Zarr3

.github/workflows/tests.yaml

@@ -11,7 +11,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.10", "3.11", "3.12"]
+        python-version: ["3.11", "3.12", "3.13"]
         resolution: ["highest", "lowest-direct"]
 
     services:

.github/workflows/mypy.yaml → .github/workflows/ty.yaml

@@ -1,15 +1,15 @@
-name: mypy
+name: ty
 
 on: [push, pull_request]
 
 jobs:
   static-analysis:
-    name: Python mypy
+    name: Python ty
     runs-on: ubuntu-latest
     steps:
       - name: Setup checkout
         uses: actions/checkout@master
       - name: Install uv
         uses: astral-sh/setup-uv@main
-      - name: mypy
-        run: uv run --extra dev mypy funlib/persistence tests
+      - name: ty
+        run: uv run --extra dev ty check src tests

.gitignore

@@ -130,3 +130,5 @@ dmypy.json
 .vscode/
 
 *.sw[pmno]
+daisy_logs
+uv.lock

README.md

@@ -1,6 +1,6 @@
 [![tests](https://github.com/funkelab/funlib.persistence/actions/workflows/tests.yaml/badge.svg)](https://github.com/funkelab/funlib.persistence/actions/workflows/tests.yaml)
 [![ruff](https://github.com/funkelab/funlib.persistence/actions/workflows/ruff.yaml/badge.svg)](https://github.com/funkelab/funlib.persistence/actions/workflows/ruff.yaml)
-[![mypy](https://github.com/funkelab/funlib.persistence/actions/workflows/mypy.yaml/badge.svg)](https://github.com/funkelab/funlib.persistence/actions/workflows/mypy.yaml)
+[![ty](https://github.com/funkelab/funlib.persistence/actions/workflows/ty.yaml/badge.svg)](https://github.com/funkelab/funlib.persistence/actions/workflows/ty.yaml)
 [![pypi](https://github.com/funkelab/funlib.persistence/actions/workflows/publish.yaml/badge.svg)](https://pypi.org/project/funlib.persistence/)
 
 # funlib.persistence

pyproject.toml

@@ -13,25 +13,21 @@ authors = [
 ]
 dynamic = ['version']
 
-requires-python = ">=3.10"
+requires-python = ">=3.11"
 classifiers = ["Programming Language :: Python :: 3"]
 keywords = []
 
 dependencies = [
-    "zarr>=2,<3",
-    # ImportError: cannot import name 'cbuffer_sizes' from 'numcodecs.blosc'
-    # We can pin zarr to >2.18.7 but then we have to drop python 3.10
-    # pin numcodecs to avoid breaking change
-    "numcodecs>0.13,<0.16.0",
-    "iohub>=0.2.0b0",
+    "zarr>=3,<4",
+    "iohub>=0.3.0a5",
     "funlib.geometry>=0.3.0",
     "networkx>=3.0.0",
     "pymongo>=4.0.0",
     "numpy>=2.0.0",
     "pydantic>=2.0.0",
     "dask>=2024.0.0",
     "toml>=0.10.0",
-    "psycopg2-binary>=2.9.5",
+    "psycopg2-binary>=2.9.11",
 ]
 
 [tool.setuptools.dynamic]
@@ -40,10 +36,10 @@ version = { attr = "funlib.persistence.__version__" }
 [project.optional-dependencies]
 dev = [
     "coverage>=7.7.1",
-    "mypy>=1.15.0",
     "pytest>=8.3.5",
     "pytest-mock>=3.14.0",
     "ruff>=0.11.2",
+    "ty>=0.0.16",
     "types-networkx",
     "types-psycopg2",
     "types-toml",
@@ -56,10 +52,8 @@ lint.select = ["F", "W", "I001"]
 [tool.setuptools.package-data]
 "funlib.persistence" = ["py.typed"]
 
-[tool.mypy]
-explicit_package_bases = true
-
 # # module specific overrides
 [[tool.mypy.overrides]]
 module = ["zarr.*", "iohub.*"]
 ignore_missing_imports = true
+

funlib/persistence/__init__.py → src/funlib/persistence/__init__.py

@@ -1,4 +1,4 @@
 from .arrays import Array, open_ds, prepare_ds, open_ome_ds, prepare_ome_ds  # noqa
 
-__version__ = "0.6.1"
+__version__ = "0.7.0"
 __version_info__ = tuple(int(i) for i in __version__.split("."))

funlib/persistence/arrays/array.py → src/funlib/persistence/arrays/array.py

@@ -6,9 +6,8 @@
 import dask.array as da
 import numpy as np
 from dask.array.optimization import fuse_slice
-from zarr import Array as ZarrArray
-
 from funlib.geometry import Coordinate, Roi
+from zarr import Array as ZarrArray
 
 from .freezable import Freezable
 from .lazy_ops import LazyOp
@@ -135,7 +134,7 @@ def attrs(self) -> dict:
 
     @property
     def chunk_shape(self) -> Coordinate:
-        return Coordinate(self.data.chunksize)
+        return Coordinate(self.data.chunksize)  # ty: ignore[unresolved-attribute]
 
     def uncollapsed_dims(self, physical: bool = False) -> list[bool]:
         """
@@ -344,18 +343,21 @@ def __getitem__(self, key) -> np.ndarray:
         else:
             return self.data[key].compute()
 
-    def __setitem__(self, key, value: np.ndarray):
-        """Set the data of this array within the given ROI.
+    def __setitem__(self, key: Roi | slice | tuple, value: np.ndarray | float | int):
+        """Set the data of this array.
 
         Args:
 
-            key (`class:Roi`):
+            key (`class:Roi` or any numpy compatible key):
 
-                The ROI to write to.
+                The region to write to. Can be a `Roi` for world-unit indexing,
+                or any numpy-compatible key (e.g. ``np.s_[:]``, a slice, a tuple
+                of slices).
 
-            value (``ndarray``):
+            value (``ndarray`` or scalar):
 
-                The value to write.
+                The value to write. Can be a numpy array or a scalar that will
+                be broadcast.
         """
 
         if self.is_writeable:
@@ -474,7 +476,7 @@ def _is_slice(self, lazy_op: LazyOp, writeable: bool = False) -> bool:
         elif isinstance(lazy_op, list) and all([isinstance(a, int) for a in lazy_op]):
             return True
         elif isinstance(lazy_op, tuple) and all(
-            [self._is_slice(a, writeable) for a in lazy_op]
+            [self._is_slice(a, writeable) for a in lazy_op]  # type: ignore[arg-type]  # ty can't narrow parameterized tuple iteration
         ):
             return True
         elif (
@@ -508,7 +510,7 @@ def validate(self, strict: bool = False):
             )
 
     def to_pixel_space(
-        self, world_loc: Roi | Coordinate | Sequence[int | float]
+        self, world_loc: Roi | Coordinate | Sequence[int | float] | np.ndarray
     ) -> Roi | Coordinate | np.ndarray:
         """Convert a point or roi in world space into the pixel space of this array.
         Works on sequences of floats by returning a numpy array that is not guaranteed
@@ -539,7 +541,7 @@ def to_pixel_space(
             )
 
     def to_world_space(
-        self, pixel_loc: Roi | Coordinate | Sequence[int | float]
+        self, pixel_loc: Roi | Coordinate | Sequence[int | float] | np.ndarray
     ) -> Roi | Coordinate:
         """Convert a point or roi from pixel space in this array to the world
         coordinate system defined by this array's roi and voxel size.