skip redundant testing and Merge pull request #715 from bioimage-io/dev

fix packaging to same folder and improve logging

Author: FynnBe

.github/workflows/build.yml

@@ -188,11 +188,6 @@ jobs:
           pip --version
           pip install --upgrade build
           pip install .
-          pip install pytest
-      - name: Test with pytest
-        run: pytest --disable-pytest-warnings
-      - name: Check version submodule imports
-        run: python scripts/generate_version_submodule_imports.py check
       - name: Check if there is a parent commit
         id: check-parent-commit
         run: |

bioimageio/spec/__init__.py

@@ -1,9 +1,12 @@
 """
 .. include:: ../../README.md
 """
+# ruff: noqa: E402
 
-__version__ = "0.5.5.0"
+__version__ = "0.5.5.1"
+from loguru import logger
 
+logger.disable("bioimageio.spec")
 
 from . import (
     application,

bioimageio/spec/_internal/_settings.py

@@ -13,7 +13,9 @@
 from .root_url import RootHttpUrl
 
 
-class Settings(BaseSettings, extra="ignore"):
+class Settings(
+    BaseSettings, extra="ignore", allow_inf_nan=False, validate_assignment=True
+):
     """environment variables for bioimageio.spec"""
 
     model_config = SettingsConfigDict(

bioimageio/spec/_internal/io_utils.py

@@ -287,6 +287,16 @@ def write_content_to_zip(
             else:
                 reader = get_reader(file)
 
+            if (
+                isinstance(reader.original_root, ZipFile)
+                and reader.original_root.filename == zip.filename
+                and reader.original_file_name == arc_name
+            ):
+                logger.debug(
+                    f"Not copying {reader.original_root}/{reader.original_file_name} to itself."
+                )
+                continue
+
             with zip.open(arc_name, "w") as dest:
                 shutil.copyfileobj(reader, dest, 1024 * 8)
 

bioimageio/spec/_package.py

@@ -188,7 +188,23 @@ def save_bioimageio_package_as_folder(
     for name, src in package_content.items():
         if isinstance(src, collections.abc.Mapping):
             write_yaml(src, output_path / name)
+        elif (
+            isinstance(src.original_root, Path)
+            and src.original_root / src.original_file_name
+            == (output_path / name).resolve()
+        ):
+            logger.debug(
+                f"Not copying {src.original_root / src.original_file_name} to itself."
+            )
         else:
+            if isinstance(src.original_root, Path):
+                logger.debug(
+                    f"Copying from path {src.original_root / src.original_file_name} to {output_path / name}."
+                )
+            else:
+                logger.debug(
+                    f"Copying {src.original_root}/{src.original_file_name} to {output_path / name}."
+                )
             with (output_path / name).open("wb") as dest:
                 _ = shutil.copyfileobj(src, dest)
 

changelog.md

@@ -10,6 +10,10 @@ In this file we log both:
 
 This changelog includes implementation details and my reference the [changes to the Resource Description Format](#changes-to-the-resource-description-format), e.g. in entry [bioimageio.spec 0.5.2](#bioimageiospec-052).
 
+#### bioimageio.spec 0.5.5.1
+
+- fix package export to the same directory as model source (avoid 'deleting' files by overwriting them in-place)
+
 #### bioimageio.spec 0.5.5.0
 
 - added programmatic `uplaod` (alpha stage)