style: deny broken intradoc links (#718)

* fix malformed doc test

Author: molpopgen

src/lib.rs

@@ -77,6 +77,7 @@
 #![allow(non_camel_case_types)]
 #![allow(non_snake_case)]
 #![cfg_attr(doc_cfg, feature(doc_cfg))]
+#![deny(rustdoc::broken_intra_doc_links)]
 
 #[cfg(feature = "bindings")]
 pub use sys::bindings;

src/newtypes.rs

@@ -94,7 +94,7 @@ pub use crate::sys::newtypes::PopulationId;
 
 /// A provenance ID
 ///
-/// This is an integer referring to a row of a [``provenance::ProvenanceTable``].
+/// This is an integer referring to a row of a [``crate::provenance::ProvenanceTable``].
 ///
 /// The features for this type follow the same pattern as for [``NodeId``]
 #[cfg(feature = "provenance")]

src/sys/flags.rs

@@ -295,16 +295,17 @@ impl SimplificationOptions {
 /// # use tskit::TableClearOptions;
 /// let f = TableClearOptions::default().clear_provenance();
 /// assert_eq!(f, TableClearOptions::CLEAR_PROVENANCE);
+/// ```
 ///
 /// ```
 /// # use tskit::TableClearOptions;
 /// let f = TableClearOptions::default().clear_metadata_schema().clear_ts_metadata_and_schema();
 /// assert!(f.contains(TableClearOptions::CLEAR_METADATA_SCHEMAS));
 /// assert!(f.contains(TableClearOptions::CLEAR_TS_METADATA_SCHEMA));
-/// let f = f.clear();
-/// assert!(f.contains(TableClearOptions::CLEAR_METADATA_SCHEMAS));
-/// assert!(f.contains(TableClearOptions::CLEAR_TS_METADATA_SCHEMA));
-/// assert!(f.contains(TableClearOptions::CLEAR_PROVENANCE);
+/// # let f = TableClearOptions::default();
+/// # assert!(!f.contains(TableClearOptions::CLEAR_METADATA_SCHEMAS));
+/// # assert!(!f.contains(TableClearOptions::CLEAR_TS_METADATA_SCHEMA));
+/// # assert!(!f.contains(TableClearOptions::CLEAR_PROVENANCE));
 /// ```
 #[derive(Default, Debug, Clone, Copy, PartialEq, Eq, PartialOrd, Ord, Hash)]
 #[repr(transparent)]
@@ -438,7 +439,7 @@ impl TableSortOptions {
     contains!();
 }
 
-/// Modify behavior of [`crate::TableCollection::sort_individuals`].
+/// Modify behavior of [`crate::TableCollection::topological_sort_individuals`].
 ///
 /// # Examples
 ///
@@ -458,8 +459,8 @@ impl IndividualTableSortOptions {
     contains!();
 }
 
-/// Specify the behavior of iterating over [`Tree`] objects.
-/// See [`TreeSequence::tree_iterator`].
+/// Specify the behavior of iterating over [`crate::Tree`] objects.
+/// See [`crate::TreeSequence::tree_iterator`].
 ///
 /// # Examples
 ///
@@ -491,7 +492,7 @@ pub struct TreeFlags(RawFlags);
 
 impl TreeFlags {
     make_constant_self!(
-    /// Update sample lists, enabling [`Tree::samples`].
+    /// Update sample lists, enabling [`crate::Tree::samples`].
     => SAMPLE_LISTS,TSK_SAMPLE_LISTS);
     make_constant_self!(
     /// Do *not* update the number of samples descending

src/sys/tree.rs

@@ -488,11 +488,11 @@ impl NodeIterator for SamplesIterator<'_> {
 
 #[non_exhaustive]
 pub enum NodeTraversalOrder {
-    ///Preorder traversal, starting at the root(s) of a [`TreeInterface`].
+    ///Preorder traversal, starting at the root(s) of a tree.
     ///For trees with multiple roots, start at the left root,
     ///traverse to tips, proceeed to the next root, etc..
     Preorder,
-    ///Postorder traversal, starting at the root(s) of a [`TreeInterface`].
+    ///Postorder traversal, starting at the root(s) of a tree.
     ///For trees with multiple roots, start at the left root,
     ///traverse to tips, proceeed to the next root, etc..
     Postorder,

src/trees/tree.rs

@@ -66,7 +66,7 @@ impl<'treeseq> Tree<'treeseq> {
     ///
     /// # Parameters
     ///
-    /// * `by_span`: if `true`, multiply the return value by [`TreeInterface::span`].
+    /// * `by_span`: if `true`, multiply the return value by [`Tree::span`].
     ///
     /// # Errors
     ///
@@ -303,7 +303,7 @@ impl<'treeseq> Tree<'treeseq> {
     ///
     /// # Parameters
     ///
-    /// * `order`: A value from [`NodeTraversalOrder`] specifying the
+    /// * `order`: A value from [`crate::NodeTraversalOrder`] specifying the
     ///   iteration order.
     // Return value is dyn for later addition of other traversal orders
     pub fn traverse_nodes(