_path: Path):
+def test_save_bioimageio_package_as_folder(unet2d_path: Path, tmp_path: Path):
     from bioimageio.spec import load_description, save_bioimageio_package_as_folder
 
-    with TemporaryDirectory() as tmp_dir:
-        tmp_dir = Path(tmp_dir)
-
-        package_folder = tmp_dir / "package"
-        _ = save_bioimageio_package_as_folder(unet2d_path, output_path=package_folder)
-
-        # load package
-        model = load_description(package_folder)
-        assert isinstance(model, v0_5.ModelDescr)
-
-        # alter package
-        doc = model.documentation
-        assert isinstance(doc, v0_5.RelativeFilePath)
-        new_doc = f"copy_{doc}"
-        shutil.move(str(package_folder / str(doc)), str(package_folder / new_doc))
-        model.documentation = package_folder / new_doc
-
-        # export altered package
-        altered_package = tmp_dir / "altered_package"
-        altered_package = save_bioimageio_package_as_folder(
-            model, output_path=altered_package, weights_priority_order=["onnx"]
-        )
-        assert (altered_package / new_doc).exists(), altered_package / new_doc
-
-        # load altered package
-        reloaded_model = load_description(altered_package)
-        assert isinstance(reloaded_model, v0_5.ModelDescr)
-        assert str(reloaded_model.documentation).startswith("copy_")
+    package_folder = tmp_path / "package"
+    _ = save_bioimageio_package_as_folder(unet2d_path, output_path=package_folder)
+
+    # load package
+    model = load_description(package_folder)
+    assert isinstance(model, v0_5.ModelDescr)
+
+    # alter package
+    doc = model.documentation
+    assert isinstance(doc, v0_5.RelativeFilePath)
+    new_doc = f"copy_{doc}"
+    shutil.move(str(package_folder / str(doc)), str(package_folder / new_doc))
+    model.documentation = package_folder / new_doc
+
+    # export altered package
+    altered_package = tmp_path / "altered_package"
+    altered_package = save_bioimageio_package_as_folder(
+        model, output_path=altered_package, weights_priority_order=["onnx"]
+    )
+    assert (altered_package / new_doc).exists(), altered_package / new_doc
+
+    # load altered package
+    reloaded_model = load_description(altered_package)
+    assert isinstance(reloaded_model, v0_5.ModelDescr)
+    assert str(reloaded_model.documentation).startswith("copy_")