chore: bump to tskit C API 1.2.0 (#789)

BREAKING CHANGE: conversion of table collection
to tree sequence will require mutation parents
to be computed for cases with multiple mutations
at a site.

Author: molpopgen

src/test_fixtures.rs

@@ -301,10 +301,7 @@ pub mod simulation {
 
         // state variables for site/mutation tables
         let num_sites = f64::from(seqlen.into()) as usize;
-        let mut site_last_mutation_order = vec![0usize; num_sites];
-
-        let mut site_last_mutation_tables = vec![MutationId::NULL; num_sites];
-        let mut site_last_mutation_tr_tbls = vec![MutationId::NULL; num_sites];
+        let site_last_mutation_order = vec![0usize; num_sites];
 
         let mut site_id_map_tables = vec![SiteId::NULL; num_sites];
         let mut site_id_map_tr_tbls = vec![SiteId::NULL; num_sites];
@@ -387,14 +384,10 @@ pub mod simulation {
                                 tables.add_site(mut_pos as f64, Some(b"a")).unwrap();
                         }
                         // add mutation
-                        let parent_mut = site_last_mutation_tables[mut_pos];
                         let site = site_id_map_tables[mut_pos];
-                        let new_mutation = tables
-                            .add_mutation(site, c, parent_mut, t, Some(derived_state))
+                        let _ = tables
+                            .add_mutation(site, c, MutationId::NULL, t, Some(derived_state))
                             .unwrap();
-
-                        site_last_mutation_tables[mut_pos] = new_mutation;
-                        site_last_mutation_order[mut_pos] += 1;
                     }
 
                     find_overlaps(s, e, &intervals, &mut buffer);
@@ -410,12 +403,10 @@ pub mod simulation {
                                     tr_tbls.add_site(mut_pos as f64, Some(b"a")).unwrap();
                             }
                             // add mutation
-                            let parent_mut = site_last_mutation_tr_tbls[mut_pos];
                             let site = site_id_map_tr_tbls[mut_pos];
-                            let new_mutation = tr_tbls
-                                .add_mutation(site, c, parent_mut, t, Some(derived_state))
+                            let _ = tr_tbls
+                                .add_mutation(site, c, MutationId::NULL, t, Some(derived_state))
                                 .unwrap();
-                            site_last_mutation_tr_tbls[mut_pos] = new_mutation;
                         }
                     }
                 }
@@ -448,6 +439,23 @@ pub mod simulation {
         tables.build_index().unwrap();
         tr_tbls.build_index().unwrap();
 
+        // Calculate mutation parents
+        // TODO: need safe API for this.
+        let code = unsafe {
+            crate::sys::bindings::tsk_table_collection_compute_mutation_parents(
+                tables.as_mut_ptr(),
+                0,
+            )
+        };
+        assert_eq!(code, 0);
+        let code = unsafe {
+            crate::sys::bindings::tsk_table_collection_compute_mutation_parents(
+                tr_tbls.as_mut_ptr(),
+                0,
+            )
+        };
+        assert_eq!(code, 0);
+
         // to tree sequences
         let treeseq_opts = TreeSequenceFlags::default();
         let full_trees = TreeSequence::new(tables, treeseq_opts).unwrap();

subprojects/tskit/tskit.h

@@ -1,7 +1,7 @@
 /*
  * MIT License
  *
- * Copyright (c) 2019 Tskit Developers
+ * Copyright (c) 2019-2024 Tskit Developers
  *
  * Permission is hereby granted, free of charge, to any person obtaining a copy
  * of this software and associated documentation files (the "Software"), to deal

subprojects/tskit/tskit/convert.c

@@ -1,7 +1,7 @@
 /*
  * MIT License
  *
- * Copyright (c) 2018-2021 Tskit Developers
+ * Copyright (c) 2018-2025 Tskit Developers
  * Copyright (c) 2015-2017 University of Oxford
  *
  * Permission is hereby granted, free of charge, to any person obtaining a copy
@@ -68,11 +68,11 @@ tsk_newick_converter_run(
     const char *label_format = ms_labels ? "%d" : "n%d";
 
     if (root < 0 || root >= (tsk_id_t) self->tree->num_nodes) {
-        ret = TSK_ERR_NODE_OUT_OF_BOUNDS;
+        ret = tsk_trace_error(TSK_ERR_NODE_OUT_OF_BOUNDS);
         goto out;
     }
     if (buffer == NULL) {
-        ret = TSK_ERR_BAD_PARAM_VALUE;
+        ret = tsk_trace_error(TSK_ERR_BAD_PARAM_VALUE);
         goto out;
     }
     root_parent = tree->parent[root];
@@ -82,7 +82,7 @@ tsk_newick_converter_run(
         v = stack[stack_top];
         if (tree->left_child[v] != TSK_NULL && v != u) {
             if (s >= buffer_size) {
-                ret = TSK_ERR_BUFFER_OVERFLOW;
+                ret = tsk_trace_error(TSK_ERR_BUFFER_OVERFLOW);
                 goto out;
             }
             buffer[s] = '(';
@@ -104,17 +104,17 @@ tsk_newick_converter_run(
             }
             if (label != -1) {
                 if (s >= buffer_size) {
-                    ret = TSK_ERR_BUFFER_OVERFLOW;
+                    ret = tsk_trace_error(TSK_ERR_BUFFER_OVERFLOW);
                     goto out;
                 }
                 r = snprintf(buffer + s, buffer_size - s, label_format, label);
                 if (r < 0) {
-                    ret = TSK_ERR_IO;
+                    ret = tsk_trace_error(TSK_ERR_IO);
                     goto out;
                 }
                 s += (size_t) r;
                 if (s >= buffer_size) {
-                    ret = TSK_ERR_BUFFER_OVERFLOW;
+                    ret = tsk_trace_error(TSK_ERR_BUFFER_OVERFLOW);
                     goto out;
                 }
             }
@@ -123,12 +123,12 @@ tsk_newick_converter_run(
                 r = snprintf(buffer + s, buffer_size - s, ":%.*f", (int) self->precision,
                     branch_length);
                 if (r < 0) {
-                    ret = TSK_ERR_IO;
+                    ret = tsk_trace_error(TSK_ERR_IO);
                     goto out;
                 }
                 s += (size_t) r;
                 if (s >= buffer_size) {
-                    ret = TSK_ERR_BUFFER_OVERFLOW;
+                    ret = tsk_trace_error(TSK_ERR_BUFFER_OVERFLOW);
                     goto out;
                 }
                 if (v == tree->right_child[u]) {
@@ -141,7 +141,7 @@ tsk_newick_converter_run(
         }
     }
     if ((s + 1) >= buffer_size) {
-        ret = TSK_ERR_BUFFER_OVERFLOW;
+        ret = tsk_trace_error(TSK_ERR_BUFFER_OVERFLOW);
         goto out;
     }
     buffer[s] = ';';
@@ -164,7 +164,7 @@ tsk_newick_converter_init(tsk_newick_converter_t *self, const tsk_tree_t *tree,
     self->traversal_stack
         = tsk_malloc(tsk_tree_get_size_bound(tree) * sizeof(*self->traversal_stack));
     if (self->traversal_stack == NULL) {
-        ret = TSK_ERR_NO_MEMORY;
+        ret = tsk_trace_error(TSK_ERR_NO_MEMORY);
         goto out;
     }
 out: