clean up code

src/lib.rs

@@ -493,20 +493,21 @@ pub fn main() -> Result<(), Error> {
 
  log::info!("Reaging input genomes");
  let path = Path::new(genome_ids);
- let file = File::open(&path)?;
+ let file = File::open(path)?;
  let reader = std::io::BufReader::new(file);
 
  // Read in genomes to
- let ids: Vec<String> = reader.lines().filter_map(|line| line.ok()).collect();
-
+ // let ids: Vec<String> = reader.lines().filter_map(|line| line.ok()).collect();
+ let ids: Vec<String> = reader.lines().map_while(Result::ok).collect();
+
  log::info!("Reading input metadata");
  let mut sketches: MultiSketch = MultiSketch::load(ref_db)
  .unwrap_or_else(|_| panic!("Could not read sketch metadata from {}.skm", ref_db));
 
 
  println!("BLUB");
  // write new .skm 
- sketches.remove_metadata(ref_db, output_file, &ids);
+ let _ = sketches.remove_metadata(output_file, &ids);
 
  // remove samples from .skd file
  log::info!("Remove genomes and writing output");

src/multisketch.rs

@@ -193,7 +193,6 @@ impl MultiSketch {
  }
  pub fn remove_metadata(
  &mut self,
- input_prefix: &str,
  output_file_name: &str,
  genome_ids_to_remove: &[String],
  ) -> std::io::Result<()> {
@@ -207,7 +206,7 @@ impl MultiSketch {
  }
  }
  self.sketch_metadata = new_sketch_metadata;
- self.save_metadata(output_file_name);
+ let _ = self.save_metadata(output_file_name);
  Ok(())
  }
 
@@ -255,23 +254,6 @@ impl MultiSketch {
  Ok(())
  }
 
- // pub fn get_genome_positions(&self, genome_ids: &[String], positions: &mut Vec<usize>) {
- // let mut missing_ids = Vec::new();
-
- // for id in genome_ids {
- // if let Some(&position) = self.name_map.get(id) {
- // positions.push(position);
- // } else {
- // missing_ids.push(id.clone());
- // }
- // }
-
- // if !missing_ids.is_empty() {
- // panic!("The following genome IDs were not found: {:?}", missing_ids);
- // }
-
- // positions.sort();
- // }
 
  // This function is called when sketches are merged, not when they are
  // first sketched (this is handled by sketch::sketch_files())

tests/common/mod.rs

@@ -37,44 +37,20 @@ impl TestSetup {
  pub fn setup() -> Self {
  let wd = assert_fs::TempDir::new().unwrap();
 
- println!("Current working directory: {:?}", std::env::current_dir().unwrap());
-
- // Debug: Print FILE_IN and FILE_TEST paths
- println!("FILE_IN constant value: {:?}", FILE_IN);
- println!("FILE_TEST constant value: {:?}", FILE_TEST);
-
- let file_in_path = Path::new(FILE_IN);
- let file_test_path = Path::new(FILE_TEST);
-
- println!("FILE_IN absolute path: {:?}", file_in_path.canonicalize());
- println!("FILE_TEST absolute path: {:?}", file_test_path.canonicalize());
-
- // Check if the directories exist
- println!("FILE_IN exists: {}", file_in_path.exists());
- println!("FILE_TEST exists: {}", file_test_path.exists());
-
- // Attempt to create symlink for SYM_IN
- match wd.child(SYM_IN).symlink_to_dir(file_in_path.canonicalize().unwrap_or_else(|e| {
- panic!("Failed to canonicalize FILE_IN path: {:?}. Error: {:?}", file_in_path, e);
- })) {
- Ok(_) => println!("Successfully created symlink for {}", SYM_IN),
- Err(e) => println!("Failed to create symlink for {}: {:?}", SYM_IN, e),
- }
-
- // Attempt to create symlink for SYM_TEST
- match wd.child(SYM_TEST).symlink_to_dir(file_test_path.canonicalize().unwrap_or_else(|e| {
- panic!("Failed to canonicalize FILE_TEST path: {:?}. Error: {:?}", file_test_path, e);
- })) {
- Ok(_) => println!("Successfully created symlink for {}", SYM_TEST),
- Err(e) => println!("Failed to create symlink for {}: {:?}", SYM_TEST, e),
- }
-
- // Debug: Print contents of temporary directory
- println!("Contents of temporary directory:");
- for entry in std::fs::read_dir(&wd.path()).unwrap() {
- let entry = entry.unwrap();
- println!(" {:?}", entry.path());
- }
+ wd.child(SYM_IN)
+ .symlink_to_dir(
+ Path::new(FILE_IN)
+ .canonicalize()
+ .expect("Could not link expected files"),
+ )
+ .unwrap();
+ wd.child(SYM_TEST)
+ .symlink_to_dir(
+ Path::new(FILE_TEST)
+ .canonicalize()
+ .expect("Could not link expected files"),
+ )
+ .unwrap();
 
  Self { wd }
  }