feature/migrate-writers

bioio/__init__.py

@@ -1,4 +1,4 @@
-# -*- coding: utf-8 -*-
+#!/usr/bin/env python
 
 """Top-level package for bioio."""
 

bioio/bio_image.py

@@ -1156,7 +1156,17 @@ def save(
         ids in each Image's name attribute but IDs will be generated. The order of the
         scenes will be the same (or whatever order was specified / provided).
         """
-        from .writers import OmeTiffWriter
+        import bioio.writers as _writers  # type: ignore[attr-defined]
+
+        OmeTiffWriter = getattr(_writers, "OmeTiffWriter", None)
+
+        if OmeTiffWriter is None:
+            log.warning(
+                "TIFF writing support (OmeTiffWriter) is not available. "
+                "To enable it, install the plugin:\n"
+                "    pip install bioio-ome-tiff"
+            )
+            return
 
         # Get all parameters as dict of lists, or static because of unchanging values
         datas: List[biob.types.ArrayLike] = []
@@ -1165,15 +1175,11 @@ def save(
         image_names: List[Optional[str]] = []
         physical_pixel_sizes: List[biob.types.PhysicalPixelSizes] = []
 
-        # Get selected scenes / handle None scenes
         if select_scenes is None:
             select_scenes = self.scenes
 
-        # Iter through scenes to get data
         for scene in select_scenes:
             self.set_scene(scene)
-
-            # Append this scene details
             datas.append(self.dask_data)
             dim_orders.append(self.dims.order)
             channel_names.append(self.channel_names)

bioio/tests/__init__.py

@@ -1,3 +1,3 @@
-# -*- coding: utf-8 -*-
+#!/usr/bin/env python
 
 """Unit test package for bioio."""

bioio/tests/dummy-plugin/dummy_plugin/writer.py

@@ -0,0 +1,22 @@
+from typing import Any
+
+import bioio_base as biob
+from bioio_base.writer import Writer
+
+
+class DummyWriter(Writer):
+    """
+    A dummy writer for testing bioio.writers entry-point discovery.
+    """
+
+    @staticmethod
+    def save(
+        data: biob.types.ArrayLike,
+        uri: biob.types.PathLike,
+        dim_order: str = biob.dimensions.DEFAULT_DIMENSION_ORDER,
+        **kwargs: Any,
+    ) -> None:
+        """
+        Stub implementation that deliberately isn’t implemented.
+        """
+        raise NotImplementedError("DummyWriter.save is a stub")

bioio/tests/dummy-plugin/pyproject.toml

@@ -47,6 +47,9 @@ test = [
 [project.entry-points."bioio.readers"]
 dummy-plugin = "dummy_plugin"
 
+[project.entry-points."bioio.writers"]
+DummyWriter = "dummy_plugin.writer:DummyWriter"
+
 # build settings
 # https://setuptools.pypa.io/en/latest/userguide/pyproject_config.html
 [tool.setuptools]

bioio/tests/test_writer.py

@@ -0,0 +1,28 @@
+from importlib.metadata import entry_points
+
+import pytest
+
+
+def test_dummy_writer_discovery_and_api(dummy_plugin: str) -> None:
+    # Entry-point registration
+    eps = entry_points(group="bioio.writers")
+    names = {ep.name for ep in eps}
+    assert "DummyWriter" in names, f"found: {sorted(names)}"
+
+    # Public API (__all__)
+    import bioio.writers as pkg
+
+    assert "DummyWriter" in getattr(pkg, "__all__", [])
+
+    # Import works (dynamic, so ignore mypy attr-defined error)
+    from bioio.writers import DummyWriter  # type: ignore[attr-defined]
+
+    assert DummyWriter.__name__ == "DummyWriter"
+
+
+def test_dummy_writer_save_stub(dummy_plugin: str) -> None:
+    # The save() stub should raise NotImplementedError
+    from bioio.writers import DummyWriter  # type: ignore[attr-defined]
+
+    with pytest.raises(NotImplementedError):
+        DummyWriter.save(data=[1], uri="unused", dim_order="XYZ")