Create read only copy if needed when opening a store path #3156

maxrjones · 2025-06-19T16:21:19Z

This PR makes a read-only copy of a store when using StorePath.open(mode="r").

See discussion in #3068. This augments #3068 (it still errors when attempting to open a writeable store path using a read-only store). This is an alternative to #3155.

Closes #3147

TODO:

Add unit tests and/or doctests in docstrings
Add docstrings and API docs for any new/modified user-facing classes and functions
New/modified features documented in docs/user-guide/*.rst
Changes documented as a new file in changes/
GitHub Actions have all passed
Test coverage is 100% (Codecov passes)

src/zarr/storage/_common.py

Co-authored-by: Davis Bennett <[email protected]>

dstansby

Looks good to me. Requesting changes because:

This should get a release note
My old release note from when I added the error should be deleted

src/zarr/core/common.py

src/zarr/storage/_common.py

Co-authored-by: David Stansby <[email protected]>

maxrjones · 2025-06-20T12:26:07Z

This should get a release note
My old release note from when I added the error should be deleted

Thanks, done in 10e50e4 (#3156)

This reverts commit 7ad760f.

src/zarr/storage/_common.py

TomNicholas · 2025-06-24T19:39:54Z

FYI I tried running xarray's zarr tests with this PR and while it fixes the basic read_only failure that #3068 caused (see for example this test, which passes with this PR), I still see a lot of other errors. I'm just trying to work out if those errors are caused by this PR or by zarr's dtypes refactor.

I also see a lot of things like this

FAILED xarray/tests/test_backends.py::TestZarrDictStore::test_warning_on_bad_chunks[2] - AssertionError: Got 1 unexpected warning(s): ["UserWarning('Store is not read-only but mode is 'r'. Creating a read-only copy. This behavior may change in the future with a more granular permissions model.'))"]

suggesting that xarray might need to swallow the warning being raised in this PR.

d-v-b · 2025-06-24T19:43:55Z

Why do we need to raise a warning here? Doesn't the new with_read_only method fully legitimize the creation of a new store in read-only mode?

TomNicholas · 2025-06-24T19:46:00Z

I agree, this isn't something to warn for, it's just a change of behaviour to be documented.

rabernat · 2025-06-24T20:00:33Z

I agree, this isn't something to warn for, it's just a change of behaviour to be documented.

👍 to this. FWIW I think we have been way to eager to issue warnings in Zarr. No warning is needed here.

TomNicholas · 2025-06-24T20:01:11Z

I'm just trying to work out if those errors are caused by this PR or by zarr's dtypes refactor.

After talking to @ianhi I think those other errors are related to the dtypes changes rather than to the changes in this PR.

maxrjones · 2025-06-24T20:13:14Z

I'm just trying to work out if those errors are caused by this PR or by zarr's dtypes refactor.

After talking to @ianhi I think those other errors are related to the dtypes changes rather than to the changes in this PR.

Yes they are definitely unrelated to this and instead are relevant to the dtypes changes.

Co-authored-by: Tom Nicholas <[email protected]>

maxrjones · 2025-06-24T20:41:46Z

Why do we need to raise a warning here? Doesn't the new with_read_only method fully legitimize the creation of a new store in read-only mode?

thanks for this suggestion, Davis, and the affirmations, Tom and Ryan. The PR no longer includes a warning. My decision to initially include one was influenced by the prevalence of warnings elsewhere so it's helpful to have that general correction.

rabernat

It would be good to get coverage back up before merging.

David's comments have clearly been addressed, he's on vacation and can't approve. GH won't let us merge with pending changes requested..

d-v-b · 2025-06-30T09:02:18Z

@meeseeksdev backport to 3.0.9

lumberbot-app · 2025-06-30T09:02:26Z

Owee, I'm MrMeeseeks, Look at me.

There seem to be a conflict, please backport manually. Here are approximate instructions:

Checkout backport branch and update it.

git checkout 3.0.9
git pull

Cherry pick the first parent branch of the this PR on top of the older branch:

git cherry-pick -x -m1 5731c6c88ef0c5a3cb7f9701a7fbcee2814febf3

You will likely have some merge/cherry-pick conflict here, fix them and commit:

git commit -am 'Backport PR #3156: Create read only copy if needed when opening a store path'

Push to a named branch:

git push YOURFORK 3.0.9:auto-backport-of-pr-3156-on-3.0.9

Create a PR against branch 3.0.9, I would have named this PR:

"Backport PR #3156 on branch 3.0.9 (Create read only copy if needed when opening a store path)"

And apply the correct labels and milestones.

Congratulations — you did some good work! Hopefully your backport PR will be tested by the continuous integration and merged soon!

Remember to remove the Still Needs Manual Backport label once the PR gets merged.

If these instructions are inaccurate, feel free to suggest an improvement.

d-v-b · 2025-06-30T09:17:45Z

@meeseeksdev backport to 3.0.9

lumberbot-app · 2025-06-30T09:17:56Z

Owee, I'm MrMeeseeks, Look at me.

There seem to be a conflict, please backport manually. Here are approximate instructions:

Checkout backport branch and update it.

git checkout 3.0.9
git pull

Cherry pick the first parent branch of the this PR on top of the older branch:

git cherry-pick -x -m1 5731c6c88ef0c5a3cb7f9701a7fbcee2814febf3

You will likely have some merge/cherry-pick conflict here, fix them and commit:

git commit -am 'Backport PR #3156: Create read only copy if needed when opening a store path'

Push to a named branch:

git push YOURFORK 3.0.9:auto-backport-of-pr-3156-on-3.0.9

Create a PR against branch 3.0.9, I would have named this PR:

"Backport PR #3156 on branch 3.0.9 (Create read only copy if needed when opening a store path)"

And apply the correct labels and milestones.

Congratulations — you did some good work! Hopefully your backport PR will be tested by the continuous integration and merged soon!

Remember to remove the Still Needs Manual Backport label once the PR gets merged.

If these instructions are inaccurate, feel free to suggest an improvement.

…opers#3156) * Create read only copy if needed when opening a store path * Add ValueError to Raises section * Update expected warning * Update src/zarr/storage/_common.py Co-authored-by: Davis Bennett <[email protected]> * Use ANY_ACCESS_MODE * Update src/zarr/storage/_common.py Co-authored-by: David Stansby <[email protected]> * Update src/zarr/storage/_common.py Co-authored-by: David Stansby <[email protected]> * Update changes * Try using get_args on definition * Revert "Try using get_args on definition" This reverts commit 7ad760f. * Add test * Remove warning * Apply suggestion for try; except shortening Co-authored-by: Tom Nicholas <[email protected]> * Improve code coverage --------- Co-authored-by: Davis Bennett <[email protected]> Co-authored-by: David Stansby <[email protected]> Co-authored-by: Tom Nicholas <[email protected]> (cherry picked from commit 5731c6c)

) * Create read only copy if needed when opening a store path * Add ValueError to Raises section * Update expected warning * Update src/zarr/storage/_common.py * Use ANY_ACCESS_MODE * Update src/zarr/storage/_common.py * Update src/zarr/storage/_common.py * Update changes * Try using get_args on definition * Revert "Try using get_args on definition" This reverts commit 7ad760f. * Add test * Remove warning * Apply suggestion for try; except shortening * Improve code coverage --------- (cherry picked from commit 5731c6c) Co-authored-by: Max Jones <[email protected]> Co-authored-by: David Stansby <[email protected]> Co-authored-by: Tom Nicholas <[email protected]>

* Create read only copy if needed when opening a store path (#3156) * Create read only copy if needed when opening a store path * Add ValueError to Raises section * Update expected warning * Update src/zarr/storage/_common.py Co-authored-by: Davis Bennett <[email protected]> * Use ANY_ACCESS_MODE * Update src/zarr/storage/_common.py Co-authored-by: David Stansby <[email protected]> * Update src/zarr/storage/_common.py Co-authored-by: David Stansby <[email protected]> * Update changes * Try using get_args on definition * Revert "Try using get_args on definition" This reverts commit 7ad760f. * Add test * Remove warning * Apply suggestion for try; except shortening Co-authored-by: Tom Nicholas <[email protected]> * Improve code coverage --------- Co-authored-by: Davis Bennett <[email protected]> Co-authored-by: David Stansby <[email protected]> Co-authored-by: Tom Nicholas <[email protected]> (cherry picked from commit 5731c6c) * release notes --------- Co-authored-by: Max Jones <[email protected]> Co-authored-by: David Stansby <[email protected]> Co-authored-by: Tom Nicholas <[email protected]>

* Enable tests on 3.0.x branch (#3135) * Changelog for 3.0.9 * Backport PR #3149: Add GroupNotFound error to API docs (#3179) Co-authored-by: David Stansby <[email protected]> * Backport PR #3140: Suppress FileNotFoundError when deleting keys in the obstore adapter (#3180) Co-authored-by: Lukas Bindreiter <[email protected]> * Backport PR #3138: Add with_read_only() convenience method to store (#3181) Co-authored-by: Max Jones <[email protected]> * Create read only copy if needed when opening a store path (#3156) * Create read only copy if needed when opening a store path * Add ValueError to Raises section * Update expected warning * Update src/zarr/storage/_common.py Co-authored-by: Davis Bennett <[email protected]> * Use ANY_ACCESS_MODE * Update src/zarr/storage/_common.py Co-authored-by: David Stansby <[email protected]> * Update src/zarr/storage/_common.py Co-authored-by: David Stansby <[email protected]> * Update changes * Try using get_args on definition * Revert "Try using get_args on definition" This reverts commit 7ad760f. * Add test * Remove warning * Apply suggestion for try; except shortening Co-authored-by: Tom Nicholas <[email protected]> * Improve code coverage --------- Co-authored-by: Davis Bennett <[email protected]> Co-authored-by: David Stansby <[email protected]> Co-authored-by: Tom Nicholas <[email protected]> (cherry picked from commit 5731c6c) * Create read only copy if needed when opening a store path (#3156) (#3182) * Create read only copy if needed when opening a store path * Add ValueError to Raises section * Update expected warning * Update src/zarr/storage/_common.py * Use ANY_ACCESS_MODE * Update src/zarr/storage/_common.py * Update src/zarr/storage/_common.py * Update changes * Try using get_args on definition * Revert "Try using get_args on definition" This reverts commit 7ad760f. * Add test * Remove warning * Apply suggestion for try; except shortening * Improve code coverage --------- (cherry picked from commit 5731c6c) Co-authored-by: Max Jones <[email protected]> Co-authored-by: David Stansby <[email protected]> Co-authored-by: Tom Nicholas <[email protected]> * Remove breaking check about `auto_mkdir` for FSSpecStore (#3193) * Remove breaking check from _make_async * Update expected error * Change import structure to protect against AttributeError * changelog * add test to ensure that we can create a read-only copy of the store with auto_mkdir=False * only test if the async wrapper is available --------- Co-authored-by: Davis Bennett <[email protected]> (cherry picked from commit 5a24487) * Remove breaking check about `auto_mkdir` for FSSpecStore (#3193) (#3203) * Remove breaking check from _make_async * Update expected error * Change import structure to protect against AttributeError * changelog * add test to ensure that we can create a read-only copy of the store with auto_mkdir=False * only test if the async wrapper is available --------- (cherry picked from commit 5a24487) Co-authored-by: Max Jones <[email protected]> * Add missing import for AsyncFileSystemWrapper for `_make_async` in `_fsspec.py` (#3195) * Add missing import for AsyncFileSystemWrapper in `_fsspec.py` * Add missing changelog entry for AsyncFileSystemWrapper import fix * Move AsyncFileSystemWrapper import past the version check in `_fsspec.py` * Add newline after AsyncFileSystemWrapper import in `_fsspec.py` * Simplify import statement for AsyncFileSystemWrapper in `_fsspec.py` --------- Co-authored-by: Altay Sansal <[email protected]> (cherry picked from commit 97aa42f) * Auto backport of pr 3195 on 3.0.10 (#3204) * Remove breaking check about `auto_mkdir` for FSSpecStore (#3193) * Remove breaking check from _make_async * Update expected error * Change import structure to protect against AttributeError * changelog * add test to ensure that we can create a read-only copy of the store with auto_mkdir=False * only test if the async wrapper is available --------- Co-authored-by: Davis Bennett <[email protected]> (cherry picked from commit 5a24487) * Add missing import for AsyncFileSystemWrapper for `_make_async` in `_fsspec.py` (#3195) * Add missing import for AsyncFileSystemWrapper in `_fsspec.py` * Add missing changelog entry for AsyncFileSystemWrapper import fix * Move AsyncFileSystemWrapper import past the version check in `_fsspec.py` * Add newline after AsyncFileSystemWrapper import in `_fsspec.py` * Simplify import statement for AsyncFileSystemWrapper in `_fsspec.py` --------- Co-authored-by: Altay Sansal <[email protected]> (cherry picked from commit 97aa42f) --------- Co-authored-by: Max Jones <[email protected]> Co-authored-by: Altay Sansal <[email protected]> Co-authored-by: Altay Sansal <[email protected]> * 3.0.9 release notes (#3183) * Create read only copy if needed when opening a store path (#3156) * Create read only copy if needed when opening a store path * Add ValueError to Raises section * Update expected warning * Update src/zarr/storage/_common.py Co-authored-by: Davis Bennett <[email protected]> * Use ANY_ACCESS_MODE * Update src/zarr/storage/_common.py Co-authored-by: David Stansby <[email protected]> * Update src/zarr/storage/_common.py Co-authored-by: David Stansby <[email protected]> * Update changes * Try using get_args on definition * Revert "Try using get_args on definition" This reverts commit 7ad760f. * Add test * Remove warning * Apply suggestion for try; except shortening Co-authored-by: Tom Nicholas <[email protected]> * Improve code coverage --------- Co-authored-by: Davis Bennett <[email protected]> Co-authored-by: David Stansby <[email protected]> Co-authored-by: Tom Nicholas <[email protected]> (cherry picked from commit 5731c6c) * release notes --------- Co-authored-by: Max Jones <[email protected]> Co-authored-by: David Stansby <[email protected]> Co-authored-by: Tom Nicholas <[email protected]> * release notes --------- Co-authored-by: Lumberbot (aka Jack) <[email protected]> Co-authored-by: Lukas Bindreiter <[email protected]> Co-authored-by: Max Jones <[email protected]> Co-authored-by: Davis Bennett <[email protected]> Co-authored-by: Tom Nicholas <[email protected]> Co-authored-by: Altay Sansal <[email protected]> Co-authored-by: Altay Sansal <[email protected]>

Create read only copy if needed when opening a store path

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github-actions bot added the needs release notes Automatically applied to PRs which haven't added release notes label Jun 19, 2025

Add ValueError to Raises section

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Update expected warning

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maxrjones and others added 2 commits June 19, 2025 13:19

Update src/zarr/storage/_common.py

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Co-authored-by: Davis Bennett <[email protected]>

Use ANY_ACCESS_MODE

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maxrjones mentioned this pull request Jun 19, 2025

Only warn if opening writeable store with mode='r' #3155

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maxrjones and others added 3 commits June 20, 2025 08:21

Update src/zarr/storage/_common.py

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Co-authored-by: David Stansby <[email protected]>

Update src/zarr/storage/_common.py

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Update changes

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maxrjones added 3 commits June 20, 2025 08:26

Merge branch 'main' into maybe-copy-store

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Try using get_args on definition

7ad760f

Revert "Try using get_args on definition"

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This reverts commit 7ad760f.

maxrjones requested a review from dstansby June 20, 2025 13:41

Add test

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Merge branch 'main' into maybe-copy-store

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maxrjones and others added 3 commits June 24, 2025 16:35

Remove warning

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Apply suggestion for try; except shortening

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Merge branch 'main' into maybe-copy-store

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rabernat merged commit 5731c6c into zarr-developers:main Jun 24, 2025
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maxrjones deleted the maybe-copy-store branch June 25, 2025 00:09

d-v-b added this to the 3.0.9 milestone Jun 30, 2025

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3.0.9 release notes #3183

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This was referenced Jun 30, 2025

⚠️ Nightly upstream-dev CI failed ⚠️ pydata/xarray#10261

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ODD PI 25.3 Objective 5: Foundational Zarr-Python and Xarray Contributions NASA-IMPACT/veda-odd#165

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maxrjones mentioned this pull request Jul 6, 2025

Use a release checklist and narrative announcement for breaking changes #3209

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Create read only copy if needed when opening a store path #3156

Create read only copy if needed when opening a store path #3156

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