docs: changelog for v0.3.1 release

CHANGELOG.md

@@ -23,6 +23,19 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 - PLACEHOLDER
 
+
+## [0.3.1]
+
+### Fixed
+
+- Wrong theta angle specification for pi-pi interactions
+- Reduced unnecessary cloning of objects and strings
+
+### Changed
+
+- Defaults to searching for all intra- and inter-chain interactions when `-g '/'` is passed to `contacts`
+
+
 ## [0.3.0] - 2024-08-14
 
 ### Added
@@ -62,7 +75,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Initial release
 - Detection of common protein-protein interactions in a PDB or mmCIF file
 
-[unreleased]: https://github.com/y1zhou/arpeggia/compare/v0.3.0...HEAD
-[0.2.0]: https://github.com/y1zhou/arpeggia/releases/tag/v0.3.0
+[unreleased]: https://github.com/y1zhou/arpeggia/compare/v0.3.1...HEAD
+[0.3.1]: https://github.com/y1zhou/arpeggia/releases/tag/v0.3.1
+[0.3.0]: https://github.com/y1zhou/arpeggia/releases/tag/v0.3.0
 [0.2.0]: https://github.com/y1zhou/arpeggia/releases/tag/v0.2.0
 [0.1.0]: https://github.com/y1zhou/arpeggia/releases/tag/v0.1.0

Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "arpeggia"
-version = "0.3.0"
+version = "0.3.1"
 description = "A port of the Arpeggio library for Rust"
 edition = "2021"
 authors = ["Yi Zhou <[email protected]>"]

src/cli/sasa.rs

@@ -60,7 +60,6 @@ pub(crate) fn run(args: &Args) {
     let mut df_sasa = get_atom_sasa(&pdb, args.probe_radius, args.n_points);
 
     // Prepare output directory
-    // let file_id = input_path.file_stem().unwrap().to_str().unwrap();
     let output_path = Path::new(&args.output).canonicalize().unwrap();
     let _ = std::fs::create_dir_all(output_path.clone());
     let output_file = match output_path.is_dir() {