feat: initialise from ArrayMetadata and store (#104)

* (chore): handle new zarr dtype API

* (fix): dep in pyproject toml for zarr from main

* (fix): use local store for v2

* fix: don't use `default_filters`/`default_compressor`

* feat: initialise from `ArrayMetadata` and store

* Apply suggestion from @ilan-gold

Co-authored-by: Ilan Gold <[email protected]>

* chore: add spy for pipeline (#105)

---------

Co-authored-by: ilan-gold <[email protected]>

Author: LDeakin

pyproject.toml

@@ -31,6 +31,7 @@ test = [
     "pytest",
     "pytest-asyncio",
     "pytest-xdist",
+    "pytest-mock",
 ]
 doc = ["sphinx>=7.4.6", "myst-parser"]
 dev = [

python/zarrs/_internal.pyi

@@ -13,7 +13,8 @@ class Basic:
 class CodecPipelineImpl:
     def __new__(
         cls,
-        metadata: builtins.str,
+        array_metadata: builtins.str,
+        store_config: StoreConfig,
         *,
         validate_checksums: builtins.bool | None = None,
         chunk_concurrent_minimum: builtins.int | None = None,

python/zarrs/pipeline.py

@@ -2,20 +2,22 @@
 
 import asyncio
 import json
-import re
 from dataclasses import dataclass
 from typing import TYPE_CHECKING, TypedDict
+from warnings import warn
 
 import numpy as np
 from zarr.abc.codec import Codec, CodecPipeline
+from zarr.codecs._v2 import V2Codec
 from zarr.core import BatchedCodecPipeline
 from zarr.core.config import config
+from zarr.core.metadata import ArrayMetadata, ArrayV2Metadata, ArrayV3Metadata
 
 if TYPE_CHECKING:
     from collections.abc import Generator, Iterable, Iterator
     from typing import Any, Self
 
-    from zarr.abc.store import ByteGetter, ByteSetter
+    from zarr.abc.store import ByteGetter, ByteSetter, Store
     from zarr.core.array_spec import ArraySpec
     from zarr.core.buffer import Buffer, NDArrayLike, NDBuffer
     from zarr.core.chunk_grids import ChunkGrid
@@ -40,10 +42,14 @@ class UnsupportedMetadataError(Exception):
     pass
 
 
-def get_codec_pipeline_impl(codec_metadata_json: str) -> CodecPipelineImpl | None:
+def get_codec_pipeline_impl(
+    metadata: ArrayMetadata, store: Store
+) -> CodecPipelineImpl | None:
     try:
+        array_metadata_json = json.dumps(metadata.to_dict())
         return CodecPipelineImpl(
-            codec_metadata_json,
+            array_metadata_json,
+            store_config=store,
             validate_checksums=config.get("codec_pipeline.validate_checksums", None),
             chunk_concurrent_minimum=config.get(
                 "codec_pipeline.chunk_concurrent_minimum", None
@@ -54,10 +60,11 @@ def get_codec_pipeline_impl(codec_metadata_json: str) -> CodecPipelineImpl | Non
             num_threads=config.get("threading.max_workers", None),
         )
     except TypeError as e:
-        if re.match(r"codec (delta|zlib) is not supported", str(e)):
-            return None
-        else:
-            raise e
+        warn(
+            f"Array is unsupported by ZarrsCodecPipeline: {e}",
+            category=UserWarning,
+        )
+        return None
 
 
 def codecs_to_dict(codecs: Iterable[Codec]) -> Generator[dict[str, Any], None, None]:
@@ -88,37 +95,47 @@ class ZarrsCodecPipelineState(TypedDict):
     codecs: tuple[Codec, ...]
 
 
+def array_metadata_to_codecs(metadata: ArrayMetadata) -> list[Codec]:
+    if isinstance(metadata, ArrayV3Metadata):
+        return metadata.codecs
+    elif isinstance(metadata, ArrayV2Metadata):
+        v2_codec = V2Codec(filters=metadata.filters, compressor=metadata.compressor)
+        return [v2_codec]
+
+
 @dataclass
 class ZarrsCodecPipeline(CodecPipeline):
-    codecs: tuple[Codec, ...]
+    metadata: ArrayMetadata
+    store: Store
     impl: CodecPipelineImpl | None
-    codec_metadata_json: str
     python_impl: BatchedCodecPipeline
 
     def __getstate__(self) -> ZarrsCodecPipelineState:
-        return {"codec_metadata_json": self.codec_metadata_json, "codecs": self.codecs}
+        return {"metadata": self.metadata, "store": self.store}
 
     def __setstate__(self, state: ZarrsCodecPipelineState):
-        self.codecs = state["codecs"]
-        self.codec_metadata_json = state["codec_metadata_json"]
-        self.impl = get_codec_pipeline_impl(self.codec_metadata_json)
-        self.python_impl = BatchedCodecPipeline.from_codecs(self.codecs)
+        self.metadata = state["metadata"]
+        self.store = state["store"]
+        self.impl = get_codec_pipeline_impl(self.metadata, self.store)
+        codecs = array_metadata_to_codecs(self.metadata)
+        self.python_impl = BatchedCodecPipeline.from_codecs(codecs)
 
     def evolve_from_array_spec(self, array_spec: ArraySpec) -> Self:
-        raise NotImplementedError("evolve_from_array_spec")
+        return self
 
     @classmethod
     def from_codecs(cls, codecs: Iterable[Codec]) -> Self:
-        codec_metadata = list(codecs_to_dict(codecs))
-        codec_metadata_json = json.dumps(codec_metadata)
-        # TODO: upstream zarr-python has not settled on how to deal with configs yet
-        # Should they be checked when an array is created, or when an operation is performed?
-        # https://github.com/zarr-developers/zarr-python/issues/2409
-        # https://github.com/zarr-developers/zarr-python/pull/2429#issuecomment-2566976567
+        return BatchedCodecPipeline.from_codecs(codecs)
+
+    @classmethod
+    def from_array_metadata_and_store(
+        cls, array_metadata: ArrayMetadata, store: Store
+    ) -> Self:
+        codecs = array_metadata_to_codecs(array_metadata)
         return cls(
-            codec_metadata_json=codec_metadata_json,
-            codecs=tuple(codecs),
-            impl=get_codec_pipeline_impl(codec_metadata_json),
+            metadata=array_metadata,
+            store=store,
+            impl=get_codec_pipeline_impl(array_metadata, store),
             python_impl=BatchedCodecPipeline.from_codecs(codecs),
         )
 

src/chunk_item.rs

@@ -14,10 +14,9 @@ use zarrs::{
     storage::StoreKey,
 };
 
-use crate::{store::StoreConfig, utils::PyErrExt};
+use crate::utils::PyErrExt;
 
 pub(crate) trait ChunksItem {
-    fn store_config(&self) -> StoreConfig;
     fn key(&self) -> &StoreKey;
     fn representation(&self) -> &ChunkRepresentation;
 }
@@ -26,7 +25,6 @@ pub(crate) trait ChunksItem {
 #[gen_stub_pyclass]
 #[pyclass]
 pub(crate) struct Basic {
-    store: StoreConfig,
     key: StoreKey,
     representation: ChunkRepresentation,
 }
@@ -62,7 +60,6 @@ fn fill_value_to_bytes(dtype: &str, fill_value: &Bound<'_, PyAny>) -> PyResult<V
 impl Basic {
     #[new]
     fn new(byte_interface: &Bound<'_, PyAny>, chunk_spec: &Bound<'_, PyAny>) -> PyResult<Self> {
-        let store: StoreConfig = byte_interface.getattr("store")?.extract()?;
         let path: String = byte_interface.getattr("path")?.extract()?;
 
         let chunk_shape = chunk_spec.getattr("shape")?.extract()?;
@@ -79,7 +76,6 @@ impl Basic {
         let fill_value: Bound<'_, PyAny> = chunk_spec.getattr("fill_value")?;
         let fill_value_bytes = fill_value_to_bytes(&dtype, &fill_value)?;
         Ok(Self {
-            store,
             key: StoreKey::new(path).map_py_err::<PyValueError>()?,
             representation: get_chunk_representation(chunk_shape, &dtype, fill_value_bytes)?,
         })
@@ -118,9 +114,6 @@ impl WithSubset {
 }
 
 impl ChunksItem for Basic {
-    fn store_config(&self) -> StoreConfig {
-        self.store.clone()
-    }
     fn key(&self) -> &StoreKey {
         &self.key
     }
@@ -130,9 +123,6 @@ impl ChunksItem for Basic {
 }
 
 impl ChunksItem for WithSubset {
-    fn store_config(&self) -> StoreConfig {
-        self.item.store.clone()
-    }
     fn key(&self) -> &StoreKey {
         &self.item.key
     }

src/lib.rs

@@ -20,14 +20,15 @@ use unsafe_cell_slice::UnsafeCellSlice;
 use utils::is_whole_chunk;
 use zarrs::array::codec::{
     ArrayPartialDecoderTraits, ArrayToBytesCodecTraits, CodecOptions, CodecOptionsBuilder,
+    StoragePartialDecoder,
 };
 use zarrs::array::{
-    copy_fill_value_into, update_array_bytes, ArrayBytes, ArrayBytesFixedDisjointView, ArraySize,
-    CodecChain, FillValue,
+    copy_fill_value_into, update_array_bytes, Array, ArrayBytes, ArrayBytesFixedDisjointView,
+    ArrayMetadata, ArraySize, CodecChain, FillValue,
 };
 use zarrs::array_subset::ArraySubset;
-use zarrs::metadata::v3::MetadataV3;
-use zarrs::storage::StoreKey;
+use zarrs::storage::store::MemoryStore;
+use zarrs::storage::{ReadableWritableListableStorage, StorageHandle, StoreKey};
 
 mod chunk_item;
 mod concurrency;
@@ -41,14 +42,14 @@ mod utils;
 use crate::chunk_item::ChunksItem;
 use crate::concurrency::ChunkConcurrentLimitAndCodecOptions;
 use crate::metadata_v2::codec_metadata_v2_to_v3;
-use crate::store::StoreManager;
+use crate::store::StoreConfig;
 use crate::utils::{PyErrExt as _, PyUntypedArrayExt as _};
 
 // TODO: Use a OnceLock for store with get_or_try_init when stabilised?
 #[gen_stub_pyclass]
 #[pyclass]
 pub struct CodecPipelineImpl {
-    pub(crate) stores: StoreManager,
+    pub(crate) store: ReadableWritableListableStorage,
     pub(crate) codec_chain: Arc<CodecChain>,
     pub(crate) codec_options: CodecOptions,
     pub(crate) chunk_concurrent_minimum: usize,
@@ -63,7 +64,7 @@ impl CodecPipelineImpl {
         codec_chain: &CodecChain,
         codec_options: &CodecOptions,
     ) -> PyResult<ArrayBytes<'a>> {
-        let value_encoded = self.stores.get(item)?;
+        let value_encoded = self.store.get(item.key()).map_py_err::<PyRuntimeError>()?;
         let value_decoded = if let Some(value_encoded) = value_encoded {
             let value_encoded: Vec<u8> = value_encoded.into(); // zero-copy in this case
             codec_chain
@@ -94,15 +95,17 @@ impl CodecPipelineImpl {
             .map_py_err::<PyValueError>()?;
 
         if value_decoded.is_fill_value(item.representation().fill_value()) {
-            self.stores.erase(item)
+            self.store.erase(item.key()).map_py_err::<PyRuntimeError>()
         } else {
             let value_encoded = codec_chain
                 .encode(value_decoded, item.representation(), codec_options)
                 .map(Cow::into_owned)
                 .map_py_err::<PyRuntimeError>()?;
 
             // Store the encoded chunk
-            self.stores.set(item, value_encoded.into())
+            self.store
+                .set(item.key(), value_encoded.into())
+                .map_py_err::<PyRuntimeError>()
         }
     }
 
@@ -204,7 +207,8 @@ impl CodecPipelineImpl {
 #[pymethods]
 impl CodecPipelineImpl {
     #[pyo3(signature = (
-        metadata,
+        array_metadata,
+        store_config,
         *,
         validate_checksums=None,
         chunk_concurrent_minimum=None,
@@ -213,16 +217,21 @@ impl CodecPipelineImpl {
     ))]
     #[new]
     fn new(
-        metadata: &str,
+        array_metadata: &str,
+        store_config: StoreConfig,
         validate_checksums: Option<bool>,
         chunk_concurrent_minimum: Option<usize>,
         chunk_concurrent_maximum: Option<usize>,
         num_threads: Option<usize>,
     ) -> PyResult<Self> {
-        let metadata: Vec<MetadataV3> =
-            serde_json::from_str(metadata).map_py_err::<PyTypeError>()?;
-        let codec_chain =
-            Arc::new(CodecChain::from_metadata(&metadata).map_py_err::<PyTypeError>()?);
+        let metadata: ArrayMetadata =
+            serde_json::from_str(array_metadata).map_py_err::<PyTypeError>()?;
+
+        // TODO: Add a direct metadata -> codec chain method to zarrs
+        let store = Arc::new(MemoryStore::new());
+        let array = Array::new_with_metadata(store, "/", metadata).map_py_err::<PyTypeError>()?;
+        let codec_chain = Arc::new(array.codecs().clone());
+
         let mut codec_options = CodecOptionsBuilder::new();
         if let Some(validate_checksums) = validate_checksums {
             codec_options = codec_options.validate_checksums(validate_checksums);
@@ -235,8 +244,11 @@ impl CodecPipelineImpl {
             chunk_concurrent_maximum.unwrap_or(rayon::current_num_threads());
         let num_threads = num_threads.unwrap_or(rayon::current_num_threads());
 
+        let store: ReadableWritableListableStorage =
+            (&store_config).try_into().map_py_err::<PyTypeError>()?;
+
         Ok(Self {
-            stores: StoreManager::default(),
+            store,
             codec_chain,
             codec_options,
             chunk_concurrent_minimum,
@@ -276,7 +288,9 @@ impl CodecPipelineImpl {
                 partial_chunk_descriptions,
                 map,
                 |item| {
-                    let input_handle = self.stores.decoder(item)?;
+                    let storage_handle = Arc::new(StorageHandle::new(self.store.clone()));
+                    let input_handle =
+                        StoragePartialDecoder::new(storage_handle, item.key().clone());
                     let partial_decoder = self
                         .codec_chain
                         .clone()
@@ -326,7 +340,9 @@ impl CodecPipelineImpl {
                     && chunk_subset.shape() == item.representation().shape_u64()
                 {
                     // See zarrs::array::Array::retrieve_chunk_into
-                    if let Some(chunk_encoded) = self.stores.get(&item)? {
+                    if let Some(chunk_encoded) =
+                        self.store.get(item.key()).map_py_err::<PyRuntimeError>()?
+                    {
                         // Decode the encoded data into the output buffer
                         let chunk_encoded: Vec<u8> = chunk_encoded.into();
                         self.codec_chain.decode_into(

src/store.rs

@@ -15,13 +15,11 @@ use crate::{runtime::tokio_block_on, utils::PyErrExt};
 
 mod filesystem;
 mod http;
-mod manager;
 
 pub use self::filesystem::FilesystemStoreConfig;
 pub use self::http::HttpStoreConfig;
-pub(crate) use self::manager::StoreManager;
 
-#[derive(Debug, Clone, Hash, PartialEq, Eq, PartialOrd, Ord)]
+#[derive(Debug, Clone)]
 #[gen_stub_pyclass_enum]
 pub enum StoreConfig {
     Filesystem(FilesystemStoreConfig),

src/store/filesystem.rs

@@ -6,7 +6,7 @@ use zarrs::{filesystem::FilesystemStore, storage::ReadableWritableListableStorag
 
 use crate::utils::PyErrExt;
 
-#[derive(Debug, Clone, Hash, PartialEq, Eq, PartialOrd, Ord)]
+#[derive(Debug, Clone)]
 #[gen_stub_pyclass]
 #[pyclass]
 pub struct FilesystemStoreConfig {

src/store/http.rs

@@ -6,7 +6,7 @@ use zarrs::storage::ReadableWritableListableStorage;
 
 use super::opendal_builder_to_sync_store;
 
-#[derive(Debug, Clone, Hash, PartialEq, Eq, PartialOrd, Ord)]
+#[derive(Debug, Clone)]
 #[gen_stub_pyclass]
 #[pyclass]
 pub struct HttpStoreConfig {