Clean up imports and use full relative paths

.gitattributes

@@ -1,2 +1,5 @@
+# Normalize all text files to LF on commit
+* text=auto eol=lf
+
 # SCM syntax highlighting & preventing 3-way merges
 pixi.lock merge=binary linguist-language=YAML linguist-generated=true

.gitignore

@@ -70,6 +70,7 @@ target/
 .idea/
 venv/
 .vscode/
+.venv*/
 
 # IPython Notebook
 .ipynb_checkpoints

src/ndevio/__init__.py

@@ -5,19 +5,21 @@
 except ImportError:
     __version__ = 'unknown'
 
-from .utils import helpers
-
-# Type stub for lazy import - lets type checkers know nImage exists
 if TYPE_CHECKING:
     from .nimage import nImage as nImage
+    from .utils import helpers as helpers
 
 
-def __getattr__(name: str):
-    """Lazily import nImage to speed up package import."""
+def __getattr__(name: str) -> object:
+    """Lazily import heavy submodules to speed up package import."""
     if name == 'nImage':
         from .nimage import nImage
 
         return nImage
+    if name == 'helpers':
+        from .utils import helpers
+
+        return helpers
     raise AttributeError(f'module {__name__!r} has no attribute {name!r}')
 
 

src/ndevio/_napari_reader.py

@@ -4,13 +4,11 @@
 from functools import partial
 from typing import TYPE_CHECKING
 
-from ndev_settings import get_settings
-
-from .nimage import nImage
-
 if TYPE_CHECKING:
     from napari.types import LayerDataTuple, PathLike, ReaderFunction
 
+    from .nimage import nImage
+
 logger = logging.getLogger(__name__)
 
 
@@ -40,6 +38,8 @@ def napari_get_reader(
         The reader function for the given path
     """
 
+    from ndev_settings import get_settings
+
     settings = get_settings()
 
     open_first_scene_only = (
@@ -93,6 +93,8 @@ def napari_reader_function(
     """
     from bioio_base.exceptions import UnsupportedFileFormatError
 
+    from .nimage import nImage
+
     try:
         img = nImage(path)  # nImage handles preferred reader and fallback
     except UnsupportedFileFormatError:
@@ -125,7 +127,7 @@ def _open_scene_container(path: PathLike, img: nImage) -> None:
 
     import napari
 
-    from .widgets import DELIMITER, nImageSceneWidget
+    from .widgets._scene_widget import DELIMITER, nImageSceneWidget
 
     viewer = napari.current_viewer()
     viewer.window.add_dock_widget(
@@ -155,7 +157,7 @@ def _open_plugin_installer(path: PathLike) -> None:
     from bioio_base.exceptions import UnsupportedFileFormatError
 
     from .bioio_plugins._manager import ReaderPluginManager
-    from .widgets import PluginInstallerWidget
+    from .widgets._plugin_install_widget import PluginInstallerWidget
 
     # Get viewer, handle case where no viewer available
     viewer = napari.current_viewer()

src/ndevio/napari.yaml

@@ -10,28 +10,28 @@ contributions:
       python_name: ndevio._napari_reader:napari_get_reader
       title: Open file with ndevio
     - id: ndevio.make_plugin_installer_widget
-      python_name: ndevio.widgets:PluginInstallerWidget
+      python_name: ndevio.widgets._plugin_install_widget:PluginInstallerWidget
       title: Install BioIO Reader Plugins
     - id: ndevio.make_utilities_widget
-      python_name: ndevio.widgets:UtilitiesContainer
+      python_name: ndevio.widgets._utilities_container:UtilitiesContainer
       title: I/O Utilities
     - id: ndevio.make_ndev_logo
-      python_name: ndevio.sampledata:ndev_logo
+      python_name: ndevio.sampledata._sample_data:ndev_logo
       title: Load ndev logo
     - id: ndevio.make_scratch_assay
-      python_name: ndevio.sampledata:scratch_assay
+      python_name: ndevio.sampledata._sample_data:scratch_assay
       title: Load scratch assay data
     - id: ndevio.make_neocortex
-      python_name: ndevio.sampledata:neocortex
+      python_name: ndevio.sampledata._sample_data:neocortex
       title: Load neocortex data
     - id: ndevio.make_neuron_raw
-      python_name: ndevio.sampledata:neuron_raw
+      python_name: ndevio.sampledata._sample_data:neuron_raw
       title: Load raw neuron data
     - id: ndevio.make_neuron_labels
-      python_name: ndevio.sampledata:neuron_labels
+      python_name: ndevio.sampledata._sample_data:neuron_labels
       title: Load neuron labels data
     - id: ndevio.make_neuron_labels_processed
-      python_name: ndevio.sampledata:neuron_labels_processed
+      python_name: ndevio.sampledata._sample_data:neuron_labels_processed
       title: Load processed neuron labels data
   readers:
     - command: ndevio.get_reader

src/ndevio/nimage.py

@@ -7,8 +7,6 @@
 from typing import TYPE_CHECKING
 
 from bioio import BioImage
-from bioio_base.reader import Reader
-from bioio_base.types import ImageLike
 
 from .bioio_plugins._manager import raise_unsupported_with_suggestions
 from .utils._layer_utils import (

src/ndevio/sampledata/__init__.py

@@ -1,19 +1 @@
 """Sample data for ndevio and the ndev-kit ecosystem."""
-
-from ndevio.sampledata._sample_data import (
-    ndev_logo,
-    neocortex,
-    neuron_labels,
-    neuron_labels_processed,
-    neuron_raw,
-    scratch_assay,
-)
-
-__all__ = [
-    'ndev_logo',
-    'neocortex',
-    'neuron_labels',
-    'neuron_labels_processed',
-    'neuron_raw',
-    'scratch_assay',
-]

src/ndevio/sampledata/_sample_data.py

@@ -10,12 +10,6 @@
 from pathlib import Path
 from typing import TYPE_CHECKING
 
-import pooch
-from bioio_imageio import Reader as ImageIOReader
-from bioio_ome_tiff import Reader as OmeTiffReader
-
-from ndevio import nImage
-
 if TYPE_CHECKING:
     from napari.types import LayerDataTuple
 
@@ -24,6 +18,10 @@
 
 def ndev_logo() -> list[LayerDataTuple]:
     """Load the ndev logo image."""
+    from bioio_imageio import Reader as ImageIOReader
+
+    from ..nimage import nImage
+
     return nImage(
         SAMPLE_DIR / 'ndev-logo.png',
         reader=ImageIOReader,
@@ -32,6 +30,11 @@ def ndev_logo() -> list[LayerDataTuple]:
 
 def scratch_assay() -> list[LayerDataTuple]:
     """Load scratch assay data with labeled nuclei and cytoplasm."""
+    import pooch
+    from bioio_ome_tiff import Reader as OmeTiffReader
+
+    from ..nimage import nImage
+
     scratch_assay_raw_path = pooch.retrieve(
         url='doi:10.5281/zenodo.17845346/scratch-assay-labeled-10T-2Ch.tiff',
         known_hash='md5:2b98c4ea18cd741a1545e59855348a2f',
@@ -58,6 +61,11 @@ def scratch_assay() -> list[LayerDataTuple]:
 
 def neocortex() -> list[LayerDataTuple]:
     """Load neocortex 3-channel image data."""
+    import pooch
+    from bioio_ome_tiff import Reader as OmeTiffReader
+
+    from ..nimage import nImage
+
     neocortex_raw_path = pooch.retrieve(
         url='doi:10.5281/zenodo.17845346/neocortex-3Ch.tiff',
         known_hash='md5:eadc3fac751052461fb2e5f3c6716afa',
@@ -75,6 +83,11 @@ def neuron_raw() -> list[LayerDataTuple]:
 
     This sample is downloaded from Zenodo if not present locally.
     """
+    import pooch
+    from bioio_ome_tiff import Reader as OmeTiffReader
+
+    from ..nimage import nImage
+
     neuron_raw_path = pooch.retrieve(
         url='doi:10.5281/zenodo.17845346/neuron-4Ch_raw.tiff',
         known_hash='md5:5d3e42bca2085e8588b6f23cf89ba87c',
@@ -94,6 +107,10 @@ def neuron_raw() -> list[LayerDataTuple]:
 
 def neuron_labels() -> list[LayerDataTuple]:
     """Load neuron labels data."""
+    from bioio_ome_tiff import Reader as OmeTiffReader
+
+    from ..nimage import nImage
+
     return nImage(
         SAMPLE_DIR / 'neuron-4Ch_labels.tiff',
         reader=OmeTiffReader,
@@ -104,6 +121,10 @@ def neuron_labels() -> list[LayerDataTuple]:
 
 def neuron_labels_processed() -> list[LayerDataTuple]:
     """Load processed neuron labels data."""
+    from bioio_ome_tiff import Reader as OmeTiffReader
+
+    from ..nimage import nImage
+
     return nImage(
         SAMPLE_DIR / 'neuron-4Ch_labels_processed.tiff',
         reader=OmeTiffReader,

src/ndevio/widgets/__init__.py

@@ -1,14 +1 @@
 """Widgets for ndevio package."""
-
-from ..bioio_plugins._manager import ReaderPluginManager
-from ._plugin_install_widget import PluginInstallerWidget
-from ._scene_widget import DELIMITER, nImageSceneWidget
-from ._utilities_container import UtilitiesContainer
-
-__all__ = [
-    'PluginInstallerWidget',
-    'nImageSceneWidget',
-    'UtilitiesContainer',
-    'DELIMITER',
-    'ReaderPluginManager',
-]

tests/test_nimage.py

@@ -42,6 +42,40 @@ def test_nImage_zarr(resources_dir: Path):
     assert img.data.shape == (1, 1, 2, 4, 4)
 
 
+def test_nImage_zarr_trailing_slash(resources_dir: Path):
+    """Test that a string path with a trailing slash is handled correctly.
+
+    Regression test: bioio's extension-based reader detection fails when the
+    path ends with '/', e.g. 'store.zarr/'. nImage strips the slash on init.
+    See https://github.com/ndev-kit/ndevio/issues/XX
+    """
+    path_with_slash = str(resources_dir / ZARR) + '/'
+    img = nImage(path_with_slash)
+    assert img.data is not None
+    # path stored without the trailing slash
+    assert not img.path.endswith('/')
+    assert img.path == str(resources_dir / ZARR)
+    assert img.data.shape == (1, 1, 2, 4, 4)
+
+
+@pytest.mark.network
+def test_nImage_remote_zarr_trailing_slash():
+    """Test that a remote Zarr URL with a trailing slash is read correctly.
+
+    Regression test: 'https://...9846152.zarr/' crashed with
+    'Reader ndevio returned no data' because the trailing slash prevented
+    bioio from matching the '*.zarr' extension pattern.
+    """
+    remote_zarr = (
+        'https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.4/idr0048A/9846152.zarr/'
+    )
+    img = nImage(remote_zarr)
+    assert img._is_remote
+    assert not img.path.endswith('/')
+    assert img.path == remote_zarr.rstrip('/')
+    assert img.xarray_dask_data is not None
+
+
 @pytest.mark.network
 def test_nImage_remote_zarr():
     """Test that nImage can read a remote Zarr file."""

tests/test_sampledata/test_sampledata.py

@@ -4,7 +4,7 @@
 
 import pytest
 
-from ndevio.sampledata import (
+from ndevio.sampledata._sample_data import (
     ndev_logo,
     neocortex,
     neuron_labels,

tests/test_widgets/test_plugin_installer_widget.py

@@ -16,7 +16,7 @@ class TestPluginInstallerWidget:
 
     def test_standalone_mode(self):
         """Test widget in standalone mode - no path, shows generic title."""
-        from ndevio.widgets import PluginInstallerWidget
+        from ndevio.widgets._plugin_install_widget import PluginInstallerWidget
 
         widget = PluginInstallerWidget()
 
@@ -27,7 +27,7 @@ def test_standalone_mode(self):
     def test_error_mode_with_path(self):
         """Test widget in error mode - has path, preselects suggested plugin."""
         from ndevio.bioio_plugins._manager import ReaderPluginManager
-        from ndevio.widgets import PluginInstallerWidget
+        from ndevio.widgets._plugin_install_widget import PluginInstallerWidget
 
         # Mock installed plugins to NOT include bioio-czi
         # This simulates the error case where file can't be read
@@ -48,7 +48,7 @@ def test_error_mode_with_path(self):
 
     def test_install_button_behavior(self):
         """Test install button: queues installation and updates status."""
-        from ndevio.widgets import PluginInstallerWidget
+        from ndevio.widgets._plugin_install_widget import PluginInstallerWidget
 
         widget = PluginInstallerWidget()
         widget._plugin_select.value = 'bioio-imageio'
@@ -64,7 +64,7 @@ def test_install_button_behavior(self):
 
     def test_install_without_selection_shows_error(self):
         """Test that clicking install with no selection shows error."""
-        from ndevio.widgets import PluginInstallerWidget
+        from ndevio.widgets._plugin_install_widget import PluginInstallerWidget
 
         widget = PluginInstallerWidget()
         widget._plugin_select.value = None