refactor: TableCollection now stores internal tables directly (#723)

Author: molpopgen

Cargo.lock

@@ -28,7 +28,6 @@ serde = {version = "1.0.203", features = ["derive"], optional = true}
 serde_json = {version = "1.0.120", optional = true}
 bincode = {version = "1.3.1", optional = true}
 tskit-derive = {version = "0.2.0", path = "tskit-derive", optional = true}
-delegate = "0.12.0"
 
 [dev-dependencies]
 anyhow = {version = "1.0.86"}

Cargo.toml

@@ -120,96 +120,6 @@ macro_rules! build_table_column_slice_mut_getter {
     };
 }
 
-macro_rules! delegate_table_view_api {
-    () => {
-        delegate::delegate! {
-            to self.views {
-                /// Get reference to the [``EdgeTable``](crate::EdgeTable).
-                pub fn edges(&self) -> &crate::EdgeTable;
-                /// Get reference to the [``IndividualTable``](crate::IndividualTable).
-                pub fn individuals(&self) -> &crate::IndividualTable;
-                /// Get reference to the [``MigrationTable``](crate::MigrationTable).
-                pub fn migrations(&self) -> &crate::MigrationTable;
-                /// Get reference to the [``MutationTable``](crate::MutationTable).
-                pub fn mutations(&self) -> &crate::MutationTable;
-                /// Get reference to the [``NodeTable``](crate::NodeTable).
-                pub fn nodes(&self) -> &crate::NodeTable;
-                /// Get reference to the [``PopulationTable``](crate::PopulationTable).
-                pub fn populations(&self) -> &crate::PopulationTable;
-                /// Get reference to the [``SiteTable``](crate::SiteTable).
-                pub fn sites(&self) -> &crate::SiteTable;
-
-                #[cfg(feature = "provenance")]
-                #[cfg_attr(doc_cfg, doc(cfg(feature = "provenance")))]
-                /// Get reference to the [``ProvenanceTable``](crate::provenance::ProvenanceTable)
-                pub fn provenances(&self) -> &crate::provenance::ProvenanceTable ;
-
-                /// Return an iterator over the individuals.
-                pub fn individuals_iter(&self) -> impl Iterator<Item = crate::IndividualTableRow> + '_;
-                /// Return an iterator over the nodes.
-                pub fn nodes_iter(&self) -> impl Iterator<Item = crate::NodeTableRow> + '_;
-                /// Return an iterator over the edges.
-                pub fn edges_iter(&self) -> impl Iterator<Item = crate::EdgeTableRow> + '_;
-                /// Return an iterator over the migrations.
-                pub fn migrations_iter(&self) -> impl Iterator<Item = crate::MigrationTableRow> + '_;
-                /// Return an iterator over the mutations.
-                pub fn mutations_iter(&self) -> impl Iterator<Item = crate::MutationTableRow> + '_;
-                /// Return an iterator over the populations.
-                pub fn populations_iter(&self) -> impl Iterator<Item = crate::PopulationTableRow> + '_;
-                /// Return an iterator over the sites.
-                pub fn sites_iter(&self) -> impl Iterator<Item = crate::SiteTableRow> + '_;
-
-                #[cfg(feature = "provenance")]
-                #[cfg_attr(doc_cfg, doc(cfg(feature = "provenance")))]
-                /// Return an iterator over provenances
-                pub fn provenances_iter(&self,) -> impl Iterator<Item = crate::provenance::ProvenanceTableRow> + '_;
-
-                /// Obtain a vector containing the indexes ("ids")
-                /// of all nodes for which [`crate::NodeFlags::is_sample`]
-                /// is `true`.
-                ///
-                /// The provided implementation dispatches to
-                /// [`crate::NodeTable::samples_as_vector`].
-                pub fn samples_as_vector(&self) -> Vec<crate::NodeId>;
-
-                /// Obtain a vector containing the indexes ("ids") of all nodes
-                /// satisfying a certain criterion.
-                ///
-                /// The provided implementation dispatches to
-                /// [`crate::NodeTable::create_node_id_vector`].
-                ///
-                /// # Parameters
-                ///
-                /// * `f`: a function.  The function is passed the current table
-                ///    collection and each [`crate::node_table::NodeTableRow`].
-                ///    If `f` returns `true`, the index of that row is included
-                ///    in the return value.
-                ///
-                /// # Examples
-                ///
-                /// Get all nodes with time > 0.0:
-                ///
-                /// ```
-                /// let mut tables = tskit::TableCollection::new(100.).unwrap();
-                /// tables
-                ///     .add_node(tskit::NodeFlags::new_sample(), 0.0, tskit::PopulationId::NULL,
-                ///     tskit::IndividualId::NULL)
-                ///     .unwrap();
-                /// tables
-                ///     .add_node(tskit::NodeFlags::new_sample(), 1.0, tskit::PopulationId::NULL,
-                ///     tskit::IndividualId::NULL)
-                ///     .unwrap();
-                /// let samples = tables.create_node_id_vector(
-                ///     |row: &tskit::NodeTableRow| row.time > 0.,
-                /// );
-                /// assert_eq!(samples[0], 1);
-                /// ```
-                pub fn create_node_id_vector(&self, f: impl FnMut(&crate::NodeTableRow) -> bool) -> Vec<crate::NodeId>;
-            }
-        }
-    };
-}
-
 #[cfg(test)]
 mod test {
     use crate::error::TskitError;

src/_macros.rs

@@ -98,7 +98,6 @@ mod site_table;
 mod sys;
 mod table_collection;
 mod table_iterator;
-mod table_views;
 mod traits;
 mod trees;
 pub mod types;