feat: Added flexible backends with the Zarr(s)-Python and Tensorstore support.

.github/workflows/docs.yml

@@ -15,7 +15,7 @@ jobs:
       - uses: actions/checkout@v5
       - uses: astral-sh/setup-uv@v7
         with:
-          python-version: "3.11"
+          python-version: "3.13"
           enable-cache: true
       - run: uv sync --group doc
       - run: uv run zensical build --clean

.github/workflows/pr.yml

@@ -22,7 +22,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.11", "3.12", "3.13"]
+        python-version: ["3.12", "3.13", "3.14"]
 
     steps:
       - uses: actions/checkout@v4
@@ -47,7 +47,7 @@ jobs:
       - uses: actions/checkout@v4
       - uses: astral-sh/setup-uv@v7
         with:
-          python-version: "3.11"
+          python-version: "3.12"
           enable-cache: true
       - run: uv sync --group doc
       - run: uv run zensical build --clean

.github/workflows/test.yml

@@ -13,7 +13,7 @@ jobs:
       max-parallel: 2
       matrix:
         platform: [ubuntu-latest, windows-latest, macos-latest]
-        python-version: ["3.11", "3.12", "3.13"]
+        python-version: ["3.12", "3.13", "3.14"]
     steps:
       - uses: actions/checkout@v4
 

README.md

@@ -4,7 +4,7 @@
 | :----------: | :-------------------------------------------------------------------------------------------------------------------------------------------------------------------------: |
 |  **Status**  | [![Docs][badge-docs]][link-docs] [![Tests][badge-tests]][link-tests]                                                                                                        |
 | **Package**  | [![PyPI][badge-pypi]][link-pypi] [![Python][badge-python]][link-pypi]                                                                                                       |
-|   **Meta**   | [![Hatch][badge-hatch]][link-hatch] [![uv][badge-uv]][link-uv] [![Ruff][badge-ruff]][link-ruff] [![prek][badge-prek]][link-prek] [![License][badge-license]][link-license]  |
+|   **Meta**   | [![SPEC 0][badge-spec0]][link-spec0] [![Hatch][badge-hatch]][link-hatch] [![uv][badge-uv]][link-uv] [![Ruff][badge-ruff]][link-ruff] [![prek][badge-prek]][link-prek] [![License][badge-license]][link-license]  |
 |   **Cite**   | [![DOI][badge-doi]][link-doi]                                                                                                                                               |
 
 [badge-docs]: https://github.com/czbiohub-sf/iohub/actions/workflows/docs.yml/badge.svg
@@ -13,6 +13,8 @@
 [badge-python]: https://img.shields.io/pypi/pyversions/iohub
 [badge-hatch]: https://img.shields.io/badge/%F0%9F%A5%9A-Hatch-4051b5.svg
 [badge-uv]: https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/uv/main/assets/badge/v0.json
+[badge-spec0]: https://img.shields.io/badge/SPEC-0-green?labelColor=%23004811&color=%235CA038
+[link-spec0]: https://scientific-python.org/specs/spec-0000/
 [badge-ruff]: https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json
 [badge-prek]: https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/j178/prek/master/docs/assets/badge-v0.json
 [badge-license]: https://img.shields.io/badge/License-BSD--3--Clause-blue.svg
@@ -44,8 +46,7 @@ used at the Biohub and in the broader imaging community.
 
 ### Write
 
-- OME-Zarr ([OME-NGFF v0.5](https://ngff.openmicroscopy.org/0.5/), OME-NGFF v0.4)
-- Multi-page TIFF stacks organized in a directory hierarchy that mimics OME-NGFF (WIP)
+- OME-Zarr ([OME-NGFF v0.5](https://ngff.openmicroscopy.org/0.5/))
 
 ## Quick start
 

docs/examples/run_multi_fov_hcs_ome_zarr.py

@@ -38,10 +38,7 @@
 )
 
 with open_ome_zarr(
-    store_path,
-    layout="hcs",
-    mode="w-",
-    channel_names=["DAPI", "GFP", "Brightfield"],
+    store_path, layout="hcs", mode="w-", channel_names=["DAPI", "GFP", "Brightfield"], implementation="tensorstore"
 ) as dataset:
     # Create and write to positions
     # This affects the tile arrangement in visualization

pyproject.toml

@@ -1,44 +1,45 @@
 [build-system]
 build-backend = "hatchling.build"
-requires = ["hatchling", "uv-dynamic-versioning>=0.7.0"]
+requires = ["hatchling", "uv-dynamic-versioning>=0.14.0"]
 
 [project]
 name = "iohub"
 description = "N-dimensional bioimaging data I/O with OME metadata in Python"
 authors = [
-    {name = "CZ Biohub and iohub contributors", email = "iohub@czbiohub.org"},
+    {name = "Biohub and iohub contributors", email = "iohub@czbiohub.org"},
 ]
 license = {file = "LICENSE"}
 readme = "README.md"
-requires-python = ">=3.11"
+requires-python = ">=3.12"
 classifiers = [
     "Development Status :: 3 - Alpha",
     "Intended Audience :: Science/Research",
     "License :: OSI Approved :: BSD License",
     "Programming Language :: Python :: 3 :: Only",
-    "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.12",
     "Programming Language :: Python :: 3.13",
+    "Programming Language :: Python :: 3.14",
     "Topic :: Scientific/Engineering",
     "Topic :: Scientific/Engineering :: Image Processing",
     "Operating System :: Microsoft :: Windows",
     "Operating System :: POSIX :: Linux",
     "Operating System :: MacOS :: MacOS X",
 ]
 dependencies = [
-    "pandas>=1.5.2",
+    "pandas>=2",
     "pydantic>=2.8.2",
     "pydantic_extra_types>=2.9.0",
     "tifffile>=2025.5.21",
-    "natsort>=7.1.1",
+    "natsort>=8.4.0",
     "ndtiff>=2.2.1",
-    "zarr>=3.0.8",
+    "zarr>=3.1.6",
     "rich",
     "tqdm",
     "pillow>=9.4.0",
     "blosc2",
     "xarray>=2024.1.1",
     "dask[array]",
+    "zarrs>=0.2.3",
 ]
 dynamic = ["version"]
 
@@ -52,13 +53,18 @@ Source = "https://github.com/czbiohub-sf/iohub"
 tensorstore = [
     "tensorstore>=0.1.64",
 ]
+
+[project.entry-points."iohub.zarr-implementations"]
+zarr = "iohub.core.implementations.zarr_python:ZarrPythonImplementation"
+tensorstore = "iohub.core.implementations.tensorstore:TensorStoreImplementation"
+
 [dependency-groups]
 test = [
     "iohub[tensorstore]",
     "ngff-zarr[validate]",
-    "pytest>=5.0.0",
+    "pytest>=9.0.2",
     "pytest-cov",
-    "hypothesis>=6.61.0",
+    "hypothesis>=6.151.0",
     "requests>=2.22.0",
     "wget>=3.2",
     "ome-zarr>=0.12.0",
@@ -67,7 +73,7 @@ acquire-zarr = [
     "acquire-zarr",
 ]
 doc = [
-    "zensical>=0.0.11",
+    "zensical>=0.0.29",
     "mkdocstrings-python>=2.0.2",
     "mkdocs-click>=0.8",
 ]
@@ -93,15 +99,58 @@ style = "pep440"
 bump = true
 fallback-version = "0.0.0"
 
+[tool.pytest]
+minversion="9.0"
+strict = true
+testpaths = [ "tests" ]
+addopts = [
+    "-ra",
+    "--import-mode=importlib",
+]
+
 [tool.ruff]
 line-length = 120
-
-[tool.ruff.format]
-quote-style = "double"
-indent-style = "space"
-docstring-code-format = true
-docstring-code-line-length = "dynamic"
-
-[tool.ruff.lint]
-select = ["E", "F", "W", "I"]
-ignore = ["E203", "E731"]
+src = [ "src" ]
+extend-include = [ "*.ipynb" ]
+format.quote-style = "double"
+format.indent-style = "space"
+format.docstring-code-format = true
+format.docstring-code-line-length = "dynamic"
+lint.select = [
+    "B",    # flake8-bugbear
+    "BLE",  # flake8-blind-except
+    "C4",   # flake8-comprehensions
+    "D",    # pydocstyle
+    "E",    # pycodestyle errors
+    "F",    # pyflakes
+    "I",    # isort
+    "NPY",  # NumPy-specific rules
+    "PERF", # Perflint
+    "PT",   # pytest
+    "PTH",  # pathlib
+    "RUF",  # Ruff-specific rules
+    "TID",  # flake8-tidy-imports
+    "UP",   # pyupgrade
+    "W",    # pycodestyle warnings
+]
+lint.ignore = [
+    "B008",  # function calls in argument defaults are fine when result is immutable
+    "D100",  # Missing docstring in public module
+    "D101",  # Missing docstring in public class
+    "D102",  # Missing docstring in public method
+    "D103",  # Missing docstring in public function
+    "D104",  # Missing docstring in public package
+    "D105",  # __magic__ methods are often self-explanatory
+    "D107",  # Missing docstring in __init__
+    "D203",  # no blank line before class docstring (conflicts with D211)
+    "D213",  # docstrings start immediately after opening triple quote (conflicts with D212)
+    "D400",  # first line should end with period (doesn't work with single-line docstrings)
+    "D401",  # first line in imperative mood
+    "E203",  # slice whitespace (handled by formatter)
+    "E501",  # line too long (formatter handles code; long comments are acceptable)
+    "E731",  # lambda assignments are convenient
+]
+lint.per-file-ignores."*/__init__.py" = [ "F401" ]
+lint.per-file-ignores."docs/*" = [ "D", "I", "NPY002", "PTH", "PERF401", "BLE001" ]
+lint.per-file-ignores."tests/*" = [ "D" ]
+lint.pydocstyle.convention = "numpy"

src/iohub/__init__.py

@@ -1,5 +1,6 @@
 """
 iohub
+
 =====
 
 N-dimensional bioimaging data I/O with OME metadata in Python