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fix: bring back zarr #21

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fix: bring back zarr #21

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2 changes: 2 additions & 0 deletions Cargo.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,7 @@
members = [
"anndata",
"anndata-hdf5",
"anndata-zarr",
"pyanndata",
"anndata-test-utils",
"python",
Expand All @@ -11,4 +12,5 @@ resolver = "2"
[workspace.dependencies]
anndata = { path = "anndata" }
anndata-hdf5 = { path = "anndata-hdf5" }
anndata-zarr = { path = "anndata-zarr" }
pyanndata = { path = "pyanndata" }
2 changes: 1 addition & 1 deletion anndata-hdf5/Cargo.toml
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@@ -1,6 +1,6 @@
[package]
name = "anndata-hdf5"
version = "0.5.2"
version = "0.5.1"
edition = "2021"
rust-version = "1.65"
authors = ["Kai Zhang <kai@kzhang.org>"]
Expand Down
1 change: 1 addition & 0 deletions anndata-test-utils/Cargo.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -18,6 +18,7 @@ itertools = "0.14"

[dev-dependencies]
anndata-hdf5 = { workspace = true }
anndata-zarr = { workspace = true }
tempfile = "3.2"
proptest = "1"
bincode = { version = "2", features = ["serde"] }
Expand Down
16 changes: 14 additions & 2 deletions anndata-test-utils/tests/tests.rs
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Original file line number Diff line number Diff line change
@@ -1,11 +1,13 @@
use anndata_test_utils as utils;
use anndata_test_utils::with_tmp_dir;
use anndata_hdf5::H5;
use anndata_zarr::Zarr;
use anndata::{AnnData, Backend};

#[test]
fn test_basic() {
utils::test_basic::<H5>();
utils::test_basic::<Zarr>();
}

#[test]
Expand All @@ -15,6 +17,9 @@ fn test_complex_dataframe() {
let file = dir.join("test.h5");
let adata = AnnData::<H5>::open(H5::open(&input).unwrap()).unwrap();
adata.write::<H5, _>(file, None, None).unwrap();

let file = dir.join("test.zarr");
adata.write::<Zarr, _>(file, None, None).unwrap();
})
}

Expand All @@ -31,11 +36,10 @@ fn test_speacial_cases() {
let adata_gen = || AnnData::<H5>::new(&file).unwrap();
utils::test_speacial_cases(|| adata_gen());

/*
let file = dir.join("test.zarr");
let adata_gen = || AnnData::<Zarr>::new(&file).unwrap();
utils::test_speacial_cases(|| adata_gen());
*/

})
}

Expand All @@ -45,6 +49,10 @@ fn test_noncanonical() {
let file = dir.join("test.h5");
let adata_gen = || AnnData::<H5>::new(&file).unwrap();
utils::test_noncanonical(|| adata_gen());

let file = dir.join("test.zarr");
let adata_gen = || AnnData::<Zarr>::new(&file).unwrap();
utils::test_noncanonical(|| adata_gen());
})
}

Expand Down Expand Up @@ -80,5 +88,9 @@ fn test_iterator() {
let file = dir.join("test.h5");
let adata_gen = || AnnData::<H5>::new(&file).unwrap();
utils::test_iterator(|| adata_gen());

let file = dir.join("test.zarr");
let adata_gen = || AnnData::<Zarr>::new(&file).unwrap();
utils::test_iterator(|| adata_gen());
})
}
12 changes: 9 additions & 3 deletions anndata-zarr/Cargo.toml
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Expand Up @@ -14,6 +14,12 @@ homepage = "https://github.com/kaizhang/anndata-rs"
anndata = { workspace = true }
serde_json = "1.0"
anyhow = "1.0"
ndarray = { version = "0.16", features = ["serde"] }
zarrs = "0.21"
smallvec = "1.15"
ndarray = { version = "0.17", features = ["serde"] }
zarrs = "0.23"
smallvec = "1.15"

[dev-dependencies]
tempfile = "3.2"
proptest = "1"
rand = "0.9"
ndarray-rand = "0.16"
118 changes: 75 additions & 43 deletions anndata-zarr/src/lib.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -7,17 +7,27 @@ use anyhow::{bail, Context, Result};
use ndarray::{Array, ArrayD, ArrayView, CowArray, Dimension, IxDyn, SliceInfoElem};
use std::{
borrow::Cow,
num::NonZeroU64,
ops::{Deref, Index},
path::{Path, PathBuf},
};
use std::{sync::Arc, vec};
use zarrs::array::codec::bytes_to_bytes::zstd::ZstdCodec;
use zarrs::array::{
codec::bytes_to_bytes::zstd::ZstdCodec,
data_type::{
BoolDataType, Float32DataType, Float64DataType, Int16DataType, Int32DataType,
Int64DataType, Int8DataType, StringDataType, UInt16DataType, UInt32DataType,
UInt64DataType, UInt8DataType,
},
};
use zarrs::filesystem::FilesystemStore;
use zarrs::group::Group;
use zarrs::{array::ElementOwned, storage::ReadableWritableListableStorageTraits};
use zarrs::{
array::{codec::ShardingCodecBuilder, data_type::DataType, ArrayShardedReadableExt, Element},
array_subset::ArraySubset,
array::{
codec::ShardingCodecBuilder, data_type, ArrayShardedReadableExt, ArraySubset, Element,
FillValue,
},
storage::StorePrefix,
};

Expand Down Expand Up @@ -344,20 +354,32 @@ impl AttributeOp<Zarr> for ZarrDataset {

impl DatasetOp<Zarr> for ZarrDataset {
fn dtype(&self) -> Result<ScalarType> {
match self.dataset.data_type() {
DataType::UInt8 => Ok(ScalarType::U8),
DataType::UInt16 => Ok(ScalarType::U16),
DataType::UInt32 => Ok(ScalarType::U32),
DataType::UInt64 => Ok(ScalarType::U64),
DataType::Int8 => Ok(ScalarType::I8),
DataType::Int16 => Ok(ScalarType::I16),
DataType::Int32 => Ok(ScalarType::I32),
DataType::Int64 => Ok(ScalarType::I64),
DataType::Float32 => Ok(ScalarType::F32),
DataType::Float64 => Ok(ScalarType::F64),
DataType::Bool => Ok(ScalarType::Bool),
DataType::String => Ok(ScalarType::String),
ty => bail!("Unsupported type: {:?}", ty),
if self.dataset.data_type().is::<UInt8DataType>() {
Ok(ScalarType::U8)
} else if self.dataset.data_type().is::<UInt16DataType>() {
Ok(ScalarType::U16)
} else if self.dataset.data_type().is::<UInt32DataType>() {
Ok(ScalarType::U32)
} else if self.dataset.data_type().is::<UInt64DataType>() {
Ok(ScalarType::U64)
} else if self.dataset.data_type().is::<Int8DataType>() {
Ok(ScalarType::I8)
} else if self.dataset.data_type().is::<Int16DataType>() {
Ok(ScalarType::I16)
} else if self.dataset.data_type().is::<Int32DataType>() {
Ok(ScalarType::I32)
} else if self.dataset.data_type().is::<Int64DataType>() {
Ok(ScalarType::I64)
} else if self.dataset.data_type().is::<Float32DataType>() {
Ok(ScalarType::F32)
} else if self.dataset.data_type().is::<Float64DataType>() {
Ok(ScalarType::F64)
} else if self.dataset.data_type().is::<BoolDataType>() {
Ok(ScalarType::Bool)
} else if self.dataset.data_type().is::<StringDataType>() {
Ok(ScalarType::String)
} else {
bail!("Unsupported type: {:?}", self.dataset.data_type())
}
}

Expand All @@ -371,7 +393,7 @@ impl DatasetOp<Zarr> for ZarrDataset {

fn reshape(&mut self, shape: &Shape) -> Result<()> {
self.dataset
.set_shape(shape.as_ref().iter().map(|x| *x as u64).collect());
.set_shape(shape.as_ref().iter().map(|x| *x as u64).collect())?;
self.dataset.store_metadata()?;
Ok(())
}
Expand All @@ -395,7 +417,7 @@ impl DatasetOp<Zarr> for ZarrDataset {
.retrieve_array_subset_ndarray_sharded_opt(
&dataset.cache,
&subset,
&zarrs::array::codec::CodecOptions::default(),
&zarrs::array::CodecOptions::default(),
)?
.into_dimensionality::<D>()?;
Ok(arr)
Expand All @@ -406,7 +428,7 @@ impl DatasetOp<Zarr> for ZarrDataset {
.retrieve_array_subset_ndarray_sharded_opt(
&dataset.cache,
&dataset.dataset.subset_all(),
&zarrs::array::codec::CodecOptions::default(),
&zarrs::array::CodecOptions::default(),
)?
.into_dimensionality::<D>()?;
Ok(select(arr.view(), selection))
Expand Down Expand Up @@ -463,7 +485,7 @@ impl DatasetOp<Zarr> for ZarrDataset {
if starts.len() == selection.ndim() {
container
.dataset
.store_array_subset_ndarray(starts.as_slice(), arr.into_owned())?;
.store_array_subset_ndarray(starts.as_slice(), &arr)?;
} else {
panic!("Not implemented");
}
Expand Down Expand Up @@ -567,23 +589,27 @@ fn new_empty_dataset_helper<T: BackendData, S: ?Sized>(
config: WriteConfig,
) -> Result<zarrs::array::Array<S>> {
let (datatype, fill) = match T::DTYPE {
ScalarType::U8 => (DataType::UInt8, 0u8.into()),
ScalarType::U16 => (DataType::UInt16, 0u16.into()),
ScalarType::U32 => (DataType::UInt32, 0u32.into()),
ScalarType::U64 => (DataType::UInt64, 0u64.into()),
ScalarType::I8 => (DataType::Int8, 0i8.into()),
ScalarType::I16 => (DataType::Int16, 0i16.into()),
ScalarType::I32 => (DataType::Int32, 0i32.into()),
ScalarType::I64 => (DataType::Int64, 0i64.into()),
ScalarType::F32 => (DataType::Float32, zarrs::array::ZARR_NAN_F32.into()),
ScalarType::F64 => (DataType::Float64, zarrs::array::ZARR_NAN_F64.into()),
ScalarType::Bool => (DataType::Bool, false.into()),
ScalarType::String => (DataType::String, "".into()),
ScalarType::U8 => (data_type::uint8(), FillValue::from(0u8)),
ScalarType::U16 => (data_type::uint16(), FillValue::from(0u16)),
ScalarType::U32 => (data_type::uint32(), FillValue::from(0u32)),
ScalarType::U64 => (data_type::uint64(), FillValue::from(0u64)),
ScalarType::I8 => (data_type::int8(), FillValue::from(0i8)),
ScalarType::I16 => (data_type::int16(), FillValue::from(0i16)),
ScalarType::I32 => (data_type::int32(), FillValue::from(0i32)),
ScalarType::I64 => (data_type::int64(), FillValue::from(0i64)),
ScalarType::F32 => (data_type::float32(), FillValue::from(0f32)),
ScalarType::F64 => (data_type::float64(), FillValue::from(0f64)),
ScalarType::Bool => (data_type::bool(), FillValue::from(false)),
ScalarType::String => (data_type::string(), FillValue::from("")),
};

let shape = shape.as_ref();
let chunk_size: Vec<u64> = match config.block_size {
Some(s) => s.as_ref().into_iter().map(|x| (*x).max(1) as u64).collect(),
Some(s) => s
.as_ref()
.into_iter()
.map(|x| (*x).max(1) as u64)
.collect::<Vec<_>>(),
_ => {
if shape.len() == 1 {
vec![shape[0].min(16384).max(1) as u64]
Expand All @@ -594,29 +620,35 @@ fn new_empty_dataset_helper<T: BackendData, S: ?Sized>(
};

let mut use_sharding = true;
if matches!(datatype, DataType::String) {//|| shape.iter().sum::<usize>() == 0 {
if datatype == data_type::string() {
//|| shape.iter().sum::<usize>() == 0 {
// Strings are not sharded, they are stored as a single chunk.
use_sharding = false;
}

let array = if use_sharding {
let shard_shape = chunk_size.iter().map(|&x| x * 8).collect::<Vec<_>>();
let mut sharding_codec_builder =
ShardingCodecBuilder::new(chunk_size.try_into()?);
let mut sharding_codec_builder = ShardingCodecBuilder::new(
chunk_size
.iter()
.map(|e| NonZeroU64::try_from(*e))
.collect::<Result<Vec<NonZeroU64>, _>>()?,
&datatype,
);
sharding_codec_builder.bytes_to_bytes_codecs(vec![Arc::new(ZstdCodec::new(7, false))]);
zarrs::array::ArrayBuilder::new(
shape.iter().map(|x| *x as u64).collect(),
shape.iter().map(|x| *x as u64).collect::<Vec<_>>(),
shard_shape.as_slice(),
datatype,
shard_shape.try_into()?,
fill,
)
.array_to_bytes_codec(sharding_codec_builder.build_arc())
.build(store, path)?
} else {
zarrs::array::ArrayBuilder::new(
shape.iter().map(|x| *x as u64).collect(),
shape.iter().map(|x| *x as u64).collect::<Vec<_>>(),
chunk_size.as_slice(),
datatype,
chunk_size.try_into()?,
fill,
)
.bytes_to_bytes_codecs(vec![Arc::new(ZstdCodec::new(7, false))])
Expand Down Expand Up @@ -710,15 +742,15 @@ mod tests {
let mut dataset =
group.new_empty_dataset::<i32>("test", &[20, 50].as_slice().into(), config)?;

let arr = Array::random((10, 10), Uniform::new(0, 100));
let arr = Array::random((10, 10), Uniform::new(0, 100).unwrap());
dataset.write_array_slice(arr.view().into(), s![5..15, 10..20].as_ref())?;
assert_eq!(
arr,
dataset.read_array_slice::<i32, _, _>(s![5..15, 10..20].as_ref())?
);

// Repeatitive writes
let arr = Array::random((20, 50), Uniform::new(0, 100));
let arr = Array::random((20, 50), Uniform::new(0, 100).unwrap());
dataset.write_array_slice(arr.view().into(), s![.., ..].as_ref())?;
dataset.write_array_slice(arr.view().into(), s![.., ..].as_ref())?;

Expand Down
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