Type safety...

2021-08-31, Version 0.4.0

Commits

• [a7d78b16aa] Bump version to 0.4.0 (molpopogen)
• [b5e2c265dd] Add newtype row IDs to prelude. (#161) (Kevin R. Thornton)
• [3dbe8c4b5e] Fix implementation of tree preorder stacking. (#160) (Kevin R. Thornton)
• [fafd457033] Refactor metadata encoding: (#158) (Kevin R. Thornton)
• [258b4ee5f0] replace IdIsNull trait with associated fn (#156) (Kevin R. Thornton)
• [9987fc0472] Release build optimizations: (#155) (Kevin R. Thornton)
• [58ac4a92d7] Refine what "NULL"-ness means for an Id type: (#154) (Kevin R. Thornton)
• [ad4975fc70] Update bindgen requirement from 0.58.1 to 0.59.1 (#152) (dependabot[bot])
• [8a553eaa80] fix clippy warnings that showed up in rust 1.54 (#153) (Kevin R. Thornton)
• [bef4bb6c7a] Allow empty provenance records. (#151) (Kevin R. Thornton)
• [86df702040] Improve test coverage of "adding rows to table collections" (#143): (Kevin R. Thornton)
• [036680050b] * Update trees API to use NodeId (#145) (Kevin R. Thornton)
• [7a716bbe76] Add additional member functions to TableCollection to (#141) (Kevin R. Thornton)
• [baf6f17430] Fix Into< > type for TableCollection::add_individual_* (#142) (Kevin R. Thornton)
• [689938eee7] fix link from ProvenanceId to ProvenanceTable in docs (#140) (Kevin R. Thornton)
• [1203a5d523] strong id type cleanup (#139) (Kevin R. Thornton)
• [6bae100e61] Add EdgeId (#138) (Kevin R. Thornton)
• [9baff077b5] Add MigrationId and ProvenanceId (#137) (Kevin R. Thornton)
• [7713ef669e] Add SiteId and MutationId (#136) (Kevin R. Thornton)
• [de006a1f0e] Add PopulationId (#135) (Kevin R. Thornton)
• [630ccd5f5e] Add IndividualId. (#133) (Kevin R. Thornton)
• [8bf7d4b954] NodeTable::metadata now uses Into. (#134) (Kevin R. Thornton)
• [3ac3d50f7b] * Establish a pattern for stronger ID types (#129) (Kevin R. Thornton)
• [e19095d9a9] clippy vs bindgen (#130) (Kevin R. Thornton)
• [d9abda5bb6] Change links in Cargo.toml to tskit-dev (#127) (Kevin R. Thornton)

Several API fixes, ready to transfer!

2021-05-19, Version 0.3.0

This release has a few API changes, etc., that streamline the public interface.

The C code is updated to 0.99.12.

Commits

• [ec0adc36ae] streamline API for creating table row objects (#126) (Kevin R. Thornton)
• [edd36fa886] Add mutable access to NodeTable flag and time arrays. (#125) (Kevin R. Thornton)
• [634df568af] Fix docs for Tree::total_branch_length. Fixes #114. (#124) (Kevin R. Thornton)
• [202bcded3f] Give access to TableCollection edge indexes. (#123) (Kevin R. Thornton)
• [3888fe5f10] update C code to version 0.99.12 (#122) (Kevin R. Thornton)
• [6fa2057af6] Add prelude.rs (#119) (Kevin R. Thornton)
• [a592126594] replace crate with $crate for all macros (#113) (Kevin R. Thornton)
• [b618d75e5b] Add macro to aid returning from MetadataRoundtrip functions. (#110) (Kevin R. Thornton)
• [79adaa1a4a] Add macro to remove code duplication (#111) (Kevin R. Thornton)
• [159bbfe926] Add convenience macro to use all public traits. (#106) (Kevin R. Thornton)
• [e912f7b2c8] Bump bindgen version. (#109) (Kevin R. Thornton)
• [15fae9327b] Update clap requirement from ~2.27.0 to ~2.33.3 (#107) (dependabot[bot])
• [55f18a1a4f] Refactor MetadataError: (#105) (Kevin R. Thornton)
• [fbce6ca894] API fixes. (#104) (Kevin R. Thornton)

Object lifetime fix

2021-04-27, Version 0.2.2

This release fixes issues with the lifetime relationships of Tree and the raw C arrays.
Technically, this is an API change, but only with respect to return type and the integer type used to index that return type.

Commits

• [89d234f674] Replace WrappedTskArray with idiomatic slices. Closes #99 (#101) (Kevin R. Thornton)
• [ed8329b89e] Completely hide NodeIterator from public name spaces. (#100) (Kevin R. Thornton)

Provenance table support

2021-04-26, Version 0.2.1

• [ff1c7ced82] Add Provenance trait as optional feature (#98). (Kevin R. Thornton)
• [0fdd30067e] Fix error in transmitting nodes. Closes #96 (#97) (Kevin R. Thornton)
• [299c83ae35] Update repo/homepage name in Cargo.toml (molpopgen)
• [35ecf29933] Remove re-exports that are part of existing bitflags types. (#95) (Kevin R. Thornton)

0.2.0

2021-04-21, Version 0.2.0

Commits

• [daffeda43e] bump version to 0.2.0 (molpopgen)
• [0dad5e39d2] Update docs (#93) (Kevin R. Thornton)
• [f905b9c384] Add reverse tree iteration. (#92) (Kevin R. Thornton)
• [a1a033f901] Add development documentation. (#91) (Kevin R. Thornton)
• [ce3d8f4849] Refine forward sim example (#90) (Kevin R. Thornton)
• [b1022e1f59] Refactor how tskit flags are handled. (#89) (Kevin R. Thornton)
• [56e43cb0ff] Add forward simulation example. Closes #71. (#86) (Kevin R. Thornton)
• [5530d7b234] Refactor all examples into examples/ (#85) (Kevin R. Thornton)
• [651e4edcac] Collect public traits in traits.rs. Closes #81. (#84) (Kevin R. Thornton)
• [11ad49f0e1] Remove mention of use NodeIterator. Closes #68. (#83) (Kevin R. Thornton)
• [df28231d9a] Add test fixtures module. Closes #73 (#80) (Kevin R. Thornton)
• [3a8a82637e] Rename Tree::nodes to Tree::traverse_nodes. (#79) (Kevin R. Thornton)
• [4e7af98ac5] Update GitHub actions. (#78) (Kevin R. Thornton)
• [43e14bb8a6] Add NodeListGenerator trait bound to TableAccess. Closes #67. (#75) (Kevin R. Thornton)
• [ae203769f4] add id field to table row types. Closes #76 (#77) (Kevin R. Thornton)
• [346c804be8] Make tree arrays public. Closes #70 (#74) (Kevin R. Thornton)
• [a2dfcfe8f6] Add TableCollection and TreeSequence simplification (#64) (Kevin R. Thornton)
• [c62ccd21aa] Add TableAccess trait and implement for TableCollection and TreeSequence. (#66) (Kevin R. Thornton)
• [167209466a] Remove duplication of entire table collection when creating a tree sequence. (#65) (Kevin R. Thornton)
• [df258ad8d1] Fix useless conversion in lib::c_api_version (#63) (Kevin R. Thornton)
• [fcca8bb682] remove unnecessary function from util (#62) (Kevin R. Thornton)
• [0ee9f86db4] Merge pull request #61 from molpopgen/add_individual_and_migration_tables (Kevin R. Thornton)
• [8f072c47d1] Add migrations and individuals tables. (molpopogen)
• [b2c891300b] Merge pull request #60 from molpopgen/tskit_C_version (Kevin R. Thornton)
• [f48b2fed57] Add functions to return C API version info (molpopogen)
• [87593d4bdc] Merge pull request #59 from molpopgen/add_test_metadata_some_columns_only (Kevin R. Thornton)
• [5ab8e8c9d0] Add test of metadata decoding when not all rows have metadata. (molpopogen)
• [adcc321cc8] Merge pull request #58 from molpopgen/table_row_access (Kevin R. Thornton)
• [860a647bf3] * Add ::row for all tables (molpopgen)
• [6b0a77e106] Add util.rs (molpopgen)
• [6b9631e1f1] Merge pull request #57 from molpopgen/unify_table_iteration (Kevin R. Thornton)
• [3d79f8bbfa] Add ability to iterate tables from a TableCollection: (molpopogen)
• [392ce57e0a] Merge pull request #52 from molpopgen/table_iteration (Kevin R. Thornton)
• [2fe5912c34] Add table iteration w/optional handling of metadata. (molpopgen)
• [9a59a148f7] Merge pull request #55 from molpopgen/wrapped_tsk_array_iter_adapter (Kevin R. Thornton)
• [84b0b496c1] Replace built-in iteration with iterator adapter for WrappedTskArray (molpopgen)
• [18234998ea] Merge pull request #56 from molpopgen/metadata_macro_fixes (Kevin R. Thornton)
• [49bbd0f2f4] metadata_to_vector macro is now a simple return (no ? operator). (molpopgen)
• [6e293acf14] Remove unused paramter to metadata_to_vector. Fixes #54. (molpopgen)
• [45347a576c] Change log for 0.1.2 (molpopgen)

0.1.2

This release is all about iteration: trees, nodes, etc..

First release as "tskit"

• Crate name changed to tskit
• Added methods to encode/decode table row meta data.
• tskit/kastore C code updated to tskit 0.3.5

First release.

0.1.0

Fix README. Fixes #16