update to CAPI 1.0.0 (#229)

Author: molpopgen

src/error.rs

@@ -79,7 +79,7 @@ pub fn panic_on_tskit_error(code: i32) {
 ///
 /// ```
 /// let x = tskit::error::get_tskit_error_message(-207);
-/// assert_eq!(x, "Individual out of bounds");
+/// assert!(x.contains("Individual out of bounds"));
 /// ```
 ///
 /// # Panics
@@ -121,14 +121,14 @@ mod test {
         let x = mock_error();
         let mut s: String = "nope!".to_string();
         x.map_or_else(|e: TskitError| s = format!("{}", e), |_| ());
-        assert_eq!(s, "Individual out of bounds");
+        assert!(s.contains("Individual out of bounds"));
     }
 
     #[test]
     fn test_extract_error_message() {
         let x = mock_error();
         match extract_error_message(x) {
-            Some(s) => assert_eq!(s, "Individual out of bounds"),
+            Some(s) => assert!(s.contains("Individual out of bounds")),
             None => panic!(),
         }
 

src/flags.rs

@@ -43,28 +43,28 @@ bitflags! {
     pub struct SimplificationOptions: RawFlags {
         /// Default behavior
         const NONE = 0;
-        const FILTER_SITES = ll_bindings::TSK_FILTER_SITES;
+        const FILTER_SITES = ll_bindings::TSK_SIMPLIFY_FILTER_SITES;
         /// If True, remove any populations that are not referenced by
         /// nodes after simplification; new population IDs are allocated
         /// sequentially from zero.
         /// If False, the population table will not be altered in any way.
-        const FILTER_POPULATIONS = ll_bindings::TSK_FILTER_POPULATIONS;
+        const FILTER_POPULATIONS = ll_bindings::TSK_SIMPLIFY_FILTER_POPULATIONS;
         /// If True, remove any individuals that are not referenced by nodes
         /// after simplification; new individual IDs are allocated sequentially
         /// from zero. If False, the individual table will not be altered in any way.
-        const FILTER_INDIVIDUALS = ll_bindings::TSK_FILTER_INDIVIDUALS;
+        const FILTER_INDIVIDUALS = ll_bindings::TSK_SIMPLIFY_FILTER_INDIVIDUALS;
         /// Whether to reduce the topology down to the trees that are present at sites.
-        const REDUCE_TO_SITE_TOPOLOGY = ll_bindings::TSK_REDUCE_TO_SITE_TOPOLOGY;
+        const REDUCE_TO_SITE_TOPOLOGY = ll_bindings::TSK_SIMPLIFY_REDUCE_TO_SITE_TOPOLOGY;
         /// If True, preserve unary nodes (i.e. nodes with exactly one child)
         /// that exist on the path from samples to root.
-        const KEEP_UNARY  = ll_bindings::TSK_KEEP_UNARY;
+        const KEEP_UNARY  = ll_bindings::TSK_SIMPLIFY_KEEP_UNARY;
         /// Whether to retain history ancestral to the MRCA of the samples.
-        const KEEP_INPUT_ROOTS = ll_bindings::TSK_KEEP_INPUT_ROOTS;
+        const KEEP_INPUT_ROOTS = ll_bindings::TSK_SIMPLIFY_KEEP_INPUT_ROOTS;
         ///  If True, preserve unary nodes that exist on the path from samples
         ///  to root, but only if they are associated with an individual
         ///  in the individuals table.
         ///  Cannot be specified at the same time as `KEEP_UNARY`.
-        const KEEP_UNARY_IN_INDIVIDUALS  = ll_bindings::TSK_KEEP_UNARY_IN_INDIVIDUALS;
+        const KEEP_UNARY_IN_INDIVIDUALS  = ll_bindings::TSK_SIMPLIFY_KEEP_UNARY_IN_INDIVIDUALS;
     }
 }
 
@@ -161,7 +161,7 @@ bitflags! {
         /// Default behavior
         const NONE = 0;
         /// If used, then build table indexes if they are not present.
-        const BUILD_INDEXES = ll_bindings::TSK_BUILD_INDEXES;
+        const BUILD_INDEXES = ll_bindings::TSK_TS_INIT_BUILD_INDEXES;
     }
 }
 

src/trees.rs

@@ -722,7 +722,6 @@ impl<'a> PostorderNodeIterator<'a> {
         let rv = unsafe {
             ll_bindings::tsk_tree_postorder(
                 tree.as_ptr(),
-                NodeId::NULL.into(), // start from virtual root
                 nodes.as_mut_ptr().cast::<tsk_id_t>(),
                 ptr,
             )
@@ -1509,7 +1508,6 @@ pub(crate) mod test_trees {
                 unsafe {
                     ll_bindings::tsk_tree_preorder(
                         tree.as_ptr(),
-                        -1,
                         nodes.as_mut_ptr() as *mut tsk_id_t,
                         ptr,
                     );

subprojects/kastore/VERSION.txt

@@ -0,0 +1 @@
+2.1.1