0.9.dev2: non-feature improvements by clbarnes · Pull Request #201 · ome/ngff-spec

clbarnes · 2026-09-02T10:08:28Z

This dev release is intended to improve the contributor and possibly reader experience without introducing any normative changes to the spec itself.

The nature of this dev version means there look like a lot of changes to review. Most of this is fixing many years' worth of accrued whitespace errors and inconsistent formatting. This PR adds config to make sure we never have to worry about this again, so it's worth the one-time pain to get that config in place.

Goals

Keep in sync with recent changes to main
resolve Remove "strict" jsonschemas and test cases #138
Add additional lints and some auto-format jobs to improve consistency end reduce e.g. whitespace-only git churn
- resolve Pre-commit hooks for enforcing formatting #123
- resolve lint/validate JSONs in the repository #194

Stretch

Format object definitions as tables #191
- This is currently implemented as a PR on top of this one, at Add object definition tables to the spec clbarnes/ngff-spec#3

Catalogue of changes

Because the diff is nightmarish.

Incorporating recent fixes to main/ 0.9.dev:

Schemas allow the minor version as well as prereleases of it (first introduced in v0.6) d4b2c1d
Fix some JSON typos from 0.9.dev1: 5c76733
describe byDimension input/outputAxes as indices, not names, and fix image schema typo: eb227a4
bump jupyter-book dependency to 2.0.2 per deps: bump jupyter book version #204
manually apply changes from

Lint and CI configuration:

Previously, codespell configuration was split between .codespellrc and pyproject.toml; now it's all in pyproject.toml. Also, added codespell to the dependencies https://github.com/ome/ngff-spec/pull/201/changes#diff-50c86b7ed8ac2cf95bd48334961bf0530cdc77b5a56f852c5c61b89d735fd711R33
Minor .editorconfig changes to better suit our use of certain file formats https://github.com/ome/ngff-spec/pull/201/changes#diff-0947e2727d6bad8cd0ac4122f5314bb5b04e337393075bc4b5ef143b17fcbd5bR9
prek configuration for running pre-commit hooks (similar to pre-commit and compatible with most of the same recipes, but much faster) https://github.com/ome/ngff-spec/pull/201/changes#diff-72359463e1c50ddcb8dfabe900898a8f1d92416bbe6754f2e497f62d96232021 The configured hooks are
- remove trailing whitespace
- ensure every text file has a newline at the end of it
- ensure that LF is used as the line ending
- check that YAML files are valid
- check that JSON files are valid
- format JSON files consistently
- check that all files are consistent with the .editorconfig
- run codespell
document use of pre-commit hooks https://github.com/ome/ngff-spec/pull/201/changes#diff-0e6105c1be2a3256539260ca3c7fe14f58a845005496d30e7e897cf9cf9c65e8R50
run pre-commit hooks on CI https://github.com/ome/ngff-spec/pull/201/changes#diff-c707f934fe56964ebe4e68cbf0eb00915fb01d8af63d6b37a06dbf365e9cf937R16
use uv and just throughout the CI configuration (see .github/workflows/*.yml)
add a CI job which actually builds the site and could run lints on the built artefact https://github.com/ome/ngff-spec/pull/201/changes#diff-3c3f6dcb27eee72f5e9c8e081a7487447b247fe8a7097d1bd973bc180fd0869dR1
- I wanted to use htmlproofer here, as ome/ngff does, but it ran for half an hour and produced thousands of lines of output which wasn't very helpful
Run CI jobs on every push/PR

Schema simplification

Remove strict schemas and test cases as discussed in Remove "strict" jsonschemas and test cases #138
Rename the "strict" examples (included in the document - see examples/*_strict

Environment management

Previously, a "testing" extra was used to install test-only dependencies. While this isn't a python package so the usual distinction between runtime and development dependencies is not so clear, it is preferred today to use a dependency group, which is implemented here https://github.com/ome/ngff-spec/pull/201/changes#diff-50c86b7ed8ac2cf95bd48334961bf0530cdc77b5a56f852c5c61b89d735fd711R22
Previously, pip was recommended for package management, environment management was left unspecified, there was no lock file, and tox was used for controlling the test environment. This, plus installing python itself, is now managed by uv, which should also speed up build times on CI https://github.com/ome/ngff-spec/pull/201/changes#diff-0e6105c1be2a3256539260ca3c7fe14f58a845005496d30e7e897cf9cf9c65e8R24

Build scripts

Previously, common tasks like building or viewing the docs, generating the citations file, and running the tests required different commands which were scattered across different documentation and configuration files. Contributors can now use just (whose normal usage is very similar to how Make is abused in python development); the justfile makes for a nice self-documenting catalogue of those commands https://github.com/ome/ngff-spec/pull/201/changes#diff-deb9bb56fb122db0b605aa5b63f95a4665c905b18dd670e1fa6c877576a94ff1
- installation of just is managed by uv

Minor changes in major volume

update 0.9.dev1 to 0.9.dev2
fix whitespace and minor formatting issues to suit the new editorconfig/ pre-commit configuration
some very minor formatting in python scripts (mainly sorting imports)

feat: no future 0.6rc1 without version bump feat: update schema store URL feat: use correct schema keys feat: list current version first feat: allow future 0.6rc1 as verion

fix: allow 0.6 as version in 0.6rcX

feat: no future 0.6rc1 without version bump feat: update schema store URL feat: use correct schema keys feat: list current version first feat: allow future 0.6rc1 as verion

Also, skip .venv/, .tox/, _build/, and css files

Also bump version of checkout action on CI

Co-authored-by: Draga Doncila <ddon0001@student.monash.edu>

Also add some useful recipes

…ome#195) * fix: describe byDimension inputAxes and outputAxes as indices The two descriptions read "Names of the input axes" and "Names of the output axes" while both arrays hold numbers. The spec text is already explicit that these are positions: the transformation table gives "inputAxes": List[number], the byDimension section states that the values are arrays of integers, and tests/attributes/spec/invalid holds a fixture that uses axis names precisely so it is rejected. Also fixes a typo in the sequence description of image.schema. Closes ome#179 * docs: add Valentin Boussot to the authors CITATION.cff regenerated with `jupyter book build --cff`, as the contribution guide asks.

Intrinsic is not a defined coordinate system.

* Fix table formatting for multiscale image metadata Updated table formatting for fields in index.md to correct alignment. * Fix table formatting in multiscales section * Move the "multiscale-md" heading up Give the multiscale specification a position higher up in the document * Fix typos in index.md documentation affine --> rotation in the rotation section; a object -> an object * Revert "Move the "multiscale-md" heading up" This reverts commit e9f7468. --------- Co-authored-by: Johannes Soltwedel <38459088+jo-mueller@users.noreply.github.com>

github-actions · 2026-09-02T10:08:40Z

Automated Review URLs

Readthedocs

- allow variation in markdown indentation - add config for .toml, .schema

Supercedes ome#197 Co-authored-by: Johannes Soltwedel <38459088+jo-mueller@users.noreply.github.com>

As implemented in ome#198 Co-authored-by: Johannes Soltwedel <38459088+jo-mueller@users.noreply.github.com>

Use dependency-groups rather than extras

Add object definition tables to the spec

clbarnes · 2026-09-23T10:49:45Z

Note that I have merged the object tables, as well as making the remainder of the cross-schema references absolute IRIs.

version bump script

jo-mueller and others added 18 commits August 17, 2026 11:28

fix: allow 0.6 as version in 0.6rc1

d4b2c1d

feat: no future 0.6rc1 without version bump feat: update schema store URL feat: use correct schema keys feat: list current version first feat: allow future 0.6rc1 as verion

Merge pull request ome#186 from jo-mueller/allow-06

91652df

fix: allow 0.6 as version in 0.6rcX

fix: allow 0.6 as version in 0.6rc1

5e521cf

feat: no future 0.6rc1 without version bump feat: update schema store URL feat: use correct schema keys feat: list current version first feat: allow future 0.6rc1 as verion

Consolidate codespell config in pyproject.toml

8eafab8

Also, skip .venv/, .tox/, _build/, and css files

Add dev commands to justfile

9ca5e53

Remove tox

f852414

Also bump version of checkout action on CI

Fix: use extras correctly in uv run

38b3b49

Fix version strings (ome#193)

5c76733

Co-authored-by: Draga Doncila <ddon0001@student.monash.edu>

feat: remove warning about experimental nature (ome#189)

4dde15b

Merge branch '0.9dev' into justfile

fbe0f13

Add just to dependencies

8c8d074

Also add some useful recipes

Update contributing to use uv, just

d9e9eab

More just docs

2213106

Merge branch 'main' into justfile

f9c70b6

Change input name from 'intrinsic' to 'physical' (ome#199)

c9c1851

Intrinsic is not a defined coordinate system.

Merge branch 'main' into 0.9.dev2

ab15835

clbarnes and others added 5 commits September 2, 2026 11:57

Remove strict schemas and tests

a1189a1

0.9.dev1 -> 0.9.dev2

f76fe7f

Update editorconfig

ff76dd9

- allow variation in markdown indentation - add config for .toml, .schema

Fix broken cross-reference

5726f70

Supercedes ome#197 Co-authored-by: Johannes Soltwedel <38459088+jo-mueller@users.noreply.github.com>

Fix anchors and references

ea44b60

As implemented in ome#198 Co-authored-by: Johannes Soltwedel <38459088+jo-mueller@users.noreply.github.com>

This was referenced Sep 2, 2026

chore: fix anchors and references #198

Closed

chore: fix broken cross-reference #197

Closed

Remove strict jsonchemas and conformance test cases (v2) #176

Closed

Merge branch 'justfile' into 0.9.dev2

5c56d86

clbarnes mentioned this pull request Sep 2, 2026

General build configuration improvements #183

Closed

Update dependencies

d561e11

Use dependency-groups rather than extras

clbarnes and others added 11 commits September 23, 2026 09:36

Axes tables

c2c3e27

Coordinate transformation tables

10f77ca

multiscales tables

0f4acab

label tables

485d7ee

plate tables

f5db8e5

well table

5998a61

scene table

8f994e5

Rework table referencing

a92c76a

rework referencing

953d9c2

Use only 1 type of anchor definition

a454224

Merge pull request #3 from clbarnes/0.9.dev2-tables

ab0ab96

Add object definition tables to the spec

clbarnes and others added 17 commits September 23, 2026 11:51

version bump script

13fea68

WIP version-bumping script

0e0c9ef

Remove text-replacing functions

43507e9

Use myst-substitutions

5591563

Use myst-substitutions in bumpversion

75c59d9

Update citing.md

ccecfff

fix typo

a6da3e7

Roll back myst-substitutions

6524bbd

Remove vestigial templating

0d17576

Check git history before applying changes

5651629

sort imports

aed51f1

Fix broken zarr test cases

b01d76b

get current version in test_validation

d27e164

fix bump script

7ee729e

List files to check manually

d7ce754

Give a grep command for finding lines

5267b0b

Merge pull request #4 from clbarnes/0.9.dev2-bump

8e97977

version bump script

clbarnes merged commit ae7f608 into ome:0.9dev Sep 24, 2026
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0.9.dev2: non-feature improvements - #201

0.9.dev2: non-feature improvements#201
clbarnes merged 86 commits into
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clbarnes commented Sep 2, 2026 •

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clbarnes commented Sep 2, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

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Goals

Stretch

Catalogue of changes

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clbarnes commented Sep 2, 2026 •

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clbarnes commented Sep 23, 2026 •

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