merge

.pre-commit-config.yaml

@@ -9,11 +9,12 @@ repos:
 - repo: https://github.com/astral-sh/ruff-pre-commit
   rev: v0.1.13
   hooks:
+    - id: ruff-format
     - id: ruff
       args: [ --fix, --exit-non-zero-on-fix ]
 - repo: https://github.com/doublify/pre-commit-rust
   rev: v1.0
   hooks:
   - id: fmt
-    entry: bash -c 'cd rust'
+    entry: bash -c 'cd rust && cargo fmt'
     args: ['--verbose', '--']

rust/src/lib.rs

@@ -22,16 +22,15 @@ pub struct ChainLifter {
 impl ChainLifter {
     #[new]
     pub fn new(chainfile_path: &str) -> PyResult<ChainLifter> {
-        let Ok(chainfile_file) = File::open(&chainfile_path) else {
+        let Ok(chainfile_file) = File::open(chainfile_path) else {
             return Err(PyFileNotFoundError::new_err(format!(
                 "Unable to open chainfile located at \"{}\"",
                 &chainfile_path
             )));
         };
         let data = BufReader::new(chainfile_file);
         let reader = chain::Reader::new(data);
-        let Ok(machine) = chain::liftover::machine::Builder::default().try_build_from(reader)
-        else {
+        let Ok(machine) = chain::liftover::machine::Builder.try_build_from(reader) else {
             return Err(ChainfileError::new_err(format!(
                 "Encountered error while reading chainfile at \"{}\"",
                 &chainfile_path

tests/test_liftover.py

@@ -7,45 +7,45 @@ def test_hg19_to_hg38():
     ch = ChainLifter(Genome.HG19, Genome.HG38)
 
     result = ch.convert_coordinate("chr7", 140439611)
-    assert result is not None
+    assert result
     assert len(result) == 1
     assert result[0] == ["chr7", "140739811", "+"]
 
     result = ch.convert_coordinate("chr7", 140439746)
-    assert result is not None
+    assert result
     assert len(result) == 1
     assert result[0] == ["chr7", "140739946", "+"]
 
     result = ch.convert_coordinate("chr7", 140439703)
-    assert result is not None
+    assert result
     assert len(result) == 1
     assert result[0] == ["chr7", "140739903", "+"]
 
     result = ch.convert_coordinate("chr7", 140453136)
-    assert result is not None
+    assert result
     assert len(result) == 1
     assert result[0] == ["chr7", "140753336", "+"]
 
     # coordinate exceeds bounds
     result = ch.convert_coordinate("chr7", 14040053136)
-    assert result is None
+    assert result == []
 
 
 def test_hg38_to_hg19():
     """Test hg38 to hg19 lifter."""
     ch = ChainLifter(Genome.HG38, Genome.HG19)
 
     result = ch.convert_coordinate("chr7", 140739811)
-    assert result is not None
+    assert result
     assert len(result) == 1
     assert result[0] == ["chr7", "140439611", "+"]
 
     result = ch.convert_coordinate("chr7", 140759820)
-    assert result is not None
+    assert result
     assert len(result) == 1
     assert result[0] == ["chr7", "140459620", "+"]
 
     result = ch.convert_coordinate("chr7", 60878240)
-    assert result is not None
+    assert result
     assert len(result) == 1
     assert result[0] == ["chr7", "61646115", "+"]