chore: bump rust-toolchain version

rust-toolchain.toml

@@ -1,5 +1,5 @@
 [toolchain]
-channel = "1.87.0"
+channel = "1.92.0"
 components = [ "rustfmt", "clippy" ]
 targets = ["x86_64-unknown-linux-gnu", "i686-unknown-linux-gnu"]
 profile = "minimal"

src/edge_table.rs

@@ -292,7 +292,7 @@ impl EdgeTable {
         crate::table_iterator::make_table_iterator::<&EdgeTable>(self)
     }
 
-    pub fn lending_iter(&self) -> EdgeTableRowView {
+    pub fn lending_iter<'table>(&'table self) -> EdgeTableRowView<'table> {
         EdgeTableRowView::new(self)
     }
 
@@ -320,7 +320,10 @@ impl EdgeTable {
     ///
     /// * `Some(row_view)` if `r` is valid
     /// * `None` otherwise
-    pub fn row_view<E: Into<EdgeId> + Copy>(&self, r: E) -> Option<EdgeTableRowView> {
+    pub fn row_view<'table, E: Into<EdgeId> + Copy>(
+        &'table self,
+        r: E,
+    ) -> Option<EdgeTableRowView<'table>> {
         let view = EdgeTableRowView {
             table: self,
             id: r.into(),

src/individual_table.rs

@@ -422,7 +422,7 @@ match tables.individuals().metadata::<MutationMetadata>(0)
         crate::table_iterator::make_table_iterator::<&IndividualTable>(self)
     }
 
-    pub fn lending_iter(&self) -> IndividualTableRowView {
+    pub fn lending_iter(&'_ self) -> IndividualTableRowView<'_> {
         IndividualTableRowView::new(self)
     }
 
@@ -451,7 +451,10 @@ match tables.individuals().metadata::<MutationMetadata>(0)
     ///
     /// * `Some(row view)` if `r` is valid
     /// * `None` otherwise
-    pub fn row_view<I: Into<IndividualId> + Copy>(&self, r: I) -> Option<IndividualTableRowView> {
+    pub fn row_view<I: Into<IndividualId> + Copy>(
+        &'_ self,
+        r: I,
+    ) -> Option<IndividualTableRowView<'_>> {
         let view = IndividualTableRowView {
             table: self,
             id: r.into(),

src/migration_table.rs

@@ -325,7 +325,7 @@ impl MigrationTable {
         crate::table_iterator::make_table_iterator::<&MigrationTable>(self)
     }
 
-    pub fn lending_iter(&self) -> MigrationTableRowView {
+    pub fn lending_iter(&'_ self) -> MigrationTableRowView<'_> {
         MigrationTableRowView::new(self)
     }
 
@@ -354,7 +354,10 @@ impl MigrationTable {
     ///
     /// * `Some(row view)` if `r` is valid
     /// * `None` otherwise
-    pub fn row_view<M: Into<MigrationId> + Copy>(&self, r: M) -> Option<MigrationTableRowView> {
+    pub fn row_view<M: Into<MigrationId> + Copy>(
+        &'_ self,
+        r: M,
+    ) -> Option<MigrationTableRowView<'_>> {
         let view = MigrationTableRowView {
             table: self,
             id: r.into(),

src/mutation_table.rs

@@ -315,7 +315,7 @@ impl MutationTable {
         crate::table_iterator::make_table_iterator::<&MutationTable>(self)
     }
 
-    pub fn lending_iter(&self) -> MutationTableRowView {
+    pub fn lending_iter(&'_ self) -> MutationTableRowView<'_> {
         MutationTableRowView::new(self)
     }
 
@@ -344,7 +344,10 @@ impl MutationTable {
     ///
     /// * `Some(row view)` if `r` is valid
     /// * `None` otherwise
-    pub fn row_view<M: Into<MutationId> + Copy>(&self, r: M) -> Option<MutationTableRowView> {
+    pub fn row_view<M: Into<MutationId> + Copy>(
+        &'_ self,
+        r: M,
+    ) -> Option<MutationTableRowView<'_>> {
         let view = MutationTableRowView {
             table: self,
             id: r.into(),

src/node_table.rs

@@ -607,7 +607,7 @@ impl NodeTable {
         crate::table_iterator::make_table_iterator::<&NodeTable>(self)
     }
 
-    pub fn lending_iter(&self) -> NodeTableRowView {
+    pub fn lending_iter(&'_ self) -> NodeTableRowView<'_> {
         NodeTableRowView::new(self)
     }
 
@@ -636,7 +636,7 @@ impl NodeTable {
     ///
     /// * `Some(row view)` if `r` is valid
     /// * `None` otherwise
-    pub fn row_view<N: Into<NodeId> + Copy>(&self, r: N) -> Option<NodeTableRowView> {
+    pub fn row_view<N: Into<NodeId> + Copy>(&'_ self, r: N) -> Option<NodeTableRowView<'_>> {
         let view = NodeTableRowView {
             table: self,
             id: r.into(),

src/population_table.rs

@@ -211,7 +211,7 @@ impl PopulationTable {
         crate::table_iterator::make_table_iterator::<&PopulationTable>(self)
     }
 
-    pub fn lending_iter(&self) -> PopulationTableRowView {
+    pub fn lending_iter(&'_ self) -> PopulationTableRowView<'_> {
         PopulationTableRowView::new(self)
     }
 
@@ -240,7 +240,10 @@ impl PopulationTable {
     ///
     /// * `Some(row view)` if `r` is valid
     /// * `None` otherwise
-    pub fn row_view<P: Into<PopulationId> + Copy>(&self, r: P) -> Option<PopulationTableRowView> {
+    pub fn row_view<P: Into<PopulationId> + Copy>(
+        &'_ self,
+        r: P,
+    ) -> Option<PopulationTableRowView<'_>> {
         match SizeType::try_from(r.into()).ok() {
             Some(row) if row < self.num_rows() => {
                 let view = PopulationTableRowView {

src/provenance.rs

@@ -242,7 +242,10 @@ impl ProvenanceTable {
     ///
     /// * `Some(row view)` if `r` is valid
     /// * `None` otherwise
-    pub fn row_view<P: Into<ProvenanceId> + Copy>(&self, row: P) -> Option<ProvenanceTableRowView> {
+    pub fn row_view<P: Into<ProvenanceId> + Copy>(
+        &'_ self,
+        row: P,
+    ) -> Option<ProvenanceTableRowView<'_>> {
         match row.into().to_usize() {
             Some(x) if (x as u64) < self.num_rows() => {
                 let view = ProvenanceTableRowView {
@@ -263,7 +266,7 @@ impl ProvenanceTable {
         crate::table_iterator::make_table_iterator::<&ProvenanceTable>(self)
     }
 
-    pub fn lending_iter(&self) -> ProvenanceTableRowView {
+    pub fn lending_iter(&'_ self) -> ProvenanceTableRowView<'_> {
         ProvenanceTableRowView::new(self)
     }
 

src/site_table.rs

@@ -250,7 +250,7 @@ impl SiteTable {
         crate::table_iterator::make_table_iterator::<&SiteTable>(self)
     }
 
-    pub fn lending_iter(&self) -> SiteTableRowView {
+    pub fn lending_iter(&'_ self) -> SiteTableRowView<'_> {
         SiteTableRowView::new(self)
     }
 
@@ -279,7 +279,7 @@ impl SiteTable {
     ///
     /// * `Some(row view)` if `r` is valid
     /// * `None` otherwise
-    pub fn row_view<S: Into<SiteId> + Copy>(&self, r: S) -> Option<SiteTableRowView> {
+    pub fn row_view<S: Into<SiteId> + Copy>(&'_ self, r: S) -> Option<SiteTableRowView<'_>> {
         let view = SiteTableRowView {
             table: self,
             id: r.into(),

src/sys/bindings.rs

@@ -28,5 +28,5 @@
 //! This module contains the same types/functions with the same names.
 
 #![allow(clippy::all)]
-
+#![allow(unnecessary_transmutes)]
 include!(concat!(env!("OUT_DIR"), "/auto_bindings.rs"));

src/test_fixtures.rs

@@ -1,51 +1,3 @@
-#[cfg(test)]
-use crate::*;
-
-#[cfg(test)]
-#[derive(serde::Serialize, serde::Deserialize, Debug, Eq, PartialEq, Copy, Clone)]
-pub struct GenericMetadata {
-    pub data: i64,
-}
-
-#[cfg(test)]
-impl Default for GenericMetadata {
-    fn default() -> Self {
-        Self { data: 42 }
-    }
-}
-
-#[cfg(test)]
-impl crate::metadata::MetadataRoundtrip for GenericMetadata {
-    fn encode(&self) -> Result<Vec<u8>, crate::metadata::MetadataError> {
-        handle_metadata_return!(bincode::serialize(&self))
-    }
-
-    fn decode(md: &[u8]) -> Result<Self, crate::metadata::MetadataError> {
-        handle_metadata_return!(bincode::deserialize(md))
-    }
-}
-
-#[cfg(test)]
-impl crate::metadata::MutationMetadata for GenericMetadata {}
-
-#[cfg(test)]
-impl crate::metadata::SiteMetadata for GenericMetadata {}
-
-#[cfg(test)]
-impl crate::metadata::EdgeMetadata for GenericMetadata {}
-
-#[cfg(test)]
-impl crate::metadata::NodeMetadata for GenericMetadata {}
-
-#[cfg(test)]
-impl crate::metadata::IndividualMetadata for GenericMetadata {}
-
-#[cfg(test)]
-impl crate::metadata::PopulationMetadata for GenericMetadata {}
-
-#[cfg(test)]
-impl crate::metadata::MigrationMetadata for GenericMetadata {}
-
 #[cfg(test)]
 pub mod bad_metadata {
     #[derive(serde::Serialize, serde::Deserialize, Debug)]

src/trees/tree.rs

@@ -77,7 +77,7 @@ impl<'treeseq> Tree<'treeseq> {
 
     /// # Failing examples
     ///
-    /// An error will be returned if ['crate::TreeFlags::SAMPLE_LISTS`] is not used:
+    /// An error will be returned if ['TreeFlags::SAMPLE_LISTS`](crate::TreeFlags::SAMPLE_LISTS) is not used:
     ///
     /// ```should_panic
     /// use tskit::StreamingIterator;
@@ -337,7 +337,7 @@ impl<'treeseq> Tree<'treeseq> {
 
     /// # Failing examples
     ///
-    /// An error will be returned if ['crate::TreeFlags::SAMPLE_LISTS`] is not used:
+    /// An error will be returned if ['TreeFlags::SAMPLE_LISTS`](crate::TreeFlags::SAMPLE_LISTS) is not used:
     ///
     /// ```should_panic
     /// use tskit::StreamingIterator;
@@ -371,7 +371,7 @@ impl<'treeseq> Tree<'treeseq> {
 
     /// # Failing examples
     ///
-    /// An error will be returned if ['crate::TreeFlags::SAMPLE_LISTS`] is not used:
+    /// An error will be returned if ['TreeFlags::SAMPLE_LISTS`](crate::TreeFlags::SAMPLE_LISTS) is not used:
     ///
     /// ```should_panic
     /// use tskit::StreamingIterator;
@@ -405,7 +405,7 @@ impl<'treeseq> Tree<'treeseq> {
 
     /// # Failing examples
     ///
-    /// An error will be returned if ['crate::TreeFlags::SAMPLE_LISTS`] is not used:
+    /// An error will be returned if ['TreeFlags::SAMPLE_LISTS`](crate::TreeFlags::SAMPLE_LISTS) is not used:
     ///
     /// ```should_panic
     /// use tskit::StreamingIterator;

src/trees/treeseq.rs

@@ -249,7 +249,10 @@ impl TreeSequence {
     /// while let Some(tree) = tree_sequence.tree_iterator(tskit::TreeFlags::default()).unwrap().next() {
     /// }
     /// ```
-    pub fn tree_iterator<F: Into<TreeFlags>>(&self, flags: F) -> Result<Tree, TskitError> {
+    pub fn tree_iterator<'ts, F: Into<TreeFlags>>(
+        &'ts self,
+        flags: F,
+    ) -> Result<Tree<'ts>, TskitError> {
         let tree = Tree::new(&self.inner, flags)?;
 
         Ok(tree)
@@ -262,11 +265,11 @@ impl TreeSequence {
     /// # Errors
     ///
     /// * [`TskitError`] if `at` is not valid
-    pub fn tree_iterator_at_position<F: Into<TreeFlags>, P: Into<Position>>(
-        &self,
+    pub fn tree_iterator_at_position<'ts, F: Into<TreeFlags>, P: Into<Position>>(
+        &'ts self,
         flags: F,
         at: P,
-    ) -> Result<Tree, TskitError> {
+    ) -> Result<Tree<'ts>, TskitError> {
         Tree::new_at_position(&self.inner, flags, at)
     }
 
@@ -277,11 +280,11 @@ impl TreeSequence {
     /// # Errors
     ///
     /// * [`TskitError`] if `at` is not valid
-    pub fn tree_iterator_at_index<F: Into<TreeFlags>>(
-        &self,
+    pub fn tree_iterator_at_index<'ts, F: Into<TreeFlags>>(
+        &'ts self,
         flags: F,
         at: i32,
-    ) -> Result<Tree, TskitError> {
+    ) -> Result<Tree<'ts>, TskitError> {
         Tree::new_at_index(&self.inner, flags, at)
     }
 
@@ -481,7 +484,9 @@ impl TreeSequence {
     }
 
     /// Build an iterator over edge differences.
-    pub fn edge_differences_iter(&self) -> crate::edge_differences::EdgeDifferencesIterator {
+    pub fn edge_differences_iter<'ts>(
+        &'ts self,
+    ) -> crate::edge_differences::EdgeDifferencesIterator<'ts> {
         crate::edge_differences::EdgeDifferencesIterator::new(self)
     }