chore: docs and clippy

Author: mobiusklein

src/io/mzml/reader.rs

@@ -857,7 +857,7 @@ impl<C: CentroidLike + BuildFromArrayMap, D: DeconvolutedCentroidLike + BuildFro
                                             dp_set = true;
                                             break;
                                         },
-                                        Err(msg) => return Err(self.handle_xml_error(msg.into(), state))
+                                        Err(msg) => return Err(self.handle_xml_error(msg, state))
                                     }
                                 }
                                 _ => {}
@@ -1732,7 +1732,7 @@ impl<
         result.ok()
     }
 
-    pub fn iter_chromatograms(&mut self) -> ChromatogramIter<R, C, D> {
+    pub fn iter_chromatograms(&mut self) -> ChromatogramIter<'_, R, C, D> {
         ChromatogramIter::new(self)
     }
 }

src/io/mzml/writer.rs

@@ -1754,7 +1754,7 @@ where
         attrib!("encodedLength", encoded_len, outer);
         if let Some(dp_id) = array.data_processing_reference() {
             if let Some(dp_global) = self.run.default_data_processing_id.as_deref() {
-                if dp_id.as_ref() != dp_global {
+                if dp_id != dp_global {
                     attrib!("dataProcessingRef", dp_id, outer);
                 }
             }

src/io/offset_index.rs

@@ -82,7 +82,7 @@ impl OffsetIndex {
     }
 
     /// Iterate over the keys and indices
-    pub fn iter(&self) -> Iter<Box<str>, u64> {
+    pub fn iter(&self) -> Iter<'_, Box<str>, u64> {
         self.offsets.iter()
     }
 

src/io/traits/frame.rs

@@ -138,7 +138,7 @@ pub trait IonMobilityFrameSource<
     }
 
     /// Open a new iterator over this stream
-    fn iter(&mut self) -> IonMobilityFrameIterator<C, D, S, Self>
+    fn iter(&mut self) -> IonMobilityFrameIterator<'_, C, D, S, Self>
     where
         Self: Sized,
     {

src/params.rs

@@ -1208,7 +1208,7 @@ macro_rules! find_param_method {
     };
     ($meth:ident, $curie:expr, $desc:literal) => {
         #[doc=$desc]
-        pub fn $meth(&self) -> Option<$crate::params::ValueRef> {
+        pub fn $meth(&self) -> Option<$crate::params::ValueRef<'_>> {
             self.get_param_by_curie($curie)
                 .map(|p| $crate::params::ParamLike::value(p))
         }
@@ -1433,7 +1433,7 @@ pub fn curie_to_num(curie: &str) -> (Option<ControlledVocabulary>, Option<Access
 /// Describe a controlled vocabulary parameter or a user-defined parameter
 pub trait ParamLike {
     fn name(&self) -> &str;
-    fn value(&self) -> ValueRef;
+    fn value(&self) -> ValueRef<'_>;
     fn accession(&self) -> Option<AccessionIntCode>;
     fn controlled_vocabulary(&self) -> Option<ControlledVocabulary>;
     fn unit(&self) -> Unit;
@@ -2302,12 +2302,12 @@ pub trait ParamDescribed {
     }
 
     /// Iterate over the encapsulated parameter list
-    fn iter_params(&self) -> std::slice::Iter<Param> {
+    fn iter_params(&self) -> std::slice::Iter<'_, Param> {
         self.params().iter()
     }
 
     /// Iterate mutably over the encapsulated parameter list
-    fn iter_params_mut(&mut self) -> std::slice::IterMut<Param> {
+    fn iter_params_mut(&mut self) -> std::slice::IterMut<'_, Param> {
         self.params_mut().iter_mut()
     }
 }

src/spectrum/bindata/array.rs

@@ -894,8 +894,8 @@ impl<'transient, 'lifespan: 'transient> DataArray {
     }
 
     /// Get the identifier referencing a [`DataProcessing`](crate::meta::DataProcessing)
-    pub fn data_processing_reference(&self) -> Option<&Box<str>> {
-        self.data_processing_reference.as_ref()
+    pub fn data_processing_reference(&self) -> Option<&str> {
+        self.data_processing_reference.as_deref()
     }
 
     /// Set the identifier referencing a [`DataProcessing`](crate::meta::DataProcessing)
@@ -927,7 +927,7 @@ impl<'transient, 'lifespan: 'transient> ByteArrayView<'transient, 'lifespan> for
         self.unit
     }
 
-    fn data_processing_reference(&self) -> Option<&Box<str>> {
+    fn data_processing_reference(&self) -> Option<&str> {
         self.data_processing_reference()
     }
 
@@ -996,7 +996,7 @@ impl<'transient, 'lifespan: 'transient> ByteArrayView<'transient, 'lifespan>
         self.source.name()
     }
 
-    fn data_processing_reference(&self) -> Option<&Box<str>> {
+    fn data_processing_reference(&self) -> Option<&str> {
         self.source.data_processing_reference()
     }
 }

src/spectrum/bindata/map.rs

@@ -45,7 +45,7 @@ impl BinaryArrayMap {
     }
 
     /// Iterate over references to the key-value pairs of this map
-    pub fn iter(&self) -> Iter<ArrayType, DataArray> {
+    pub fn iter(&self) -> Iter<'_, ArrayType, DataArray> {
         self.byte_buffer_map.iter()
     }
 
@@ -55,7 +55,7 @@ impl BinaryArrayMap {
     }
 
     /// Iterate over mutable references to the key-value pairs of this map
-    pub fn iter_mut(&mut self) -> IterMut<ArrayType, DataArray> {
+    pub fn iter_mut(&mut self) -> IterMut<'_, ArrayType, DataArray> {
         self.byte_buffer_map.iter_mut()
     }
 

src/spectrum/bindata/traits.rs

@@ -80,7 +80,7 @@ pub trait ByteArrayView<'transient, 'lifespan: 'transient> {
     fn unit(&self) -> Unit;
 
     /// Get the identifier referencing a [`DataProcessing`](crate::meta::DataProcessing)
-    fn data_processing_reference(&self) -> Option<&Box<str>> {
+    fn data_processing_reference(&self) -> Option<&str> {
         None
     }
 

src/spectrum/frame.rs

@@ -293,7 +293,7 @@ pub trait IonMobilityFrameLike<
 
     fn raw_arrays(&'_ self) -> Option<&'_ BinaryArrayMap3D>;
 
-    fn features(&self) -> RefFeatureDataLevel<C, D>;
+    fn features(&self) -> RefFeatureDataLevel<'_, C, D>;
 
     fn into_features_and_parts(self) -> (FeatureDataLevel<C, D>, IonMobilityFrameDescription);
 }