Update to C API 0.99.15 (breaking) (#183)

* manually update C API files

* minimal updates for build/tests/docs

Author: molpopgen

src/trees.rs

@@ -337,7 +337,12 @@ impl Tree {
 
     /// Return the `[left, right)` coordinates of the tree.
     pub fn interval(&self) -> (f64, f64) {
-        unsafe { ((*self.as_ptr()).left, (*self.as_ptr()).right) }
+        unsafe {
+            (
+                (*self.as_ptr()).interval.left,
+                (*self.as_ptr()).interval.right,
+            )
+        }
     }
 
     /// Return the length of the genome for which this
@@ -681,7 +686,7 @@ impl<'a> RootIterator<'a> {
     fn new(tree: &'a Tree) -> Self {
         RootIterator {
             current_root: None,
-            next_root: tree.inner.left_root.into(),
+            next_root: unsafe { ll_bindings::tsk_tree_get_left_root(tree.as_ptr()).into() },
             tree,
         }
     }
@@ -905,9 +910,10 @@ impl TreeSequence {
     /// tskit::TreeSequenceFlags::default()).unwrap();
     /// ```
     pub fn new(tables: TableCollection, flags: TreeSequenceFlags) -> Result<Self, TskitError> {
+        let mut t = tables;
         let mut treeseq = Self::wrap();
         let rv = unsafe {
-            ll_bindings::tsk_treeseq_init(treeseq.as_mut_ptr(), tables.as_ptr(), flags.bits())
+            ll_bindings::tsk_treeseq_init(treeseq.as_mut_ptr(), t.as_mut_ptr(), flags.bits())
         };
         handle_tsk_return_value!(rv, treeseq)
     }

subprojects/kastore/kastore.c

@@ -9,7 +9,10 @@
 
 /* Private flag used to indicate when we have opened the file ourselves
  * and need to free it. */
-#define OWN_FILE (1 << 31)
+/* Note: we use 1<<14 to keep this flag at the end of the flag space,
+ * and this is the highest bit that can be guaranteed to fit into
+ * an int. */
+#define OWN_FILE (1 << 14)
 
 const char *
 kas_strerror(int err)
@@ -261,7 +264,7 @@ kastore_read_descriptors(kastore_t *self)
     if (size + KAS_HEADER_SIZE > self->file_size) {
         goto out;
     }
-    read_buffer = malloc(size);
+    read_buffer = (char *) malloc(size);
     if (read_buffer == NULL) {
         ret = KAS_ERR_NO_MEMORY;
         goto out;
@@ -386,7 +389,7 @@ kastore_read_file(kastore_t *self)
     assert(size > offset);
     size -= offset;
 
-    self->read_buffer = malloc(size);
+    self->read_buffer = (char *) malloc(size);
     if (self->read_buffer == NULL) {
         ret = KAS_ERR_NO_MEMORY;
         goto out;
@@ -480,7 +483,7 @@ kastore_read(kastore_t *self)
         goto out;
     }
     if (self->num_items > 0) {
-        self->items = calloc(self->num_items, sizeof(*self->items));
+        self->items = (kaitem_t *) calloc(self->num_items, sizeof(*self->items));
         if (self->items == NULL) {
             ret = KAS_ERR_NO_MEMORY;
             goto out;
@@ -559,6 +562,7 @@ kastore_open(kastore_t *self, const char *filename, const char *mode, int flags)
         tmp.file = NULL;
         if (err != 0) {
             ret = KAS_ERR_IO;
+            goto out;
         }
     }
     file = fopen(filename, file_mode);
@@ -690,7 +694,7 @@ kastore_get(kastore_t *self, const char *key, size_t key_len, void **array,
     int ret = KAS_ERR_KEY_NOT_FOUND;
     kaitem_t search;
     kaitem_t *item;
-    search.key = malloc(key_len);
+    search.key = (char *) malloc(key_len);
     search.key_len = key_len;
 
     if (self->mode != KAS_READ) {
@@ -733,7 +737,7 @@ static int KAS_WARN_UNUSED
 kastore_gets_type(
     kastore_t *self, const char *key, void **array, size_t *array_len, int type)
 {
-    int loaded_type;
+    int loaded_type = -1;
     int ret;
 
     ret = kastore_get(self, key, strlen(key), array, array_len, &loaded_type);
@@ -847,7 +851,7 @@ kastore_oput(kastore_t *self, const char *key, size_t key_len, void *array,
 {
     int ret = 0;
     kaitem_t *new_item;
-    void *p;
+    kaitem_t *p;
     size_t j;
 
     if (self->mode != KAS_WRITE) {
@@ -864,7 +868,7 @@ kastore_oput(kastore_t *self, const char *key, size_t key_len, void *array,
     }
     /* This isn't terribly efficient, but we're not expecting large
      * numbers of items. */
-    p = realloc(self->items, (self->num_items + 1) * sizeof(*self->items));
+    p = (kaitem_t *) realloc(self->items, (self->num_items + 1) * sizeof(*self->items));
     if (p == NULL) {
         ret = KAS_ERR_NO_MEMORY;
         goto out;
@@ -877,7 +881,7 @@ kastore_oput(kastore_t *self, const char *key, size_t key_len, void *array,
     new_item->key_len = key_len;
     new_item->array_len = array_len;
     new_item->array = array;
-    new_item->key = malloc(key_len);
+    new_item->key = (char *) malloc(key_len);
     if (new_item->key == NULL) {
         kas_safe_free(new_item->key);
         ret = KAS_ERR_NO_MEMORY;

subprojects/kastore/kastore.h

@@ -24,8 +24,6 @@ extern "C" {
 #include <stddef.h>
 #include <stdio.h>
 
-/** @} */
-
 /**
 @defgroup ERROR_GROUP Error return values.
 @{
@@ -155,7 +153,7 @@ 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   0
+#define KAS_VERSION_PATCH   2
 /** @} */
 
 #define KAS_HEADER_SIZE             64

subprojects/tskit/tskit/convert.c

@@ -57,12 +57,15 @@ tsk_newick_converter_run(
     const tsk_tree_t *tree = self->tree;
     tsk_id_t *stack = self->traversal_stack;
     const double *time = self->tree->tree_sequence->tables->nodes.time;
+    const tsk_flags_t *flags = self->tree->tree_sequence->tables->nodes.flags;
     int stack_top = 0;
     int label;
     size_t s = 0;
     int r;
     tsk_id_t u, v, w, root_parent;
     double branch_length;
+    bool ms_labels = self->options & TSK_NEWICK_LEGACY_MS_LABELS;
+    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;
@@ -91,15 +94,20 @@ tsk_newick_converter_run(
         } else {
             u = tree->parent[v];
             stack_top--;
-            if (tree->left_child[v] == TSK_NULL) {
+            label = -1;
+            if (ms_labels) {
+                if (tree->left_child[v] == TSK_NULL) {
+                    label = (int) v + 1;
+                }
+            } else if (flags[v] & TSK_NODE_IS_SAMPLE) {
+                label = (int) v;
+            }
+            if (label != -1) {
                 if (s >= buffer_size) {
                     ret = TSK_ERR_BUFFER_OVERFLOW;
                     goto out;
                 }
-                /* We do this for ms-compatability. This should be a configurable option
-                 * via the flags attribute */
-                label = (int) v + 1;
-                r = snprintf(buffer + s, buffer_size - s, "%d", label);
+                r = snprintf(buffer + s, buffer_size - s, label_format, label);
                 if (r < 0) {
                     ret = TSK_ERR_IO;
                     goto out;
@@ -154,8 +162,7 @@ tsk_newick_converter_init(tsk_newick_converter_t *self, const tsk_tree_t *tree,
     self->options = options;
     self->tree = tree;
     self->traversal_stack
-        = tsk_malloc(tsk_treeseq_get_num_nodes(self->tree->tree_sequence)
-                     * sizeof(*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;
         goto out;

subprojects/tskit/tskit/convert.h

@@ -32,6 +32,8 @@ extern "C" {
 
 #include <tskit/trees.h>
 
+#define TSK_NEWICK_LEGACY_MS_LABELS (1 << 0)
+
 int tsk_convert_newick(const tsk_tree_t *tree, tsk_id_t root, unsigned int precision,
     tsk_flags_t options, size_t buffer_size, char *buffer);