diff --git a/forrustts_examples/neutral_wf.rs b/forrustts_examples/neutral_wf.rs index 6576270a..96af6202 100644 --- a/forrustts_examples/neutral_wf.rs +++ b/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, ); diff --git a/src/lib.rs b/src/lib.rs index 8592433d..8967ea68 100644 --- a/src/lib.rs +++ b/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. diff --git a/src/test_simplify_tables.rs b/src/test_simplify_tables.rs index 3d5f997c..bdabbbf6 100644 --- a/src/test_simplify_tables.rs +++ b/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, ); diff --git a/src/tskit.rs b/src/tskit_tools.rs similarity index 94% rename from src/tskit.rs rename to src/tskit_tools.rs index 4c65be54..df075290 100644 --- a/src/tskit.rs +++ b/src/tskit_tools.rs @@ -31,7 +31,7 @@ pub fn simple_time_reverser(x: Time) -> Box 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 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(v: &mut Vec) { /// 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(v: &mut Vec) { /// 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, /// );