fix: update deps, make clippy happy

Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "alevin-fry"
-version = "0.8.1"
+version = "0.8.2"
 authors = [
   "Avi Srivastava <avi.srivastava@nyu.edu>",
   "Hirak Sarkar <hirak_sarkar@hms.harvard.edu>",
@@ -16,7 +16,6 @@ repository = "https://github.com/COMBINE-lab/alevin-fry"
 homepage = "https://github.com/COMBINE-lab/alevin-fry"
 documentation = "https://alevin-fry.readthedocs.io/en/latest/"
 include = [
-  "/libradicl/src/*.rs",
   "/src/*.rs",
   "/Cargo.toml",
   "/README.md",

src/collate.rs

@@ -24,7 +24,7 @@ use serde_json::json;
 use std::collections::HashMap;
 use std::fs::File;
 use std::io::BufReader;
-use std::io::{BufWriter, Cursor, Read, Seek, SeekFrom, Write};
+use std::io::{BufWriter, Cursor, Read, Seek, Write};
 use std::iter::FromIterator;
 use std::path::{Path, PathBuf};
 use std::str::FromStr;
@@ -370,7 +370,7 @@ where
     // the exact position at the end of the header,
     // precisely sizeof(u64) bytes beyond the num_chunks field.
     let end_header_pos =
-        br.get_ref().seek(SeekFrom::Current(0)).unwrap() - (br.buffer().len() as u64);
+        br.get_ref().stream_position().unwrap() - (br.buffer().len() as u64);
 
     info!(
         log,
@@ -398,7 +398,7 @@ where
     let umit = rl_tags.tags[1].typeid;
 
     // the exact position at the end of the header + file tags
-    let pos = br.get_ref().seek(SeekFrom::Current(0)).unwrap() - (br.buffer().len() as u64);
+    let pos = br.get_ref().stream_position().unwrap() - (br.buffer().len() as u64);
 
     // copy the header
     {

src/convert.rs

@@ -167,7 +167,7 @@ where
 
     // keep a pointer to header pos
     let end_header_pos =
-        data.seek(SeekFrom::Current(0)).unwrap() - std::mem::size_of::<u64>() as u64;
+        data.stream_position().unwrap() - std::mem::size_of::<u64>() as u64;
 
     // check header position
     info!(log, "end header pos: {:?}", end_header_pos,);

src/quant.rs

@@ -47,18 +47,13 @@ use libradicl::rad_types;
 
 type BufferedGzFile = BufWriter<GzEncoder<fs::File>>;
 
-#[derive(PartialEq, Eq, Debug, Clone, Copy, Serialize)]
+#[derive(PartialEq, Eq, Debug, Default, Clone, Copy, Serialize)]
 pub enum SplicedAmbiguityModel {
     PreferAmbiguity,
+    #[default]
     WinnerTakeAll,
 }
 
-impl Default for SplicedAmbiguityModel {
-    fn default() -> Self {
-        SplicedAmbiguityModel::WinnerTakeAll
-    }
-}
-
 // Implement the trait
 impl FromStr for SplicedAmbiguityModel {
     type Err = &'static str;
@@ -71,9 +66,10 @@ impl FromStr for SplicedAmbiguityModel {
     }
 }
 
-#[derive(PartialEq, Eq, Debug, Clone, Copy, Serialize)]
+#[derive(PartialEq, Eq, Debug, Default, Clone, Copy, Serialize)]
 pub enum ResolutionStrategy {
     Trivial,
+    #[default]
     CellRangerLike,
     CellRangerLikeEm,
     ParsimonyEm,
@@ -82,12 +78,6 @@ pub enum ResolutionStrategy {
     ParsimonyGene,
 }
 
-impl Default for ResolutionStrategy {
-    fn default() -> Self {
-        ResolutionStrategy::CellRangerLike
-    }
-}
-
 impl fmt::Display for ResolutionStrategy {
     fn fmt(&self, f: &mut fmt::Formatter<'_>) -> fmt::Result {
         write!(f, "{:?}", self)