fix tests

snapatac2-core/src/preprocessing/bam.rs

@@ -42,7 +42,7 @@ use crate::utils::{open_file_for_write, Compression};
 ///     result in faster sorting and greater memory usage.
 /// * `compression` - Compression algorithm to use for the output file. Valid values are `gzip` and `zstandard`.
 /// * `compression_level` - Compression level to use for the output file. Valid values are 0-9 for `gzip` and 1-22 for `zstandard`.
-pub fn make_fragment_file<P1: AsRef<Path>, P2: AsRef<Path>>(
+pub fn make_fragment_file<P1: AsRef<Path>, P2: AsRef<Path>, P3: AsRef<Path>>(
     bam_file: P1,
     output_file: P2,
     is_paired: bool,
@@ -56,10 +56,17 @@ pub fn make_fragment_file<P1: AsRef<Path>, P2: AsRef<Path>>(
     chunk_size: usize,
     compression: Option<Compression>,
     compression_level: Option<u32>,
+    temp_dir: Option<P3>,
 ) -> Result<FlagStat> {
-    let tmp_dir = Builder::new()
-        .tempdir_in("./")
-        .expect("failed to create tmperorary directory");
+    let temp_dir = if let Some(tmp) = temp_dir {
+        Builder::new()
+            .tempdir_in(tmp)
+            .expect("failed to create tmperorary directory")
+    } else {
+        Builder::new()
+            .tempdir()
+            .expect("failed to create tmperorary directory")
+    };
 
     if barcode_regex.is_some() && barcode_tag.is_some() {
         bail!("Can only set barcode_tag or barcode_regex but not both");
@@ -99,7 +106,7 @@ pub fn make_fragment_file<P1: AsRef<Path>, P2: AsRef<Path>>(
         &barcode,
         umi.as_ref(),
         is_paired,
-        tmp_dir.path().to_path_buf(),
+        temp_dir.path().to_path_buf(),
         chunk_size,
     )
     .into_fragments(&header)

snapatac2-python/snapatac2/_version.py

@@ -1 +1 @@
-__version__ = "2.5.2.dev0"
+__version__ = "2.5.2.dev1"

snapatac2-python/snapatac2/preprocessing/_basic.py

@@ -28,6 +28,7 @@ def make_fragment_file(
     chunk_size: int = 50000000,
     compression: Literal["gzip", "zstandard"] | None = None,
     compression_level: int | None = None,
+    tempdir: Path | None = None,
 ) -> internal.PyFlagStat:
     """
     Convert a BAM file to a fragment file.
@@ -87,6 +88,9 @@ def make_fragment_file(
     compression_level
         Compression level. 1-9 for gzip, 1-22 for zstandard.
         If `None`, it is set to 6 for gzip and 3 for zstandard.
+    tempdir
+        Location to store temporary files. If `None`, system temporary directory
+        will be used.
 
     Returns
     -------
@@ -110,7 +114,8 @@ def make_fragment_file(
 
     return internal.make_fragment_file(
         bam_file, output_file, is_paired, shift_left, shift_right, chunk_size,
-        barcode_tag, barcode_regex, umi_tag, umi_regex, min_mapq, compression, compression_level,
+        barcode_tag, barcode_regex, umi_tag, umi_regex, min_mapq,
+        compression, compression_level, tempdir,
     )
 
 def import_data(

snapatac2-python/src/preprocessing.rs

@@ -45,6 +45,7 @@ pub(crate) fn make_fragment_file(
     mapq: Option<u8>,
     compression: Option<&str>,
     compression_level: Option<u32>,
+    temp_dir: Option<PathBuf>,
 ) -> Result<PyFlagStat>
 {
     fn parse_tag(tag: &str) -> [u8; 2] {
@@ -60,7 +61,7 @@ pub(crate) fn make_fragment_file(
         barcode_tag.map(|x| parse_tag(x)), barcode_regex,
         umi_tag.map(|x| parse_tag(x)), umi_regex,
         shift_left, shift_right, mapq, chunk_size,
-        compression.map(|x| utils::Compression::from_str(x).unwrap()), compression_level,
+        compression.map(|x| utils::Compression::from_str(x).unwrap()), compression_level, temp_dir,
     )?;
     Ok(PyFlagStat(stat))
 }

snapatac2-python/tests/test_pipeline.py

@@ -10,12 +10,9 @@ def h5ad(dir=Path("./")):
 def test_exclude():
     fragment_file = snap.datasets.pbmc500(downsample=True)
 
-    chr_sizes = snap.genome.hg38.chrom_sizes
-    chr_sizes.pop('chr1', None)
-    chr_sizes.pop('chr10', None)
     data1 = snap.pp.import_data(
         fragment_file,
-        chrom_sizes=chr_sizes,
+        chrom_sizes={chr: size for chr, size in snap.genome.hg38.chrom_sizes.items() if chr not in ["chr1", "chr10"]},
         sorted_by_barcode=False
     )
     snap.pp.add_tile_matrix(data1, exclude_chroms=None)

snapatac2-python/tests/test_tools.py

@@ -7,7 +7,7 @@
 from natsort import natsorted
 from collections import defaultdict
 import pytest
-from hypothesis import given, example, settings, HealthCheck, strategies as st
+from hypothesis import given, settings, HealthCheck, strategies as st
 from hypothesis.extra.numpy import *
 from scipy.sparse import csr_matrix
 import gzip
@@ -136,7 +136,7 @@ def test_import(datadir):
             sorted_by_barcode=False,
         )
 
-        data.obs['group'] = '1'
-        snap.ex.export_fragments(data, groupby="group", suffix='.bed.gz')
+        data.obs['group'] = 'test_import'
+        outputs = snap.ex.export_fragments(data, groupby="group", out_dir=str(datadir), suffix='.bed.gz')
 
-        assert read_bed("1.bed.gz") == read_bed(fl)
+        assert read_bed(list(outputs.values())[0]) == read_bed(fl)