0.9.dev2: non-feature improvements

.editorconfig

@@ -6,10 +6,13 @@ insert_final_newline = true
 charset = utf-8
 trim_trailing_whitespace = true
 
-[*.{py,md,ini}]
+[*.md]
+indent_style = space
+
+[*.{py,ini}]
 indent_style = space
 indent_size = 4
 
-[*.{json,yaml,yml,cff}]
+[*.{json,yaml,yml,cff,toml,schema}]
 indent_style = space
 indent_size = 2

.github/workflows/build-lint.yml

@@ -0,0 +1,23 @@
+name: "Build and Lint Site"
+
+on:
+  workflow_dispatch:
+  push:
+  pull_request:
+
+concurrency:
+  group: build-lint-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  build-site:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v7
+      - uses: astral-sh/setup-uv@v9.0.0
+      - uses: extractions/setup-just@v4
+      - run: just build
+      - name: Ensure no unexpected encoded HTML in output
+        run: |
+          ! fgrep -R 'lt;blockquote' _build/html
+      # TODO: htmlproofer would be nice to have, but currently generates a lot of noise

.github/workflows/codespell.yml

@@ -1,12 +1,10 @@
-# Codespell configuration is within .codespellrc
+# Codespell configuration is within pyproject.toml
 ---
 name: Codespell
 
 on:
   push:
-    branches: [main]
   pull_request:
-    branches: [main]
 
 permissions:
   contents: read
@@ -18,6 +16,6 @@ jobs:
 
     steps:
       - name: Checkout
-        uses: actions/checkout@v4
+        uses: actions/checkout@v7
       - name: Codespell
         uses: codespell-project/actions-codespell@v2

.github/workflows/validation.yml

@@ -8,9 +8,16 @@ jobs:
     name: Validation
     runs-on: ubuntu-24.04
     steps:
-      - uses: actions/checkout@v4
-      - uses: actions/setup-python@v5
-        with:
-          python-version: '3.12'
-      - run: python -mpip install --upgrade wheel tox
-      - run: tox
+      - uses: actions/checkout@v7
+      - uses: astral-sh/setup-uv@v9.0.0
+      - uses: extractions/setup-just@v4
+      - run: just test
+
+  pre-commit:
+    name: Pre-commit
+    runs-on: ubuntu-24.04
+    steps:
+      - uses: actions/checkout@v7
+      - uses: astral-sh/setup-uv@v9.0.0
+      - uses: extractions/setup-just@v4
+      - run: just pre-commit

.readthedocs.yaml

@@ -8,13 +8,13 @@ build:
     post_install:
       - pip install uv
       - UV_PROJECT_ENVIRONMENT=$READTHEDOCS_VIRTUALENV_PATH uv sync --link-mode=copy
-      
+
     pre_build:
       # Run the script that autogenerates content before building the docs
       - "uv run python pre_build.py"
 
     build:
-      html: 
+      html:
         - jupyter book build --html --ci
         - mkdir -p $READTHEDOCS_OUTPUT
         - mv ./_build/html $READTHEDOCS_OUTPUT

CITATION.cff

@@ -92,6 +92,9 @@ authors:
   - family-names: Best
     given-names: Benedikt T.
     orcid: 0000-0001-6965-1117
+  - family-names: Boussot
+    given-names: Valentin
+    orcid: 0009-0003-2465-5458
   - family-names: Comparin
     given-names: Tommaso
     orcid: 0000-0001-6853-5931

README.md

@@ -9,6 +9,11 @@ as well as [json schemas](./schemas) to validate written ome-zarr image data.
 
 The built documentation including contribution hints can be found **[here](https://ngff-spec.readthedocs.io/en/latest/)**.
 
+## Development
+
+Use [`just`](https://github.com/casey/just) for common development tasks like building, linting, testing.
+Run `just` to see a list of commands.
+
 ## Conformance tests
 
 Conformance can be tested at several levels.

_version.py

@@ -1 +1 @@
-__version__ = '0.9.dev1'
+__version__ = "0.9.dev2"

authors.yml

@@ -111,6 +111,9 @@ project:
     - name: Benedikt T. Best
       github: btbest
       orcid: 0000-0001-6965-1117
+    - name: Valentin Boussot
+      github: vboussot
+      orcid: 0009-0003-2465-5458
 
     # C
     - name: Tommaso Comparin
@@ -169,7 +172,7 @@ project:
       github: ziw-liu
       orcid: 0000-0001-7482-1299
     - name: Tiago Lubiana
-      orrcid: 0000-0003-2473-2313
+      orcid: 0000-0003-2473-2313
       github: lubianat
 
     # N
@@ -189,7 +192,7 @@ project:
     - name: Constantin Pape
       github: constantinpape
       orcid: 0000-0001-6562-7187
-    
+
     # R
     - name: Sebastian Rhode
       github: sebi06

citing.md

@@ -7,9 +7,9 @@ author: ""
 [Next-generation file format (NGFF) specifications for storing bioimaging data in the cloud.](https://ngff.openmicroscopy.org/0.4)
 J. Moore, *et al*. Open Microscopy Environment Consortium, 8 February 2022.
 
-This edition of the specification is [https://ngff.openmicroscopy.org/{{version}}](https://ngff.openmicroscopy.org/{{version}}]).
+This edition of the specification is [https://ngff.openmicroscopy.org/{{version}}](https://ngff.openmicroscopy.org/{{version}}).
 The latest edition is publicly available {cite}`ngff_spec_latest`.
 
 ```{bibliography}
 :style: unsrt
-```
+```

conformance/ome_zarr_conformance.py

@@ -8,17 +8,19 @@
 """
 
 from __future__ import annotations
-from concurrent.futures import Future, ThreadPoolExecutor
+
+import json
+import logging
 import os
+import re
 import subprocess as sp
-from argparse import ArgumentParser
-from pathlib import Path
 import sys
-import re
-import json
+from argparse import ArgumentParser
+from collections.abc import Iterable
+from concurrent.futures import Future, ThreadPoolExecutor
 from dataclasses import dataclass
-from typing import Any, Iterable, Literal, Self
-import logging
+from pathlib import Path
+from typing import Any, Literal, Self
 
 logger = logging.getLogger("ome_zarr_conformance")
 
@@ -80,14 +82,11 @@ def __init__(
         self,
         exclude_patterns: list[re.Pattern] | None = None,
         include_patterns: list[re.Pattern] | None = None,
-        exclude_strict=False,
         exclude_invalid=False,
     ) -> None:
         self.exclude_patterns = exclude_patterns or []
         self.include_patterns = include_patterns or []
 
-        if exclude_strict:
-            self.exclude_patterns.append(re.compile(r"^strict/"))
         if exclude_invalid:
             self.exclude_patterns.append(re.compile(r"^\w+/invalid/"))
 
@@ -172,7 +171,7 @@ def main(raw_args=None):
         description=(
             "Feed sample Zarr data into a dingus CLI for validation. "
             "After the arguments shown, add a -- followed by the dingus CLI call; "
-            "e.g., `ome_zarr_conformance attributes --exclude-strict -- path/to/my/dingus -cli +args`. "
+            "e.g., `ome_zarr_conformance attributes -- path/to/my/dingus -cli +args`. "
             "The path to the attributes file or root of the zarr container will be appended to the dingus call."
         )
     )
@@ -201,12 +200,6 @@ def main(raw_args=None):
         action="append",
         help="regular expression pattern for test names to exclude; can be given multiple times",
     )
-    parser.add_argument(
-        "--exclude-strict",
-        "-S",
-        action="store_true",
-        help="exclude strict tests",
-    )
     parser.add_argument(
         "--exclude-invalid",
         "-I",
@@ -241,7 +234,7 @@ def main(raw_args=None):
         3: logging.DEBUG,
     }.get(args.verbose, logging.DEBUG)
     logging.basicConfig(level=lvl)
-    logging.debug("Got args: %s", args)
+    logger.debug("Got args: %s", args)
 
     if dingus_args is None:
         print(
@@ -267,7 +260,6 @@ def main(raw_args=None):
     req = Requested(
         exclude_patterns=args.exclude_pattern,
         include_patterns=args.include_pattern,
-        exclude_strict=bool(args.exclude_strict),
         exclude_invalid=bool(args.exclude_invalid),
     )
 

contribute.md

@@ -13,10 +13,15 @@ Major changes should follow the RFC process as it was laid out in [RFC1](https:/
 ## Building the documentation
 
 Build and inspect changes to the documentation before submitting a PR.
-To do so, you first need to install the necessary dependencies:
+
+This project uses [`uv`](https://docs.astral.sh/uv) to manage its required (python) tooling,
+and [`just`](https://github.com/casey/just) to run common development tasks.
+
+[Install `uv`](https://docs.astral.sh/uv/#installation),
+then set up an environment with the correct python version and development dependencies with
 
 ```bash
-pip install .
+uv sync
 ```
 
 This document uses [jupyter-book](https://jupyterbook.org) to generate the pages
@@ -25,12 +30,33 @@ After installing these via the dependencies,
 navigate into the repository on your machine and build the book using the following command:
 
 ```bash
-python pre_build.py
-jupyter book start
+just serve
 ```
 
 This will build the book and start a local server to inspect the changes in your browser.
 
+To generate the "production" output in the `./_build/` directory, use
+
+```bash
+just build
+```
+
+To see all available recipes, use
+
+```bash
+just
+```
+
+## Code quality
+
+To maximise consistency and minimise non-meaningful git churn,
+pre-commit hooks are used to lint and format some types of contribution.
+This is enforced on CI.
+
+When you clone the repository, install the hooks with `just pre-commit-install`.
+These will run whenever you make a commit;
+you can run them manually with `just pre-commit`.
+
 ## First contribution
 
 If you haven't contributed to the spec before,
@@ -51,7 +77,7 @@ make sure to rebuild the `CITATION.cff` file in the root of this repository.
 To do so, run the following command:
 
 ```bash
-jupyter book build --cff
+just cff
 ```
 
 Make sure the updated `CITATION.cff` file is included in your PR.
@@ -70,19 +96,35 @@ MyST allows a number of ways to reference and cross-reference inside this text
 and across several of the pages in this repo.
 For an overview of supported referencing syntax,
 see the [MyST doc pages](https://mystmd.org/guide/cross-references).
-It is recommended to use the following syntax in this document for consistency:
+It is recommended to use the following syntax for references:
+
+```markdown
+[This is the visible text](#your-reference-name)
+```
+
+Use `(your-reference)=` on the line before an element like a section header to set the target for that element.
 
 ```markdown
-anchor: (your-reference-name)=
-reference: [This is a reference](#your-reference-name)
+(version0.9:some-section)=
+## Some section
+
+(version0.9:some-note)=
+:::{note}
+
+The content of a note.
+:::
+
+## Another section
+
+See the [note](#some-note) in the [previous section](#some-section).
 ```
 
 For cross-referencing in the spec document,
 make sure to prepend the reference anchor with `versionX` like so:
 
 ```markdown
-## Some header
 (version0.9:some-header)=
+## Some header
 ```
 
 Otherwise, the same anchors may not be possible to resolve
@@ -112,7 +154,7 @@ This is a citation {cite:t}`citation_key`.
 
 where `citation_key` is the key of the bibtex entry in the `references.bib` file.
 
-#### Json examples
+#### JSON examples
 
 We suggest using [dropdowns](https://mystmd.org/guide/dropdowns-cards-and-tabs) for example code and other highlighting.
 For examples, please use the following syntax to wrap your examples:
@@ -162,4 +204,4 @@ Before creating a release, please make sure to go through the following items to
 - [ ] Update versions in examples. Go through the examples in the `examples/` and make sure that all version numbers in the `.json` files are up-to-date.
 - [ ] Update the specification number in the spec text. The [spec text](./index.md) mentions its own version number in several places. Please make sure to update those to the new version.
 - [ ] Make sure all tests are passing. Run the test suite to make sure that all tests are passing before creating a release.
-- [ ] Update the version history. Add a new entry to the [version history](#ngff-spec:history) file with the new version number and date, and a summary of the changes made in this release.
+- [ ] Update the version history. Add a new entry to the [version history](#ngff-spec:history) file with the new version number and date, and a summary of the changes made in this release.

examples/bf2raw/image.json

@@ -3,7 +3,7 @@
   "node_type": "group",
   "attributes": {
     "ome": {
-      "version": "0.9.dev1",
+      "version": "0.9.dev2",
       "bioformats2raw.layout": 3
     }
   }

examples/bf2raw/plate.json

@@ -3,7 +3,7 @@
   "node_type": "group",
   "attributes": {
     "ome": {
-      "version": "0.9.dev1",
+      "version": "0.9.dev2",
       "bioformats2raw.layout": 3,
       "plate": {
         "columns": [

examples/label/.config.json

@@ -0,0 +1,3 @@
+{
+  "schema": "schemas/label.schema"
+}