Alpha release

Alpha release of 0.15. The changelog is not updated. This release is a placeholder so that others can pull from crates.io.

0.14.1

[0.14.1] - 2023-04-16

Bug Fixes

• Tree now tied to TreeSequence lifetime (#497)

Miscellaneous Tasks

• Update delegate requirement from 0.8.0 to 0.9.0 (#494)

0.14.0

[0.14.0] - 2023-03-17

Documentation

• Book section on node defaults (#491)

Features

• Allow use of bookmark in examples/haploid_wright_fisher (#479)
• Impl Default for row id types (#484)
• Impl Default for Bookmark (#486)
• Implement Builder pattern for flags (#487)
• Support adding nodes with defaults (#488)

Miscellaneous Tasks

• [breaking] Bump MSRV to 1.60.0 (#478)

Refactor

• Remove internal impl Deref/DerefMut for edge diff iterator. (#482)
• Mod table_view is no longer pub (#483)
• [breaking] TableCollection::simplify now takes &[NodeId] (#485)
• Replace macros with fn for adding node table rows (#489)
• Manually impl Default for NodeDefaultsWithMetadata (#490)

0.12.0

[0.12.0] - 2022-12-23

Documentation

• Book section on lending row iterators (#406)
• Advanced metadata topics in book (#407)
• Book chapter on edge differences (#417)

Features

• TreeSequence::edge_differences_iter (#410)
• Add convience functions to get usize from row ids. (#413)
• Tree::total_branch_length now works. (#429)
• Add getters/setters for Bookmark. (#437)

Miscellaneous Tasks

• Update bindgen requirement from 0.61.0 to 0.63.0 (#415)

Refactor

• [breaking] Replace Deref with delegation of TableViews API (#409)
• [breaking] Remove TskitTypeAccess trait (#411)
• Allow TreeSequence::edge_differences_iter to Err. (#412)
• [breaking] Usize to SizeType conversion is now fallible. (#419)
• Macros only use newtype public API. (#420)
• Move newtypes into module (#421)
• The raw_metadata fn for tables now takes Into. (#425)
• Add low-level table wrappers to sys (#426)
• Generalize slice building in sys (#427)
• Remove many unsafe calls from tree_interface.rs (#428)
• Add sys::LLTreeSeq. (#430)
• Sys module no longer depends on TskitError (#431)
• Move Drop details for TreeSequence to sys. (#432)
• Add low level owning tables to sys (#433)
• Tidy up table definitions (#434)

Styling

• [breaking] Rename all OwnedX tables to OwningX. (#408)
• Replace column access macro with generic fn (#422)
• Generic fns for ragged column access (#423)
• Use fn to get array slices from Trees. (#424)

v0.12.0-alpha.1

[0.12.0-alpha.1] - 2022-11-09

Bug Fixes

• [breaking] MetadataError::RoundtripError now requires Send + Sync (#396)

Documentation

• Add haploid WF example to book (#397)

Features

• Add examples/haploid_wright_fisher.rs (#394)
• Add lending iterators over table row "views" (#398)
• Impl PartialEq for table row views. (#400)
• Add ProvenenceTableRowView (#401)
• Add row_view() for tables (#402)
• Column slice getters for tables (#404)

Refactor

• [breaking] Return &str from provenance table getters (#403)
• Deprecate NodeTable::flags_array_mut and NodeTable::time_array_mut (#405)

v0.12.0-alpha.0

[0.12.0-alpha.0] - 2022-11-06

Documentation

• Add book sections on table data access (#379)
• Remove chapter number from book intro (#380)
• Start book sections on tree sequences (#381)
• Book section on the tree API. (#382)
• Add book section on misc. ops on treeseqs (#385)
• Appendix material for book (#386)
• Rewrite book intro (#389)
• Show prelude contents as book appendix (#390)
• Book sections on metadata (#391)
• Book section on error handling (#393)

Refactor

• [breaking] Improve Tree iterator ergonomics (#384)
• [breaking] Improve Tree interface ergonomics (#388)

v0.11.1

[0.11.1] - 2022-11-04

Documentation

• Add mdbook (#378)

Refactor

• Apply functional style for NodeTable fns (#377)

v0.11.0

[0.11.0] - 2022-11-04

Bug Fixes

• Derive Debug for all table row types (#361)
• [breaking] Update generic bounds on metadata getters (#370)
• Impl DerefMut for "owned" tables. (#371)

Documentation

• Add migration guide (#376)

Features

• [breaking] Add TskitError::LibraryError (#342)

Refactor

• Streamline code for generating table rows. (#340)
• Replace unwrap with expect in _macros.rs (#341)
• Replace unwrap with errors in table_collection.rs (#343)
• Remove unwraps in trees source files. (#344)
• Streamline building individual table rows (#345)
• Remove unwraps from node_table.rs (#346)
• Unwrap to expect in error.rs (#347)
• Remove type info from Display for newtypes. (#349)
• [breaking] Return None for out-of-range row indexes. (#350)
• [breaking] Return None for out-of-range row indexes, part II. (#351)
• [breaking] Return None for out-of-range row indexes, part III. (#355)
• Improve safety of tsk array access (#362)
• Tree now stores tsk_tree_t in MBox. (#367)
• [breaking] Provenance table getters now return Option (#369)
• [breaking] Remove lifetime annotation from table types (#373)

Styling

• Fix lints from rust 1.65.0 (#374)
• Fix lints from nightly (#375)

Testing

• Rewrite table API tests (#356)
• Add doc tests for node table (#359)

v0.10.0

[0.10.0] - 2022-10-28

Documentation

• Display feature flags in docs.rs (#338)

Miscellaneous Tasks

• Set msrv to 1.57.0 (result of cargo msrv) (#322)
• Fix tag_pattern in cliff.toml (#330)
• Update github actions (#332)
• Add github actions to monthly dependabot (#333)
• Update bindgen requirement from 0.60.1 to 0.61.0 (#336)
• Bump styfle/cancel-workflow-action from 0.6.0 to 0.11.0 (#334)

Performance

• Use Bookmark in forward simulation example (#318)

Refactor

• Streamline internal macros for adding nodes (#309)
• Remove internal ffi module (#310)
• Panics compatible with earlier rustc (#311)
• Remove type name from SizeType Display output. (#315)
• [breaking] TableCollection::simplify returns Option<&[NodeId]> (#316)
• [breaking] Conversion from row id to usize is now fallible. (#319)
• Use clap::Parser in example program. (#320)
• Remove pontential panic! when instantiating table rows. (#329)
• Examples/tree_traversals.rs now uses clap derive (#337)

Styling

• Remove unneeded ( ) from match. (#323)
• Use auto-deref for pointer deref. (#325)
• Fix +nightly clippy lints for all targets/features. (#326)

Testing

• Improve test work flow (#331)

[0.10.0-alpha.1] - 2022-07-31

Bug Fixes

• Replace crate with $crate in macros (#287)

Features

• Add tskit::OwnedMutationTable (#281)
• Add tskit::OwnedSiteTable (#283)
• Add tskit::OwnedIndividualTable (#284)
• Add tskit::OwnedMigrationTable (#285)
• Add tskit::provenance::OwnedProvenanceTable (#286)
• Set tables in collection from owned tables. (#288)
• [breaking] Impl Send/Sync for TreeSequence (#297)

Miscellaneous Tasks

• Update to C API 1.1.1 (#304)

Performance

• [breaking] Implement slice access to individual data (#292)
• [breaking] Eliminate several copies from C to rust (#293)

Refactor

• Deduplicate code for adding node table rows. (#278)
• Use macros to implement adding table rows. (#279)
• Add new macro to build owned tables (#282)
• Separate tree ownership from API. (#300)
• Bring back generic syntax for adding node table rows. (#302)
• [breaking] Display for new types now omits type name. (#305)
• Remove MBox for tsk_treeseq_t storage (#306)

[0.10.0-alpha.0] - 2022-07-19

Bug Fixes

• Fix memory leak in TreeSequence::simplify (#274)
• Fix leak in TableCollection::deepcopy (#275)
• Fix leak in TreeSequence::dump_tables (#276)

Documentation

• Fix warnings from "cargo doc" (#255)

Features

• Make load from file generic over AsRef (#254)
• Add tskit::OwnedPopulationTable (#267)
• Add tskit::OwnedEdgeTable (#268)
• Add tskit::OwnedNodeTable (#273)

Miscellaneous Tasks

• Add cliff.toml (config file for git-cliff) (#257)
• Prefix "chore: " to dependabot.yml (#258)
• Use cargo-hack to streamline CI. (#259)
• Add cargo-valgrind CI workflow (#277)

Refactor

• Macro metadata_to_vector intputs changed. (#263)
• Add macros to implement owned tables. (#269)

Testing

• Add another experimental trait idea for metadata. (#261)
• Redo doctest: TableCollection::new_from_file (#272)

Second alpha release for 0.10.0

v0.10.0-alpha.1

Bump to version 0.10.0-alpha.1