obstore-based Store implementation

[kylebarron]

A Zarr store based on obstore, which is a Python library that uses the Rust object_store crate under the hood.

object-store is a rust crate for interoperating with remote object stores like S3, GCS, Azure, etc. See the highlights section of its docs.

obstore maps async Rust functions to async Python functions, and is able to stream GET and LIST requests, which all make it a good candidate for use with the Zarr v3 Store protocol.

You should be able to test this branch with the latest pre-release version of obstore:

pip install --pre --upgrade obstore

TODO:

• Examples
• 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)

[jhamman]

Amazing @kylebarron! I'll spend some time playing with this today.

[kylebarron]

With roeap/object-store-python#9 it should be possible to fetch multiple ranges within a file concurrently with range coalescing (using get_ranges_async). Note that this object-store API accepts multiple ranges within one object, which is still not 100% aligned with the Zarr get_partial_values because that allows fetches across multiple objects.

That PR also adds a get_opts function which now supports "offset" and "suffix" ranges, of the sort Range:N- and Range:-N, which would allow removing the raise NotImplementedError on line 37.

[martindurant]

martindurant/rfsspec#3

[normanrz]

Great work @kylebarron!
What are everbody's thoughts on having this in zarr-python vs. spinning it out as a separate package?

[martindurant]

What are everbody's thoughts on having this in zarr-python vs. spinning it out as a separate package?

I suggest we see whether it makes any improvements first, so it's author's choice for now.

[kylebarron]

While @rabernat has seen some impressive perf improvements in some settings when making many requests with Rust's tokio runtime, which would possibly also trickle down to a Python binding, the biggest advantage I see is improved ease of use in installation.

A common hurdle I've seen is handling dependency management, especially around boto3, aioboto3, etc dependencies. Versions need to be compatible at runtime with any other libraries the user also has in their environment. And Python doesn't allow multiple versions of the same dependency at the same time in one environment. With a Python library wrapping a statically-linked Rust binary, you can remove all Python dependencies and remove this class of hardship.

The underlying Rust object-store crate is stable and under open governance via the Apache Arrow project. We'll just have to wait on some discussion in object-store-python for exactly where that should live.

I don't have an opinion myself on where this should live, but it should be on the order of 100 lines of code wherever it is (unless the v3 store api changes dramatically)

[jhamman]

I suggest we see whether it makes any improvements first, so it's author's choice for now.

👍

What are everbody's thoughts on having this in zarr-python vs. spinning it out as a separate package?

I want to keep an open mind about what the core stores provided by Zarr-Python are. My current thinking is that we should just do a MemoryStore and a LocalFilesystemStore. Everything else can be opt-in by installing a 3rd party package. That said, I like having a few additional stores in the mix as we develop the store interface since it helps us think about the design more broadly.

[martindurant]

A common hurdle I've seen is handling dependency management, especially around boto3, aioboto3, etc dependencies.

This is no longer an issue, s3fs has much more relaxed deps than it used to. Furthermore, it's very likely to be already part of an installation environment.

[normanrz]

I want to keep an open mind about what the core stores provided by Zarr-Python are. My current thinking is that we should just do a MemoryStore and a LocalFilesystemStore. Everything else can be opt-in by installing a 3rd party package.

I agree with that. I think it is beneficial to keep the number of dependencies of core zarr-python small. But, I am open for discussion.

That said, I like having a few additional stores in the mix as we develop the store interface since it helps us think about the design more broadly.

Sure! That is certainly useful.

[itsgifnotjiff]

This is awesome work, thank you all!!!

[kylebarron]

The object-store-python package is not very well maintained roeap/object-store-python#24, so I took a few days to implement my own wrapper around the Rust object_store crate: https://github.com/developmentseed/object-store-rs

I'd like to update this PR soonish to use that library instead.

[martindurant]

If the zarr group prefers object-store-rs, we can move it into the zarr-developers org, if you like. I would like to be involved in developing it, particularly if it can grow more explicit fsspec compatible functionality.

[kylebarron]

I have a few questions because the Store API has changed a bit since the spring.

• There's a new BufferPrototype object. Is the BufferPrototype chosen by the store implementation or the caller? It would be very nice if this prototype could be chosen by the store implementation, because then we could return a RustBuffer object that implements the Python buffer protocol, but doesn't need to copy the buffer into Python memory.
• Similarly for puts, is Buffer guaranteed to implement the buffer protocol? Contrary to fetching, we can't do zero-copy puts right now with object-store

I like that list now returns an AsyncGenerator. That aligns well with the underlying object-store rust API, but for technical reasons we can't expose that as an async iterable to Python yet (apache/arrow-rs#6587), even though we do expose the readable stream to Python as an async iterable.

[TomAugspurger]

Is the BufferPrototype chosen by the store implementation or the caller? It would be very nice if this prototype could be chosen by the store implementation, because then we could return a RustBuffer object that implements the Python buffer protocol, but doesn't need to copy the buffer into Python memory.

This came up in the discussion at https://github.com/zarr-developers/zarr-python/pull/2426/files/5e0ffe80d039d9261517d96ce87220ce8d48e4f2#diff-bb6bb03f87fe9491ef78156256160d798369749b4b35c06d4f275425bdb6c4ad. By default, it's passed as default_buffer_prototype though I think the user can override at the call site or globally.

Does it look compatible with what you need?

[kylebarron]

It looks like this is now passing all tests, with just Read the docs and codecov targets not hit.

What are the final steps for this PR? Where should we write documentation?

[jhamman]

It looks like this is now passing all tests, with just Read the docs and codecov targets not hit.

🎉

What are the final steps for this PR? Where should we write documentation?

• Make CI happy (@maxrjones is on this)
• Write a short bit of documentation here: https://github.com/zarr-developers/zarr-python/blob/main/docs/user-guide/storage.rst. Note that this store is "currently experimental".

[kylebarron]

obstore 0.4.0 was released and this PR was updated to use that latest version.

Optional dependency

From comment above

1. We want to include this in Zarr-Python so long as obstore is an optional dependency

CI had been failing because (I think) obstore was marked as an optional dependency but then unconditionally exported from zarr.storage.

I removed the re-export from zarr.storage but renamed _object.py to obstore.py. So anyone who wishes to use the obstore-backed class needs to run

import zarr.storage.obstore

themselves. When that import is run, obstore will be imported, and so obstore must exist in the environment at that time.

Alternatively

We could keep the re-export but ensure that obstore.py doesn't import obstore in any public scope. Thoughts?

Future follow up PRs:

• BytesLike type should accept collections.abc.Buffer #2814. This PR added # type: ignore[arg-type] to satisfy passing a buffer protocol object into prototype.buffer.from_bytes

[jhamman]

Regarding the import of obstore, I suggest moving all imports from obstore into the class itself. Users should get an ImportError if they attempt to instantiate the Store without the required dependency.

[martindurant]

You can have

import obstore
self.obs = obstore

in __init__ to avoid having to have import all over the place.

[kylebarron]

We can move the imports into the class; that's fine.

You can have

import obstore
self.obs = obstore

in __init__ to avoid having to have import all over the place.

It's not clear to me how the typing would work there? How would you define the type hint for obs so that self.obs.get would correctly access the same type hint as obstore.get? I'd rather import obstore a bunch than lose that type safety.

[martindurant]

I'm not usually too worried by typing. I'm sure it can be fixed, but fighting with mypy is never fun.

[kylebarron]

We can move the imports into the class; that's fine.

Hmm, moving the imports inside the class caused a pickling error. Maybe this won't work:

FAILED tests/test_store/test_object.py::TestObjectStore::test_serializable_store - TypeError: cannot pickle 'module' object

https://github.com/zarr-developers/zarr-python/actions/runs/13295245421/job/37125558963?pr=1661#step:6:299