update to tskit 0.1.1

Cargo.toml

@@ -15,4 +15,4 @@ keywords = ["simulation", "tree_sequences", "tskit", "population_genetics"]
 bitflags = "1.2.1"
 thiserror = "1.0"
 GSL = "2.0.1"
-tskit_rust = "0.1.0"
+tskit = "0.1.1"

forrustts_examples/Cargo.toml

@@ -10,7 +10,7 @@ edition = "2018"
 path = "../"
 
 [dependencies]
-tskit_rust = { git = "https://github.com/molpopgen/tskit_rust", branch = "main" }
+tskit = "0.1.1"
 clap = "~2.27.0"
 
 [[bin]]

forrustts_examples/neutral_wf.rs

@@ -77,7 +77,7 @@ fn main() {
     let psurvival = value_t!(matches.value_of("psurvival"), f64).unwrap_or(0.0);
     let seed = value_t_or_exit!(matches.value_of("seed"), usize);
     let outfile = value_t_or_exit!(matches.value_of("outfile"), String);
-    let validate_tables =  matches.is_present("validate_tables");
+    let validate_tables = matches.is_present("validate_tables");
 
     // TODO: parameter validation..
 
@@ -129,7 +129,7 @@ fn main() {
         tskit_tables.dump(&outfile, 0).unwrap();
     } else {
         tskit_tables
-            .dump(&outfile, tskit_rust::TSK_NO_BUILD_INDEXES)
+            .dump(&outfile, tskit::TSK_NO_BUILD_INDEXES)
             .unwrap();
     }
 }

src/simplification_logic.rs

@@ -37,12 +37,10 @@ impl SegmentOverlapper {
     fn num_overlaps(&self) -> usize {
         assert!(
             self.oend - self.obeg <= self.overlapping.len(),
-            format!(
-                "overlap details = {} {} {}",
-                self.oend,
-                self.obeg,
-                self.overlapping.len()
-            )
+            "overlap details = {} {} {}",
+            self.oend,
+            self.obeg,
+            self.overlapping.len()
         );
         self.oend - self.obeg
     }

src/test_simplify_tables.rs

@@ -1,9 +1,9 @@
 #[cfg(test)]
 mod test {
     // NOTE: Currently, these tests are both testing
-    // stuff from tskit_rust and forrusts, which isn't great.
+    // stuff from tskit and forrusts, which isn't great.
     // We'll clean this up later when we get better abstractions
-    // into tskit_rust.
+    // into tskit.
     use crate::simplify_tables_without_state;
     use crate::tsdef::{IdType, Position, Time};
     use crate::wright_fisher::*;
@@ -13,11 +13,10 @@ mod test {
     use crate::SimplificationOutput;
     use crate::TableCollection;
     use std::mem::MaybeUninit;
-    use tskit_rust::bindings as tskr;
+    use tskit::bindings as tskr;
+    use tskit::ffi::TskitType;
 
-    fn tables_to_treeseq(
-        tables: &mut tskit_rust::TableCollection,
-    ) -> MaybeUninit<tskr::tsk_treeseq_t> {
+    fn tables_to_treeseq(tables: &mut tskit::TableCollection) -> MaybeUninit<tskr::tsk_treeseq_t> {
         let mut tsk_ts: MaybeUninit<tskr::tsk_treeseq_t> = MaybeUninit::uninit();
         unsafe {
             let rv = tskr::tsk_table_collection_build_index(tables.as_mut_ptr(), 0);

src/tskit.rs

@@ -1,4 +1,4 @@
-//! Data interchange to ``tskit`` format using [``tskit_rust``].
+//! Data interchange to ``tskit`` format using [``tskit``].
 //!
 //! # Note
 //!
@@ -11,7 +11,7 @@
 
 use crate::tsdef::Time;
 use crate::TableCollection;
-use tskit_rust::{tsk_flags_t, tsk_id_t, TSK_NODE_IS_SAMPLE, TSK_NULL};
+use tskit::{tsk_flags_t, tsk_id_t, TSK_NODE_IS_SAMPLE, TSK_NULL};
 
 /// Return a closure to help reverse time.
 ///
@@ -44,7 +44,7 @@ pub fn simple_time_reverser(x: Time) -> Box<dyn Fn(Time) -> f64> {
 ///
 /// # Returns
 ///
-/// A [``tskit_rust::TableCollection``].
+/// A [``tskit::TableCollection``].
 ///
 /// # Example
 ///
@@ -69,8 +69,8 @@ pub fn convert_to_tskit_minimal(
     is_sample: &[i32],
     convert_time: impl Fn(Time) -> f64,
     build_indexes: bool,
-) -> tskit_rust::TableCollection {
-    let mut tsk_tables = tskit_rust::TableCollection::new(tables.genome_length() as f64).unwrap();
+) -> tskit::TableCollection {
+    let mut tsk_tables = tskit::TableCollection::new(tables.genome_length() as f64).unwrap();
 
     for e in tables.edges() {
         tsk_tables
@@ -133,7 +133,7 @@ fn swap_with_empty<T>(v: &mut Vec<T>) {
 ///
 /// # Returns
 ///
-/// A [``tskit_rust::TableCollection``].
+/// A [``tskit::TableCollection``].
 ///
 /// # Example
 ///
@@ -166,8 +166,8 @@ pub fn convert_to_tskit_and_drain_minimal(
     convert_time: impl Fn(Time) -> f64,
     build_indexes: bool,
     tables: &mut TableCollection,
-) -> tskit_rust::TableCollection {
-    let mut tsk_tables = tskit_rust::TableCollection::new(tables.genome_length() as f64).unwrap();
+) -> tskit::TableCollection {
+    let mut tsk_tables = tskit::TableCollection::new(tables.genome_length() as f64).unwrap();
 
     let mut max_pop: tsk_id_t = -1;
     for (i, n) in tables.enumerate_nodes() {