Add TableCollection::topological_sort_individuals.

Closes #195

Author: molpopgen

examples/forward_simulation.rs

@@ -18,7 +18,7 @@
  *   and numbers of crossovers, etc.., from being entered
  *   on the command line.
  */
-use clap::{Command, Arg};
+use clap::{Arg, Command};
 use rand::rngs::StdRng;
 use rand::Rng;
 use rand::SeedableRng;

examples/tree_traversals.rs

@@ -1,4 +1,4 @@
-use clap::{Command, Arg};
+use clap::{Arg, Command};
 use tskit::prelude::*;
 
 // "Manual" traversal from samples to root

src/flags.rs

@@ -103,6 +103,15 @@ bitflags! {
     }
 }
 
+bitflags! {
+    /// Modify behavior of [`crate::TableCollection::sort_individuals`].
+    #[derive(Default)]
+    pub struct IndividualTableSortOptions : tsk_flags_t {
+        /// Default behavior.
+        const NONE = 0;
+    }
+}
+
 bitflags! {
     /// Specify the behavior of iterating over [`Tree`] objects.
     /// See [`TreeSequence::tree_iterator`].

src/table_collection.rs

@@ -5,6 +5,7 @@ use crate::metadata::*;
 use crate::types::Bookmark;
 use crate::EdgeTable;
 use crate::IndividualTable;
+use crate::IndividualTableSortOptions;
 use crate::Location;
 use crate::MigrationTable;
 use crate::MutationTable;
@@ -597,6 +598,12 @@ impl TableCollection {
     /// Sort the tables.  
     /// The [``bookmark``](crate::types::Bookmark) can
     /// be used to affect where sorting starts from for each table.
+    ///
+    /// # Warning
+    ///
+    /// As of `0.7.0`, this function does not sort the individual table!
+    /// See
+    /// [``topological_sort_individuals``](crate::TableCollection::topological_sort_individuals).
     pub fn sort(&mut self, start: &Bookmark, options: TableSortOptions) -> TskReturnValue {
         let rv = unsafe {
             ll_bindings::tsk_table_collection_sort(
@@ -611,11 +618,73 @@ impl TableCollection {
 
     /// Fully sort all functions.
     /// Implemented via a call to [``sort``](crate::TableCollection::sort).
+    ///
+    /// # Warning
+    ///
+    /// As of `0.7.0`, this function does not sort the individual table!
+    /// See
+    /// [``topological_sort_individuals``](crate::TableCollection::topological_sort_individuals).
     pub fn full_sort(&mut self, options: TableSortOptions) -> TskReturnValue {
         let b = Bookmark::new();
         self.sort(&b, options)
     }
 
+    /// Sorts the individual table in place, so that parents come before children,
+    /// and the parent column is remapped as required. Node references to individuals
+    /// are also updated.
+    ///
+    /// This function is needed because neither [``sort``](crate::TableCollection::sort) nor
+    /// [``full_sort``](crate::TableCollection::full_sort) sorts
+    /// the individual table!
+    ///
+    /// # Examples
+    ///
+    /// ```
+    /// // Parent comes AFTER the child
+    /// let mut tables = tskit::TableCollection::new(1.0).unwrap();
+    /// let i0 = tables.add_individual::<i32, f64>(0,&[],&[1]).unwrap();
+    /// assert_eq!(i0, 0);
+    /// let i1 = tables.add_individual::<i32, f64>(0,&[],&[]).unwrap();
+    /// assert_eq!(i1, 1);
+    /// let n0 = tables.add_node(0, 0.0, -1, i1).unwrap();
+    /// assert_eq!(n0, 0);
+    /// let n1 = tables.add_node(0, 1.0, -1, i0).unwrap();
+    /// assert_eq!(n1, 1);
+    ///
+    /// // Testing for valid individual order will Err:
+    /// match tables.check_integrity(tskit::TableIntegrityCheckFlags::CHECK_INDIVIDUAL_ORDERING) {
+    ///     Ok(_) => panic!("expected Err"),
+    ///     Err(_) => (),
+    /// };
+    ///
+    /// // The standard sort doesn't fix the Err...:
+    /// tables.full_sort(tskit::TableSortOptions::default()).unwrap();
+    /// match tables.check_integrity(tskit::TableIntegrityCheckFlags::CHECK_INDIVIDUAL_ORDERING) {
+    ///     Ok(_) => panic!("expected Err"),
+    ///     Err(_) => (),
+    /// };
+    ///
+    /// // ... so we need to intentionally sort the individuals.
+    /// let _ = tables.topological_sort_individuals(tskit::IndividualTableSortOptions::default()).unwrap();
+    /// tables.check_integrity(tskit::TableIntegrityCheckFlags::CHECK_INDIVIDUAL_ORDERING).unwrap();
+    /// ```
+    ///
+    /// # Errors
+    ///
+    /// Will return an error code if the underlying `C` function returns an error.
+    pub fn topological_sort_individuals(
+        &mut self,
+        options: IndividualTableSortOptions,
+    ) -> TskReturnValue {
+        let rv = unsafe {
+            ll_bindings::tsk_table_collection_individual_topological_sort(
+                self.as_mut_ptr(),
+                options.bits(),
+            )
+        };
+        handle_tsk_return_value!(rv)
+    }
+
     /// Dump the table collection to file.
     ///
     pub fn dump(&self, filename: &str, options: TableOutputOptions) -> TskReturnValue {