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0.9.dev2: non-feature improvements - #201

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clbarnes wants to merge 43 commits into
ome:0.9devfrom
clbarnes:0.9.dev2
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0.9.dev2: non-feature improvements#201
clbarnes wants to merge 43 commits into
ome:0.9devfrom
clbarnes:0.9.dev2

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@clbarnes

@clbarnes clbarnes commented Sep 2, 2026

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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

Stretch

Catalogue of changes

Because the diff is nightmarish.

Incorporating recent fixes to main:

  • 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

Lint and CI configuration:

Schema simplification

Environment management

Build scripts

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)

jo-mueller and others added 18 commits August 17, 2026 11:28
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>
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clbarnes and others added 5 commits September 2, 2026 11:57
- 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
@clbarnes
clbarnes marked this pull request as ready for review September 2, 2026 15:51
@jni

jni commented Sep 3, 2026

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Thanks @clbarnes! Can you add more details about the changes due to the large number of files?

Keep in sync with recent changes to main

which recent changes? Can you list them? Is this all a straight back/forward port or have you made the changes here optimistically, expecting that dev will become main soon?

Add additional lints and some auto-format jobs to improve consistency end reduce e.g. whitespace-only git churn

Can you list the configuration, or link to the specific files to review?

Basically, it would be good if this PR had a good record of exactly the changes that were made, since the diff itself is enormous and thus difficult to review.

Otherwise, full support! 🚀

@clbarnes

clbarnes commented Sep 3, 2026

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Good feedback @jni ; I've added a change catalogue to the top post.

@clbarnes

clbarnes commented Sep 3, 2026

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I got nerdsniped into adding JSONC support to prek; not sure if it'll be accepted, but it would allow us to check that the examples are valid JSON(C).

@clbarnes

clbarnes commented Sep 3, 2026

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Object definitions as tables where fields' types are linked to their own definition gives you a nice hover preview. From https://ngff-spec-clbarnes.readthedocs.io/en/0.9.dev2-tables

Screenshot 2026-09-03 at 17 13 33

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This pull request has been mentioned on Image.sc Forum. There might be relevant details there:

https://forum.image.sc/t/ngff-weekly-dev-update-thread/110810/143

@lubianat

lubianat commented Sep 3, 2026

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@clbarnes would you mind adding also

it could be a PR on top of a PR on top of a PR...

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8 participants