basic support for v2 and v3 groups by jhamman · Pull Request #1590 · zarr-developers/zarr-python

jhamman · 2023-12-05T20:06:48Z

This begins the work of harmonizing the V2 and V3 group APIs from Zarrita with the Zarr-Python Group API.

I'll leave some comments inline.

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)

pep8speaks · 2023-12-05T20:07:00Z

Hello @jhamman! Thanks for updating this PR. We checked the lines you've touched for PEP 8 issues, and found:

In the file zarr/v3/__init__.py:

Line 30:1: W293 blank line contains whitespace

Comment last updated at 2023-12-06 15:13:06 UTC

jhamman

A few thoughts below 👇

jhamman · 2023-12-05T20:08:47Z

 attributes: Dict[str, Any] = field(factory=dict)
- zarr_format: Literal[3] = 3
- node_type: Literal["group"] = "group"
+ zarr_format: Literal[2, 3] = 3 # field(default=3, validator=validators.in_([2, 3]))


@normanrz - I tried this and failed! Happy to return to it later.

jhamman · 2023-12-05T20:21:24Z

+
+ @abstractmethod
+ def __setitem__(self, key: str, value: Union[SyncArray, "SyncGroup"]) -> None:
+ """get child"""


Suggested change
"""get child"""
Proposing that we do away with Group.__setitem__ all together. It really doesn't make sense to include in the api.

jhamman · 2023-12-05T20:22:03Z

+ @abstractmethod
+ def group_keys(self) -> AsyncIterator[str]:
+ """iterate over child group keys"""
+ ...


all of these iterators need listable stores before they can be built.

jhamman · 2023-12-05T20:31:28Z

+@frozen
+class SyncConfiguration:
+ concurrency: Optional[int] = None
+ asyncio_loop: Optional[AbstractEventLoop] = None


this was a half hearted attempt at rethinking the config topic. I expect this to go away soon.

jhamman · 2023-12-05T20:32:54Z

+ def __setitem__(self, key, value):
+ raise NotImplementedError


Suggested change
def__setitem__(self, key, value):
raiseNotImplementedError

jhamman · 2023-12-05T20:35:16Z

+ return self._sync(self._async_group.nchildren)
+
+ @property
+ def children(self) -> List[Array, "Group"]:


some exploratory work is needed to figure out how to make this (and similar methods) a proper iterator/generator instead of a list. The tricky bit is that the async method is returning an AsyncIterator and we need to synchronize that into a regular Iterator.

normanrz · 2023-12-06T09:59:24Z

Now that there is only 1 Group and AsyncGroup. Do we actually want to keep the Group ABC?

@d-v-b and I were just talking about that last night. I think the answer is NO. For ABCs, I we probably only need the Store and Codec base classes.

normanrz · 2023-12-06T10:07:38Z

+ # TODO: consider trying to autodiscover the zarr-format here
+ if zarr_format == 3:
+ # V3 groups are comprised of a zarr.json object
+ # (it is optional in the case of implicit groups)


Are implicit groups really a thing? I don't think they show up in the v3 spec.

They do show up in the spec (in quite a few places actually)! https://zarr-specs.readthedocs.io/en/latest/v3/core/v3.0.html#explicit-vs-implicit-groups

I didn't know that!

normanrz · 2023-12-06T10:08:28Z

+ if self.zarr_format == 3:
+ zarr_json_bytes = await (store_path / ZARR_JSON).get_async()
+ if zarr_json_bytes is None:
+ # implicit group?


This is a bit dangerous because we have no good way of telling whether this path even exists.

I agree and we should return to this. For now I'm going to put a log statement there and we can address this later.

normanrz · 2023-12-06T10:09:42Z

+ store_path, zarr_json, runtime_configuration=self.runtime_configuration
+ )
+ elif self.zarr_format == 2:
+ # Q: how do we like optimistically fetching .zgroup, .zarray, and .zattrs?


I think the overfetching is fine because it is happening in parallel.

I was thinking about this issue the other day. One possible behavior when you "open" anything in Zarr would be to call the store.tree(depth=1) method, fetching all existing metadata docs at the root level and one level below.

- removed abcs for groups/arrays - improved return types in group.py - warn (temporarily) when an implicit group is found - add attributes.py with Attributes class

d-v-b · 2023-12-06T17:00:12Z

+ elif self.zarr_format == 2:
+ return {
+ ZGROUP_JSON: self.zarr_format,
+ ZATTRS_JSON: json.dumps(self.attributes).encode(),


how would custom JSON serialization of user attributes plug in here? e.g., i don't think numpy dtype objects serialize to JSON easily. Maybe to_bytes can take a attrs_serializer kwarg or something.

d-v-b · 2023-12-06T17:08:39Z

+ def create_array(self, name: str, **kwargs) -> Array:
+ return Array(self._sync(self._async_group.create_array(name, **kwargs)))
+
+ def empty(self, **kwargs) -> Array:


thoughts on ultimately putting these routines in a dedicated namespace?

d-v-b · 2023-12-06T17:09:14Z

+ try:
+ if self.store == other.store and self.path == other.path:
+ return True
+ except Exception:


we can probably be a bit more specific about the exception type here

jhamman · 2023-12-05T20:06:48Z

This begins the work of harmonizing the V2 and V3 group APIs from Zarrita with the Zarr-Python Group API.

I'll leave some comments inline.

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)

pep8speaks · 2023-12-05T20:07:00Z

Hello @jhamman! Thanks for updating this PR. We checked the lines you've touched for PEP 8 issues, and found:

In the file zarr/v3/__init__.py:

Line 30:1: W293 blank line contains whitespace

Comment last updated at 2023-12-06 15:13:06 UTC

jhamman

A few thoughts below 👇

jhamman · 2023-12-05T20:08:47Z

 attributes: Dict[str, Any] = field(factory=dict)
- zarr_format: Literal[3] = 3
- node_type: Literal["group"] = "group"
+ zarr_format: Literal[2, 3] = 3 # field(default=3, validator=validators.in_([2, 3]))


@normanrz - I tried this and failed! Happy to return to it later.

jhamman · 2023-12-05T20:21:24Z

+
+ @abstractmethod
+ def __setitem__(self, key: str, value: Union[SyncArray, "SyncGroup"]) -> None:
+ """get child"""


Suggested change
"""get child"""
Proposing that we do away with Group.__setitem__ all together. It really doesn't make sense to include in the api.

jhamman · 2023-12-05T20:22:03Z

+ @abstractmethod
+ def group_keys(self) -> AsyncIterator[str]:
+ """iterate over child group keys"""
+ ...


all of these iterators need listable stores before they can be built.

jhamman · 2023-12-05T20:31:28Z

+@frozen
+class SyncConfiguration:
+ concurrency: Optional[int] = None
+ asyncio_loop: Optional[AbstractEventLoop] = None


this was a half hearted attempt at rethinking the config topic. I expect this to go away soon.

jhamman · 2023-12-05T20:32:54Z

+ def __setitem__(self, key, value):
+ raise NotImplementedError


Suggested change
def__setitem__(self, key, value):
raiseNotImplementedError

jhamman · 2023-12-05T20:35:16Z

+ return self._sync(self._async_group.nchildren)
+
+ @property
+ def children(self) -> List[Array, "Group"]:


some exploratory work is needed to figure out how to make this (and similar methods) a proper iterator/generator instead of a list. The tricky bit is that the async method is returning an AsyncIterator and we need to synchronize that into a regular Iterator.

normanrz · 2023-12-06T09:59:24Z

Now that there is only 1 Group and AsyncGroup. Do we actually want to keep the Group ABC?

@d-v-b and I were just talking about that last night. I think the answer is NO. For ABCs, I we probably only need the Store and Codec base classes.

normanrz · 2023-12-06T10:07:38Z

+ # TODO: consider trying to autodiscover the zarr-format here
+ if zarr_format == 3:
+ # V3 groups are comprised of a zarr.json object
+ # (it is optional in the case of implicit groups)


Are implicit groups really a thing? I don't think they show up in the v3 spec.

They do show up in the spec (in quite a few places actually)! https://zarr-specs.readthedocs.io/en/latest/v3/core/v3.0.html#explicit-vs-implicit-groups

I didn't know that!

normanrz · 2023-12-06T10:08:28Z

+ if self.zarr_format == 3:
+ zarr_json_bytes = await (store_path / ZARR_JSON).get_async()
+ if zarr_json_bytes is None:
+ # implicit group?


This is a bit dangerous because we have no good way of telling whether this path even exists.

I agree and we should return to this. For now I'm going to put a log statement there and we can address this later.

normanrz · 2023-12-06T10:09:42Z

+ store_path, zarr_json, runtime_configuration=self.runtime_configuration
+ )
+ elif self.zarr_format == 2:
+ # Q: how do we like optimistically fetching .zgroup, .zarray, and .zattrs?


I think the overfetching is fine because it is happening in parallel.

I was thinking about this issue the other day. One possible behavior when you "open" anything in Zarr would be to call the store.tree(depth=1) method, fetching all existing metadata docs at the root level and one level below.

- removed abcs for groups/arrays - improved return types in group.py - warn (temporarily) when an implicit group is found - add attributes.py with Attributes class

d-v-b · 2023-12-06T17:00:12Z

+ elif self.zarr_format == 2:
+ return {
+ ZGROUP_JSON: self.zarr_format,
+ ZATTRS_JSON: json.dumps(self.attributes).encode(),


how would custom JSON serialization of user attributes plug in here? e.g., i don't think numpy dtype objects serialize to JSON easily. Maybe to_bytes can take a attrs_serializer kwarg or something.

d-v-b · 2023-12-06T17:08:39Z

+ def create_array(self, name: str, **kwargs) -> Array:
+ return Array(self._sync(self._async_group.create_array(name, **kwargs)))
+
+ def empty(self, **kwargs) -> Array:


thoughts on ultimately putting these routines in a dedicated namespace?

d-v-b · 2023-12-06T17:09:14Z

+ try:
+ if self.store == other.store and self.path == other.path:
+ return True
+ except Exception:


we can probably be a bit more specific about the exception type here

jhamman · 2023-12-05T20:06:48Z

This begins the work of harmonizing the V2 and V3 group APIs from Zarrita with the Zarr-Python Group API.

I'll leave some comments inline.

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)

pep8speaks · 2023-12-05T20:07:00Z

Hello @jhamman! Thanks for updating this PR. We checked the lines you've touched for PEP 8 issues, and found:

In the file zarr/v3/__init__.py:

Line 30:1: W293 blank line contains whitespace

Comment last updated at 2023-12-06 15:13:06 UTC

jhamman

A few thoughts below 👇

jhamman · 2023-12-05T20:08:47Z

 attributes: Dict[str, Any] = field(factory=dict)
- zarr_format: Literal[3] = 3
- node_type: Literal["group"] = "group"
+ zarr_format: Literal[2, 3] = 3 # field(default=3, validator=validators.in_([2, 3]))


@normanrz - I tried this and failed! Happy to return to it later.

jhamman · 2023-12-05T20:21:24Z

+
+ @abstractmethod
+ def __setitem__(self, key: str, value: Union[SyncArray, "SyncGroup"]) -> None:
+ """get child"""


Suggested change
"""get child"""
Proposing that we do away with Group.__setitem__ all together. It really doesn't make sense to include in the api.

jhamman · 2023-12-05T20:22:03Z

+ @abstractmethod
+ def group_keys(self) -> AsyncIterator[str]:
+ """iterate over child group keys"""
+ ...


all of these iterators need listable stores before they can be built.

jhamman · 2023-12-05T20:31:28Z

+@frozen
+class SyncConfiguration:
+ concurrency: Optional[int] = None
+ asyncio_loop: Optional[AbstractEventLoop] = None


this was a half hearted attempt at rethinking the config topic. I expect this to go away soon.

jhamman · 2023-12-05T20:32:54Z

+ def __setitem__(self, key, value):
+ raise NotImplementedError


Suggested change
def__setitem__(self, key, value):
raiseNotImplementedError

jhamman · 2023-12-05T20:35:16Z

+ return self._sync(self._async_group.nchildren)
+
+ @property
+ def children(self) -> List[Array, "Group"]:


some exploratory work is needed to figure out how to make this (and similar methods) a proper iterator/generator instead of a list. The tricky bit is that the async method is returning an AsyncIterator and we need to synchronize that into a regular Iterator.

normanrz · 2023-12-06T09:59:24Z

Now that there is only 1 Group and AsyncGroup. Do we actually want to keep the Group ABC?

@d-v-b and I were just talking about that last night. I think the answer is NO. For ABCs, I we probably only need the Store and Codec base classes.

normanrz · 2023-12-06T10:07:38Z

+ # TODO: consider trying to autodiscover the zarr-format here
+ if zarr_format == 3:
+ # V3 groups are comprised of a zarr.json object
+ # (it is optional in the case of implicit groups)


Are implicit groups really a thing? I don't think they show up in the v3 spec.

They do show up in the spec (in quite a few places actually)! https://zarr-specs.readthedocs.io/en/latest/v3/core/v3.0.html#explicit-vs-implicit-groups

I didn't know that!

normanrz · 2023-12-06T10:08:28Z

+ if self.zarr_format == 3:
+ zarr_json_bytes = await (store_path / ZARR_JSON).get_async()
+ if zarr_json_bytes is None:
+ # implicit group?


This is a bit dangerous because we have no good way of telling whether this path even exists.

I agree and we should return to this. For now I'm going to put a log statement there and we can address this later.

normanrz · 2023-12-06T10:09:42Z

+ store_path, zarr_json, runtime_configuration=self.runtime_configuration
+ )
+ elif self.zarr_format == 2:
+ # Q: how do we like optimistically fetching .zgroup, .zarray, and .zattrs?


I think the overfetching is fine because it is happening in parallel.

I was thinking about this issue the other day. One possible behavior when you "open" anything in Zarr would be to call the store.tree(depth=1) method, fetching all existing metadata docs at the root level and one level below.

- removed abcs for groups/arrays - improved return types in group.py - warn (temporarily) when an implicit group is found - add attributes.py with Attributes class

d-v-b · 2023-12-06T17:00:12Z

+ elif self.zarr_format == 2:
+ return {
+ ZGROUP_JSON: self.zarr_format,
+ ZATTRS_JSON: json.dumps(self.attributes).encode(),


how would custom JSON serialization of user attributes plug in here? e.g., i don't think numpy dtype objects serialize to JSON easily. Maybe to_bytes can take a attrs_serializer kwarg or something.

d-v-b · 2023-12-06T17:08:39Z

+ def create_array(self, name: str, **kwargs) -> Array:
+ return Array(self._sync(self._async_group.create_array(name, **kwargs)))
+
+ def empty(self, **kwargs) -> Array:


thoughts on ultimately putting these routines in a dedicated namespace?

d-v-b · 2023-12-06T17:09:14Z

+ try:
+ if self.store == other.store and self.path == other.path:
+ return True
+ except Exception:


we can probably be a bit more specific about the exception type here

jhamman · 2023-12-05T20:06:48Z

This begins the work of harmonizing the V2 and V3 group APIs from Zarrita with the Zarr-Python Group API.

I'll leave some comments inline.

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)

pep8speaks · 2023-12-05T20:07:00Z

Hello @jhamman! Thanks for updating this PR. We checked the lines you've touched for PEP 8 issues, and found:

In the file zarr/v3/__init__.py:

Line 30:1: W293 blank line contains whitespace

Comment last updated at 2023-12-06 15:13:06 UTC

jhamman

A few thoughts below 👇

jhamman · 2023-12-05T20:08:47Z

 attributes: Dict[str, Any] = field(factory=dict)
- zarr_format: Literal[3] = 3
- node_type: Literal["group"] = "group"
+ zarr_format: Literal[2, 3] = 3 # field(default=3, validator=validators.in_([2, 3]))


@normanrz - I tried this and failed! Happy to return to it later.

jhamman · 2023-12-05T20:21:24Z

+
+ @abstractmethod
+ def __setitem__(self, key: str, value: Union[SyncArray, "SyncGroup"]) -> None:
+ """get child"""


Suggested change
"""get child"""
Proposing that we do away with Group.__setitem__ all together. It really doesn't make sense to include in the api.

jhamman · 2023-12-05T20:22:03Z

+ @abstractmethod
+ def group_keys(self) -> AsyncIterator[str]:
+ """iterate over child group keys"""
+ ...


all of these iterators need listable stores before they can be built.

jhamman · 2023-12-05T20:31:28Z

+@frozen
+class SyncConfiguration:
+ concurrency: Optional[int] = None
+ asyncio_loop: Optional[AbstractEventLoop] = None


this was a half hearted attempt at rethinking the config topic. I expect this to go away soon.

jhamman · 2023-12-05T20:32:54Z

+ def __setitem__(self, key, value):
+ raise NotImplementedError


Suggested change
def__setitem__(self, key, value):
raiseNotImplementedError

jhamman · 2023-12-05T20:35:16Z

+ return self._sync(self._async_group.nchildren)
+
+ @property
+ def children(self) -> List[Array, "Group"]:


some exploratory work is needed to figure out how to make this (and similar methods) a proper iterator/generator instead of a list. The tricky bit is that the async method is returning an AsyncIterator and we need to synchronize that into a regular Iterator.

normanrz · 2023-12-06T09:59:24Z

Now that there is only 1 Group and AsyncGroup. Do we actually want to keep the Group ABC?

@d-v-b and I were just talking about that last night. I think the answer is NO. For ABCs, I we probably only need the Store and Codec base classes.

normanrz · 2023-12-06T10:07:38Z

+ # TODO: consider trying to autodiscover the zarr-format here
+ if zarr_format == 3:
+ # V3 groups are comprised of a zarr.json object
+ # (it is optional in the case of implicit groups)


Are implicit groups really a thing? I don't think they show up in the v3 spec.

They do show up in the spec (in quite a few places actually)! https://zarr-specs.readthedocs.io/en/latest/v3/core/v3.0.html#explicit-vs-implicit-groups

I didn't know that!

normanrz · 2023-12-06T10:08:28Z

+ if self.zarr_format == 3:
+ zarr_json_bytes = await (store_path / ZARR_JSON).get_async()
+ if zarr_json_bytes is None:
+ # implicit group?


This is a bit dangerous because we have no good way of telling whether this path even exists.

I agree and we should return to this. For now I'm going to put a log statement there and we can address this later.

normanrz · 2023-12-06T10:09:42Z

+ store_path, zarr_json, runtime_configuration=self.runtime_configuration
+ )
+ elif self.zarr_format == 2:
+ # Q: how do we like optimistically fetching .zgroup, .zarray, and .zattrs?


I think the overfetching is fine because it is happening in parallel.

I was thinking about this issue the other day. One possible behavior when you "open" anything in Zarr would be to call the store.tree(depth=1) method, fetching all existing metadata docs at the root level and one level below.

- removed abcs for groups/arrays - improved return types in group.py - warn (temporarily) when an implicit group is found - add attributes.py with Attributes class

d-v-b · 2023-12-06T17:00:12Z

+ elif self.zarr_format == 2:
+ return {
+ ZGROUP_JSON: self.zarr_format,
+ ZATTRS_JSON: json.dumps(self.attributes).encode(),


how would custom JSON serialization of user attributes plug in here? e.g., i don't think numpy dtype objects serialize to JSON easily. Maybe to_bytes can take a attrs_serializer kwarg or something.

d-v-b · 2023-12-06T17:08:39Z

+ def create_array(self, name: str, **kwargs) -> Array:
+ return Array(self._sync(self._async_group.create_array(name, **kwargs)))
+
+ def empty(self, **kwargs) -> Array:


thoughts on ultimately putting these routines in a dedicated namespace?

d-v-b · 2023-12-06T17:09:14Z

+ try:
+ if self.store == other.store and self.path == other.path:
+ return True
+ except Exception:


we can probably be a bit more specific about the exception type here

jhamman · 2023-12-05T20:06:48Z

This begins the work of harmonizing the V2 and V3 group APIs from Zarrita with the Zarr-Python Group API.

I'll leave some comments inline.

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)

pep8speaks · 2023-12-05T20:07:00Z

Hello @jhamman! Thanks for updating this PR. We checked the lines you've touched for PEP 8 issues, and found:

In the file zarr/v3/__init__.py:

Line 30:1: W293 blank line contains whitespace

Comment last updated at 2023-12-06 15:13:06 UTC

jhamman

A few thoughts below 👇

jhamman · 2023-12-05T20:08:47Z

 attributes: Dict[str, Any] = field(factory=dict)
- zarr_format: Literal[3] = 3
- node_type: Literal["group"] = "group"
+ zarr_format: Literal[2, 3] = 3 # field(default=3, validator=validators.in_([2, 3]))


@normanrz - I tried this and failed! Happy to return to it later.

jhamman · 2023-12-05T20:21:24Z

+
+ @abstractmethod
+ def __setitem__(self, key: str, value: Union[SyncArray, "SyncGroup"]) -> None:
+ """get child"""


Suggested change
"""get child"""
Proposing that we do away with Group.__setitem__ all together. It really doesn't make sense to include in the api.

jhamman · 2023-12-05T20:22:03Z

+ @abstractmethod
+ def group_keys(self) -> AsyncIterator[str]:
+ """iterate over child group keys"""
+ ...


all of these iterators need listable stores before they can be built.

jhamman · 2023-12-05T20:31:28Z

+@frozen
+class SyncConfiguration:
+ concurrency: Optional[int] = None
+ asyncio_loop: Optional[AbstractEventLoop] = None


this was a half hearted attempt at rethinking the config topic. I expect this to go away soon.

jhamman · 2023-12-05T20:32:54Z

+ def __setitem__(self, key, value):
+ raise NotImplementedError


Suggested change
def__setitem__(self, key, value):
raiseNotImplementedError

jhamman · 2023-12-05T20:35:16Z

+ return self._sync(self._async_group.nchildren)
+
+ @property
+ def children(self) -> List[Array, "Group"]:


some exploratory work is needed to figure out how to make this (and similar methods) a proper iterator/generator instead of a list. The tricky bit is that the async method is returning an AsyncIterator and we need to synchronize that into a regular Iterator.

normanrz · 2023-12-06T09:59:24Z

Now that there is only 1 Group and AsyncGroup. Do we actually want to keep the Group ABC?

@d-v-b and I were just talking about that last night. I think the answer is NO. For ABCs, I we probably only need the Store and Codec base classes.

normanrz · 2023-12-06T10:07:38Z

+ # TODO: consider trying to autodiscover the zarr-format here
+ if zarr_format == 3:
+ # V3 groups are comprised of a zarr.json object
+ # (it is optional in the case of implicit groups)


Are implicit groups really a thing? I don't think they show up in the v3 spec.

They do show up in the spec (in quite a few places actually)! https://zarr-specs.readthedocs.io/en/latest/v3/core/v3.0.html#explicit-vs-implicit-groups

I didn't know that!

normanrz · 2023-12-06T10:08:28Z

+ if self.zarr_format == 3:
+ zarr_json_bytes = await (store_path / ZARR_JSON).get_async()
+ if zarr_json_bytes is None:
+ # implicit group?


This is a bit dangerous because we have no good way of telling whether this path even exists.

I agree and we should return to this. For now I'm going to put a log statement there and we can address this later.

normanrz · 2023-12-06T10:09:42Z

+ store_path, zarr_json, runtime_configuration=self.runtime_configuration
+ )
+ elif self.zarr_format == 2:
+ # Q: how do we like optimistically fetching .zgroup, .zarray, and .zattrs?


I think the overfetching is fine because it is happening in parallel.

I was thinking about this issue the other day. One possible behavior when you "open" anything in Zarr would be to call the store.tree(depth=1) method, fetching all existing metadata docs at the root level and one level below.

- removed abcs for groups/arrays - improved return types in group.py - warn (temporarily) when an implicit group is found - add attributes.py with Attributes class

d-v-b · 2023-12-06T17:00:12Z

+ elif self.zarr_format == 2:
+ return {
+ ZGROUP_JSON: self.zarr_format,
+ ZATTRS_JSON: json.dumps(self.attributes).encode(),


how would custom JSON serialization of user attributes plug in here? e.g., i don't think numpy dtype objects serialize to JSON easily. Maybe to_bytes can take a attrs_serializer kwarg or something.

d-v-b · 2023-12-06T17:08:39Z

+ def create_array(self, name: str, **kwargs) -> Array:
+ return Array(self._sync(self._async_group.create_array(name, **kwargs)))
+
+ def empty(self, **kwargs) -> Array:


thoughts on ultimately putting these routines in a dedicated namespace?

d-v-b · 2023-12-06T17:09:14Z

+ try:
+ if self.store == other.store and self.path == other.path:
+ return True
+ except Exception:


we can probably be a bit more specific about the exception type here

jhamman · 2023-12-05T20:06:48Z

This begins the work of harmonizing the V2 and V3 group APIs from Zarrita with the Zarr-Python Group API.

I'll leave some comments inline.

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)

pep8speaks · 2023-12-05T20:07:00Z

Hello @jhamman! Thanks for updating this PR. We checked the lines you've touched for PEP 8 issues, and found:

In the file zarr/v3/__init__.py:

Line 30:1: W293 blank line contains whitespace

Comment last updated at 2023-12-06 15:13:06 UTC

jhamman

A few thoughts below 👇

jhamman · 2023-12-05T20:08:47Z

 attributes: Dict[str, Any] = field(factory=dict)
- zarr_format: Literal[3] = 3
- node_type: Literal["group"] = "group"
+ zarr_format: Literal[2, 3] = 3 # field(default=3, validator=validators.in_([2, 3]))


@normanrz - I tried this and failed! Happy to return to it later.

jhamman · 2023-12-05T20:21:24Z

+
+ @abstractmethod
+ def __setitem__(self, key: str, value: Union[SyncArray, "SyncGroup"]) -> None:
+ """get child"""


Suggested change
"""get child"""
Proposing that we do away with Group.__setitem__ all together. It really doesn't make sense to include in the api.

jhamman · 2023-12-05T20:22:03Z

+ @abstractmethod
+ def group_keys(self) -> AsyncIterator[str]:
+ """iterate over child group keys"""
+ ...


all of these iterators need listable stores before they can be built.

jhamman · 2023-12-05T20:31:28Z

+@frozen
+class SyncConfiguration:
+ concurrency: Optional[int] = None
+ asyncio_loop: Optional[AbstractEventLoop] = None


this was a half hearted attempt at rethinking the config topic. I expect this to go away soon.

jhamman · 2023-12-05T20:32:54Z

+ def __setitem__(self, key, value):
+ raise NotImplementedError


Suggested change
def__setitem__(self, key, value):
raiseNotImplementedError

jhamman · 2023-12-05T20:35:16Z

+ return self._sync(self._async_group.nchildren)
+
+ @property
+ def children(self) -> List[Array, "Group"]:


some exploratory work is needed to figure out how to make this (and similar methods) a proper iterator/generator instead of a list. The tricky bit is that the async method is returning an AsyncIterator and we need to synchronize that into a regular Iterator.

normanrz · 2023-12-06T09:59:24Z

Now that there is only 1 Group and AsyncGroup. Do we actually want to keep the Group ABC?

@d-v-b and I were just talking about that last night. I think the answer is NO. For ABCs, I we probably only need the Store and Codec base classes.

normanrz · 2023-12-06T10:07:38Z

+ # TODO: consider trying to autodiscover the zarr-format here
+ if zarr_format == 3:
+ # V3 groups are comprised of a zarr.json object
+ # (it is optional in the case of implicit groups)


Are implicit groups really a thing? I don't think they show up in the v3 spec.

They do show up in the spec (in quite a few places actually)! https://zarr-specs.readthedocs.io/en/latest/v3/core/v3.0.html#explicit-vs-implicit-groups

I didn't know that!

normanrz · 2023-12-06T10:08:28Z

+ if self.zarr_format == 3:
+ zarr_json_bytes = await (store_path / ZARR_JSON).get_async()
+ if zarr_json_bytes is None:
+ # implicit group?


This is a bit dangerous because we have no good way of telling whether this path even exists.

I agree and we should return to this. For now I'm going to put a log statement there and we can address this later.

normanrz · 2023-12-06T10:09:42Z

+ store_path, zarr_json, runtime_configuration=self.runtime_configuration
+ )
+ elif self.zarr_format == 2:
+ # Q: how do we like optimistically fetching .zgroup, .zarray, and .zattrs?


I think the overfetching is fine because it is happening in parallel.

I was thinking about this issue the other day. One possible behavior when you "open" anything in Zarr would be to call the store.tree(depth=1) method, fetching all existing metadata docs at the root level and one level below.

- removed abcs for groups/arrays - improved return types in group.py - warn (temporarily) when an implicit group is found - add attributes.py with Attributes class

d-v-b · 2023-12-06T17:00:12Z

+ elif self.zarr_format == 2:
+ return {
+ ZGROUP_JSON: self.zarr_format,
+ ZATTRS_JSON: json.dumps(self.attributes).encode(),


how would custom JSON serialization of user attributes plug in here? e.g., i don't think numpy dtype objects serialize to JSON easily. Maybe to_bytes can take a attrs_serializer kwarg or something.

d-v-b · 2023-12-06T17:08:39Z

+ def create_array(self, name: str, **kwargs) -> Array:
+ return Array(self._sync(self._async_group.create_array(name, **kwargs)))
+
+ def empty(self, **kwargs) -> Array:


thoughts on ultimately putting these routines in a dedicated namespace?

d-v-b · 2023-12-06T17:09:14Z

+ try:
+ if self.store == other.store and self.path == other.path:
+ return True
+ except Exception:


we can probably be a bit more specific about the exception type here

jhamman · 2023-12-05T20:06:48Z

This begins the work of harmonizing the V2 and V3 group APIs from Zarrita with the Zarr-Python Group API.

I'll leave some comments inline.

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)

pep8speaks · 2023-12-05T20:07:00Z

Hello @jhamman! Thanks for updating this PR. We checked the lines you've touched for PEP 8 issues, and found:

In the file zarr/v3/__init__.py:

Line 30:1: W293 blank line contains whitespace

Comment last updated at 2023-12-06 15:13:06 UTC

jhamman

A few thoughts below 👇

jhamman · 2023-12-05T20:08:47Z

 attributes: Dict[str, Any] = field(factory=dict)
- zarr_format: Literal[3] = 3
- node_type: Literal["group"] = "group"
+ zarr_format: Literal[2, 3] = 3 # field(default=3, validator=validators.in_([2, 3]))


@normanrz - I tried this and failed! Happy to return to it later.

jhamman · 2023-12-05T20:21:24Z

+
+ @abstractmethod
+ def __setitem__(self, key: str, value: Union[SyncArray, "SyncGroup"]) -> None:
+ """get child"""


Suggested change
"""get child"""
Proposing that we do away with Group.__setitem__ all together. It really doesn't make sense to include in the api.

jhamman · 2023-12-05T20:22:03Z

+ @abstractmethod
+ def group_keys(self) -> AsyncIterator[str]:
+ """iterate over child group keys"""
+ ...


all of these iterators need listable stores before they can be built.

jhamman · 2023-12-05T20:31:28Z

+@frozen
+class SyncConfiguration:
+ concurrency: Optional[int] = None
+ asyncio_loop: Optional[AbstractEventLoop] = None


this was a half hearted attempt at rethinking the config topic. I expect this to go away soon.

jhamman · 2023-12-05T20:32:54Z

+ def __setitem__(self, key, value):
+ raise NotImplementedError


Suggested change
def__setitem__(self, key, value):
raiseNotImplementedError

jhamman · 2023-12-05T20:35:16Z

+ return self._sync(self._async_group.nchildren)
+
+ @property
+ def children(self) -> List[Array, "Group"]:


some exploratory work is needed to figure out how to make this (and similar methods) a proper iterator/generator instead of a list. The tricky bit is that the async method is returning an AsyncIterator and we need to synchronize that into a regular Iterator.

normanrz · 2023-12-06T09:59:24Z

Now that there is only 1 Group and AsyncGroup. Do we actually want to keep the Group ABC?

@d-v-b and I were just talking about that last night. I think the answer is NO. For ABCs, I we probably only need the Store and Codec base classes.

normanrz · 2023-12-06T10:07:38Z

+ # TODO: consider trying to autodiscover the zarr-format here
+ if zarr_format == 3:
+ # V3 groups are comprised of a zarr.json object
+ # (it is optional in the case of implicit groups)


Are implicit groups really a thing? I don't think they show up in the v3 spec.

They do show up in the spec (in quite a few places actually)! https://zarr-specs.readthedocs.io/en/latest/v3/core/v3.0.html#explicit-vs-implicit-groups

I didn't know that!

normanrz · 2023-12-06T10:08:28Z

+ if self.zarr_format == 3:
+ zarr_json_bytes = await (store_path / ZARR_JSON).get_async()
+ if zarr_json_bytes is None:
+ # implicit group?


This is a bit dangerous because we have no good way of telling whether this path even exists.

I agree and we should return to this. For now I'm going to put a log statement there and we can address this later.

normanrz · 2023-12-06T10:09:42Z

+ store_path, zarr_json, runtime_configuration=self.runtime_configuration
+ )
+ elif self.zarr_format == 2:
+ # Q: how do we like optimistically fetching .zgroup, .zarray, and .zattrs?


I think the overfetching is fine because it is happening in parallel.

I was thinking about this issue the other day. One possible behavior when you "open" anything in Zarr would be to call the store.tree(depth=1) method, fetching all existing metadata docs at the root level and one level below.

- removed abcs for groups/arrays - improved return types in group.py - warn (temporarily) when an implicit group is found - add attributes.py with Attributes class

d-v-b · 2023-12-06T17:00:12Z

+ elif self.zarr_format == 2:
+ return {
+ ZGROUP_JSON: self.zarr_format,
+ ZATTRS_JSON: json.dumps(self.attributes).encode(),


how would custom JSON serialization of user attributes plug in here? e.g., i don't think numpy dtype objects serialize to JSON easily. Maybe to_bytes can take a attrs_serializer kwarg or something.

d-v-b · 2023-12-06T17:08:39Z

+ def create_array(self, name: str, **kwargs) -> Array:
+ return Array(self._sync(self._async_group.create_array(name, **kwargs)))
+
+ def empty(self, **kwargs) -> Array:


thoughts on ultimately putting these routines in a dedicated namespace?

d-v-b · 2023-12-06T17:09:14Z

+ try:
+ if self.store == other.store and self.path == other.path:
+ return True
+ except Exception:


we can probably be a bit more specific about the exception type here

jhamman · 2023-12-05T20:06:48Z

This begins the work of harmonizing the V2 and V3 group APIs from Zarrita with the Zarr-Python Group API.

I'll leave some comments inline.

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)

pep8speaks · 2023-12-05T20:07:00Z

Hello @jhamman! Thanks for updating this PR. We checked the lines you've touched for PEP 8 issues, and found:

In the file zarr/v3/__init__.py:

Line 30:1: W293 blank line contains whitespace

Comment last updated at 2023-12-06 15:13:06 UTC

jhamman

A few thoughts below 👇

jhamman · 2023-12-05T20:08:47Z

 attributes: Dict[str, Any] = field(factory=dict)
- zarr_format: Literal[3] = 3
- node_type: Literal["group"] = "group"
+ zarr_format: Literal[2, 3] = 3 # field(default=3, validator=validators.in_([2, 3]))


@normanrz - I tried this and failed! Happy to return to it later.

jhamman · 2023-12-05T20:21:24Z

+
+ @abstractmethod
+ def __setitem__(self, key: str, value: Union[SyncArray, "SyncGroup"]) -> None:
+ """get child"""


Suggested change
"""get child"""
Proposing that we do away with Group.__setitem__ all together. It really doesn't make sense to include in the api.

jhamman · 2023-12-05T20:22:03Z

+ @abstractmethod
+ def group_keys(self) -> AsyncIterator[str]:
+ """iterate over child group keys"""
+ ...


all of these iterators need listable stores before they can be built.

jhamman · 2023-12-05T20:31:28Z

+@frozen
+class SyncConfiguration:
+ concurrency: Optional[int] = None
+ asyncio_loop: Optional[AbstractEventLoop] = None


this was a half hearted attempt at rethinking the config topic. I expect this to go away soon.

jhamman · 2023-12-05T20:32:54Z

+ def __setitem__(self, key, value):
+ raise NotImplementedError


Suggested change
def__setitem__(self, key, value):
raiseNotImplementedError

jhamman · 2023-12-05T20:35:16Z

+ return self._sync(self._async_group.nchildren)
+
+ @property
+ def children(self) -> List[Array, "Group"]:


some exploratory work is needed to figure out how to make this (and similar methods) a proper iterator/generator instead of a list. The tricky bit is that the async method is returning an AsyncIterator and we need to synchronize that into a regular Iterator.

normanrz · 2023-12-06T09:59:24Z

Now that there is only 1 Group and AsyncGroup. Do we actually want to keep the Group ABC?

@d-v-b and I were just talking about that last night. I think the answer is NO. For ABCs, I we probably only need the Store and Codec base classes.

normanrz · 2023-12-06T10:07:38Z

+ # TODO: consider trying to autodiscover the zarr-format here
+ if zarr_format == 3:
+ # V3 groups are comprised of a zarr.json object
+ # (it is optional in the case of implicit groups)


Are implicit groups really a thing? I don't think they show up in the v3 spec.

They do show up in the spec (in quite a few places actually)! https://zarr-specs.readthedocs.io/en/latest/v3/core/v3.0.html#explicit-vs-implicit-groups

I didn't know that!

normanrz · 2023-12-06T10:08:28Z

+ if self.zarr_format == 3:
+ zarr_json_bytes = await (store_path / ZARR_JSON).get_async()
+ if zarr_json_bytes is None:
+ # implicit group?


This is a bit dangerous because we have no good way of telling whether this path even exists.

I agree and we should return to this. For now I'm going to put a log statement there and we can address this later.

normanrz · 2023-12-06T10:09:42Z

+ store_path, zarr_json, runtime_configuration=self.runtime_configuration
+ )
+ elif self.zarr_format == 2:
+ # Q: how do we like optimistically fetching .zgroup, .zarray, and .zattrs?


I think the overfetching is fine because it is happening in parallel.

I was thinking about this issue the other day. One possible behavior when you "open" anything in Zarr would be to call the store.tree(depth=1) method, fetching all existing metadata docs at the root level and one level below.

- removed abcs for groups/arrays - improved return types in group.py - warn (temporarily) when an implicit group is found - add attributes.py with Attributes class

d-v-b · 2023-12-06T17:00:12Z

+ elif self.zarr_format == 2:
+ return {
+ ZGROUP_JSON: self.zarr_format,
+ ZATTRS_JSON: json.dumps(self.attributes).encode(),


how would custom JSON serialization of user attributes plug in here? e.g., i don't think numpy dtype objects serialize to JSON easily. Maybe to_bytes can take a attrs_serializer kwarg or something.

d-v-b · 2023-12-06T17:08:39Z

+ def create_array(self, name: str, **kwargs) -> Array:
+ return Array(self._sync(self._async_group.create_array(name, **kwargs)))
+
+ def empty(self, **kwargs) -> Array:


thoughts on ultimately putting these routines in a dedicated namespace?

d-v-b · 2023-12-06T17:09:14Z

+ try:
+ if self.store == other.store and self.path == other.path:
+ return True
+ except Exception:


we can probably be a bit more specific about the exception type here

jhamman commented Dec 5, 2023
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basic support for v2 and v3 groups
fae9028

second rev on group apis
7f6a715
- removed abcs for groups/arrays - improved return types in group.py - warn (temporarily) when an implicit group is found - add attributes.py with Attributes class

add test file
84b497f

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implement group.members#1726
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jhamman added 3 commits December 6, 2023 16:22

basic support for v2 and v3 groups
fae9028

second rev on group apis
7f6a715
- removed abcs for groups/arrays - improved return types in group.py - warn (temporarily) when an implicit group is found - add attributes.py with Attributes class

add test file
84b497f

jhamman force-pushed the basic-v2-and-v3-group-support branch from 888551a to 84b497fCompare December 6, 2023 15:24

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This was referenced Jan 16, 2024
Listable V3 Stores #1634
Merged
doc(v3): add v3 roadmap and design document #1583
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jhamman mentioned this pull request Mar 30, 2024
implement group.members#1726
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jhamman added 3 commits December 6, 2023 16:22

basic support for v2 and v3 groups
fae9028

second rev on group apis
7f6a715
- removed abcs for groups/arrays - improved return types in group.py - warn (temporarily) when an implicit group is found - add attributes.py with Attributes class

add test file
84b497f

jhamman force-pushed the basic-v2-and-v3-group-support branch from 888551a to 84b497fCompare December 6, 2023 15:24

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This was referenced Jan 16, 2024
Listable V3 Stores #1634
Merged
doc(v3): add v3 roadmap and design document #1583
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jhamman mentioned this pull request Mar 30, 2024
implement group.members#1726
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jhamman added 3 commits December 6, 2023 16:22

basic support for v2 and v3 groups
fae9028

second rev on group apis
7f6a715
- removed abcs for groups/arrays - improved return types in group.py - warn (temporarily) when an implicit group is found - add attributes.py with Attributes class

add test file
84b497f

jhamman force-pushed the basic-v2-and-v3-group-support branch from 888551a to 84b497fCompare December 6, 2023 15:24

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basic support for v2 and v3 groups
fae9028

second rev on group apis
7f6a715
- removed abcs for groups/arrays - improved return types in group.py - warn (temporarily) when an implicit group is found - add attributes.py with Attributes class

add test file
84b497f

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basic support for v2 and v3 groups
fae9028

second rev on group apis
7f6a715
- removed abcs for groups/arrays - improved return types in group.py - warn (temporarily) when an implicit group is found - add attributes.py with Attributes class

add test file
84b497f

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basic support for v2 and v3 groups
fae9028

second rev on group apis
7f6a715
- removed abcs for groups/arrays - improved return types in group.py - warn (temporarily) when an implicit group is found - add attributes.py with Attributes class

add test file
84b497f

jhamman force-pushed the basic-v2-and-v3-group-support branch from 888551a to 84b497fCompare December 6, 2023 15:24

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Listable V3 Stores #1634
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doc(v3): add v3 roadmap and design document #1583
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implement group.members#1726
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basic support for v2 and v3 groups
fae9028

second rev on group apis
7f6a715
- removed abcs for groups/arrays - improved return types in group.py - warn (temporarily) when an implicit group is found - add attributes.py with Attributes class

add test file
84b497f

jhamman force-pushed the basic-v2-and-v3-group-support branch from 888551a to 84b497fCompare December 6, 2023 15:24

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Listable V3 Stores #1634
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implement group.members#1726
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Uh oh!

Uh oh!

Conversation

jhamman commented Dec 5, 2023

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Comment last updated at 2023-12-06 15:13:06 UTC

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jhamman commented Dec 5, 2023

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pep8speaks commented Dec 5, 2023• edited Loading Uh oh! There was an error while loading. Please reload this page.

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Comment last updated at 2023-12-06 15:13:06 UTC

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pep8speaks commented Dec 5, 2023•
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pep8speaks commented Dec 5, 2023•
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