fix tests [wheel]

kaizhang · Dec 13, 2024 · 908524a · 908524a
1 parent 1f870ac
commit 908524a
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Showing 4 changed files with 16 additions and 9 deletions.
diff --git a/docs/changelog.md b/docs/changelog.md
@@ -1,5 +1,12 @@
 # Release Notes
 
+## Nightly (unreleased)
+
+### Features:
+
+  - Support python 3.13.
+  - Add Zarr backend support for AnnData.
+
 ## Release 2.8.0 (released December 13, 2024)
 
 ### Features:

diff --git a/snapatac2-core/src/utils/similarity.rs b/snapatac2-core/src/utils/similarity.rs
@@ -363,7 +363,7 @@ where
             }
         }).collect::<Vec<_>>()
     }).collect();
-    ArrayBase::from_vec(cor).into_shape((n1, n2)).unwrap()
+    ArrayBase::from_vec(cor).into_shape_with_order((n1, n2)).unwrap()
 }
 
 pub fn spearman2<T1, T2>(
@@ -381,7 +381,7 @@ where
         let vec: Vec<_> = mat.rows().into_iter().flat_map(|row|
             Data::new(row.into_iter().map(|x| x.to_f64().unwrap()).collect::<Vec<_>>()).ranks(RankTieBreaker::Average)
         ).collect();
-        ArrayBase::from_vec(vec).into_shape((mat.shape()[0], mat.shape()[1])).unwrap()
+        ArrayBase::from_vec(vec).into_shape_with_order((mat.shape()[0], mat.shape()[1])).unwrap()
     }
     let mat1_ = rank(mat1);
     let mat2_ = rank(mat2);
@@ -406,5 +406,5 @@ where
     let n2 = mat_y.nrows();
     let dists = (0..n1).cartesian_product(0..n2).collect::<Vec<_>>().into_par_iter()
         .map(|(i, j)| dist_fn(mat_x.get_row(i).unwrap(), mat_y.get_row(j).unwrap())).collect();
-    ArrayBase::from_vec(dists).into_shape((n1, n2)).unwrap()
+    ArrayBase::from_vec(dists).into_shape_with_order((n1, n2)).unwrap()
 }
diff --git a/snapatac2-python/tests/test_pipeline.py b/snapatac2-python/tests/test_pipeline.py
@@ -10,15 +10,15 @@ def h5ad(dir=Path("./")):
 def test_exclude():
     fragment_file = snap.datasets.pbmc500(downsample=True)
 
-    data1 = snap.pp.import_data(
+    data1 = snap.pp.import_fragments(
         fragment_file,
         chrom_sizes={chr: size for chr, size in snap.genome.hg38.chrom_sizes.items() if chr not in ["chr1", "chr10"]},
         sorted_by_barcode=False,
         min_num_fragments=0,
     )
     snap.pp.add_tile_matrix(data1, exclude_chroms=None)
 
-    data2 = snap.pp.import_data(
+    data2 = snap.pp.import_fragments(
         fragment_file,
         chrom_sizes=snap.genome.hg38,
         sorted_by_barcode=False,
@@ -57,7 +57,7 @@ def pipeline(data):
 def test_backed(tmp_path):
     fragment_file = snap.datasets.pbmc500(downsample=True)
 
-    data = snap.pp.import_data(
+    data = snap.pp.import_fragments(
         fragment_file,
         chrom_sizes=snap.genome.hg38,
         file=h5ad(tmp_path),
@@ -68,7 +68,7 @@ def test_backed(tmp_path):
 def test_in_memory():
     fragment_file = snap.datasets.pbmc500(downsample=True)
 
-    data = snap.pp.import_data(
+    data = snap.pp.import_fragments(
         fragment_file,
         chrom_sizes=snap.genome.hg38,
         sorted_by_barcode=False,

diff --git a/snapatac2-python/tests/test_tools.py b/snapatac2-python/tests/test_tools.py
@@ -129,7 +129,7 @@ def test_import(datadir):
     test_files = [snap.datasets.pbmc500(downsample=True), str(datadir.join('test_clean.tsv.gz'))]
 
     for fl in test_files:
-        data = snap.pp.import_data(
+        data = snap.pp.import_fragments(
             fl,
             chrom_sizes=snap.genome.hg38,
             min_num_fragments=0,
@@ -150,7 +150,7 @@ def total_count(adata, bin_size):
             counting_strategy='insertion',
             ).X.sum()
 
-    data = snap.pp.import_data(
+    data = snap.pp.import_fragments(
         snap.datasets.pbmc500(downsample=True),
         chrom_sizes=snap.genome.hg38,
         min_num_fragments=0,