Migration to zarr 3 by konstntokas · Pull Request #112 · bcdev/zappend

konstntokas · 2026-10-28T14:46:47Z

Migrated to the Zarr v3 Python API. Supports writing Zarr v2 and v3 stores, with Zarr v2 as the default.

closes #111

Checklist (strike out non-applicable):

Changes documented in CHANGES.md
Related issue exists and is referred to in the PR description and CHANGES.md
Added docstrings and API docs for any new/modified user-facing classes and functions
Changes/features documented in docs/*
Unit-tests adapted/added for changes/features
Test coverage remains or increases (target 100%)

codecov · 2026-10-28T15:28:27Z

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 100.00%. Comparing base (e9c8677) to head (afc5a1a).

Additional details and impacted files

@@             Coverage Diff             @@
##             main      #112      +/-   ##
===========================================
+ Coverage   99.92%   100.00%   +0.07%     
===========================================
  Files          30        30              
  Lines        1418      1467      +49     
===========================================
+ Hits         1417      1467      +50     
+ Misses          1         0       -1

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forman

Implementation looks good!

However, I'd like to go for the following changes which would need also some documentation changes:

Make Zarr 3 the new default format, because it is the better format.
zarr_version should be deprecated, zarr_format be used instead to align with the API.
~~Require zarr_format setting in new configurations. If it is missing assume an old config that refers to the old default zarr_version=2 and so zarr_format=2. Emit a warning in this case.~~
shards setting should be ignored with a warning if it is not applicable.

EDIT

Require zarr_format=2|3 setting in new configurations and accept zarr_version=2 in old configurations. If either is missing, raise.

forman · 2026-11-02T12:05:04Z

 desired and the variable's data array will be persisted as one block. 

+For Zarr v3, `shards` may additionally be configured for a variable. A shard
+contains an integer number of regular chunks, reducing object counts while


Suggested change

contains an integer number of regular chunks, reducing object counts while

contains an integer number of regular chunks, reducing file or object counts while

forman · 2026-11-02T12:06:11Z

+contains an integer number of regular chunks, reducing object counts while
+retaining smaller read/write chunks. Each shard size must be at least its
+corresponding chunk size and an exact multiple of it. Shards are not available
+for Zarr v2.


Suggested change

for Zarr v2.

for Zarr v2, hence the `shards` setting will be ignored.

forman · 2026-11-02T12:12:29Z

@@ -603,7 +611,7 @@
        "zarr_version": {


Deprecate zarr_version and introduce zarr_format (to align with Zarr API).

forman · 2026-11-02T12:12:52Z

            "description": "The Zarr version to be used.",
-            "const": DEFAULT_ZARR_VERSION,
+            "enum": [2, 3],
            "default": DEFAULT_ZARR_VERSION,


Suggested change

"default": DEFAULT_ZARR_VERSION,

"default": DEFAULT_ZARR_FORMAT,

forman · 2026-11-02T12:13:13Z

Suggested change

DEFAULT_ZARR_FORMAT,

forman · 2026-11-02T12:18:29Z

    target_store: collections.abc.MutableMapping,
    target_ds: xr.Dataset,
    target_attrs: dict[str, Any],
+    zarr_version: int,


Suggested change

zarr_version: int,

zarr_format: int,

forman · 2026-11-02T12:20:28Z

@@ -1,5 +1,7 @@
 ## Version 0.8.1 (in development)

+* Migrated to the Zarr v3 Python API. Supports writing Zarr v2 and v3 stores, 


Suggested change

* Migrated to the Zarr v3 Python API. Supports writing Zarr v2 and v3 stores,

* Migrated to use `zarr >=3`. Supports writing Zarr v2 and v3 stores,

forman · 2026-11-02T12:22:14Z

@@ -1,5 +1,7 @@
 ## Version 0.8.1 (in development)


Suggested change

## Version 0.8.1 (in development)

## Version 0.9.0 (in development)

This PR is a major change of the implementation and a capability enhancement. This justifies a minor number increase.

forman · 2026-11-02T12:24:54Z

 ## Version 0.8.1 (in development)

+* Migrated to the Zarr v3 Python API. Supports writing Zarr v2 and v3 stores, 
+  with Zarr v2 as the default. (#111)


Suggested change

with Zarr v2 as the default. (#111)

with Zarr 3 as the new default format. (#111)

forman · 2026-11-02T12:26:06Z

+[Zarr format](https://zarr.readthedocs.io/en/stable/). Targets use Zarr v2 by
+default and may opt into Zarr v3. If an error


Suggested change

[Zarr format](https://zarr.readthedocs.io/en/stable/). Targets use Zarr v2 by

default and may opt into Zarr v3. If an error

[Zarr format](https://zarr.readthedocs.io/en/stable/). Targets use Zarr 3 format by

default and may opt into Zarr 2 format, if needed. If an error

konstntokas · 2026-11-02T14:23:44Z

* `zarr_version` should be deprecated, `zarr_format` be used instead to align with the API.

Linking related issue: #107

konstntokas · 2026-11-03T08:33:39Z

Closes #107

forman

All good, but the package version is still "0.8.1.dev0". Please change to "0.9.0.dev0".

konstntokas added 2 commits October 28, 2026 15:04

backup

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double check

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konstntokas added 3 commits October 29, 2026 14:53

coverage increased

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ready for review

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run ruff

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konstntokas marked this pull request as ready for review October 29, 2026 16:59

link issue

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konstntokas requested a review from forman October 29, 2026 17:05

ready

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forman requested changes Nov 2, 2026

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renanme module

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konstntokas force-pushed the konstntokas/migrate_zarr3 branch from 34577db to 242b875 Compare November 2, 2026 15:43

konstntokas added 3 commits November 2, 2026 17:19

address review

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konstntokas requested a review from forman November 3, 2026 08:33

forman requested changes Nov 3, 2026

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update version

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konstntokas requested a review from forman November 3, 2026 12:56

forman approved these changes Nov 3, 2026

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forman merged commit 38a530e into main Nov 3, 2026
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konstntokas mentioned this pull request Nov 3, 2026

Replace deprecated zarr_version argument with zarr_format #107

Closed

konstntokas deleted the konstntokas/migrate_zarr3 branch November 3, 2026 13:09

	contains an integer number of regular chunks, reducing object counts while
	contains an integer number of regular chunks, reducing file or object counts while

	for Zarr v2.
	for Zarr v2, hence the `shards` setting will be ignored.

	"default": DEFAULT_ZARR_VERSION,
	"default": DEFAULT_ZARR_FORMAT,

		@@ -1,5 +1,7 @@
		## Version 0.8.1 (in development)

		* Migrated to the Zarr v3 Python API. Supports writing Zarr v2 and v3 stores,

	* Migrated to the Zarr v3 Python API. Supports writing Zarr v2 and v3 stores,
	* Migrated to use `zarr >=3`. Supports writing Zarr v2 and v3 stores,

	## Version 0.8.1 (in development)
	## Version 0.9.0 (in development)

	with Zarr v2 as the default. (#111)
	with Zarr 3 as the new default format. (#111)

		[Zarr format](https://zarr.readthedocs.io/en/stable/). Targets use Zarr v2 by
		default and may opt into Zarr v3. If an error

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konstntokas commented Nov 2, 2026

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konstntokas commented Oct 28, 2026 •

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