Zarr python v3 [DO NOT MERGE]

.github/workflows/ci.yml

@@ -51,7 +51,7 @@ jobs:
           python -m pip install -U pip
           # if running a cron job, we add the --pre flag to test against pre-releases
           python -m pip install .[test] ${{ github.event_name == 'schedule' && '--pre' || ''  }}
-      
+
       - name: Restore shared data cache
         id: cache-data
         uses: actions/cache@v4
@@ -79,6 +79,7 @@ jobs:
           update_existing: true
 
       - name: Coverage
+        if: success() && matrix.platform == 'ubuntu-latest'
         uses: codecov/codecov-action@v5
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
@@ -118,4 +119,4 @@ jobs:
       - uses: softprops/action-gh-release@v2
         with:
           generate_release_notes: true
-          files: './dist/*'
+          files: "./dist/*"

CHANGELOG.md

@@ -1,9 +1,27 @@
 # Changelog
 
+## [v0.5.0]
+
+### Features
+- Add support for OME-NGFF v0.5
+- Move to zarr-python v3
+- API to delete labels and tables from OME-Zarr containers and HCS plates.
+
+### API Breaking Changes
+
+- New `Roi` models, now supporting arbitrary axes.
+- The `compressor` argument has been renamed to `compressors` in all relevant functions and methods to reflect the support for multiple compressors in zarr v3.
+- The `version` argument has been renamed to `ngff_version` in all relevant functions and methods to specify the OME-NGFF version.
+- Remove the `parallel_safe` argument from all zarr related functions and methods. The locking mechanism is now handled internally and only depends on the 
+`cache`.
+- Remove the unused `parent` argument from `ZarrGroupHandler`.
+- Internal changes to `ZarrGroupHandler` to support cleanup unused apis.
+- Remove `ngio_logger` in favor of standard warnings module.
+
 ## [v0.4.6]
 
 ### Bug Fixes
-- Fix channel selection from `wavelenght_id`
+- Fix channel selection from `wavelength_id`
 - Fix table opening mode to stop wrtiting groups when opening in append mode.
 
 ## [v0.4.5]

pyproject.toml

@@ -35,8 +35,8 @@ classifiers = [
 dependencies = [
     "numpy",
     "filelock",
-    "zarr<3",
-    "anndata>=0.8.0,<0.11.4",      # To be removed when we transition to zarr v3
+    "zarr>3",
+    "anndata",
     "pydantic",
     "pandas>=1.2.0",
     "requests",
@@ -54,14 +54,23 @@ dependencies = [
 # https://peps.python.org/pep-0621/#dependencies-optional-dependencies
 # "extras" (e.g. for `pip install .[test]`)
 [project.optional-dependencies]
-test = ["pytest", "pytest-cov", "scikit-image"]
+test = [
+    "pytest",
+    "pytest-cov",
+    "scikit-image",
+    "moto[server]",
+    "boto",
+    "pytest_httpserver",
+    "devtools",
+    "s3fs",
+]
 
 dev = [
+    "zarrs",
     "Pympler",
     "napari",
     "pyqt5",
     "matplotlib",
-    "devtools",
     "notebook",
     "mypy",
     "pdbpp",        # https://github.com/pdbpp/pdbpp
@@ -155,7 +164,9 @@ minversion = "7.0"
 testpaths = ["tests"]
 filterwarnings = [
     "error",
-    "ignore::FutureWarning", # TODO remove after zarr-python v3 
+    "ignore::zarr.errors.ZarrUserWarning", # required for anndata
+    "ignore::UserWarning",                 # from ngio.utils._zarr_utils
+    "ignore::DeprecationWarning",          # temporary ignore deprecation warnings
 ]
 addopts = [
     "-vv",
@@ -224,6 +235,7 @@ test13 = { features = ["py13", "test"], solve-group = "py13" }
 
 # dev env
 dev = { features = ["dev", "test"], solve-group = "py11" }
+test = { features = ["test"], solve-group = "py11" }
 
 [tool.pixi.tasks]
 serve_docs = "mkdocs serve"

src/ngio/__init__.py

@@ -9,7 +9,7 @@
 __author__ = "Lorenzo Cerrone"
 __email__ = "[email protected]"
 
-from ngio.common import Dimensions, Roi, RoiPixels
+from ngio.common import Dimensions, Roi, RoiSlice
 from ngio.hcs import (
     OmeZarrPlate,
     OmeZarrWell,
@@ -37,6 +37,7 @@
     NgffVersions,
     PixelSize,
 )
+from ngio.utils import NgioSupportedStore, StoreOrGroup
 
 __all__ = [
     "AxesSetup",
@@ -47,12 +48,14 @@
     "ImageInWellPath",
     "Label",
     "NgffVersions",
+    "NgioSupportedStore",
     "OmeZarrContainer",
     "OmeZarrPlate",
     "OmeZarrWell",
     "PixelSize",
     "Roi",
-    "RoiPixels",
+    "RoiSlice",
+    "StoreOrGroup",
     "create_empty_ome_zarr",
     "create_empty_plate",
     "create_empty_well",

src/ngio/common/__init__.py

@@ -2,22 +2,27 @@
 
 from ngio.common._dimensions import Dimensions
 from ngio.common._masking_roi import compute_masking_roi
-from ngio.common._pyramid import consolidate_pyramid, init_empty_pyramid, on_disk_zoom
-from ngio.common._roi import (
-    Roi,
-    RoiPixels,
+from ngio.common._pyramid import (
+    ChunksLike,
+    ImagePyramidBuilder,
+    ShardsLike,
+    consolidate_pyramid,
+    on_disk_zoom,
 )
+from ngio.common._roi import Roi, RoiSlice
 from ngio.common._zoom import InterpolationOrder, dask_zoom, numpy_zoom
 
 __all__ = [
+    "ChunksLike",
     "Dimensions",
+    "ImagePyramidBuilder",
     "InterpolationOrder",
     "Roi",
-    "RoiPixels",
+    "RoiSlice",
+    "ShardsLike",
     "compute_masking_roi",
     "consolidate_pyramid",
     "dask_zoom",
-    "init_empty_pyramid",
     "numpy_zoom",
     "on_disk_zoom",
 ]

src/ngio/common/_masking_roi.py

@@ -7,7 +7,7 @@
 import scipy.ndimage as ndi
 from dask.delayed import delayed
 
-from ngio.common._roi import Roi, RoiPixels
+from ngio.common._roi import Roi
 from ngio.ome_zarr_meta import PixelSize
 from ngio.utils import NgioValueError
 
@@ -135,52 +135,23 @@ def compute_masking_roi(
     rois = []
     for label, slice_ in slices.items():
         if len(slice_) == 2:
-            min_t, max_t = None, None
-            min_z, max_z = None, None
-            min_y, min_x = slice_[0].start, slice_[1].start
-            max_y, max_x = slice_[0].stop, slice_[1].stop
+            slices = {"y": slice_[0], "x": slice_[1]}
         elif len(slice_) == 3:
-            min_t, max_t = None, None
-            min_z, min_y, min_x = slice_[0].start, slice_[1].start, slice_[2].start
-            max_z, max_y, max_x = slice_[0].stop, slice_[1].stop, slice_[2].stop
+            slices = {"z": slice_[0], "y": slice_[1], "x": slice_[2]}
         elif len(slice_) == 4:
-            min_t, min_z, min_y, min_x = (
-                slice_[0].start,
-                slice_[1].start,
-                slice_[2].start,
-                slice_[3].start,
-            )
-            max_t, max_z, max_y, max_x = (
-                slice_[0].stop,
-                slice_[1].stop,
-                slice_[2].stop,
-                slice_[3].stop,
-            )
+            slices = {
+                "t": slice_[0],
+                "z": slice_[1],
+                "y": slice_[2],
+                "x": slice_[3],
+            }
         else:
             raise ValueError("Invalid slice length.")
 
-        if max_t is None:
-            t_length = None
-        else:
-            t_length = max_t - min_t
-
-        if max_z is None:
-            z_length = None
-        else:
-            z_length = max_z - min_z
-
-        roi = RoiPixels(
-            name=str(label),
-            x_length=max_x - min_x,
-            y_length=max_y - min_y,
-            z_length=z_length,
-            t_length=t_length,
-            x=min_x,
-            y=min_y,
-            z=min_z,
-            label=label,
+        roi = Roi.from_values(
+            name=str(label), slices=slices, label=label, space="pixel"
         )
 
-        roi = roi.to_roi(pixel_size)
+        roi = roi.to_world(pixel_size=pixel_size)
         rois.append(roi)
     return rois