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Rename functions exporting to tskit #56

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Merged
merged 1 commit into from
Dec 27, 2020
Merged

Rename functions exporting to tskit #56

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2 changes: 1 addition & 1 deletion forrustts_examples/neutral_wf.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -102,7 +102,7 @@ fn main() {
)
.unwrap();

let mut tskit_tables = forrustts::tskit::convert_to_tskit_and_drain(
let mut tskit_tables = forrustts::tskit::convert_to_tskit_and_drain_minimal(
&is_sample,
forrustts::tskit::simple_time_reverser(g),
simplify.is_some(),
Expand Down
12 changes: 6 additions & 6 deletions src/test_simplify_tables.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -79,7 +79,7 @@ mod test {
)
.unwrap();

let mut tsk_tables = crate::tskit::convert_to_tskit(
let mut tsk_tables = crate::tskit::convert_to_tskit_minimal(
&tables,
&is_sample,
crate::tskit::simple_time_reverser(num_generations),
Expand Down Expand Up @@ -111,7 +111,7 @@ mod test {
*i = 1;
}

let mut simplified_rust_tables = crate::tskit::convert_to_tskit(
let mut simplified_rust_tables = crate::tskit::convert_to_tskit_minimal(
&tables,
&is_sample,
crate::tskit::simple_time_reverser(num_generations),
Expand Down Expand Up @@ -192,14 +192,14 @@ 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(
let mut tables_sorted_tskit = crate::tskit::convert_to_tskit_minimal(
&tables_sorted,
&is_sample_sorted,
crate::tskit::simple_time_reverser(num_generations),
true,
);

let mut tables_buffered_tskit = crate::tskit::convert_to_tskit(
let mut tables_buffered_tskit = crate::tskit::convert_to_tskit_minimal(
&tables_buffered,
&is_sample_buffered,
crate::tskit::simple_time_reverser(num_generations),
Expand Down Expand Up @@ -264,14 +264,14 @@ 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(
let mut tables_sorted_tskit = crate::tskit::convert_to_tskit_minimal(
&tables_sorted,
&is_sample_sorted,
crate::tskit::simple_time_reverser(num_generations),
true,
);

let mut tables_buffered_tskit = crate::tskit::convert_to_tskit(
let mut tables_buffered_tskit = crate::tskit::convert_to_tskit_minimal(
&tables_buffered,
&is_sample_buffered,
crate::tskit::simple_time_reverser(num_generations),
Expand Down
25 changes: 18 additions & 7 deletions src/tskit.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -39,6 +39,9 @@ pub fn simple_time_reverser(x: Time) -> Box<dyn Fn(Time) -> f64> {
/// If the input ``tables`` are not sorted, pass ``false`` for
/// `build_indexes`.
///
/// This function will not be part of the long-term API.
/// Rather, it is the minimum currently needed to get stuff done.
///
/// # Returns
///
/// A [``tskit_rust::TableCollection``].
Expand All @@ -51,7 +54,7 @@ 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(
/// let tsk_tables = forrustts::tskit::convert_to_tskit_minimal(
/// &tables,
/// &is_sample,
/// forrustts::tskit::simple_time_reverser(1),
Expand All @@ -61,7 +64,7 @@ pub fn simple_time_reverser(x: Time) -> Box<dyn Fn(Time) -> f64> {
/// assert_eq!(tsk_tables.edges().num_rows(), 1);
/// assert_eq!(tsk_tables.populations().num_rows(), 1);
/// ```
pub fn convert_to_tskit(
pub fn convert_to_tskit_minimal(
tables: &TableCollection,
is_sample: &[i32],
convert_time: impl Fn(Time) -> f64,
Expand Down Expand Up @@ -125,6 +128,9 @@ fn swap_with_empty<T>(v: &mut Vec<T>) {
/// If the input ``tables`` are not sorted, pass ``false`` for
/// `build_indexes`.
///
/// This function will not be part of the long-term API.
/// Rather, it is the minimum currently needed to get stuff done.
///
/// # Returns
///
/// A [``tskit_rust::TableCollection``].
Expand All @@ -137,7 +143,7 @@ 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(
/// let tsk_tables = forrustts::tskit::convert_to_tskit_and_drain_minimal(
/// &is_sample,
/// forrustts::tskit::simple_time_reverser(1),
/// true,
Expand All @@ -155,7 +161,7 @@ fn swap_with_empty<T>(v: &mut Vec<T>) {
/// assert_eq!(tables.nodes().capacity(), 0);
/// assert_eq!(tables.edges().capacity(), 0);
/// ```
pub fn convert_to_tskit_and_drain(
pub fn convert_to_tskit_and_drain_minimal(
is_sample: &[i32],
convert_time: impl Fn(Time) -> f64,
build_indexes: bool,
Expand Down Expand Up @@ -209,7 +215,8 @@ mod tests {
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 = convert_to_tskit(&tables, &is_sample, simple_time_reverser(1), true);
let tsk_tables =
convert_to_tskit_minimal(&tables, &is_sample, simple_time_reverser(1), true);
assert_eq!(tsk_tables.nodes().num_rows(), 2);
assert_eq!(tsk_tables.edges().num_rows(), 1);
assert_eq!(tsk_tables.populations().num_rows(), 1);
Expand All @@ -224,8 +231,12 @@ mod tests {
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 =
convert_to_tskit_and_drain(&is_sample, simple_time_reverser(1), true, &mut tables);
let tsk_tables = convert_to_tskit_and_drain_minimal(
&is_sample,
simple_time_reverser(1),
true,
&mut tables,
);
assert_eq!(tsk_tables.nodes().num_rows(), 2);
assert_eq!(tsk_tables.edges().num_rows(), 1);
assert_eq!(tsk_tables.populations().num_rows(), 1);
Expand Down