bump polars version

.github/workflows/ci.yml

@@ -17,17 +17,15 @@ jobs:
     - name: Install dependency
       run: |
         sudo pip install --upgrade pip
-        pip install --user pytest hypothesis \
-          Pygments==2.6.1 sphinx==4.4.0 pandoc nbsphinx \
+        pip install --user Pygments==2.6.1 sphinx==4.4.0 pandoc nbsphinx \
           sphinx-autodoc-typehints sphinx_rtd_theme \
           markupsafe==2.0.1
 
     - name: Build and test package
       run: |
         cd ${GITHUB_WORKSPACE}/anndata-hdf5 && cargo test --all --no-fail-fast
         cd ${GITHUB_WORKSPACE}/anndata && cargo test --all --no-fail-fast
-        cd ${GITHUB_WORKSPACE}/python && \
-          pip install --user .
+        cd ${GITHUB_WORKSPACE}/python && pip install --user .[test]
         pytest ${GITHUB_WORKSPACE}/python/tests
 
     - name: Build doc

anndata-hdf5/Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "anndata-hdf5"
-version = "0.1.0"
+version = "0.2.0"
 edition = "2021"
 rust-version = "1.65"
 authors = ["Kai Zhang <kai@kzhang.org>"]
@@ -11,7 +11,7 @@ repository = "https://github.com/kaizhang/anndata-rs"
 homepage = "https://github.com/kaizhang/anndata-rs"
 
 [dependencies]
-anndata = "0.2"
+anndata = "0.3"
 anyhow = "1.0"
 hdf5 = { version = "0.8" }
 hdf5-sys = { version = "0.8", features = ["static", "zlib", "threadsafe"] }
@@ -20,7 +20,8 @@ libz-sys = { version = "1", features = ["libc"], default-features = false }
 ndarray = { version = "0.15" }
 
 [dev-dependencies]
+anndata-test-utils = { path = '../anndata-test-utils' }
 tempfile = "3.2"
 proptest = "1"
 rand = "0.8.5"
-ndarray-rand = "0.14"
+ndarray-rand = "0.14"

anndata-hdf5/tests/tests.rs

@@ -0,0 +1,58 @@
+use anndata_test_utils::*;
+use anndata_hdf5::H5;
+use anndata::AnnData;
+
+#[test]
+fn test_basic_h5() {
+    test_basic::<H5>()
+}
+
+#[test]
+fn test_save_h5() {
+    test_save::<H5>()
+}
+
+#[test]
+fn test_speacial_cases_h5() {
+    with_tmp_dir(|dir| {
+        let file = dir.join("test.h5");
+        let adata_gen = || AnnData::<H5>::new(&file).unwrap();
+        test_speacial_cases(|| adata_gen());
+    })
+}
+
+#[test]
+fn test_noncanonical_h5() {
+    with_tmp_dir(|dir| {
+        let file = dir.join("test.h5");
+        let adata_gen = || AnnData::<H5>::new(&file).unwrap();
+        test_noncanonical(|| adata_gen());
+    })
+}
+
+#[test]
+fn test_io_h5() {
+    with_tmp_dir(|dir| {
+        let file = dir.join("test.h5");
+        let adata_gen = || AnnData::<H5>::new(&file).unwrap();
+        test_io(|| adata_gen());
+    })
+}
+
+#[test]
+fn test_index_h5() {
+    with_tmp_dir(|dir| {
+        let file = dir.join("test.h5");
+        let adata_gen = || AnnData::<H5>::new(&file).unwrap();
+        test_index(|| adata_gen());
+    })
+}
+
+#[test]
+fn test_iterator_h5() {
+    with_tmp_dir(|dir| {
+        let file = dir.join("test.h5");
+        let adata_gen = || AnnData::<H5>::new(&file).unwrap();
+        test_iterator(|| adata_gen());
+    })
+}

anndata-test-utils/Cargo.toml

@@ -0,0 +1,18 @@
+[package]
+name = "anndata-test-utils"
+version = "0.1.0"
+edition = "2021"
+
+[dependencies]
+anyhow = "1.0"
+ndarray = { version = "0.15" }
+anndata = ">= 0.2, < 0.4"
+num = "0.4"
+tempfile = "3.2"
+criterion = { version = "0.4", features = ["rayon", "plotters", "cargo_bench_support", "html_reports"] }
+proptest = "1"
+rand = "0.8.5"
+ndarray-rand = "0.14"
+nalgebra = { version = "0.32", features = ["rand"] }
+nalgebra-sparse = "0.9"
+itertools = "0.12"

anndata/tests/common/mod.rs → anndata-test-utils/src/common/mod.rs

@@ -26,18 +26,6 @@ pub fn with_tmp_dir<T, F: FnMut(PathBuf) -> T>(mut func: F) -> T {
     func(path)
 }
 
-pub fn with_tmp_path<T, F: FnMut(PathBuf) -> T>(mut func: F) -> T {
-    with_tmp_dir(|dir| func(dir.join("temp.h5")))
-}
-
-pub fn empty_adata<B>() -> AnnData<B>
-where
-    B: Backend,
-{
-    let file = tempfile::NamedTempFile::new().unwrap();
-    AnnData::new(file.path()).unwrap()
-}
-
 ////////////////////////////////////////////////////////////////////////////////
 /// Strategies
 ////////////////////////////////////////////////////////////////////////////////

anndata/tests/anndata_op.rs → anndata-test-utils/src/lib.rs

@@ -1,17 +1,54 @@
-#![allow(dead_code, unused)]
-
 mod common;
-use common::*;
+pub use common::*;
 
+use anndata::{*, data::CsrNonCanonical};
 use ndarray::Array2;
+use nalgebra_sparse::{CooMatrix, CsrMatrix};
 use proptest::prelude::*;
-use anndata::{*, data::{DynCscMatrix, CsrNonCanonical}};
-use anndata_hdf5::H5;
-use std::path::Path;
-use nalgebra_sparse::{CooMatrix, CscMatrix, CsrMatrix};
 
+pub fn test_basic<B: Backend>() {
+    with_tmp_dir(|dir| {
+        let ann1 = AnnData::<B>::new(dir.join("test1.h5ad")).unwrap();
+        let ann2 = AnnData::<B>::new(dir.join("test2.h5ad")).unwrap();
+        AnnDataSet::<B>::new(
+            [("ann1", ann1), ("ann2", ann2)],
+            dir.join("dataset.h5ads"),
+            "sample",
+        ).unwrap();
+    })
+}
+
+pub fn test_save<B: Backend>() {
+    with_tmp_dir(|dir| {
+        let input = dir.join("input.h5ad");
+        let output = dir.join("output.h5ad");
+        let anndatas = ((0 as usize ..100), (0 as usize ..100))
+            .prop_flat_map(|(n_obs, n_vars)|
+                ( anndata_strat::<B, _>(&input, n_obs, n_vars),
+                  select_strat(n_obs),
+                  select_strat(n_vars),
+                )
+            );
+        proptest!(ProptestConfig::with_cases(100), |((adata, slice_obs, slice_var) in anndatas)| {
+            adata.write::<B, _>(&output).unwrap();
+            let adata_in = AnnData::<B>::open(B::open(&output).unwrap()).unwrap();
+            prop_assert!(anndata_eq(&adata, &adata_in).unwrap());
+            adata_in.close().unwrap();
+
+            let index = adata.obs_names().select(&slice_obs);
+            assert_eq!(index.len(), index.into_vec().len());
+
+            let select = [slice_obs, slice_var];
+            adata.write_select::<B, _, _>(&select, &output).unwrap();
+            adata.subset(&select).unwrap();
+            let adata_in = AnnData::<B>::open(B::open(&output).unwrap()).unwrap();
+            prop_assert!(anndata_eq(&adata, &adata_in).unwrap());
+            adata_in.close().unwrap();
+        });
+    });
+}
 
-fn test_speacial_cases<F, T>(adata_gen: F)
+pub fn test_speacial_cases<F, T>(adata_gen: F)
 where
     F: Fn() -> T,
     T: AnnDataOp,
@@ -29,7 +66,7 @@ where
     adata.x().get::<Array2<f64>>().unwrap().unwrap();
 }
 
-fn test_noncanonical<F, T>(adata_gen: F)
+pub fn test_noncanonical<F, T>(adata_gen: F)
 where
     F: Fn() -> T,
     T: AnnDataOp,
@@ -42,12 +79,12 @@ where
         vec![1,2,3,4,5,6,7],
     ).unwrap();
     adata.set_x(&CsrNonCanonical::from(&coo)).unwrap();
-    adata.x().get::<CsrMatrix<i32>>().is_err();
+    assert!(adata.x().get::<CsrMatrix<i32>>().is_err());
     adata.x().get::<CsrNonCanonical<i32>>().unwrap().unwrap();
     adata.x().get::<ArrayData>().unwrap().unwrap();
 }
 
-fn test_io<F, T>(adata_gen: F)
+pub fn test_io<F, T>(adata_gen: F)
 where
     F: Fn() -> T,
     T: AnnDataOp,
@@ -60,7 +97,7 @@ where
     });
 }
 
-fn test_index<F, T>(adata_gen: F)
+pub fn test_index<F, T>(adata_gen: F)
 where
     F: Fn() -> T,
     T: AnnDataOp,
@@ -83,7 +120,7 @@ where
     });
 }
 
-fn test_iterator<F, T>(adata_gen: F)
+pub fn test_iterator<F, T>(adata_gen: F)
 where
     F: Fn() -> T,
     T: AnnDataOp,
@@ -101,54 +138,4 @@ where
             prop_assert_eq!(adata.obsm().get_item::<ArrayData>("test2").unwrap().unwrap(), x);
         }
     });
-}
-
-
-////////////////////////////////////////////////////////////////////////////////
-/// Test HDF5 backend
-////////////////////////////////////////////////////////////////////////////////
-
-#[test]
-fn test_speacial_cases_h5() {
-    with_tmp_dir(|dir| {
-        let file = dir.join("test.h5");
-        let adata_gen = || AnnData::<H5>::new(&file).unwrap();
-        test_speacial_cases(|| adata_gen());
-    })
-}
-
-#[test]
-fn test_noncanonical_h5() {
-    with_tmp_dir(|dir| {
-        let file = dir.join("test.h5");
-        let adata_gen = || AnnData::<H5>::new(&file).unwrap();
-        test_noncanonical(|| adata_gen());
-    })
-}
-
-#[test]
-fn test_io_h5() {
-    with_tmp_dir(|dir| {
-        let file = dir.join("test.h5");
-        let adata_gen = || AnnData::<H5>::new(&file).unwrap();
-        test_io(|| adata_gen());
-    })
-}
-
-#[test]
-fn test_index_h5() {
-    with_tmp_dir(|dir| {
-        let file = dir.join("test.h5");
-        let adata_gen = || AnnData::<H5>::new(&file).unwrap();
-        test_index(|| adata_gen());
-    })
-}
-
-#[test]
-fn test_iterator_h5() {
-    with_tmp_dir(|dir| {
-        let file = dir.join("test.h5");
-        let adata_gen = || AnnData::<H5>::new(&file).unwrap();
-        test_iterator(|| adata_gen());
-    })
 }

anndata/Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "anndata"
-version = "0.2.2"
+version = "0.3.1"
 edition = "2021"
 rust-version = "1.70"
 authors = ["Kai Zhang <kai@kzhang.org>"]
@@ -15,27 +15,20 @@ anyhow = "1.0"
 flate2 = "1.0"
 log = "0.4"
 indexmap = { version = "2.0", features = ["rayon"] }
-itertools = "0.11"
+itertools = "0.12"
 ndarray = { version = "0.15" }
 nalgebra-sparse = "0.9"
 num = "0.4"
-polars = { version = "0.35", features = ["lazy", "decompress-fast", "ndarray", "dtype-full"] }
+polars = { version = "0.37", features = ["lazy", "decompress-fast", "ndarray", "dtype-full"] }
 parking_lot = "0.12"
 replace_with = "0.1"
 smallvec = "1.11"
 rayon = "1.8"
 permutation = "0.4"
 
 [dev-dependencies]
-anndata-n5 = { path = '../anndata-n5' }
-anndata-hdf5 = { path = '../anndata-hdf5' }
 tempfile = "3.2"
-criterion = { version = "0.4", features = ["rayon", "plotters", "cargo_bench_support", "html_reports"] }
 proptest = "1"
 rand = "0.8.5"
 ndarray-rand = "0.14"
-nalgebra = { version = "0.32", features = ["rand"] }
-
-[[bench]]
-name = "main"
-harness = false
+nalgebra = { version = "0.32", features = ["rand"] }