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update change log #698

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150 changes: 150 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -2,6 +2,156 @@

All notable changes to this project will be documented in this file.

## [0.15.1] - 2025-01-23

### Features

- Added keep intervals for tables and tree sequences ([#635](https://github.com/tskit-dev/tskit-rust/pull/635))
- Add TreeSequence::tables ([#648](https://github.com/tskit-dev/tskit-rust/pull/648))

### Miscellaneous Tasks

- Bump serde from 1.0.199 to 1.0.203 ([#639](https://github.com/tskit-dev/tskit-rust/pull/639))
- Bump serde_json from 1.0.115 to 1.0.117 ([#637](https://github.com/tskit-dev/tskit-rust/pull/637))
- Bump thiserror from 1.0.58 to 1.0.61 ([#638](https://github.com/tskit-dev/tskit-rust/pull/638))
- Bump cc from 1.0.96 to 1.0.98 ([#640](https://github.com/tskit-dev/tskit-rust/pull/640))
- Bump libc from 0.2.154 to 0.2.155 ([#636](https://github.com/tskit-dev/tskit-rust/pull/636))
- Bump anyhow from 1.0.81 to 1.0.86 ([#641](https://github.com/tskit-dev/tskit-rust/pull/641))
- Bump bitflags from 2.5.0 to 2.6.0 ([#645](https://github.com/tskit-dev/tskit-rust/pull/645))
- Bump serde_json from 1.0.117 to 1.0.120 ([#646](https://github.com/tskit-dev/tskit-rust/pull/646))
- Bump cc from 1.0.98 to 1.0.104 ([#643](https://github.com/tskit-dev/tskit-rust/pull/643))

### Refactor

- [**breaking**] Use Into<Idtype> for metadata retrieval fns ([#633](https://github.com/tskit-dev/tskit-rust/pull/633))
- Separate keep_intervals from simplify ([#647](https://github.com/tskit-dev/tskit-rust/pull/647))
- Update to proc_macro_error2 ([#661](https://github.com/tskit-dev/tskit-rust/pull/661))
- Bump to syn 2.0 ([#663](https://github.com/tskit-dev/tskit-rust/pull/663))

### Styling

- Remove duplicated attribute ([#642](https://github.com/tskit-dev/tskit-rust/pull/642))
- Fix lints from rust 1.80.0 ([#650](https://github.com/tskit-dev/tskit-rust/pull/650))
- Fix lints from rust 1.81.0 ([#662](https://github.com/tskit-dev/tskit-rust/pull/662))
- Clippy lints for rustc 1.84.0 ([#699](https://github.com/tskit-dev/tskit-rust/pull/699))

## [0.15.0-alpha.0] - 2024-05-07

### Documentation

- Fix incomplete sentence in metadata_advanced.md ([#529](https://github.com/tskit-dev/tskit-rust/pull/529))
- Remove visible use of namespace from flags doc tests ([#618](https://github.com/tskit-dev/tskit-rust/pull/618))
- Fix lints from rustdoc ([#631](https://github.com/tskit-dev/tskit-rust/pull/631))

### Features

- Allow tree iteration to start at a given position/tree index ([#613](https://github.com/tskit-dev/tskit-rust/pull/613))
- Sys::NodeTable::raw_metadata ([#628](https://github.com/tskit-dev/tskit-rust/pull/628))

### Miscellaneous Tasks

- Add cargo-semver checks + caching to CI ([#493](https://github.com/tskit-dev/tskit-rust/pull/493))
- Update bindgen requirement from 0.63.0 to 0.65.1 ([#499](https://github.com/tskit-dev/tskit-rust/pull/499))
- [**breaking**] Update tskit C files to C API 1.1.2 ([#501](https://github.com/tskit-dev/tskit-rust/pull/501))
- Move sys into subdir ([#503](https://github.com/tskit-dev/tskit-rust/pull/503))
- Move bindings into sys ([#504](https://github.com/tskit-dev/tskit-rust/pull/504))
- Reorganize tables code in sys ([#511](https://github.com/tskit-dev/tskit-rust/pull/511))
- Reorganize treeseq code in sys ([#512](https://github.com/tskit-dev/tskit-rust/pull/512))
- Move flags into sys and re-export ([#513](https://github.com/tskit-dev/tskit-rust/pull/513))
- Reorganize tree/treeseq code ([#515](https://github.com/tskit-dev/tskit-rust/pull/515))
- Update bindgen requirement from 0.65.1 to 0.66.1 ([#523](https://github.com/tskit-dev/tskit-rust/pull/523))
- Update delegate requirement from 0.9.0 to 0.10.0 ([#525](https://github.com/tskit-dev/tskit-rust/pull/525))
- Bump dependencies ([#533](https://github.com/tskit-dev/tskit-rust/pull/533))
- Bump serde from 1.0.185 to 1.0.188 ([#538](https://github.com/tskit-dev/tskit-rust/pull/538))
- Bump actions/checkout from 2 to 4 ([#544](https://github.com/tskit-dev/tskit-rust/pull/544))
- Bump libc from 0.2.147 to 0.2.148 ([#543](https://github.com/tskit-dev/tskit-rust/pull/543))
- Bump serde_json from 1.0.105 to 1.0.107 ([#542](https://github.com/tskit-dev/tskit-rust/pull/542))
- Bump thiserror from 1.0.47 to 1.0.49 ([#541](https://github.com/tskit-dev/tskit-rust/pull/541))
- Bump bindgen from 0.66.1 to 0.68.1 ([#540](https://github.com/tskit-dev/tskit-rust/pull/540))
- Audit and remove unused dependencies ([#545](https://github.com/tskit-dev/tskit-rust/pull/545))
- Bump clap version ([#548](https://github.com/tskit-dev/tskit-rust/pull/548))
- Replace cargo-msrv with cargo check + specific version ([#549](https://github.com/tskit-dev/tskit-rust/pull/549))
- Pin clap in Cargo.toml ([#550](https://github.com/tskit-dev/tskit-rust/pull/550))
- Bump thiserror from 1.0.49 to 1.0.50 ([#559](https://github.com/tskit-dev/tskit-rust/pull/559))
- Bump styfle/cancel-workflow-action from 0.11.0 to 0.12.0 ([#556](https://github.com/tskit-dev/tskit-rust/pull/556))
- Bump serde_json from 1.0.107 to 1.0.108 ([#558](https://github.com/tskit-dev/tskit-rust/pull/558))
- Bump libc from 0.2.148 to 0.2.149 ([#557](https://github.com/tskit-dev/tskit-rust/pull/557))
- Bump serde from 1.0.188 to 1.0.190 ([#560](https://github.com/tskit-dev/tskit-rust/pull/560))
- Bump libc from 0.2.149 to 0.2.150 ([#561](https://github.com/tskit-dev/tskit-rust/pull/561))
- Bump serde from 1.0.190 to 1.0.193 ([#563](https://github.com/tskit-dev/tskit-rust/pull/563))
- Bump bindgen from 0.68.1 to 0.69.1 ([#562](https://github.com/tskit-dev/tskit-rust/pull/562))
- Bump serde_json from 1.0.108 to 1.0.109 ([#568](https://github.com/tskit-dev/tskit-rust/pull/568))
- Bump thiserror from 1.0.50 to 1.0.56 ([#572](https://github.com/tskit-dev/tskit-rust/pull/572))
- Bump libc from 0.2.150 to 0.2.151 ([#565](https://github.com/tskit-dev/tskit-rust/pull/565))
- Bump pkg-config from 0.3.27 to 0.3.28 ([#567](https://github.com/tskit-dev/tskit-rust/pull/567))
- Bump anyhow from 1.0.75 to 1.0.79 ([#571](https://github.com/tskit-dev/tskit-rust/pull/571))
- Bump delegate from 0.10.0 to 0.12.0 ([#566](https://github.com/tskit-dev/tskit-rust/pull/566))
- Bump shlex from 1.1.0 to 1.3.0 ([#574](https://github.com/tskit-dev/tskit-rust/pull/574))
- Bump bindgen from 0.69.1 to 0.69.2 ([#577](https://github.com/tskit-dev/tskit-rust/pull/577))
- Bump serde from 1.0.193 to 1.0.196 ([#579](https://github.com/tskit-dev/tskit-rust/pull/579))
- Bump libc from 0.2.151 to 0.2.153 ([#576](https://github.com/tskit-dev/tskit-rust/pull/576))
- Bump pkg-config from 0.3.28 to 0.3.29 ([#578](https://github.com/tskit-dev/tskit-rust/pull/578))
- Bump styfle/cancel-workflow-action from 0.12.0 to 0.12.1 ([#575](https://github.com/tskit-dev/tskit-rust/pull/575))
- Bump serde from 1.0.196 to 1.0.197 ([#583](https://github.com/tskit-dev/tskit-rust/pull/583))
- Bump bindgen from 0.69.2 to 0.69.4 ([#584](https://github.com/tskit-dev/tskit-rust/pull/584))
- Bump serde_json from 1.0.109 to 1.0.114 ([#586](https://github.com/tskit-dev/tskit-rust/pull/586))
- Bump cc from 1.0.83 to 1.0.88 ([#585](https://github.com/tskit-dev/tskit-rust/pull/585))
- Bump thiserror from 1.0.56 to 1.0.57 ([#581](https://github.com/tskit-dev/tskit-rust/pull/581))
- Bump pkg-config from 0.3.29 to 0.3.30 ([#582](https://github.com/tskit-dev/tskit-rust/pull/582))
- Bump all dependencies ([#593](https://github.com/tskit-dev/tskit-rust/pull/593))
- Bump baptiste0928/cargo-install from 2 to 3 ([#580](https://github.com/tskit-dev/tskit-rust/pull/580))
- Bump serde from 1.0.197 to 1.0.199 ([#626](https://github.com/tskit-dev/tskit-rust/pull/626))
- Bump cc from 1.0.90 to 1.0.96 ([#625](https://github.com/tskit-dev/tskit-rust/pull/625))
- Bump libc from 0.2.153 to 0.2.154 ([#627](https://github.com/tskit-dev/tskit-rust/pull/627))

### Refactor

- [**breaking**] Remove TSK_NODE_IS_SAMPLE ([#505](https://github.com/tskit-dev/tskit-rust/pull/505))
- [**breaking**] Remove tsk_flags_t from lib.rs and prelude ([#506](https://github.com/tskit-dev/tskit-rust/pull/506))
- [**breaking**] Remove tsk_size_t ([#507](https://github.com/tskit-dev/tskit-rust/pull/507))
- [**breaking**] Remove TSK_NULL ([#508](https://github.com/tskit-dev/tskit-rust/pull/508))
- [**breaking**] Remove tsk_id_t ([#509](https://github.com/tskit-dev/tskit-rust/pull/509))
- [**breaking**] C API bindings are now feature gates ([#510](https://github.com/tskit-dev/tskit-rust/pull/510))
- LLTreeSeq impl now takes flag types directly ([#514](https://github.com/tskit-dev/tskit-rust/pull/514))
- Add sys::LLTree ([#516](https://github.com/tskit-dev/tskit-rust/pull/516))
- [**breaking**] Mark all pub enums non_exhaustive. ([#519](https://github.com/tskit-dev/tskit-rust/pull/519))
- Remove unneeded private feilds from struct Tree ([#521](https://github.com/tskit-dev/tskit-rust/pull/521))
- Replace MBox with TskBox for "owning" table types ([#536](https://github.com/tskit-dev/tskit-rust/pull/536))
- Drop MBox for the storage behing TableCollection. ([#539](https://github.com/tskit-dev/tskit-rust/pull/539))
- Remove unsafe label from fn that is now safe ([#552](https://github.com/tskit-dev/tskit-rust/pull/552))
- TskBox::new now returns Result ([#553](https://github.com/tskit-dev/tskit-rust/pull/553))
- Sys::TskBox<T> now requires that T implement a private trait. ([#573](https://github.com/tskit-dev/tskit-rust/pull/573))
- [**breaking**] EdgeTable implemented using sys::EdgeTable ([#595](https://github.com/tskit-dev/tskit-rust/pull/595))
- [**breaking**] NodeTable implemented using sys::NodeTable ([#604](https://github.com/tskit-dev/tskit-rust/pull/604))
- [**breaking**] MutationTable implemented using sys::MutationTable ([#606](https://github.com/tskit-dev/tskit-rust/pull/606))
- [**breaking**] SiteTable implemented using sys::SiteTable ([#607](https://github.com/tskit-dev/tskit-rust/pull/607))
- [**breaking**] MigrationTable implemented using sys::MigrationTable ([#608](https://github.com/tskit-dev/tskit-rust/pull/608))
- [**breaking**] IndividualTable implemented using sys::IndividualTable ([#609](https://github.com/tskit-dev/tskit-rust/pull/609))
- [**breaking**] Population and Provenance tables use new sys:: types. ([#610](https://github.com/tskit-dev/tskit-rust/pull/610))
- [**breaking**] TreeSequence::dump_tables now consumes self. ([#612](https://github.com/tskit-dev/tskit-rust/pull/612))
- Use TSK_TREE_OK in StreamingIterator impl for Tree ([#614](https://github.com/tskit-dev/tskit-rust/pull/614))
- Move newtype definitions to sys module. ([#616](https://github.com/tskit-dev/tskit-rust/pull/616))
- Move TskitError to sys and reexport ([#617](https://github.com/tskit-dev/tskit-rust/pull/617))
- Use newtypes and generics for sys::NodeTable ([#619](https://github.com/tskit-dev/tskit-rust/pull/619))
- Sys:: tree sequence now uses TskBox ([#620](https://github.com/tskit-dev/tskit-rust/pull/620))
- Low level tables/tree sequences ([#622](https://github.com/tskit-dev/tskit-rust/pull/622))
- Mark TskBox::into_raw safe ([#623](https://github.com/tskit-dev/tskit-rust/pull/623))
- [**breaking**] Remove deprecated items ([#624](https://github.com/tskit-dev/tskit-rust/pull/624))
- [**breaking**] Bump bitflags to 2.5.x ([#630](https://github.com/tskit-dev/tskit-rust/pull/630))

### Styling

- Address clippy lints due to rust 1.72.0 ([#535](https://github.com/tskit-dev/tskit-rust/pull/535))
- Fix lints from rustc 1.77.1 ([#592](https://github.com/tskit-dev/tskit-rust/pull/592))
- Fix lints from rust 1.78 ([#629](https://github.com/tskit-dev/tskit-rust/pull/629))

### Testing

- Add explicit tests of empty bitflags types ([#527](https://github.com/tskit-dev/tskit-rust/pull/527))
- Rewrite test without proptest ([#534](https://github.com/tskit-dev/tskit-rust/pull/534))
- Verify MSRV in CI ([#546](https://github.com/tskit-dev/tskit-rust/pull/546))
- Remove CI pinned to an explicit MSRV ([#547](https://github.com/tskit-dev/tskit-rust/pull/547))

## [0.14.1] - 2023-04-16

### Bug Fixes
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