Update tskit C API to version 1.3.1

Author: gregorgorjanc

RcppTskit/inst/include/tskit/VERSION.txt

@@ -1 +1 @@
-1.3.0
+1.3.1

RcppTskit/inst/include/tskit/tskit/VERSION_kastore.txt

@@ -1 +1 @@
-2.1.1
+2.1.2

RcppTskit/inst/include/tskit/tskit/core.h

@@ -42,7 +42,7 @@ extern "C" {
 
 #ifdef __GNUC__
 #define TSK_WARN_UNUSED __attribute__((warn_unused_result))
-#define TSK_UNUSED(x) TSK_UNUSED_##x __attribute__((__unused__))
+#define TSK_UNUSED(x)   TSK_UNUSED_##x __attribute__((__unused__))
 #else
 #define TSK_WARN_UNUSED
 #define TSK_UNUSED(x) TSK_UNUSED_##x
@@ -93,11 +93,11 @@ missing data.
  * on the thread above.
  */
 typedef int64_t tsk_id_t;
-#define TSK_MAX_ID INT64_MAX - 1
+#define TSK_MAX_ID          INT64_MAX - 1
 #define TSK_ID_STORAGE_TYPE KAS_INT64
 #else
 typedef int32_t tsk_id_t;
-#define TSK_MAX_ID INT32_MAX - 1
+#define TSK_MAX_ID          INT32_MAX - 1
 #define TSK_ID_STORAGE_TYPE KAS_INT32
 #endif
 
@@ -109,7 +109,7 @@ The ``tsk_size_t`` type is an unsigned integer used for any size or count value.
 @endrst
 */
 typedef uint64_t tsk_size_t;
-#define TSK_MAX_SIZE UINT64_MAX
+#define TSK_MAX_SIZE          UINT64_MAX
 #define TSK_SIZE_STORAGE_TYPE KAS_UINT64
 
 /**
@@ -152,7 +152,7 @@ to the API or ABI are introduced, i.e., the addition of a new function.
 The library patch version. Incremented when any changes not relevant to the
 to the API or ABI are introduced, i.e., internal refactors of bugfixes.
 */
-#define TSK_VERSION_PATCH   0
+#define TSK_VERSION_PATCH   1
 /** @} */
 
 /*

RcppTskit/inst/include/tskit/tskit/kastore.h

@@ -157,7 +157,7 @@ to the API or ABI are introduced, i.e., the addition of a new function.
 The library patch version. Incremented when any changes not relevant to the
 to the API or ABI are introduced, i.e., internal refactors of bugfixes.
 */
-#define KAS_VERSION_PATCH   1
+#define KAS_VERSION_PATCH   2
 /** @} */
 
 #define KAS_HEADER_SIZE             64

RcppTskit/inst/include/tskit/tskit/tables.h

@@ -4607,7 +4607,7 @@ tsk_id_t tsk_table_collection_check_integrity(
 /* Undocumented methods */
 
 /* Flags for ibd_segments */
-#define TSK_IBD_STORE_PAIRS (1 << 0)
+#define TSK_IBD_STORE_PAIRS    (1 << 0)
 #define TSK_IBD_STORE_SEGMENTS (1 << 1)
 
 /* TODO be systematic about where "result" should be in the params

RcppTskit/inst/include/tskit/tskit/trees.h

@@ -663,7 +663,7 @@ sequence.
 @endrst
 
 @param self A pointer to a tsk_treeseq_t object.
-@return Returns a pointer to the time units.
+@return Returns a pointer to the null-terminated file uuid.
 */
 const char *tsk_treeseq_get_file_uuid(const tsk_treeseq_t *self);
 

RcppTskit/src/tskit/VERSION.txt

@@ -1 +1 @@
-1.3.0
+1.3.1

RcppTskit/src/tskit/VERSION_kastore.txt

@@ -1 +1 @@
-2.1.1
+2.1.2

RcppTskit/src/tskit/core.c

@@ -883,8 +883,8 @@ tsk_search_sorted(const double *restrict array, tsk_size_t size, double value)
             upper = mid;
         }
     }
-    offset = (int64_t)(array[lower] < value);
-    return (tsk_size_t)(lower + offset);
+    offset = (int64_t) (array[lower] < value);
+    return (tsk_size_t) (lower + offset);
 }
 
 /* Rounds the specified double to the closest multiple of 10**-num_digits. If

RcppTskit/src/tskit/haplotype_matching.c

@@ -572,15 +572,15 @@ static inline bool
 element_in(
     const uint64_t *restrict A, tsk_id_t u, const tsk_id_t state, tsk_size_t num_words)
 {
-    tsk_size_t index = ((tsk_size_t) u) * num_words + (tsk_size_t)(state / 64);
+    tsk_size_t index = ((tsk_size_t) u) * num_words + (tsk_size_t) (state / 64);
     return (A[index] & (1ULL << (state % 64))) != 0;
 }
 
 static inline void
 set_optimal_value(
     uint64_t *restrict A, tsk_id_t u, const tsk_size_t num_words, tsk_id_t state)
 {
-    tsk_size_t index = ((tsk_size_t) u) * num_words + (tsk_size_t)(state / 64);
+    tsk_size_t index = ((tsk_size_t) u) * num_words + (tsk_size_t) (state / 64);
     tsk_bug_assert(((tsk_size_t) state) / 64 < num_words);
     A[index] |= 1ULL << (state % 64);
 }
@@ -815,7 +815,7 @@ tsk_ls_hmm_redistribute_transitions(tsk_ls_hmm_t *self)
      * iterating over the roots. See the existing parsimony implementations
      * for an example. */
     for (root = tsk_tree_get_left_root(&self->tree); root != TSK_NULL;
-         root = right_sib[root]) {
+        root = right_sib[root]) {
         stack[0].tree_node = root;
         stack[0].old_state = T_old[T_index[root]].value_index;
         stack[0].new_state
@@ -966,7 +966,7 @@ tsk_ls_hmm_run_forward(tsk_ls_hmm_t *self, int32_t *haplotype)
     }
 
     for (t_ret = tsk_tree_first(&self->tree); t_ret == TSK_TREE_OK;
-         t_ret = tsk_tree_next(&self->tree)) {
+        t_ret = tsk_tree_next(&self->tree)) {
         ret = tsk_ls_hmm_update_tree(self, TSK_DIR_FORWARD);
         if (ret != 0) {
             goto out;
@@ -1166,7 +1166,7 @@ tsk_ls_hmm_run_backward(
     }
 
     for (t_ret = tsk_tree_last(&self->tree); t_ret == TSK_TREE_OK;
-         t_ret = tsk_tree_prev(&self->tree)) {
+        t_ret = tsk_tree_prev(&self->tree)) {
         ret = tsk_ls_hmm_update_tree(self, TSK_DIR_REVERSE);
         if (ret != 0) {
             goto out;
@@ -1492,7 +1492,7 @@ tsk_compressed_matrix_decode(tsk_compressed_matrix_t *self, double *values)
     }
 
     for (t_ret = tsk_tree_first(&tree); t_ret == TSK_TREE_OK;
-         t_ret = tsk_tree_next(&tree)) {
+        t_ret = tsk_tree_next(&tree)) {
         ret = tsk_tree_get_sites(&tree, &sites, &num_tree_sites);
         if (ret != 0) {
             goto out;