fix deadlocks

Author: brentp

Cargo.toml

@@ -19,24 +19,25 @@ path = "src/main.rs"
 [dependencies]
 rand = "0.8.5"
 smartstring = { version = "1.0.1", optional = true }
-smol_str = { version = "0.2.0", optional = true }
-compact_str = { version = "0.7.0", optional = true }
+smol_str = { version = "0.3.2", optional = true }
+compact_str = { version = "0.9.0", optional = true }
 kstring = { version = "2.0.0", optional = true }
-noodles = { version = "0.85.0" }
+noodles = { version = "0.97.0" }
 flate2 = "1.0.26"
 clap = { version = "4.2.7", features = ['derive'] }
-env_logger = "0.10.0"
+env_logger = "0.11.8"
 log = "0.4.19"
 linear-map = "1.2.0"
-hashbrown = "0.14.0"
+hashbrown = "0.15.2"
 mimalloc = "0.1.39"
 bitflags = "2.4.0"
 rust-htslib = { git = "https://github.com/brentp/rust-htslib.git", rev = "0471b48" }
 tempfile = "^3.14.0"
-simplebed = { git = "https://github.com/brentp/simplebed-rs.git", rev = "924f8e4" }
-pyo3 = {version = "0.23.4", features=["auto-initialize"]}
-pyo3-ffi = "0.23.4"
+simplebed = { git = "https://github.com/brentp/simplebed-rs.git", rev = "4471cdc" }
+pyo3 = {version = "0.24.1", features=["auto-initialize"]}
+pyo3-ffi = "0.24.1"
 mlua = {version = "0.10.3", features=["luau", "send"]}
+parking_lot = {version="0.12.3"}
 
 
 [features]
@@ -52,7 +53,7 @@ core = ["noodles/core"]
 dyn_positioned = []
 
 [dev-dependencies]
-criterion = { version = "0.4", features = ["html_reports"] }
+criterion = { version = "0.5.1", features = ["html_reports"] }
 clap = { version = "4.5.21", features = ["derive"] }
 
 [[bench]]

examples/intersect.rs

@@ -1,5 +1,5 @@
 use crate::intersection::Intersections;
-use crate::py::{CompiledPython, PyReportOptions};
+use crate::py::CompiledPython;
 use crate::report_options::ReportOptions;
 use std::sync::Arc;
 #[derive(Debug, PartialEq)]
@@ -215,21 +215,29 @@ impl ColumnReporter for Column<'_> {
                 Ok(Value::Int(total_bases))
             }
             Some(ValueParser::ChromStartEnd) => {
+                let base_interval = r
+                    .base_interval
+                    .try_lock()
+                    .expect("failed to lock base_interval");
                 let s = format!(
                     "{}\t{}\t{}",
-                    r.base_interval.chrom(),
-                    r.base_interval.start(),
-                    r.base_interval.stop()
+                    base_interval.chrom(),
+                    base_interval.start(),
+                    base_interval.stop()
                 );
                 Ok(Value::String(s))
             }
             Some(ValueParser::OriginalInterval) => {
                 // Return the original interval as a string
+                let base_interval = r
+                    .base_interval
+                    .try_lock()
+                    .expect("failed to lock base_interval");
                 let s = format!(
                     "{}\t{}\t{}",
-                    r.base_interval.chrom(),
-                    r.base_interval.start(),
-                    r.base_interval.stop()
+                    base_interval.chrom(),
+                    base_interval.start(),
+                    base_interval.stop()
                 );
                 Ok(Value::String(s))
             }