pre commit

.github/workflows/notebook-test.yml

@@ -13,4 +13,4 @@ jobs:
 
       - name: Test notebooks
         run: |
-          pixi run test-notebooks
+          pixi run test-notebooks

.github/workflows/test.yml

@@ -1,6 +1,6 @@
 name: Test
 
-on: [push,pull_request]
+on: [push, pull_request]
 
 jobs:
   test:
@@ -9,7 +9,7 @@ jobs:
       max-parallel: 5
       matrix:
         os: [ubuntu-22.04, windows-2022, macos-12, macos-14]
-        python-version: ['3.8', '3.9', '3.10', '3.11', '3.12']
+        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
 
     steps:
       - uses: actions/checkout@v4
@@ -30,4 +30,4 @@ jobs:
         if: ${{ matrix.os != 'mac-14' && matrix.package == '3.8' }}
         uses: mikepenz/action-junit-report@v2
         with:
-          report_paths: 'junit/test-results*.xml'
+          report_paths: "junit/test-results*.xml"

.pre-commit-config.yaml

@@ -0,0 +1,52 @@
+exclude: (^.pixi/|.snap|pixi.lock)
+
+ci:
+  autoupdate_commit_msg: "ENH: update pre-commit hooks"
+  autofix_commit_msg: "STYLE: pre-commit fixes"
+
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: "v4.6.0"
+    hooks:
+      - id: check-added-large-files
+      - id: check-case-conflict
+      - id: check-symlinks
+      - id: check-json
+      - id: check-merge-conflict
+      - id: check-toml
+      - id: check-xml
+      - id: check-yaml
+      - id: debug-statements
+      - id: detect-private-key
+      - id: end-of-file-fixer
+      - id: mixed-line-ending
+      - id: name-tests-test
+        args: ["--pytest-test-first"]
+      - id: requirements-txt-fixer
+      - id: trailing-whitespace
+
+  - repo: https://github.com/pre-commit/mirrors-prettier
+    rev: "v3.0.0"
+    hooks:
+      - id: prettier
+        types_or: [yaml, markdown, html, css, scss, javascript, json]
+        args: [--prose-wrap=always]
+
+  - repo: https://github.com/codespell-project/codespell
+    rev: "v2.2.5"
+    hooks:
+      - id: codespell
+        exclude: examples/
+
+  - repo: https://github.com/shellcheck-py/shellcheck-py
+    rev: "v0.9.0.5"
+    hooks:
+      - id: shellcheck
+
+  - repo: https://github.com/charliermarsh/ruff-pre-commit
+    rev: v0.5.4
+    hooks:
+      - id: ruff
+        args: [--fix, --exit-non-zero-on-fix]
+        exclude: test/conftest.py
+      - id: ruff-format

README.md

@@ -6,10 +6,11 @@
 [![image](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/python/black)
 [![DOI](https://zenodo.org/badge/379678181.svg)](https://zenodo.org/badge/latestdoi/379678181)
 
-Generate a multiscale, chunked, multi-dimensional spatial image data structure that can serialized to [OME-NGFF].
-
-Each scale is a scientific Python [Xarray] [spatial-image] [Dataset], organized into nodes of an Xarray [Datatree].
+Generate a multiscale, chunked, multi-dimensional spatial image data structure
+that can serialized to [OME-NGFF].
 
+Each scale is a scientific Python [Xarray] [spatial-image] [Dataset], organized
+into nodes of an Xarray [Datatree].
 
 ## Installation
 
@@ -32,8 +33,8 @@ image = to_spatial_image(array)
 print(image)
 ```
 
-An [Xarray] [spatial-image] [DataArray].
-Spatial metadata can also be passed during construction.
+An [Xarray] [spatial-image] [DataArray]. Spatial metadata can also be passed
+during construction.
 
 ```
 <xarray.SpatialImage 'image' (y: 128, x: 128)>
@@ -82,9 +83,11 @@ DataTree('multiscales', parent=None)
         image    (y, x) uint8 dask.array<chunksize=(16, 16), meta=np.ndarray>
 ```
 
-Store as an Open Microscopy Environment-Next Generation File Format ([OME-NGFF]) / [netCDF] [Zarr] store.
+Store as an Open Microscopy Environment-Next Generation File Format ([OME-NGFF])
+/ [netCDF] [Zarr] store.
 
-It is highly recommended to use `dimension_separator='/'` in the construction of the Zarr stores.
+It is highly recommended to use `dimension_separator='/'` in the construction of
+the Zarr stores.
 
 ```python
 store = zarr.storage.DirectoryStore('multiscale.zarr', dimension_separator='/')
@@ -96,26 +99,51 @@ released. We mean it :-).
 
 ## Examples
 
-- [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/spatial-image/multiscale-spatial-image/main?urlpath=lab/tree/examples%2FHelloMultiscaleSpatialImageWorld.ipynb) [Hello MultiscaleSpatialImage World!](./examples/HelloMultiscaleSpatialImageWorld.ipynb) 
-- [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/spatial-image/multiscale-spatial-image/main?urlpath=lab/tree/examples%2FConvertITKImage.ipynb) [Convert itk.Image](./examples/ConvertITKImage.ipynb) 
-- [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/spatial-image/multiscale-spatial-image/main?urlpath=lab/tree/examples%2FConvertImageioImageResource.ipynb) [Convert imageio ImageResource](./examples/ConvertImageioImageResource.ipynb) 
-- [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/spatial-image/multiscale-spatial-image/main?urlpath=lab/tree/examples%2FConvertPyImageJDataset.ipynb) [Convert pyimagej Dataset](./examples/ConvertPyImageJDataset.ipynb) 
+- [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/spatial-image/multiscale-spatial-image/main?urlpath=lab/tree/examples%2FHelloMultiscaleSpatialImageWorld.ipynb)
+  [Hello MultiscaleSpatialImage World!](./examples/HelloMultiscaleSpatialImageWorld.ipynb)
+- [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/spatial-image/multiscale-spatial-image/main?urlpath=lab/tree/examples%2FConvertITKImage.ipynb)
+  [Convert itk.Image](./examples/ConvertITKImage.ipynb)
+- [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/spatial-image/multiscale-spatial-image/main?urlpath=lab/tree/examples%2FConvertImageioImageResource.ipynb)
+  [Convert imageio ImageResource](./examples/ConvertImageioImageResource.ipynb)
+- [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/spatial-image/multiscale-spatial-image/main?urlpath=lab/tree/examples%2FConvertPyImageJDataset.ipynb)
+  [Convert pyimagej Dataset](./examples/ConvertPyImageJDataset.ipynb)
 
 ## Development
 
 Contributions are welcome and appreciated.
 
-To run the test suite:
+### Get the source code
 
-```
+```shell
 git clone https://github.com/spatial-image/multiscale-spatial-image
 cd multiscale-spatial-image
-pip install -e ".[test]"
-pytest
-# Notebook tests
-pytest --nbmake --nbmake-timeout=3000 examples/*ipynb
 ```
 
+### Install dependencies
+
+First install [pixi]. Then, install project dependencies:
+
+```shell
+pixi install -a
+pixi run pre-commit-install
+```
+
+### Run the test suite
+
+The unit tests:
+
+```shell
+pixi run -e test test
+```
+
+The notebooks tests:
+
+```shell
+pixi run test-notebooks
+```
+
+### Update test data
+
 To add new or update testing data, such as a new baseline for this block:
 
 ```py
@@ -150,10 +178,15 @@ gzip -9 ../data.tar
 python3 -c 'import pooch; print(pooch.file_hash("../data.tar.gz"))'
 ```
 
-Update the `test_data_sha256` variable in the *test/_data.py* file.
-Upload the data to [web3.storage](https://web3.storage).
-And update the `test_data_ipfs_cid` [Content Identifier (CID)](https://proto.school/anatomy-of-a-cid/01) variable, which is available in the web3.storage web page interface.
+Update the `test_data_sha256` variable in the _test/\_data.py_ file. Upload the
+data to [web3.storage](https://web3.storage). And update the
+`test_data_ipfs_cid`
+[Content Identifier (CID)](https://proto.school/anatomy-of-a-cid/01) variable,
+which is available in the web3.storage web page interface.
+
+### Submit the patch
 
+We use the standard [GitHub flow].
 
 [spatial-image]: https://github.com/spatial-image/spatial-image
 [Xarray]: https://xarray.pydata.org/en/stable/
@@ -164,3 +197,5 @@ And update the `test_data_ipfs_cid` [Content Identifier (CID)](https://proto.sch
 [Zarr]: https://zarr.readthedocs.io/en/stable/
 [Dask]: https://docs.dask.org/en/stable/array.html
 [netCDF]: https://www.unidata.ucar.edu/software/netcdf/
+[pixi]: https://pixi.sh
+[GitHub flow]: https://docs.github.com/en/get-started/using-github/github-flow

multiscale_spatial_image/__about__.py

@@ -1,4 +1,4 @@
 # SPDX-FileCopyrightText: 2022-present NumFOCUS <[email protected]>
 #
 # SPDX-License-Identifier: MIT
-__version__ = '1.0.0'
+__version__ = "1.0.0"

multiscale_spatial_image/__init__.py

@@ -2,15 +2,14 @@
 
 Generate a multiscale spatial image."""
 
-
 __all__ = [
-  "MultiscaleSpatialImage",
-  "Methods",
-  "to_multiscale",
-  "itk_image_to_multiscale",
-  "__version__",
+    "MultiscaleSpatialImage",
+    "Methods",
+    "to_multiscale",
+    "itk_image_to_multiscale",
+    "__version__",
 ]
 
 from .__about__ import __version__
 from .multiscale_spatial_image import MultiscaleSpatialImage
-from .to_multiscale import Methods, to_multiscale, itk_image_to_multiscale
+from .to_multiscale import Methods, to_multiscale, itk_image_to_multiscale

multiscale_spatial_image/multiscale_spatial_image.py

@@ -1,13 +1,10 @@
-from typing import Union, List
+from typing import Union
 
-import xarray as xr
 from datatree import DataTree
-from datatree.treenode import TreeNode
 import numpy as np
 from collections.abc import MutableMapping
 from pathlib import Path
 from zarr.storage import BaseStore
-import xarray as xr
 from datatree import register_datatree_accessor
 
 

multiscale_spatial_image/to_multiscale/__init__.py

@@ -1,2 +1,4 @@
-from .to_multiscale import Methods, to_multiscale 
+from .to_multiscale import Methods, to_multiscale
 from .itk_image_to_multiscale import itk_image_to_multiscale
+
+__all__ = ["Methods", "to_multiscale", "itk_image_to_multiscale"]