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Prune stores #1791

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wants to merge 30 commits into from
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Prune stores #1791

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d-v-b
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@d-v-b d-v-b commented Apr 11, 2024

Removes a lot of stores from the v2 codebase. I basically removed every store that required an extra dependency (other than fsspec), and also removed the N5 stores and the sqlite store. The logic for doing this is to thin down the v2 codebase.

Depends on #1742.

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/tutorial.rst
  • Changes documented in docs/release.rst
  • GitHub Actions have all passed
  • Test coverage is 100% (Codecov passes)

d-v-b and others added 12 commits April 4, 2024 13:14
* refactor(v3): Using appropriate types

* fix(v3): Typing fixes + minor code fixes

* fix(v3): _sync_iter works with coroutines

* docs(v3/store/core.py): clearer comment

* fix(metadata.py): Use Any outside TYPE_CHECKING for Pydantic

* fix(zarr/v3): correct zarr format + remove unused method

* fix(v3/store/core.py): Potential suggestion on handling str store_like

* refactor(zarr/v3): Add more typing

* ci(.pre-commit-config.yaml): zarr v3 mypy checks turned on in pre-commit
…elopers#1728)

* Specify v3 hatch envs using GitHub actions matrix

* Update .github/workflows/test-v3.yml

Co-authored-by: Joe Hamman <jhamman1@gmail.com>

* Update .github/workflows/test-v3.yml

Co-authored-by: Joe Hamman <jhamman1@gmail.com>

* test on 3.12 too

* no 3.12

---------

Co-authored-by: Joe Hamman <jhamman1@gmail.com>
Co-authored-by: Joe Hamman <joe@earthmover.io>
* black -> ruff + cleanup

* format

* Preserve git blame

* pre-commit fix
…ntributing.rst (zarr-developers#1643)

Co-authored-by: Joe Hamman <joe@earthmover.io>
@d-v-b d-v-b added in progress Someone is currently working on this V3 Affects the v3 branch labels Apr 11, 2024
@d-v-b
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d-v-b commented Apr 19, 2024

This PR specifically removes following the following v2 stores, and their v3 counterparts:

One question that @jhamman raised was whether we want to remove ZipStore or not. Since FSSpec supports Zip archives as a backend, is it possible that we could get ZipStore functionality via FSStore? @martindurant what do you think?

Once we decide on whether or not we keep ZipStore, then I think this PR is good to go, barring any other feedback / concerns.

@rabernat
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My feeling is that Zip stores are really an underappreciated feature of Zarr. Whatever we choose in terms of design, we should document Zip stores prominently.

I'm curious--are there performance or feature differences between the native Zip store and the fsspec version?

@martindurant
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fsspec's ZipFS ought to be able to do everything, I would have thought, with the additional plus of being able to work with remote zips too (usually "r" and "w" modes only). It has certainly not been tested for speed, convenience being the priority over performance. A more specialised, and therefore simple, implementation can be reasonable if there is someone to maintain it.

@mxmlnkn , you might be interested by another way of thinking of compressed bunch-of-files containers discussed here.

@jhamman jhamman added this to the 3.0.0.alpha milestone Apr 22, 2024
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d-v-b commented Apr 22, 2024

Updates:

  • My initial effort in this PR removed everything in one commit. I have reverted that, and broken the removals into one commit per storage class.
  • I am keeping ZipStore, since it doesn't require any external dependencies and some community members expressed an interested in keeping it.

I think the ZipStore was the only controversial aspect here, and that issue should be sorted. I would like to merge this in the next few days, unless anyone has objections.

@d-v-b d-v-b removed the in progress Someone is currently working on this label Apr 23, 2024
@d-v-b d-v-b mentioned this pull request May 21, 2024
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@jhamman jhamman modified the milestones: 3.0.0.alpha, 3.0.0 May 24, 2024
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dstansby commented Oct 2, 2024

Is this still something we want to get into zarr v3? And if so, would it be better to deprecate everything for a few releases and then remove it first? If not, and it's just going to be removed without warning, there should be a clear guide to how users can adapt their code if they were using these stores.

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jhamman commented Oct 14, 2024

closing as we have done this elsewhere

@jhamman jhamman closed this Oct 14, 2024
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9 participants