Alpha release

First alpha release of 0.10.0. Fixes some memory leaks.

New NodeFlags pub fn. Doc improvements.

2022-06-20, Version 0.9.0

Commits

• [068fdccdea] Bump version to 0.9.0 (Kevin R. Thornton)
• [d700af7294] doc sorting requirements (#243) (Kevin R. Thornton)
• [6114d2bd65] Change ffi to private visibility. (#241) (Kevin R. Thornton)
• [b53105112a] Add new_sample and is_sample to NodeFlags public API. (#238) (Kevin R. Thornton)

TreeSequence takes ownership of TableCollection

2022-05-26, Version 0.8.1

Commits

• [bd72b689ac] Bump version to 0.8.1 (molpopgen)
• [b0abdfad5c] impl TryFrom for TreeSequence (#236) (Kevin R. Thornton)
• [71e927a9bb] TreeSequence::new now takes ownership of the TableCollection. (#235) (Kevin R. Thornton)

Contains C API 1_0_0

2022-05-24, Version 0.8.0

Commits

• [e463302ced] Bump package version to 0.8.0 (molpopgen)
• [deffc58127] Replace From for usize with TryFrom. (#234) (Kevin R. Thornton)
• [a7c04213a1] update to CAPI 1.0.0 (#229) (Kevin R. Thornton)
• [7c0b6169a3] Add CI for 32 bit Linux builds (#232) (Kevin R. Thornton)
• [7458d85163] Invoke rust dependency caching after setting up rustc (#233) (Kevin R. Thornton)
• [203a43a0e8] Only run CI for rust/stable. (#231) (Kevin R. Thornton)
• [fb2128c0a5] Add dependency caching for CI. (#230) (Kevin R. Thornton)
• [aff053c786] Improvements to handling of tsk_flags_t: (#227) (Kevin R. Thornton)
• [5f558cb051] Audit pedantic lints re: integer casts (#223) (Kevin R. Thornton)
• [609546185c] Fix several "pedantic" lints from clippy: (#222) (Kevin R. Thornton)

0.7.0

2022-03-24, Version 0.7.0

Commits

• [8427c2fea7] Change order of generics to match argument order for all "add" (#221) (Kevin R. Thornton)
• [6ef0406731] Fix typo in docstring for TableCollection::full_sort. (#219) (Kevin R. Thornton)
• [a1a7e12208] Add TableCollection::topological_sort_individuals. (#218) (Kevin R. Thornton)
• [4c17ca62a2] Update clap requirement from ~3.0.0 to ~3.1.3 (#215) (dependabot[bot])
• [f40562a56a] Fix lint found by clippy. (#216) (Kevin R. Thornton)
• [4efddb6f5d] Update clap requirement from ~2.34.0 to ~3.0.0 (#214) (dependabot[bot])

0.7.0, second alpha release

2021-12-15, Version 0.7.0-alpha.1

Some minor fixes over the first alpha

Commits

• [44965969c0] Bump version to 0.7.0.alpha.1 (molpopgen)
• [5d6a289490] Fix issues with Time, Positin, Location newtypes (#212) (Kevin R. Thornton)
• [99930e8bb0] Add explicit tests of tree roots. (#211) (Kevin R. Thornton)

0.7.0, first alpha

2021-12-15, Version 0.7.0-alpha.0

Breaking changes:

• Update to tskit C API 0.99.15.
• Add newtypes for Time, Position, and Location.
• Add newtype SizeType, which wraps tsk_size_t.
• tsk_id_t and tsk_size_t removed from library prelude.
• The Provenance trait is removed and all "provenance stuff"
  is now a first-class table API supported by the TableAccess trait.

New features:

• Update to tskit C API 0.99.15.
• tskit C structs are now managed by MBox.
• Support for virtual tree roots.
• Add postorder node iterator for Tree

Commits

• [272d0736e2] bump package version to 0.7.0-alpha.0 (molpopgen)
• [b5946a4cc4] Redesign provenance feature: (#207) (Kevin R. Thornton)
• [5699aab37f] Change return time of Tree::num_tracked_samples. (#206) (Kevin R. Thornton)
• [2391c9e587] Add support for virtual roots (#205) (Kevin R. Thornton)
• [4cf3496d82] Fix metadata links in lib.rs (#204) (Kevin R. Thornton)
• [d7f70a7cfd] Use MBox to manage lifetimes of tskit C structs. (#203) (Kevin R. Thornton)
• [034204ed88] Add newtypes for Time, Position, and for Location. (#199) (Kevin R. Thornton)
• [4ba44ef0c5] Bump editions to 2021. (#198) (Kevin R. Thornton)
• [c4cc6e875a] Add tskit::SizeType (#192) (Kevin R. Thornton)
• [8429cc37d2] Use type erasure for all table row iteration functions. (#189) (Kevin R. Thornton)
• [f4cb6350e0] Add TableCollection::check_integrity. (#188) (Kevin R. Thornton)
• [562014b04f] Add preorder node traversal using latest tskit C API. (#186) (Kevin R. Thornton)
• [db8550f6d7] Replace Box with malloc'd raw pointer for tskit types. (#184) (Kevin R. Thornton)
• [90a2d84a9d] Update to C API 0.99.15 (breaking) (#183) (Kevin R. Thornton)
• [58e7c5ed73] Update clap requirement from ~2.33.3 to ~2.34.0 (#176) (dependabot[bot])

Security-related fixes

2021-11-29, Version 0.6.1

Commits

• [3eadcb161e] Replace chrono with humantime in provenance doc tests. (#175) (Kevin R. Thornton)
• [4def777ddf] Add security audit work flow. (#172) (Kevin R. Thornton)

Version 0.6.0

2021-11-23, Version 0.6.0

Commits

• [b07c035077] bump version to 0.6.0 (molpopgen)
• [8bb08be83d] Replace chrono dependency with humantime to avoid RUSTSEC-2020-0071 and RUSTSEC-2020-0159 (#171) (Momo Langenstein)
• [896b5891e0] Implement Display for Id newtypes. (#168) (Kevin R. Thornton)
• [d2c6383ae9] Update to C API 0.99.14 (#165) (Kevin R. Thornton)

Derive macros for table row metadata

2021-09-03, Version 0.5.0

Commits

• [41633b60ed] Add metadata type registration via derive macros. (#163) (Kevin R. Thornton)