upgrade pyo3 and polars

Author: kaizhang

anndata-hdf5/Cargo.toml

@@ -13,7 +13,7 @@ homepage = "https://github.com/kaizhang/anndata-rs"
 [dependencies]
 anndata = { workspace = true }
 anyhow = "1.0"
-hdf5 = { package = "hdf5-metno", version = "0.9", features = ["blosc"] }
+hdf5 = { package = "hdf5-metno", version = "0.10", features = ["blosc", "blosc-zstd"] }
 blosc-src = { version = "0.3.0", features = ["zstd"] }
 hdf5-sys = { package = "hdf5-metno-sys", version = "0.10", features = ["static", "zlib", "threadsafe"] }
 libz-sys = { version = "1", features = ["libc"], default-features = false }

anndata-zarr/Cargo.toml

@@ -15,8 +15,8 @@ anndata = { workspace = true }
 serde_json = "1.0"
 anyhow = "1.0"
 ndarray = { version = "0.16", features = ["serde"] }
-zarrs = "0.18"
-smallvec = "1.13"
+zarrs = "0.20"
+smallvec = "1.15"
 
 [dev-dependencies]
 tempfile = "3.2"

anndata/Cargo.toml

@@ -2,7 +2,7 @@
 name = "anndata"
 version = "0.6.2"
 edition = "2021"
-rust-version = "1.81"
+rust-version = "1.85"
 authors = ["Kai Zhang <kai@kzhang.org>"]
 description = "Rust APIs"
 license = "MIT"
@@ -14,15 +14,15 @@ homepage = "https://github.com/kaizhang/anndata-rs"
 anyhow = "1.0"
 flate2 = "1.0"
 log = "0.4"
-indexmap = { version = "2.6", features = ["rayon"] }
-itertools = "0.13"
+indexmap = { version = "2.9", features = ["rayon"] }
+itertools = "0.14"
 ndarray = "0.16"
 nalgebra-sparse = "0.10"
 num = "0.4"
-polars = { version = "0.46.0", features = ["lazy", "ndarray", "dtype-full"] }
+polars = { version = "0.48", features = ["lazy", "ndarray", "dtype-full"] }
 paste = "1.0"
 parking_lot = "0.12"
-smallvec = "1.13"
+smallvec = "1.15"
 serde = "1.0"
 serde_json = "1.0"
 rayon = "1.10"

pyanndata/Cargo.toml

@@ -16,19 +16,19 @@ anndata = { workspace = true }
 anndata-hdf5 = { workspace = true }
 anndata-zarr = { workspace = true }
 anyhow = "1.0"
-downcast-rs = "1.2"
-numpy = "0.23"
+downcast-rs = "2"
+numpy = "0.24"
 ndarray = "0.16"
 nalgebra-sparse = "0.10"
 hdf5 = { package = "hdf5-metno", version = "0.9" }
-polars = { version = "0.46.0", features = ["ndarray"] }
-pyo3-polars = {version = "0.20", features = ["dtype-full", "dtype-struct"] }
-rand = "0.8"
+polars = { version = "0.48", features = ["ndarray"] }
+pyo3-polars = {version = "0.21", features = ["dtype-full", "dtype-struct"] }
+rand = "0.9"
 flate2 = "1.0"
 rayon = "1.10"
 
 [dependencies.pyo3]
-version = "0.23"
+version = "0.24"
 features = ["extension-module", "multiple-pymethods", "anyhow"]
 
 [lib]

python/Cargo.toml

@@ -14,7 +14,7 @@ pyanndata = { workspace = true }
 pyo3-log = "0.12"
 
 [dependencies.pyo3]
-version = "0.23"
+version = "0.24"
 features = ["extension-module", "multiple-pymethods"]
 
 [lib]

python/tests/test_subset.py

@@ -43,6 +43,7 @@ def test_subset(x, obs, obsm, obsp, varm, varp, indices, indices2, tmp_path, bac
     adata.obsp = dict(x=obsp, y=csr_matrix(obsp))
     adata.varp = dict(x=varp, y=csr_matrix(varp))
     adata.layers["raw"] = x
+    np.testing.assert_array_equal(adata.obs["txt"], obs)
 
     for adata_subset in [ adata.subset(indices, indices2, out=h5ad(tmp_path), inplace=False, backend=backend),
                          adata.subset(indices, indices2, inplace=False)]: