tskit-dev · molpopgen · Nov 4, 2022 · Nov 3, 2022
diff --git a/examples/forward_simulation.rs b/examples/forward_simulation.rs
@@ -23,7 +23,6 @@ use rand::rngs::StdRng;
 use rand::Rng;
 use rand::SeedableRng;
 use rand_distr::{Exp, Uniform};
-use tskit::TableAccess;
 use tskit::TskitTypeAccess;
 
 #[derive(clap::Parser)]

diff --git a/src/_macros.rs b/src/_macros.rs
@@ -518,7 +518,7 @@ macro_rules! build_owned_tables {
         }
 
         impl std::ops::Deref for $name {
-            type Target = $deref<'static>;
+            type Target = $deref;
 
             fn deref(&self) -> &Self::Target {
                 // SAFETY: that T* and &T have same layout,

diff --git a/src/edge_table.rs b/src/edge_table.rs
@@ -1,3 +1,5 @@
+use std::ptr::NonNull;
+
 use crate::bindings as ll_bindings;
 use crate::metadata;
 use crate::Position;
@@ -28,7 +30,7 @@ impl PartialEq for EdgeTableRow {
 }
 
 fn make_edge_table_row(table: &EdgeTable, pos: tsk_id_t) -> Option<EdgeTableRow> {
-    let table_ref = table.table_;
+    let table_ref = table.as_ref();
     Some(EdgeTableRow {
         id: pos.into(),
         left: table.left(pos)?,
@@ -39,8 +41,8 @@ fn make_edge_table_row(table: &EdgeTable, pos: tsk_id_t) -> Option<EdgeTableRow>
     })
 }
 
-pub(crate) type EdgeTableRefIterator<'a> = crate::table_iterator::TableIterator<&'a EdgeTable<'a>>;
-pub(crate) type EdgeTableIterator<'a> = crate::table_iterator::TableIterator<EdgeTable<'a>>;
+pub(crate) type EdgeTableRefIterator<'a> = crate::table_iterator::TableIterator<&'a EdgeTable>;
+pub(crate) type EdgeTableIterator = crate::table_iterator::TableIterator<EdgeTable>;
 
 impl<'a> Iterator for EdgeTableRefIterator<'a> {
     type Item = EdgeTableRow;
@@ -52,7 +54,7 @@ impl<'a> Iterator for EdgeTableRefIterator<'a> {
     }
 }
 
-impl<'a> Iterator for EdgeTableIterator<'a> {
+impl Iterator for EdgeTableIterator {
     type Item = EdgeTableRow;
 
     fn next(&mut self) -> Option<Self::Item> {
@@ -64,22 +66,32 @@ impl<'a> Iterator for EdgeTableIterator<'a> {
 
 /// An immutable view of an edge table.
 ///
-/// These are not created directly.
-/// Instead, use [`TableAccess::edges`](crate::TableAccess::edges)
-/// to get a reference to an existing edge table;
+/// These are not created directly but are accessed
+/// by types implementing [`std::ops::Deref`] to
+/// [`crate::table_views::TableViews`]
 #[repr(transparent)]
-pub struct EdgeTable<'a> {
-    table_: &'a ll_bindings::tsk_edge_table_t,
+pub struct EdgeTable {
+    pub(crate) table_: NonNull<ll_bindings::tsk_edge_table_t>,
 }
 
-impl<'a> EdgeTable<'a> {
-    pub(crate) fn new_from_table(edges: &'a ll_bindings::tsk_edge_table_t) -> Self {
-        EdgeTable { table_: edges }
+impl EdgeTable {
+    pub(crate) fn new_from_table(
+        edges: *mut ll_bindings::tsk_edge_table_t,
+    ) -> Result<Self, TskitError> {
+        let n = NonNull::new(edges).ok_or_else(|| {
+            TskitError::LibraryError("null pointer to tsk_edge_table_t".to_string())
+        })?;
+        Ok(EdgeTable { table_: n })
+    }
+
+    pub(crate) fn as_ref(&self) -> &ll_bindings::tsk_edge_table_t {
+        // SAFETY: NonNull
+        unsafe { self.table_.as_ref() }
     }
 
     /// Return the number of rows
-    pub fn num_rows(&'a self) -> crate::SizeType {
-        self.table_.num_rows.into()
+    pub fn num_rows(&self) -> crate::SizeType {
+        self.as_ref().num_rows.into()
     }
 
     /// Return the ``parent`` value from row ``row`` of the table.
@@ -88,12 +100,12 @@ impl<'a> EdgeTable<'a> {
     ///
     /// * `Some(parent)` if `u` is valid.
     /// * `None` otherwise.
-    pub fn parent<E: Into<EdgeId> + Copy>(&'a self, row: E) -> Option<NodeId> {
+    pub fn parent<E: Into<EdgeId> + Copy>(&self, row: E) -> Option<NodeId> {
         unsafe_tsk_column_access!(
             row.into().0,
             0,
             self.num_rows(),
-            self.table_,
+            self.as_ref(),
             parent,
             NodeId
         )
@@ -105,8 +117,15 @@ impl<'a> EdgeTable<'a> {
     ///
     /// * `Some(child)` if `u` is valid.
     /// * `None` otherwise.
-    pub fn child<E: Into<EdgeId> + Copy>(&'a self, row: E) -> Option<NodeId> {
-        unsafe_tsk_column_access!(row.into().0, 0, self.num_rows(), self.table_, child, NodeId)
+    pub fn child<E: Into<EdgeId> + Copy>(&self, row: E) -> Option<NodeId> {
+        unsafe_tsk_column_access!(
+            row.into().0,
+            0,
+            self.num_rows(),
+            self.as_ref(),
+            child,
+            NodeId
+        )
     }
 
     /// Return the ``left`` value from row ``row`` of the table.
@@ -115,12 +134,12 @@ impl<'a> EdgeTable<'a> {
     ///
     /// * `Some(position)` if `u` is valid.
     /// * `None` otherwise.
-    pub fn left<E: Into<EdgeId> + Copy>(&'a self, row: E) -> Option<Position> {
+    pub fn left<E: Into<EdgeId> + Copy>(&self, row: E) -> Option<Position> {
         unsafe_tsk_column_access!(
             row.into().0,
             0,
             self.num_rows(),
-            self.table_,
+            self.as_ref(),
             left,
             Position
         )
@@ -132,8 +151,14 @@ impl<'a> EdgeTable<'a> {
     ///
     /// * `Some(position)` if `u` is valid.
     /// * `None` otherwise.
-    pub fn right<E: Into<EdgeId> + Copy>(&'a self, row: E) -> Option<Position> {
-        unsafe_tsk_column_access_and_map_into!(row.into().0, 0, self.num_rows(), self.table_, right)
+    pub fn right<E: Into<EdgeId> + Copy>(&self, row: E) -> Option<Position> {
+        unsafe_tsk_column_access_and_map_into!(
+            row.into().0,
+            0,
+            self.num_rows(),
+            self.as_ref(),
+            right
+        )
     }
 
     /// Retrieve decoded metadata for a `row`.
@@ -153,10 +178,10 @@ impl<'a> EdgeTable<'a> {
     /// The big-picture semantics are the same for all table types.
     /// See [`crate::IndividualTable::metadata`] for examples.
     pub fn metadata<T: metadata::EdgeMetadata>(
-        &'a self,
+        &self,
         row: EdgeId,
     ) -> Option<Result<T, TskitError>> {
-        let table_ref = self.table_;
+        let table_ref = self.as_ref();
         let buffer = metadata_to_vector!(self, table_ref, row.0)?;
         Some(decode_metadata_row!(T, buffer).map_err(|e| e.into()))
     }
@@ -165,7 +190,7 @@ impl<'a> EdgeTable<'a> {
     /// The value of the iterator is [`EdgeTableRow`].
     ///
     pub fn iter(&self) -> impl Iterator<Item = EdgeTableRow> + '_ {
-        crate::table_iterator::make_table_iterator::<&EdgeTable<'a>>(self)
+        crate::table_iterator::make_table_iterator::<&EdgeTable>(self)
     }
 
     /// Return row `r` of the table.

diff --git a/src/individual_table.rs b/src/individual_table.rs
@@ -1,3 +1,5 @@
+use std::ptr::NonNull;
+
 use crate::bindings as ll_bindings;
 use crate::metadata;
 use crate::IndividualFlags;
@@ -45,15 +47,15 @@ impl PartialEq for IndividualTableRow {
 
 /// An immutable view of a individual table.
 ///
-/// These are not created directly.
-/// Instead, use [`TableAccess::individuals`](crate::TableAccess::individuals)
-/// to get a reference to an existing node table;
-pub struct IndividualTable<'a> {
-    table_: &'a ll_bindings::tsk_individual_table_t,
+/// These are not created directly but are accessed
+/// by types implementing [`std::ops::Deref`] to
+/// [`crate::table_views::TableViews`]
+pub struct IndividualTable {
+    table_: NonNull<ll_bindings::tsk_individual_table_t>,
 }
 
 fn make_individual_table_row(table: &IndividualTable, pos: tsk_id_t) -> Option<IndividualTableRow> {
-    let table_ref = table.table_;
+    let table_ref = table.as_ref();
     Some(IndividualTableRow {
         id: pos.into(),
         flags: table.flags(pos)?,
@@ -64,9 +66,8 @@ fn make_individual_table_row(table: &IndividualTable, pos: tsk_id_t) -> Option<I
 }
 
 pub(crate) type IndividualTableRefIterator<'a> =
-    crate::table_iterator::TableIterator<&'a IndividualTable<'a>>;
-pub(crate) type IndividualTableIterator<'a> =
-    crate::table_iterator::TableIterator<IndividualTable<'a>>;
+    crate::table_iterator::TableIterator<&'a IndividualTable>;
+pub(crate) type IndividualTableIterator = crate::table_iterator::TableIterator<IndividualTable>;
 
 impl<'a> Iterator for IndividualTableRefIterator<'a> {
     type Item = IndividualTableRow;
@@ -78,7 +79,7 @@ impl<'a> Iterator for IndividualTableRefIterator<'a> {
     }
 }
 
-impl<'a> Iterator for IndividualTableIterator<'a> {
+impl Iterator for IndividualTableIterator {
     type Item = IndividualTableRow;
 
     fn next(&mut self) -> Option<Self::Item> {
@@ -88,16 +89,24 @@ impl<'a> Iterator for IndividualTableIterator<'a> {
     }
 }
 
-impl<'a> IndividualTable<'a> {
-    pub(crate) fn new_from_table(individuals: &'a ll_bindings::tsk_individual_table_t) -> Self {
-        IndividualTable {
-            table_: individuals,
-        }
+impl IndividualTable {
+    pub(crate) fn new_from_table(
+        individuals: *mut ll_bindings::tsk_individual_table_t,
+    ) -> Result<Self, TskitError> {
+        let n = NonNull::new(individuals).ok_or_else(|| {
+            TskitError::LibraryError("null pointer to tsk_individual_table_t".to_string())
+        })?;
+        Ok(IndividualTable { table_: n })
+    }
+
+    pub(crate) fn as_ref(&self) -> &ll_bindings::tsk_individual_table_t {
+        // SAFETY: NonNull
+        unsafe { self.table_.as_ref() }
     }
 
     /// Return the number of rows
-    pub fn num_rows(&'a self) -> crate::SizeType {
-        self.table_.num_rows.into()
+    pub fn num_rows(&self) -> crate::SizeType {
+        self.as_ref().num_rows.into()
     }
 
     /// Return the flags for a given row.
@@ -107,7 +116,13 @@ impl<'a> IndividualTable<'a> {
     /// * `Some(flags)` if `row` is valid.
     /// * `None` otherwise.
     pub fn flags<I: Into<IndividualId> + Copy>(&self, row: I) -> Option<IndividualFlags> {
-        unsafe_tsk_column_access_and_map_into!(row.into().0, 0, self.num_rows(), self.table_, flags)
+        unsafe_tsk_column_access_and_map_into!(
+            row.into().0,
+            0,
+            self.num_rows(),
+            self.as_ref(),
+            flags
+        )
     }
 
     /// Return the locations for a given row.
@@ -121,7 +136,7 @@ impl<'a> IndividualTable<'a> {
             row.into().0,
             0,
             self.num_rows(),
-            self.table_,
+            self.as_ref(),
             location,
             location_offset,
             location_length,
@@ -140,7 +155,7 @@ impl<'a> IndividualTable<'a> {
             row.into().0,
             0,
             self.num_rows(),
-            self.table_,
+            self.as_ref(),
             parents,
             parents_offset,
             parents_length,
@@ -179,7 +194,7 @@ impl<'a> IndividualTable<'a> {
     ///
     /// ```
     /// # #[cfg(feature = "derive")] {
-    /// # use tskit::TableAccess;
+    /// #
     /// # let mut tables = tskit::TableCollection::new(100.).unwrap();
     /// # #[derive(serde::Serialize, serde::Deserialize, tskit::metadata::IndividualMetadata)]
     /// # #[serializer("serde_json")]
@@ -202,7 +217,7 @@ impl<'a> IndividualTable<'a> {
     ///
     /// ```
     /// # #[cfg(feature = "derive")] {
-    /// # use tskit::TableAccess;
+    /// #
     /// # let mut tables = tskit::TableCollection::new(100.).unwrap();
     /// # #[derive(serde::Serialize, serde::Deserialize, tskit::metadata::IndividualMetadata)]
     /// # #[serializer("serde_json")]
@@ -248,7 +263,7 @@ impl<'a> IndividualTable<'a> {
 # struct MutationMetadata {
 #    x: i32,
 # }
-# use tskit::TableAccess;
+# 
 # let mut tables = tskit::TableCollection::new(10.).unwrap();
 match tables.individuals().metadata::<MutationMetadata>(0.into())
 {
@@ -280,7 +295,7 @@ match tables.individuals().metadata::<MutationMetadata>(0.into())
     ///
     /// ```
     /// # #[cfg(feature = "derive")] {
-    /// # use tskit::TableAccess;
+    /// #
     /// # #[derive(serde::Serialize, serde::Deserialize, tskit::metadata::IndividualMetadata)]
     /// # #[serializer("serde_json")]
     /// # struct IndividualMetadata {
@@ -319,10 +334,10 @@ match tables.individuals().metadata::<MutationMetadata>(0.into())
     /// types](https://doc.rust-lang.org/book/ch19-03-advanced-traits.html#specifying-placeholder-types-in-trait-definitions-with-associated-types) to enforce at *compile time* that exactly one type (`struct/enum`, etc.) is a valid
     /// metadata type for a table.
     pub fn metadata<T: metadata::IndividualMetadata>(
-        &'a self,
+        &self,
         row: IndividualId,
     ) -> Option<Result<T, TskitError>> {
-        let table_ref = self.table_;
+        let table_ref = self.as_ref();
         let buffer = metadata_to_vector!(self, table_ref, row.0)?;
         Some(decode_metadata_row!(T, buffer).map_err(|e| e.into()))
     }
@@ -331,7 +346,7 @@ match tables.individuals().metadata::<MutationMetadata>(0.into())
     /// The value of the iterator is [`IndividualTableRow`].
     ///
     pub fn iter(&self) -> impl Iterator<Item = IndividualTableRow> + '_ {
-        crate::table_iterator::make_table_iterator::<&IndividualTable<'a>>(self)
+        crate::table_iterator::make_table_iterator::<&IndividualTable>(self)
     }
 
     /// Return row `r` of the table.

diff --git a/src/lib.rs b/src/lib.rs
@@ -92,6 +92,7 @@ pub mod prelude;
 mod site_table;
 mod table_collection;
 mod table_iterator;
+pub mod table_views;
 mod traits;
 mod tree_interface;
 mod trees;
@@ -438,8 +439,6 @@ pub use site_table::{OwnedSiteTable, SiteTable, SiteTableRow};
 pub use table_collection::TableCollection;
 pub use traits::IndividualLocation;
 pub use traits::IndividualParents;
-pub use traits::NodeListGenerator;
-pub use traits::TableAccess;
 pub use traits::TskitTypeAccess;
 pub use tree_interface::{NodeTraversalOrder, TreeInterface};
 pub use trees::{Tree, TreeSequence};

diff --git a/src/metadata.rs b/src/metadata.rs
@@ -30,7 +30,7 @@
 //! ```
 //! # #[cfg(feature = "derive")] {
 //! use tskit::handle_metadata_return;
-//! use tskit::TableAccess;
+//!
 //!
 //! #[derive(serde::Serialize, serde::Deserialize, tskit::metadata::MutationMetadata)]
 //! #[serializer("serde_json")]
@@ -75,7 +75,7 @@
 //!
 //! ```
 //! # #[cfg(feature = "derive")] {
-//! use tskit::TableAccess;
+//!
 //! #[derive(serde::Serialize, serde::Deserialize, PartialEq, PartialOrd)]
 //! struct GeneticValue(f64);
 //!
@@ -101,7 +101,7 @@
 //! For fun, we'll use the Python [`pickle`](https://docs.rs/crate/serde-pickle/) format.
 //!
 //! ```
-//! use tskit::TableAccess;
+//!
 //!
 //! #[derive(serde::Serialize, serde::Deserialize)]
 //! struct Metadata {