diff --git a/examples/haploid_wright_fisher.rs b/examples/haploid_wright_fisher.rs index 07cedf99e..407da558f 100644 --- a/examples/haploid_wright_fisher.rs +++ b/examples/haploid_wright_fisher.rs @@ -156,7 +156,7 @@ fn stress_test_total_branch_length() { // stress test the branch length fn b/c it is not a trivial // wrapper around the C API. { - use streaming_iterator::StreamingIterator; + use tskit::StreamingIterator; let mut x = f64::NAN; if let Ok(mut tree_iter) = ts.tree_iterator(0) { // We will only do the first tree to save time. diff --git a/src/edge_differences.rs b/src/edge_differences.rs index 19a3bdaba..17e661f07 100644 --- a/src/edge_differences.rs +++ b/src/edge_differences.rs @@ -236,7 +236,7 @@ impl EdgeDifferencesIterator { } } -impl streaming_iterator::StreamingIterator for EdgeDifferencesIterator { +impl crate::StreamingIterator for EdgeDifferencesIterator { type Item = EdgeDifferencesIterator; fn advance(&mut self) { diff --git a/src/edge_table.rs b/src/edge_table.rs index 917fbec61..b4ccc5749 100644 --- a/src/edge_table.rs +++ b/src/edge_table.rs @@ -124,7 +124,7 @@ impl PartialEq> for EdgeTableRow { } } -impl streaming_iterator::StreamingIterator for EdgeTableRowView<'_> { +impl crate::StreamingIterator for EdgeTableRowView<'_> { type Item = Self; row_lending_iterator_get!(); diff --git a/src/individual_table.rs b/src/individual_table.rs index 0b752e031..b77cc6021 100644 --- a/src/individual_table.rs +++ b/src/individual_table.rs @@ -82,7 +82,7 @@ impl PartialEq> for IndividualTableRow { } } -impl streaming_iterator::StreamingIterator for IndividualTableRowView<'_> { +impl crate::StreamingIterator for IndividualTableRowView<'_> { type Item = Self; row_lending_iterator_get!(); diff --git a/src/lib.rs b/src/lib.rs index 69f56154f..b82ac1c25 100644 --- a/src/lib.rs +++ b/src/lib.rs @@ -82,6 +82,9 @@ #[cfg(feature = "bindings")] pub use sys::bindings; +pub use streaming_iterator::DoubleEndedStreamingIterator; +pub use streaming_iterator::StreamingIterator; + mod _macros; // Starts w/_ to be sorted at front by rustfmt! mod edge_differences; mod edge_table; @@ -117,9 +120,9 @@ pub use site_table::{SiteTable, SiteTableRow}; pub use sys::flags::*; pub use sys::NodeTraversalOrder; pub use table_collection::TableCollection; -pub use traits::TableColumn; pub use traits::IndividualLocation; pub use traits::IndividualParents; +pub use traits::TableColumn; pub use trees::{Tree, TreeSequence}; // Optional features diff --git a/src/migration_table.rs b/src/migration_table.rs index d10a3f901..90f098921 100644 --- a/src/migration_table.rs +++ b/src/migration_table.rs @@ -142,7 +142,7 @@ impl PartialEq> for MigrationTableRow { } } -impl streaming_iterator::StreamingIterator for MigrationTableRowView<'_> { +impl crate::StreamingIterator for MigrationTableRowView<'_> { type Item = Self; row_lending_iterator_get!(); diff --git a/src/mutation_table.rs b/src/mutation_table.rs index 2f9af82bd..df20ed30a 100644 --- a/src/mutation_table.rs +++ b/src/mutation_table.rs @@ -140,7 +140,7 @@ impl PartialEq> for MutationTableRow { } } -impl streaming_iterator::StreamingIterator for MutationTableRowView<'_> { +impl crate::StreamingIterator for MutationTableRowView<'_> { type Item = Self; row_lending_iterator_get!(); diff --git a/src/node_table.rs b/src/node_table.rs index 0d4bb3667..e03cc6434 100644 --- a/src/node_table.rs +++ b/src/node_table.rs @@ -125,7 +125,7 @@ impl PartialEq> for NodeTableRow { } } -impl streaming_iterator::StreamingIterator for NodeTableRowView<'_> { +impl crate::StreamingIterator for NodeTableRowView<'_> { type Item = Self; row_lending_iterator_get!(); diff --git a/src/population_table.rs b/src/population_table.rs index b69b61760..06e6d4617 100644 --- a/src/population_table.rs +++ b/src/population_table.rs @@ -95,7 +95,7 @@ impl PartialEq> for PopulationTableRow { } } -impl streaming_iterator::StreamingIterator for PopulationTableRowView<'_> { +impl crate::StreamingIterator for PopulationTableRowView<'_> { type Item = Self; row_lending_iterator_get!(); diff --git a/src/prelude.rs b/src/prelude.rs index 9392aa335..bc34211a6 100644 --- a/src/prelude.rs +++ b/src/prelude.rs @@ -1,7 +1,7 @@ //! Export commonly-use types and traits -pub use streaming_iterator::DoubleEndedStreamingIterator; -pub use streaming_iterator::StreamingIterator; +pub use crate::DoubleEndedStreamingIterator; +pub use crate::StreamingIterator; pub use { crate::EdgeId, crate::IndividualId, crate::Location, crate::MigrationId, crate::MutationId, crate::NodeId, crate::PopulationId, crate::Position, crate::RawFlags, crate::SiteId, diff --git a/src/provenance.rs b/src/provenance.rs index b883a7236..94db29db4 100644 --- a/src/provenance.rs +++ b/src/provenance.rs @@ -116,7 +116,7 @@ impl PartialEq> for ProvenanceTableRow { } } -impl streaming_iterator::StreamingIterator for ProvenanceTableRowView<'_> { +impl crate::StreamingIterator for ProvenanceTableRowView<'_> { type Item = Self; row_lending_iterator_get!(); @@ -286,7 +286,7 @@ impl ProvenanceTable { #[cfg(test)] mod test_provenances { - use streaming_iterator::StreamingIterator; + use crate::StreamingIterator; #[test] fn test_empty_record_string() { diff --git a/src/site_table.rs b/src/site_table.rs index 16453b23f..5fe5e21eb 100644 --- a/src/site_table.rs +++ b/src/site_table.rs @@ -109,7 +109,7 @@ impl PartialEq> for SiteTableRow { } } -impl streaming_iterator::StreamingIterator for SiteTableRowView<'_> { +impl crate::StreamingIterator for SiteTableRowView<'_> { type Item = Self; row_lending_iterator_get!(); diff --git a/src/table_collection.rs b/src/table_collection.rs index a5ba5a78c..d89ea9805 100644 --- a/src/table_collection.rs +++ b/src/table_collection.rs @@ -1631,7 +1631,7 @@ impl TableCollection { where P: Into, { - use streaming_iterator::StreamingIterator; + use crate::StreamingIterator; let mut tables = self; // use tables from sys to allow easier process with metadata let options = 0; diff --git a/src/trees/tree.rs b/src/trees/tree.rs index d9e0c9145..5891acd54 100644 --- a/src/trees/tree.rs +++ b/src/trees/tree.rs @@ -80,7 +80,7 @@ impl<'treeseq> Tree<'treeseq> { /// An error will be returned if ['crate::TreeFlags::SAMPLE_LISTS`] is not used: /// /// ```should_panic - /// use streaming_iterator::StreamingIterator; + /// use tskit::StreamingIterator; /// let tables = tskit::TableCollection::new(1.).unwrap(); /// let treeseq = /// tables.tree_sequence(tskit::TreeSequenceFlags::BUILD_INDEXES).unwrap(); @@ -94,7 +94,7 @@ impl<'treeseq> Tree<'treeseq> { /// The lifetime of the slice is tied to the parent object: /// /// ```compile_fail - /// use streaming_iterator::StreamingIterator; + /// use tskit::StreamingIterator; /// let tables = tskit::TableCollection::new(1.).unwrap(); /// let treeseq = /// tables.tree_sequence(tskit::TreeSequenceFlags::BUILD_INDEXES).unwrap(); @@ -204,7 +204,7 @@ impl<'treeseq> Tree<'treeseq> { /// The lifetime of the slice is tied to the parent object: /// /// ```compile_fail - /// use streaming_iterator::StreamingIterator; + /// use tskit::StreamingIterator; /// let tables = tskit::TableCollection::new(1.).unwrap(); /// let treeseq = /// tables.tree_sequence(tskit::TreeSequenceFlags::BUILD_INDEXES).unwrap(); @@ -224,7 +224,7 @@ impl<'treeseq> Tree<'treeseq> { /// The lifetime of the slice is tied to the parent object: /// /// ```compile_fail - /// use streaming_iterator::StreamingIterator; + /// use tskit::StreamingIterator; /// let tables = tskit::TableCollection::new(1.).unwrap(); /// let treeseq = /// tables.tree_sequence(tskit::TreeSequenceFlags::BUILD_INDEXES).unwrap(); @@ -244,7 +244,7 @@ impl<'treeseq> Tree<'treeseq> { /// The lifetime of the slice is tied to the parent object: /// /// ```compile_fail - /// use streaming_iterator::StreamingIterator; + /// use tskit::StreamingIterator; /// let tables = tskit::TableCollection::new(1.).unwrap(); /// let treeseq = /// tables.tree_sequence(tskit::TreeSequenceFlags::BUILD_INDEXES).unwrap(); @@ -264,7 +264,7 @@ impl<'treeseq> Tree<'treeseq> { /// The lifetime of the slice is tied to the parent object: /// /// ```compile_fail - /// use streaming_iterator::StreamingIterator; + /// use tskit::StreamingIterator; /// let tables = tskit::TableCollection::new(1.).unwrap(); /// let treeseq = /// tables.tree_sequence(tskit::TreeSequenceFlags::BUILD_INDEXES).unwrap(); @@ -284,7 +284,7 @@ impl<'treeseq> Tree<'treeseq> { /// The lifetime of the slice is tied to the parent object: /// /// ```compile_fail - /// use streaming_iterator::StreamingIterator; + /// use tskit::StreamingIterator; /// let tables = tskit::TableCollection::new(1.).unwrap(); /// let treeseq = /// tables.tree_sequence(tskit::TreeSequenceFlags::BUILD_INDEXES).unwrap(); @@ -340,7 +340,7 @@ impl<'treeseq> Tree<'treeseq> { /// An error will be returned if ['crate::TreeFlags::SAMPLE_LISTS`] is not used: /// /// ```should_panic - /// use streaming_iterator::StreamingIterator; + /// use tskit::StreamingIterator; /// let tables = tskit::TableCollection::new(1.).unwrap(); /// let treeseq = /// tables.tree_sequence(tskit::TreeSequenceFlags::BUILD_INDEXES).unwrap(); @@ -354,7 +354,7 @@ impl<'treeseq> Tree<'treeseq> { /// The lifetime of the slice is tied to the parent object: /// /// ```compile_fail - /// use streaming_iterator::StreamingIterator; + /// use tskit::StreamingIterator; /// let tables = tskit::TableCollection::new(1.).unwrap(); /// let treeseq = /// tables.tree_sequence(tskit::TreeSequenceFlags::BUILD_INDEXES).unwrap(); @@ -374,7 +374,7 @@ impl<'treeseq> Tree<'treeseq> { /// An error will be returned if ['crate::TreeFlags::SAMPLE_LISTS`] is not used: /// /// ```should_panic - /// use streaming_iterator::StreamingIterator; + /// use tskit::StreamingIterator; /// let tables = tskit::TableCollection::new(1.).unwrap(); /// let treeseq = /// tables.tree_sequence(tskit::TreeSequenceFlags::BUILD_INDEXES).unwrap(); @@ -388,7 +388,7 @@ impl<'treeseq> Tree<'treeseq> { /// The lifetime of the slice is tied to the parent object: /// /// ```compile_fail - /// use streaming_iterator::StreamingIterator; + /// use tskit::StreamingIterator; /// let tables = tskit::TableCollection::new(1.).unwrap(); /// let treeseq = /// tables.tree_sequence(tskit::TreeSequenceFlags::BUILD_INDEXES).unwrap(); @@ -408,7 +408,7 @@ impl<'treeseq> Tree<'treeseq> { /// An error will be returned if ['crate::TreeFlags::SAMPLE_LISTS`] is not used: /// /// ```should_panic - /// use streaming_iterator::StreamingIterator; + /// use tskit::StreamingIterator; /// let tables = tskit::TableCollection::new(1.).unwrap(); /// let treeseq = /// tables.tree_sequence(tskit::TreeSequenceFlags::BUILD_INDEXES).unwrap(); @@ -422,7 +422,7 @@ impl<'treeseq> Tree<'treeseq> { /// The lifetime of the slice is tied to the parent object: /// /// ```compile_fail - /// use streaming_iterator::StreamingIterator; + /// use tskit::StreamingIterator; /// let tables = tskit::TableCollection::new(1.).unwrap(); /// let treeseq = /// tables.tree_sequence(tskit::TreeSequenceFlags::BUILD_INDEXES).unwrap(); @@ -454,7 +454,7 @@ impl<'treeseq> Tree<'treeseq> { } } -impl<'ts> streaming_iterator::StreamingIterator for Tree<'ts> { +impl<'ts> crate::StreamingIterator for Tree<'ts> { type Item = Tree<'ts>; fn advance(&mut self) { assert!(!self.inner.as_ptr().is_null()); @@ -480,7 +480,7 @@ impl<'ts> streaming_iterator::StreamingIterator for Tree<'ts> { } } -impl streaming_iterator::DoubleEndedStreamingIterator for Tree<'_> { +impl crate::DoubleEndedStreamingIterator for Tree<'_> { fn advance_back(&mut self) { assert!(!self.inner.as_ptr().is_null()); // SAFETY: pointer is not null. diff --git a/src/trees/treeseq.rs b/src/trees/treeseq.rs index f916e457b..17dd79d75 100644 --- a/src/trees/treeseq.rs +++ b/src/trees/treeseq.rs @@ -204,10 +204,10 @@ impl TreeSequence { /// ``` /// // You must include streaming_iterator as a dependency /// // and import this type. - /// use streaming_iterator::StreamingIterator; + /// use tskit::StreamingIterator; /// // Import this to allow .next_back() for reverse /// // iteration over trees. - /// use streaming_iterator::DoubleEndedStreamingIterator; + /// use tskit::DoubleEndedStreamingIterator; /// /// let mut tables = tskit::TableCollection::new(1000.).unwrap(); /// tables.build_index(); @@ -222,8 +222,8 @@ impl TreeSequence { /// A `Tree`'s lifetime is tied to that of its tree sequence: /// /// ```compile_fail - /// # use streaming_iterator::StreamingIterator; - /// # use streaming_iterator::DoubleEndedStreamingIterator; + /// # use tskit::StreamingIterator; + /// # use tskit::DoubleEndedStreamingIterator; /// # let mut tables = tskit::TableCollection::new(1000.).unwrap(); /// # tables.build_index(); /// let tree_sequence = tables.tree_sequence(tskit::TreeSequenceFlags::default()).unwrap(); @@ -238,7 +238,7 @@ impl TreeSequence { /// Be sure to note the difference from the previous example. /// /// ```no_run - /// use streaming_iterator::StreamingIterator; + /// use tskit::StreamingIterator; /// /// let mut tables = tskit::TableCollection::new(1000.).unwrap(); /// tables.build_index(); diff --git a/tests/book_metadata.rs b/tests/book_metadata.rs index 1e8b20d6d..cb0122d7c 100644 --- a/tests/book_metadata.rs +++ b/tests/book_metadata.rs @@ -1,8 +1,8 @@ #[cfg(feature = "derive")] #[test] fn book_mutation_metadata() { - use streaming_iterator::StreamingIterator; use tskit::metadata::MetadataRoundtrip; + use tskit::StreamingIterator; // ANCHOR: metadata_derive #[derive(serde::Serialize, serde::Deserialize, tskit::metadata::MutationMetadata)] diff --git a/tests/test_trees.rs b/tests/test_trees.rs index 4e0777031..8064538a4 100644 --- a/tests/test_trees.rs +++ b/tests/test_trees.rs @@ -1,8 +1,8 @@ use std::sync::Arc; use std::thread; -use streaming_iterator::DoubleEndedStreamingIterator; -use streaming_iterator::StreamingIterator; +use crate::DoubleEndedStreamingIterator; +use crate::StreamingIterator; use tskit::prelude::*; use tskit::NodeFlags;