Tskit tools

forrustts_examples/neutral_wf.rs

@@ -118,9 +118,9 @@ fn main() {
     )
     .unwrap();
 
-    let mut tskit_tables = forrustts::tskit::convert_to_tskit_and_drain_minimal(
+    let mut tskit_tables = forrustts::tskit_tools::convert_to_tskit_and_drain_minimal(
         &is_sample,
-        forrustts::tskit::simple_time_reverser(g),
+        forrustts::tskit_tools::simple_time_reverser(g),
         simplify.is_some(),
         &mut tables,
     );

src/lib.rs

@@ -22,7 +22,7 @@
 //!    used during the simulation.  Thus, it is not
 //!    part of a [``TableCollection``] and is something
 //!    that would only be useful to write when transfering
-//!    final results to a [`tskit::TableCollection`](::tskit::TableCollection).
+//!    final results to a [`tskit::TableCollection`].
 //! 4. Mutation table data are different. See [``MutationRecord``].
 //! 5. Time is measured as an integer (see [``Time``]),
 //!    as are genomic locations (see [``Position``]).
@@ -60,7 +60,7 @@ pub use simplification::{simplify_tables, simplify_tables_without_state};
 pub use tables::*;
 pub use tsdef::*;
 
-pub mod tskit;
+pub mod tskit_tools;
 pub mod wright_fisher;
 
 /// Get the forrustts version number.

src/test_simplify_tables.rs

@@ -79,10 +79,10 @@ mod test {
         )
         .unwrap();
 
-        let mut tsk_tables = crate::tskit::convert_to_tskit_minimal(
+        let mut tsk_tables = crate::tskit_tools::convert_to_tskit_minimal(
             &tables,
             &is_sample,
-            crate::tskit::simple_time_reverser(num_generations),
+            crate::tskit_tools::simple_time_reverser(num_generations),
             // Do not index tables here!
             // Things are unsorted!
             false,
@@ -111,10 +111,10 @@ mod test {
             *i = 1;
         }
 
-        let mut simplified_rust_tables = crate::tskit::convert_to_tskit_minimal(
+        let mut simplified_rust_tables = crate::tskit_tools::convert_to_tskit_minimal(
             &tables,
             &is_sample,
-            crate::tskit::simple_time_reverser(num_generations),
+            crate::tskit_tools::simple_time_reverser(num_generations),
             true,
         );
 
@@ -192,17 +192,17 @@ mod test {
         let sum_times_buffered: Time = tables_buffered.nodes_.iter().map(|x| x.time).sum();
         assert_eq!(sum_times_sorted, sum_times_buffered);
 
-        let mut tables_sorted_tskit = crate::tskit::convert_to_tskit_minimal(
+        let mut tables_sorted_tskit = crate::tskit_tools::convert_to_tskit_minimal(
             &tables_sorted,
             &is_sample_sorted,
-            crate::tskit::simple_time_reverser(num_generations),
+            crate::tskit_tools::simple_time_reverser(num_generations),
             true,
         );
 
-        let mut tables_buffered_tskit = crate::tskit::convert_to_tskit_minimal(
+        let mut tables_buffered_tskit = crate::tskit_tools::convert_to_tskit_minimal(
             &tables_buffered,
             &is_sample_buffered,
-            crate::tskit::simple_time_reverser(num_generations),
+            crate::tskit_tools::simple_time_reverser(num_generations),
             true,
         );
 
@@ -264,17 +264,17 @@ mod test {
         let sum_times_buffered: Time = tables_buffered.nodes_.iter().map(|x| x.time).sum();
         assert_eq!(sum_times_sorted, sum_times_buffered);
 
-        let mut tables_sorted_tskit = crate::tskit::convert_to_tskit_minimal(
+        let mut tables_sorted_tskit = crate::tskit_tools::convert_to_tskit_minimal(
             &tables_sorted,
             &is_sample_sorted,
-            crate::tskit::simple_time_reverser(num_generations),
+            crate::tskit_tools::simple_time_reverser(num_generations),
             true,
         );
 
-        let mut tables_buffered_tskit = crate::tskit::convert_to_tskit_minimal(
+        let mut tables_buffered_tskit = crate::tskit_tools::convert_to_tskit_minimal(
             &tables_buffered,
             &is_sample_buffered,
-            crate::tskit::simple_time_reverser(num_generations),
+            crate::tskit_tools::simple_time_reverser(num_generations),
             true,
         );
 

src/tskit.rs → src/tskit_tools.rs

@@ -31,7 +31,7 @@ pub fn simple_time_reverser(x: Time) -> Box<dyn Fn(Time) -> f64> {
 ///    is a sample (`1`) or is not a sample (`0`).
 /// * `convert_time`: A callback to convert time, *e.g.* from forwards
 ///                   to backwards. For example, see
-///                   [``simple_time_reverser``](crate::tskit::simple_time_reverser).
+///                   [``simple_time_reverser``](crate::tskit_tools::simple_time_reverser).
 /// * `build_indexes`: If `true`, build the edge table indexes for the return value.
 ///
 /// # Notes
@@ -54,10 +54,10 @@ pub fn simple_time_reverser(x: Time) -> Box<dyn Fn(Time) -> f64> {
 /// tables.add_node(1, 0).unwrap(); // Add a child node at time 1
 /// tables.add_edge(0, 100, 0, 1).unwrap(); // Add an edge
 /// let is_sample = vec![0, 1]; // Mark the child node as a sample.
-/// let tsk_tables = forrustts::tskit::convert_to_tskit_minimal(
+/// let tsk_tables = forrustts::tskit_tools::convert_to_tskit_minimal(
 ///     &tables,
 ///     &is_sample,
-///     forrustts::tskit::simple_time_reverser(1),
+///     forrustts::tskit_tools::simple_time_reverser(1),
 ///     true,
 /// );
 /// assert_eq!(tsk_tables.nodes().num_rows(), 2);
@@ -119,7 +119,7 @@ fn swap_with_empty<T>(v: &mut Vec<T>) {
 ///    is a sample (`1`) or is not a sample (`0`).
 /// * `convert_time`: A callback to convert time, *e.g.* from forwards
 ///                   to backwards. For example, see
-///                   [``simple_time_reverser``](crate::tskit::simple_time_reverser).
+///                   [``simple_time_reverser``](crate::tskit_tools::simple_time_reverser).
 /// * `build_indexes`: If `true`, build the edge table indexes for the return value.
 /// * `tables`: A mutable [``TableCollection``](crate::TableCollection)
 ///
@@ -143,9 +143,9 @@ fn swap_with_empty<T>(v: &mut Vec<T>) {
 /// tables.add_node(1, 0).unwrap(); // Add a child node at time 1
 /// tables.add_edge(0, 100, 0, 1).unwrap(); // Add an edge
 /// let is_sample = vec![0, 1]; // Mark the child node as a sample.
-/// let tsk_tables = forrustts::tskit::convert_to_tskit_and_drain_minimal(
+/// let tsk_tables = forrustts::tskit_tools::convert_to_tskit_and_drain_minimal(
 ///     &is_sample,
-///     forrustts::tskit::simple_time_reverser(1),
+///     forrustts::tskit_tools::simple_time_reverser(1),
 ///     true,
 ///     &mut tables,
 /// );